[voronota] 01/09: Imported Upstream version 1.18.1877
Andrius Merkys
merkys-guest at moszumanska.debian.org
Fri Oct 13 14:37:57 UTC 2017
This is an automated email from the git hooks/post-receive script.
merkys-guest pushed a commit to branch master
in repository voronota.
commit 1ca2aa576be566deeff30847bf21e57f5e07e742
Author: Andrius Merkys <andrius.merkys at gmail.com>
Date: Fri Oct 13 13:32:14 2017 +0300
Imported Upstream version 1.18.1877
---
CMakeLists.txt | 19 +
LICENSE.txt | 21 +
Makefile.am | 4 +
Makefile.in | 1373 +
README.html | 719 +
README.txt | 792 +
aclocal.m4 | 951 +
configure | 4272 ++
configure.ac | 5 +
depcomp | 630 +
install-sh | 520 +
missing | 376 +
radii | 119 +
src/apollota/basic_operations_on_points.h | 373 +
src/apollota/basic_operations_on_spheres.h | 222 +
src/apollota/bounding_spheres_hierarchy.h | 343 +
src/apollota/constrained_contact_contour.h | 646 +
src/apollota/constrained_contact_remainder.h | 218 +
src/apollota/constrained_contacts_construction.h | 419 +
src/apollota/constrained_contacts_utilities.h | 152 +
src/apollota/hyperboloid_between_two_spheres.h | 118 +
src/apollota/polar_sorting.h | 86 +
src/apollota/polynomial_curves.h | 310 +
src/apollota/rolling_topology.h | 227 +
src/apollota/rotation.h | 79 +
src/apollota/safer_comparison_of_numbers.h | 45 +
src/apollota/safer_quadratic_equation_root.h | 57 +
src/apollota/safer_summation.h | 116 +
src/apollota/search_for_spherical_collisions.h | 104 +
src/apollota/simple_polygon_utilities.h | 262 +
src/apollota/spheres_boundary_construction.h | 48 +
src/apollota/spherical_contacts_construction.h | 124 +
src/apollota/splitting_of_spheres.h | 119 +
src/apollota/subdivided_icosahedron.h | 189 +
src/apollota/tangent_plane_of_three_spheres.h | 134 +
src/apollota/tangent_sphere_of_four_spheres.h | 170 +
src/apollota/tangent_sphere_of_three_spheres.h | 223 +
src/apollota/triangulation.h | 1265 +
src/apollota/triangulation_output.h | 77 +
src/apollota/triangulation_queries.h | 132 +
src/apollota/tuple.h | 202 +
src/auxiliaries/atom_radius_assigner.h | 93 +
src/auxiliaries/atoms_io.h | 629 +
src/auxiliaries/chain_residue_atom_descriptor.h | 664 +
src/auxiliaries/io_utilities.h | 336 +
src/auxiliaries/opengl_printer.h | 817 +
src/auxiliaries/pairwise_sequence_alignment.h | 193 +
src/auxiliaries/program_options_handler.h | 454 +
src/auxiliaries/residue_atoms_reference.h | 53 +
src/auxiliaries/residue_letters_coding.h | 76 +
src/auxiliaries/xml_writer.h | 75 +
src/compatability_macros.h | 16 +
src/main.cpp | 212 +
src/mode_calculate_contacts.cpp | 291 +
src/mode_calculate_mock_solvent.cpp | 176 +
src/mode_calculate_vertices.cpp | 59 +
src/mode_calculate_vertices_in_parallel.cpp | 450 +
src/mode_compare_contacts.cpp | 425 +
src/mode_demo_hypercut.cpp | 616 +
src/mode_demo_polygon_triangulation.cpp | 100 +
src/mode_demo_ses.cpp | 544 +
src/mode_draw_balls.cpp | 90 +
src/mode_draw_contacts.cpp | 89 +
src/mode_expand_descriptors.cpp | 78 +
src/mode_get_balls_from_atoms_file.cpp | 141 +
src/mode_place_membrane.cpp | 318 +
src/mode_plot_contacts.cpp | 278 +
src/mode_query_balls.cpp | 374 +
src/mode_query_balls_clashes.cpp | 78 +
src/mode_query_balls_sequences_pairings_stats.cpp | 76 +
src/mode_query_contacts.cpp | 342 +
src/mode_query_contacts_depth_values.cpp | 136 +
src/mode_query_contacts_simulating_unfolding.cpp | 61 +
src/mode_query_contacts_solvation_values.cpp | 55 +
src/mode_rotational_optimization_demo.cpp | 55 +
src/mode_score_contacts_energy.cpp | 71 +
src/mode_score_contacts_energy_stats.cpp | 49 +
src/mode_score_contacts_global_energy_by_cuts.cpp | 214 +
src/mode_score_contacts_potential.cpp | 322 +
src/mode_score_contacts_potentials_stats.cpp | 37 +
src/mode_score_contacts_quality.cpp | 129 +
src/mode_score_scores.cpp | 267 +
...de_simulate_potential_for_membrane_proteins.cpp | 81 +
src/mode_vectorize_contact_environments.cpp | 180 +
src/mode_vectorize_contacts.cpp | 122 +
src/mode_vectorize_points.cpp | 78 +
...alls_from_atoms_file_and_calculate_vertices.cpp | 69 +
src/mode_write_balls_to_atoms_file.cpp | 192 +
src/mode_write_qa_scores_in_casp_format.cpp | 101 +
src/modescommon/ball_value.h | 36 +
src/modescommon/contact_value.h | 80 +
src/modescommon/contacts_scoring_utilities.h | 147 +
src/modescommon/drawing_cylinder.h | 49 +
src/modescommon/drawing_links.h | 75 +
src/modescommon/drawing_nucleic_acid_cartoons.h | 221 +
src/modescommon/drawing_protein_cartoons.h | 443 +
src/modescommon/drawing_utilities.h | 185 +
src/modescommon/filepath_utilities.h | 38 +
src/modescommon/generic_utilities.h | 42 +
src/modescommon/matching_utilities.h | 189 +
src/modescommon/mock_solvent_utilities.h | 21 +
src/modescommon/properties_value.h | 81 +
src/modescommon/sequence_utilities.h | 127 +
src/modescommon/statistics_utilities.h | 63 +
src/modescommon/svg_writer.h | 83 +
src/modescommon/vectorization_utilities.h | 400 +
..._balls_from_atoms_file_and_calculate_vertices.h | 229 +
support/generate-arguments-for-query-balls.html | 226 +
support/generate-arguments-for-query-contacts.html | 317 +
voronota | Bin 0 -> 3801606 bytes
voronota-cadscore | 468 +
voronota-contacts | 237 +
voronota-resources | 51977 +++++++++++++++++++
voronota-volumes | 180 +
voronota-voromqa | 1094 +
voronota.man | 76 +
116 files changed, 83707 insertions(+)
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..0fb71c3
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,19 @@
+cmake_minimum_required(VERSION 2.6)
+
+project(Voronota)
+
+file(GLOB sources ${PROJECT_SOURCE_DIR}/src/*.cpp)
+file(GLOB headers ${PROJECT_SOURCE_DIR}/src/*.h)
+
+set(CMAKE_BUILD_TYPE Release)
+
+find_package(OpenMP)
+if (OPENMP_FOUND)
+ set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+endif()
+
+add_executable(voronota ${sources} ${headers})
+
+install(TARGETS voronota RUNTIME DESTINATION bin)
+install(PROGRAMS voronota-cadscore voronota-contacts voronota-resources voronota-voromqa voronota-volumes DESTINATION bin)
diff --git a/LICENSE.txt b/LICENSE.txt
new file mode 100644
index 0000000..bf353cc
--- /dev/null
+++ b/LICENSE.txt
@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2013-2016 Kliment Olechnovic
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 0000000..94224ac
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,4 @@
+bin_PROGRAMS = voronota
+voronota_SOURCES = src/mode_calculate_vertices.cpp src/mode_vectorize_points.cpp src/mode_compare_contacts.cpp src/mode_calculate_contacts.cpp src/mode_query_contacts_solvation_values.cpp src/modescommon/matching_utilities.h src/modescommon/drawing_links.h src/modescommon/drawing_protein_cartoons.h src/modescommon/mock_solvent_utilities.h src/modescommon/filepath_utilities.h src/modescommon/ball_value.h src/modescommon/contact_value.h src/modescommon/statistics_utilities.h src/modescommo [...]
+dist_bin_SCRIPTS = voronota-resources voronota-voromqa voronota-contacts voronota-cadscore voronota-volumes
+dist_man1_MANS = voronota.man
diff --git a/Makefile.in b/Makefile.in
new file mode 100644
index 0000000..79635d9
--- /dev/null
+++ b/Makefile.in
@@ -0,0 +1,1373 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+
+VPATH = @srcdir@
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+install_sh_DATA = $(install_sh) -c -m 644
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+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+bin_PROGRAMS = voronota$(EXEEXT)
+subdir = .
+DIST_COMMON = $(am__configure_deps) $(dist_bin_SCRIPTS) \
+ $(dist_man1_MANS) $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+ $(top_srcdir)/configure depcomp install-sh missing
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
+ configure.lineno config.status.lineno
+mkinstalldirs = $(install_sh) -d
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" \
+ "$(DESTDIR)$(man1dir)"
+PROGRAMS = $(bin_PROGRAMS)
+am_voronota_OBJECTS = mode_calculate_vertices.$(OBJEXT) \
+ mode_vectorize_points.$(OBJEXT) \
+ mode_compare_contacts.$(OBJEXT) \
+ mode_calculate_contacts.$(OBJEXT) \
+ mode_query_contacts_solvation_values.$(OBJEXT) \
+ mode_query_balls_clashes.$(OBJEXT) \
+ mode_calculate_vertices_in_parallel.$(OBJEXT) \
+ mode_get_balls_from_atoms_file.$(OBJEXT) \
+ mode_expand_descriptors.$(OBJEXT) mode_draw_balls.$(OBJEXT) \
+ mode_score_contacts_energy.$(OBJEXT) \
+ mode_score_scores.$(OBJEXT) \
+ mode_query_contacts_simulating_unfolding.$(OBJEXT) \
+ main.$(OBJEXT) mode_score_contacts_potential.$(OBJEXT) \
+ mode_vectorize_contacts.$(OBJEXT) \
+ mode_score_contacts_quality.$(OBJEXT) \
+ mode_query_balls_sequences_pairings_stats.$(OBJEXT) \
+ mode_wrapped_get_balls_from_atoms_file_and_calculate_vertices.$(OBJEXT) \
+ mode_plot_contacts.$(OBJEXT) \
+ mode_vectorize_contact_environments.$(OBJEXT) \
+ mode_calculate_mock_solvent.$(OBJEXT) \
+ mode_place_membrane.$(OBJEXT) mode_query_balls.$(OBJEXT) \
+ mode_write_qa_scores_in_casp_format.$(OBJEXT) \
+ mode_score_contacts_potentials_stats.$(OBJEXT) \
+ mode_rotational_optimization_demo.$(OBJEXT) \
+ mode_demo_ses.$(OBJEXT) \
+ mode_score_contacts_energy_stats.$(OBJEXT) \
+ mode_write_balls_to_atoms_file.$(OBJEXT) \
+ mode_demo_polygon_triangulation.$(OBJEXT) \
+ mode_demo_hypercut.$(OBJEXT) mode_draw_contacts.$(OBJEXT) \
+ mode_score_contacts_global_energy_by_cuts.$(OBJEXT) \
+ mode_query_contacts.$(OBJEXT) \
+ mode_query_contacts_depth_values.$(OBJEXT) \
+ mode_simulate_potential_for_membrane_proteins.$(OBJEXT)
+voronota_OBJECTS = $(am_voronota_OBJECTS)
+voronota_LDADD = $(LDADD)
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+ *) f=$$p;; \
+ esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+ for p in $$list; do echo "$$p $$p"; done | \
+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+ if (++n[$$2] == $(am__install_max)) \
+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+ END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
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+am__depfiles_maybe = depfiles
+am__mv = mv -f
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+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
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+voronota_SOURCES = src/mode_calculate_vertices.cpp \
+ src/mode_vectorize_points.cpp src/mode_compare_contacts.cpp \
+ src/mode_calculate_contacts.cpp \
+ src/mode_query_contacts_solvation_values.cpp \
+ src/modescommon/matching_utilities.h \
+ src/modescommon/drawing_links.h \
+ src/modescommon/drawing_protein_cartoons.h \
+ src/modescommon/mock_solvent_utilities.h \
+ src/modescommon/filepath_utilities.h \
+ src/modescommon/ball_value.h src/modescommon/contact_value.h \
+ src/modescommon/statistics_utilities.h \
+ src/modescommon/contacts_scoring_utilities.h \
+ src/modescommon/svg_writer.h \
+ src/modescommon/generic_utilities.h \
+ src/modescommon/properties_value.h \
+ src/modescommon/drawing_cylinder.h \
+ src/modescommon/vectorization_utilities.h \
+ src/modescommon/drawing_utilities.h \
+ src/modescommon/drawing_nucleic_acid_cartoons.h \
+ src/modescommon/sequence_utilities.h \
+ src/wrapper_get_balls_from_atoms_file_and_calculate_vertices.h \
+ src/mode_query_balls_clashes.cpp \
+ src/mode_calculate_vertices_in_parallel.cpp \
+ src/mode_get_balls_from_atoms_file.cpp \
+ src/mode_expand_descriptors.cpp src/compatability_macros.h \
+ src/mode_draw_balls.cpp src/mode_score_contacts_energy.cpp \
+ src/mode_score_scores.cpp \
+ src/mode_query_contacts_simulating_unfolding.cpp src/main.cpp \
+ src/mode_score_contacts_potential.cpp \
+ src/mode_vectorize_contacts.cpp \
+ src/mode_score_contacts_quality.cpp src/auxiliaries/atoms_io.h \
+ src/auxiliaries/io_utilities.h \
+ src/auxiliaries/chain_residue_atom_descriptor.h \
+ src/auxiliaries/residue_letters_coding.h \
+ src/auxiliaries/opengl_printer.h \
+ src/auxiliaries/program_options_handler.h \
+ src/auxiliaries/pairwise_sequence_alignment.h \
+ src/auxiliaries/residue_atoms_reference.h \
+ src/auxiliaries/xml_writer.h \
+ src/auxiliaries/atom_radius_assigner.h \
+ src/mode_query_balls_sequences_pairings_stats.cpp \
+ src/mode_wrapped_get_balls_from_atoms_file_and_calculate_vertices.cpp \
+ src/mode_plot_contacts.cpp \
+ src/mode_vectorize_contact_environments.cpp \
+ src/mode_calculate_mock_solvent.cpp \
+ src/mode_place_membrane.cpp src/mode_query_balls.cpp \
+ src/mode_write_qa_scores_in_casp_format.cpp \
+ src/mode_score_contacts_potentials_stats.cpp \
+ src/mode_rotational_optimization_demo.cpp \
+ src/mode_demo_ses.cpp src/mode_score_contacts_energy_stats.cpp \
+ src/mode_write_balls_to_atoms_file.cpp \
+ src/mode_demo_polygon_triangulation.cpp \
+ src/mode_demo_hypercut.cpp src/mode_draw_contacts.cpp \
+ src/apollota/subdivided_icosahedron.h \
+ src/apollota/constrained_contacts_utilities.h \
+ src/apollota/triangulation_output.h src/apollota/tuple.h \
+ src/apollota/triangulation_queries.h \
+ src/apollota/spheres_boundary_construction.h \
+ src/apollota/tangent_plane_of_three_spheres.h \
+ src/apollota/rotation.h \
+ src/apollota/tangent_sphere_of_three_spheres.h \
+ src/apollota/triangulation.h \
+ src/apollota/safer_quadratic_equation_root.h \
+ src/apollota/basic_operations_on_points.h \
+ src/apollota/bounding_spheres_hierarchy.h \
+ src/apollota/splitting_of_spheres.h \
+ src/apollota/rolling_topology.h src/apollota/polar_sorting.h \
+ src/apollota/safer_comparison_of_numbers.h \
+ src/apollota/hyperboloid_between_two_spheres.h \
+ src/apollota/tangent_sphere_of_four_spheres.h \
+ src/apollota/constrained_contact_contour.h \
+ src/apollota/basic_operations_on_spheres.h \
+ src/apollota/spherical_contacts_construction.h \
+ src/apollota/constrained_contacts_construction.h \
+ src/apollota/constrained_contact_remainder.h \
+ src/apollota/safer_summation.h \
+ src/apollota/search_for_spherical_collisions.h \
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <meta name="generator" content="pandoc" />
+ <title></title>
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+ div#TOC > ul > li > ul > li ul { display: none; }
+ </style>
+</head>
+<body>
+<h1>Voronota version 1.18</h1>
+<div id="TOC">
+<ul>
+<li><a href="#about-voronota">About Voronota</a></li>
+<li><a href="#getting-the-latest-version">Getting the latest version</a></li>
+<li><a href="#building-from-source-code">Building from source code</a><ul>
+<li><a href="#using-c-compiler-directly">Using C++ compiler directly</a></li>
+<li><a href="#using-make">Using make</a></li>
+<li><a href="#using-cmake">Using CMake</a></li>
+<li><a href="#enabling-openmp">Enabling OpenMP</a></li>
+<li><a href="#enabling-mpi">Enabling MPI</a></li>
+<li><a href="#tr1-usage-switch">TR1 usage switch</a></li>
+</ul></li>
+<li><a href="#basic-usage-example">Basic usage example</a><ul>
+<li><a href="#computing-voronoi-vertices">Computing Voronoi vertices</a></li>
+<li><a href="#computing-inter-atom-contacts">Computing inter-atom contacts</a></li>
+<li><a href="#computing-annotated-inter-atom-contacts">Computing annotated inter-atom contacts</a></li>
+<li><a href="#querying-annotated-inter-atom-contacts">Querying annotated inter-atom contacts</a></li>
+<li><a href="#getting-help-in-command-line">Getting help in command line</a></li>
+</ul></li>
+<li><a href="#command-reference">Command reference</a><ul>
+<li><a href="#list-of-all-commands">List of all commands</a></li>
+<li><a href="#command-get-balls-from-atoms-file">Command 'get-balls-from-atoms-file'</a><ul>
+<li><a href="#command-line-arguments">Command line arguments:</a></li>
+<li><a href="#input-stream">Input stream:</a></li>
+<li><a href="#output-stream">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-calculate-vertices">Command 'calculate-vertices'</a><ul>
+<li><a href="#command-line-arguments-1">Command line arguments:</a></li>
+<li><a href="#input-stream-1">Input stream:</a></li>
+<li><a href="#output-stream-1">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-calculate-vertices-in-parallel">Command 'calculate-vertices-in-parallel'</a><ul>
+<li><a href="#command-line-arguments-2">Command line arguments:</a></li>
+<li><a href="#input-stream-2">Input stream:</a></li>
+<li><a href="#output-stream-2">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-calculate-contacts">Command 'calculate-contacts'</a><ul>
+<li><a href="#command-line-arguments-3">Command line arguments:</a></li>
+<li><a href="#input-stream-3">Input stream:</a></li>
+<li><a href="#output-stream-3">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-query-balls">Command 'query-balls'</a><ul>
+<li><a href="#command-line-arguments-4">Command line arguments:</a></li>
+<li><a href="#input-stream-4">Input stream:</a></li>
+<li><a href="#output-stream-4">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-query-contacts">Command 'query-contacts'</a><ul>
+<li><a href="#command-line-arguments-5">Command line arguments:</a></li>
+<li><a href="#input-stream-5">Input stream:</a></li>
+<li><a href="#output-stream-5">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-draw-contacts">Command 'draw-contacts'</a><ul>
+<li><a href="#command-line-arguments-6">Command line arguments:</a></li>
+<li><a href="#input-stream-6">Input stream:</a></li>
+<li><a href="#output-stream-6">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-score-contacts-energy">Command 'score-contacts-energy'</a><ul>
+<li><a href="#command-line-arguments-7">Command line arguments:</a></li>
+<li><a href="#input-stream-7">Input stream:</a></li>
+<li><a href="#output-stream-7">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-score-contacts-quality">Command 'score-contacts-quality'</a><ul>
+<li><a href="#command-line-arguments-8">Command line arguments:</a></li>
+<li><a href="#input-stream-8">Input stream:</a></li>
+<li><a href="#output-stream-8">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-score-contacts-potential">Command 'score-contacts-potential'</a><ul>
+<li><a href="#command-line-arguments-9">Command line arguments:</a></li>
+<li><a href="#input-stream-9">Input stream:</a></li>
+<li><a href="#output-stream-9">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-compare-contacts">Command 'compare-contacts'</a><ul>
+<li><a href="#command-line-arguments-10">Command line arguments:</a></li>
+<li><a href="#input-stream-10">Input stream:</a></li>
+<li><a href="#output-stream-10">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-write-balls-to-atoms-file">Command 'write-balls-to-atoms-file'</a><ul>
+<li><a href="#command-line-arguments-11">Command line arguments:</a></li>
+<li><a href="#input-stream-11">Input stream:</a></li>
+<li><a href="#output-stream-11">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-query-balls-clashes">Command 'query-balls-clashes'</a><ul>
+<li><a href="#command-line-arguments-12">Command line arguments:</a></li>
+<li><a href="#input-stream-12">Input stream:</a></li>
+<li><a href="#output-stream-12">Output stream:</a></li>
+</ul></li>
+<li><a href="#command-expand-descriptors">Command 'expand-descriptors'</a><ul>
+<li><a href="#command-line-arguments-13">Command line arguments:</a></li>
+<li><a href="#input-stream-13">Input stream:</a></li>
+<li><a href="#output-stream-13">Output stream:</a></li>
+</ul></li>
+</ul></li>
+<li><a href="#wrapper-scripts">Wrapper scripts</a><ul>
+<li><a href="#voromqa-method-script">VoroMQA method script</a></li>
+<li><a href="#cad-score-method-script">CAD-score method script</a></li>
+<li><a href="#contacts-calculation-convenience-script">Contacts calculation convenience script</a></li>
+<li><a href="#volumes-calculation-convenience-script">Volumes calculation convenience script</a></li>
+</ul></li>
+</ul>
+</div>
+<h1 id="about-voronota"><a href="#TOC">About Voronota</a></h1>
+<p>The analysis of macromolecular structures often requires a comprehensive definition of atomic neighborhoods. Such a definition can be based on the Voronoi diagram of balls, where each ball represents an atom of some van der Waals radius. Voronota is a software tool for finding all the vertices of the Voronoi diagram of balls. Such vertices correspond to the centers of the empty tangent spheres defined by quadruples of balls. Voronota is especially suitable for processing three-dimensi [...]
+<p>Since version 1.2 Voronota also uses the Voronoi vertices to construct inter-atom contact surfaces and solvent accessible surfaces. Voronota provides tools to query contacts, generate contacts graphics, compare contacts and evaluate quality of protein structural models using contacts.</p>
+<p>Voronota is developed by Kliment Olechnovic (kliment at ibt.lt).</p>
+<h1 id="getting-the-latest-version"><a href="#TOC">Getting the latest version</a></h1>
+<p>Download the latest archive from the official downloads page: <a href="https://bitbucket.org/kliment/voronota/downloads">https://bitbucket.org/kliment/voronota/downloads</a>.</p>
+<p>The archive contains ready-to-use statically compiled 'voronota' program for 64 bit Linux systems. This executable can be rebuilt from the provided source code to work on any modern Linux, Mac OS X or Windows operating systems.</p>
+<p>Packages in .deb or .rpm formats are currently not available. However, installing Voronota in Linux or Mac OS X is easy: just copy Voronota executable files ('voronota' program and, if needed, the wrapper scripts) to one of the directories listed in $PATH variable.</p>
+<h1 id="building-from-source-code"><a href="#TOC">Building from source code</a></h1>
+<h2 id="using-c-compiler-directly"><a href="#TOC">Using C++ compiler directly</a></h2>
+<p>Voronota has no required external dependencies, only a standard-compliant C++ compiler is needed to build it.</p>
+<p>For example, "voronota" executable can be built from the sources in "src" directory using GNU C++ compiler:</p>
+<pre><code>g++ -O3 -o voronota src/*.cpp
+</code></pre>
+<h2 id="using-make"><a href="#TOC">Using make</a></h2>
+<p>You can generate and use a makefile:</p>
+<pre><code>./configure
+make
+</code></pre>
+<p>It allows to install and uninstall Voronota executables:</p>
+<pre><code>make install
+make uninstall
+</code></pre>
+<h2 id="using-cmake"><a href="#TOC">Using CMake</a></h2>
+<p>You can build using CMake for makefile generation. Starting in the directory containing "CMakeLists.txt" file, run the sequence of commands:</p>
+<pre><code>cmake ./
+make
+</code></pre>
+<h2 id="enabling-openmp"><a href="#TOC">Enabling OpenMP</a></h2>
+<p>To enable the usage of OpenMP for parallel processing when building using C++ compiler directly, add "-fopenmp" option:</p>
+<pre><code>g++ -O3 -fopenmp -o voronota src/*.cpp
+</code></pre>
+<p>When generating a makefile with a "configure" script, OpenMP usage can be enabled by setting CXXFLAGS variable:</p>
+<pre><code>./configure CXXFLAGS="-O3 -fopenmp"
+make
+</code></pre>
+<p>When using CMake, OpenMP usage is enabled automatically if it is possible.</p>
+<h2 id="enabling-mpi"><a href="#TOC">Enabling MPI</a></h2>
+<p>To enable the usage of MPI for parallel processing, you can use mpic++ compiler wrapper. You also need to define "ENABLE_MPI" macro when buiding:</p>
+<pre><code>mpic++ -O3 -DENABLE_MPI -o voronota ./src/*.cpp
+</code></pre>
+<h2 id="tr1-usage-switch"><a href="#TOC">TR1 usage switch</a></h2>
+<p>Voronota can be built with either modern C++ compilers or pre-C++11 compilers that support C++ Technical Report 1 (TR1) features. The voronota code has preprocessor-based checks to find out if C++ TR1 namespace is available and needs to be used. If compilation fails, it may mean that these checks failed. To troubleshoot this, try setting the value of the "USE_TR1" macro to 0 (to not use TR1 and to rely on C++11 standard) or 1 (to use TR1) when compiling, for example:</p>
+<pre><code>g++ -O3 -DUSE_TR1=1 -o voronota src/*.cpp
+</code></pre>
+<p>or</p>
+<pre><code>g++ -O3 -std=c++11 -DUSE_TR1=0 -o voronota src/*.cpp
+</code></pre>
+<h1 id="basic-usage-example"><a href="#TOC">Basic usage example</a></h1>
+<h2 id="computing-voronoi-vertices"><a href="#TOC">Computing Voronoi vertices</a></h2>
+<p>Here is a basic example of computing Voronoi vertices for a structure in a PDB file:</p>
+<pre><code>./voronota get-balls-from-atoms-file < input.pdb > balls.txt
+./voronota calculate-vertices < balls.txt > vertices.txt
+</code></pre>
+<p>The first command reads a PDB file "input.pdb" and outputs a file "balls.txt" that contains balls corresponding to the atoms in "input.pdb" (by default, Voronota ignores all heteroatoms and all hydrogen atoms when reading PDB files: this behavior can be altered using command-line options). The second command reads "balls.txt" and outputs a file "vertices.txt" that contains a quadruples and empty tangent spheres that correspond to the v [...]
+<p>In "balls.txt" the line format is "x y z r # comments". The first four values (x, y, z, r) are atomic ball coordinates and radius. Comments are not needed for further calculations, they are to assist human readers. For example, below is a part of some possible "balls.txt":</p>
+<pre><code>28.888 9.409 52.301 1.7 # 1 A 2 SER N
+27.638 10.125 52.516 1.9 # 2 A 2 SER CA
+26.499 9.639 51.644 1.75 # 3 A 2 SER C
+26.606 8.656 50.915 1.49 # 4 A 2 SER O
+27.783 11.635 52.378 1.91 # 5 A 2 SER CB
+27.69 12.033 51.012 1.54 # 6 A 2 SER OG
+</code></pre>
+<p>In "vertices.txt" the line format is "q1 q2 q3 q4 x y z r". The first four numbers (q1, q2, q3, q4) are numbers of atomic records in "balls.txt", starting from 0. The remaining four values (x, y, z, r) are the coordinates and the radius of an empty tangent sphere of the quadruple of atoms. For example, below is a part of some possible "vertices.txt":</p>
+<pre><code>0 1 2 3 27.761 8.691 51.553 -0.169
+0 1 2 23 28.275 9.804 50.131 0.588
+0 1 3 1438 24.793 -3.225 60.761 14.047
+0 1 4 5 28.785 10.604 50.721 0.283
+0 1 4 1453 30.018 10.901 55.386 1.908
+0 1 5 23 28.544 10.254 50.194 0.595
+</code></pre>
+<h2 id="computing-inter-atom-contacts"><a href="#TOC">Computing inter-atom contacts</a></h2>
+<p>Taking the "balls.txt" file described in the previous section, here is a basic example of computing inter-atom contacts:</p>
+<pre><code>./voronota calculate-contacts < balls.txt > contacts.txt
+</code></pre>
+<p>In "contacts.txt" file the line format is "b1 b2 area". The first two numbers (b1 and b2) are numbers of atomic records in "balls.txt", starting from 0. If b1 does not equal b2, then the 'area' value is the area of contact between atoms b1 and b2. If b1 equals b2, then the 'area' value is the solvent-accessible area of atom b1. For example, below is a part of some possible "contacts.txt":</p>
+<pre><code>0 0 35.440
+0 1 15.908
+0 2 0.167
+0 3 7.025
+0 4 7.021
+0 5 0.624
+0 23 2.849
+0 25 0.008
+0 26 11.323
+0 1454 0.021
+1 1 16.448
+1 2 11.608
+1 3 0.327
+1 4 14.170
+1 5 0.820
+1 6 3.902
+1 23 0.081
+2 2 3.591
+2 3 11.714
+2 4 0.305
+2 5 2.019
+</code></pre>
+<h2 id="computing-annotated-inter-atom-contacts"><a href="#TOC">Computing annotated inter-atom contacts</a></h2>
+<p>Here is a basic example of computing annotated inter-atom contacts:</p>
+<pre><code>./voronota get-balls-from-atoms-file --annotated < input.pdb > annotated_balls.txt
+./voronota calculate-contacts --annotated < annotated_balls.txt > annotated_contacts.txt
+</code></pre>
+<p>In "annotated_contacts.txt" the line format is "annotation1 annotation2 area distance tags adjuncts [graphics]". The strings 'annotation1' and 'annotation2' describe contacting atoms, the 'area' value is the area of contact between the two atoms, the 'distance' value is the distance between the centers of the contacting atoms. If 'annotation2' contains string "solvent", then the 'area' value is the solvent-accessible area of the atom described by 'annotat [...]
+<pre><code>c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<2>R<SER>A<CA> 15.908 1.456 . .
+c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<3>R<SER>A<C> 0.167 2.488 . .
+c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<4>R<SER>A<O> 7.025 2.774 . .
+c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<5>R<SER>A<CB> 7.021 2.486 . .
+c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<6>R<SER>A<OG> 0.624 3.159 . .
+c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<24>R<GLU>A<CB> 2.849 4.628 . .
+c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<26>R<GLU>A<CD> 0.008 4.792 . .
+c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<27>R<GLU>A<OE1> 11.323 3.932 . .
+c<A>r<2>a<1>R<SER>A<N> c<A>r<194>a<1501>R<LEU>A<CD2> 0.021 5.465 . .
+c<A>r<2>a<1>R<SER>A<N> c<solvent> 35.440 5.9 . .
+c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<3>R<SER>A<C> 11.608 1.514 . .
+c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<4>R<SER>A<O> 0.327 2.405 . .
+c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<5>R<SER>A<CB> 14.170 1.523 . .
+c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<6>R<SER>A<OG> 0.820 2.430 . .
+c<A>r<2>a<2>R<SER>A<CA> c<A>r<3>a<7>R<LYS>A<N> 3.902 2.371 . .
+c<A>r<2>a<2>R<SER>A<CA> c<A>r<5>a<24>R<GLU>A<CB> 0.081 4.954 . .
+c<A>r<2>a<2>R<SER>A<CA> c<solvent> 16.448 6.1 . .
+</code></pre>
+<p>Each atomic descriptor in the above text can be transformed into a space-separated list (chainID resSeq iCode serial altLoc resName name) using "voronota expand-descriptors" command:</p>
+<pre><code>cat annotated_contacts.txt | voronota expand-descriptors | column -t > expanded_table_of_contacts.txt
+</code></pre>
+<p>Below is a part of some possible "expanded_table_of_contacts.txt":</p>
+<pre><code>A 2 . 1 . SER N A 2 . 2 . SER CA 15.908 1.456 . .
+A 2 . 1 . SER N A 2 . 3 . SER C 0.167 2.488 . .
+A 2 . 1 . SER N A 2 . 4 . SER O 7.025 2.774 . .
+A 2 . 1 . SER N A 2 . 5 . SER CB 7.021 2.486 . .
+A 2 . 1 . SER N A 2 . 6 . SER OG 0.624 3.159 . .
+A 2 . 1 . SER N A 5 . 24 . GLU CB 2.849 4.628 . .
+A 2 . 1 . SER N A 5 . 26 . GLU CD 0.008 4.792 . .
+A 2 . 1 . SER N A 5 . 27 . GLU OE1 11.323 3.932 . .
+A 2 . 1 . SER N A 194 . 1501 . LEU CD2 0.021 5.465 . .
+A 2 . 1 . SER N solvent . . . . . . 35.440 5.9 . .
+A 2 . 2 . SER CA A 2 . 3 . SER C 11.608 1.514 . .
+A 2 . 2 . SER CA A 2 . 4 . SER O 0.327 2.405 . .
+A 2 . 2 . SER CA A 2 . 5 . SER CB 14.170 1.523 . .
+A 2 . 2 . SER CA A 2 . 6 . SER OG 0.820 2.430 . .
+A 2 . 2 . SER CA A 3 . 7 . LYS N 3.902 2.371 . .
+A 2 . 2 . SER CA A 5 . 24 . GLU CB 0.081 4.954 . .
+A 2 . 2 . SER CA solvent . . . . . . 16.448 6.1 . .
+</code></pre>
+<h2 id="querying-annotated-inter-atom-contacts"><a href="#TOC">Querying annotated inter-atom contacts</a></h2>
+<p>The "voronota query-contacts" command can be used to query and manipulate computed annotated contacts. For example, below is the command that selects contacts that probably correspond to salt bridges:</p>
+<pre><code>cat annotated_contacts.txt | voronota query-contacts --match-first 'R<ASP,GLU>&A<OD1,OD2,OE1,OE2,OXT>' --match-second 'R<ARG,HIS,LYS>&A<NH1,NH2,ND1,NE2,NZ>' --match-max-dist 4.0
+</code></pre>
+<p>The "support/generate-arguments-for-query-contacts.html" file in the Voronota package provides a graphical interface for generating sets of arguments for the "voronota query-contacts" command: it serves as an interactive documentation. A similar interface for the "voronota query-balls" command is provided by the "support/generate-arguments-for-query-balls.html" file.</p>
+<h2 id="getting-help-in-command-line"><a href="#TOC">Getting help in command line</a></h2>
+<p>The list of all available Voronota commands is displayed when executing Voronota without any parameters.</p>
+<p>Command help is shown when "--help" command line option is present, for example:</p>
+<pre><code>./voronota calculate-vertices --help
+</code></pre>
+<p>Using "--help" option without specific command results in printing help for all commands:</p>
+<pre><code>./voronota --help
+</code></pre>
+<h1 id="command-reference"><a href="#TOC">Command reference</a></h1>
+<h2 id="list-of-all-commands"><a href="#TOC">List of all commands</a></h2>
+<ul>
+<li>get-balls-from-atoms-file</li>
+<li>calculate-vertices</li>
+<li>calculate-vertices-in-parallel</li>
+<li>calculate-contacts</li>
+<li>query-balls</li>
+<li>query-contacts</li>
+<li>draw-contacts</li>
+<li>score-contacts-energy</li>
+<li>score-contacts-quality</li>
+<li>score-contacts-potential</li>
+<li>compare-contacts</li>
+<li>write-balls-to-atoms-file</li>
+<li>query-balls-clashes</li>
+<li>expand-descriptors</li>
+</ul>
+<h2 id="command-get-balls-from-atoms-file"><a href="#TOC">Command 'get-balls-from-atoms-file'</a></h2>
+<h3 id="command-line-arguments"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--annotated flag to enable annotated mode
+--include-heteroatoms flag to include heteroatoms
+--include-hydrogens flag to include hydrogen atoms
+--multimodel-chains flag to read multiple models in PDB format and rename chains accordingly
+--mmcif flag to input in mmCIF format
+--radii-file string path to radii configuration file
+--default-radius number default atomic radius
+--only-default-radius flag to make all radii equal to the default radius
+--hull-offset number positive offset distance enables adding artificial hull balls
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream"><a href="#TOC">Input stream:</a></h3>
+<pre><code>file in PDB or mmCIF format
+</code></pre>
+<h3 id="output-stream"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of balls
+
+ default mode line format: 'x y z r # atomSerial chainID resSeq resName atomName altLoc iCode'
+
+ annotated mode line format: 'annotation x y z r tags adjuncts'
+</code></pre>
+<h2 id="command-calculate-vertices"><a href="#TOC">Command 'calculate-vertices'</a></h2>
+<h3 id="command-line-arguments-1"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--print-log flag to print log of calculations
+--exclude-hidden-balls flag to exclude hidden input balls
+--include-surplus-quadruples flag to include surplus quadruples
+--link flag to output links between vertices
+--init-radius-for-BSH number initial radius for bounding sphere hierarchy
+--check flag to slowly check the resulting vertices (used only for testing)
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-1"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of balls (line format: 'x y z r')
+</code></pre>
+<h3 id="output-stream-1"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')
+</code></pre>
+<h2 id="command-calculate-vertices-in-parallel"><a href="#TOC">Command 'calculate-vertices-in-parallel'</a></h2>
+<h3 id="command-line-arguments-2"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--method string * parallelization method name, variants are: 'simulated'
+--parts number * number of parts for splitting, must be power of 2
+--print-log flag to print log of calculations
+--include-surplus-quadruples flag to include surplus quadruples
+--link flag to output links between vertices
+--init-radius-for-BSH number initial radius for bounding sphere hierarchy
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-2"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of balls (line format: 'x y z r')
+</code></pre>
+<h3 id="output-stream-2"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')
+</code></pre>
+<h2 id="command-calculate-contacts"><a href="#TOC">Command 'calculate-contacts'</a></h2>
+<h3 id="command-line-arguments-3"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--annotated flag to enable annotated mode
+--probe number probe radius
+--exclude-hidden-balls flag to exclude hidden input balls
+--step number curve step length
+--projections number curve optimization depth
+--sih-depth number spherical surface optimization depth
+--add-mirrored flag to add mirrored contacts to non-annnotated output
+--draw flag to output graphics for annotated contacts
+--tag-centrality flag to tag contacts centrality
+--tag-peripherial flag to tag peripherial contacts
+--old-contacts-output string file path to output spherical contacts
+--volumes-output string file path to output constrained cells volumes
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-3"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of balls
+
+ default mode line format: 'x y z r'
+
+ annotated mode line format: 'annotation x y z r tags adjuncts'
+</code></pre>
+<h3 id="output-stream-3"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of contacts
+
+ default mode line format: 'b1 b2 area'
+
+ annotated mode line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]'
+</code></pre>
+<h2 id="command-query-balls"><a href="#TOC">Command 'query-balls'</a></h2>
+<h3 id="command-line-arguments-4"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--match string selection
+--match-not string negative selection
+--match-tags string tags to match
+--match-tags-not string tags to not match
+--match-adjuncts string adjuncts intervals to match
+--match-adjuncts-not string adjuncts intervals to not match
+--match-external-annotations string file path to input matchable annotations
+--invert flag to invert selection
+--whole-residues flag to select whole residues
+--drop-atom-serials flag to drop atom serial numbers from input
+--drop-altloc-indicators flag to drop alternate location indicators from input
+--drop-tags flag to drop all tags from input
+--drop-adjuncts flag to drop all adjuncts from input
+--set-tags string set tags instead of filtering
+--set-dssp-info string file path to input DSSP file
+--set-adjuncts string set adjuncts instead of filtering
+--set-external-adjuncts string file path to input external adjuncts
+--set-external-adjuncts-name string name for external adjuncts
+--rename-chains flag to rename input chains to be in interval from 'A' to 'Z'
+--renumber-from-adjunct string adjunct name to use for input residue renumbering
+--renumber-positively flag to increment residue numbers to make them positive
+--reset-serials flag to reset atom serial numbers
+--set-seq-pos-adjunct flag to set normalized sequence position adjunct
+--set-ref-seq-num-adjunct string file path to input reference sequence
+--ref-seq-alignment string file path to output alignment with reference
+--seq-output string file path to output query result sequence string
+--chains-summary-output string file path to output chains summary
+--chains-seq-identity number sequence identity threshold for chains summary, default is 0.9
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-4"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of balls (line format: 'annotation x y z r tags adjuncts')
+</code></pre>
+<h3 id="output-stream-4"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of balls (line format: 'annotation x y z r tags adjuncts')
+</code></pre>
+<h2 id="command-query-contacts"><a href="#TOC">Command 'query-contacts'</a></h2>
+<h3 id="command-line-arguments-5"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--match-first string selection for first contacting group
+--match-first-not string negative selection for first contacting group
+--match-second string selection for second contacting group
+--match-second-not string negative selection for second contacting group
+--match-min-seq-sep number minimum residue sequence separation
+--match-max-seq-sep number maximum residue sequence separation
+--match-min-area number minimum contact area
+--match-max-area number maximum contact area
+--match-min-dist number minimum distance
+--match-max-dist number maximum distance
+--match-tags string tags to match
+--match-tags-not string tags to not match
+--match-adjuncts string adjuncts intervals to match
+--match-adjuncts-not string adjuncts intervals to not match
+--match-external-first string file path to input matchable annotations
+--match-external-second string file path to input matchable annotations
+--match-external-pairs string file path to input matchable annotation pairs
+--no-solvent flag to not include solvent accessible areas
+--no-same-chain flag to not include same chain contacts
+--invert flag to invert selection
+--drop-tags flag to drop all tags from input
+--drop-adjuncts flag to drop all adjuncts from input
+--set-tags string set tags instead of filtering
+--set-hbplus-tags string file path to input HBPLUS file
+--set-distance-bins-tags string list of distance thresholds
+--inter-residue-hbplus-tags flag to set inter-residue H-bond tags
+--set-adjuncts string set adjuncts instead of filtering
+--set-external-adjuncts string file path to input external adjuncts
+--set-external-adjuncts-name string name for external adjuncts
+--set-external-means string file path to input external values for averaging
+--set-external-means-name string name for external means
+--renaming-map string file path to input atoms renaming map
+--inter-residue flag to convert input to inter-residue contacts
+--inter-residue-after flag to convert output to inter-residue contacts
+--summing-exceptions string file path to input inter-residue summing exceptions annotations
+--summarize flag to output only summary of matched contacts
+--summarize-by-first flag to output only summary of matched contacts by first identifier
+--preserve-graphics flag to preserve graphics in output
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-5"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')
+</code></pre>
+<h3 id="output-stream-5"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')
+</code></pre>
+<h2 id="command-draw-contacts"><a href="#TOC">Command 'draw-contacts'</a></h2>
+<h3 id="command-line-arguments-6"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--drawing-for-pymol string file path to output drawing as pymol script
+--drawing-for-jmol string file path to output drawing as jmol script
+--drawing-for-scenejs string file path to output drawing as scenejs script
+--drawing-name string graphics object name for drawing output
+--default-color string default color for drawing output, in hex format, white is 0xFFFFFF
+--adjunct-gradient string adjunct name to use for gradient-based coloring
+--adjunct-gradient-blue number blue adjunct gradient value
+--adjunct-gradient-red number red adjunct gradient value
+--adjuncts-rgb flag to use RGB color values from adjuncts
+--random-colors flag to use random color for each drawn contact
+--alpha number alpha opacity value for drawing output
+--use-labels flag to use labels in drawing if possible
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-6"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')
+</code></pre>
+<h3 id="output-stream-6"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')
+</code></pre>
+<h2 id="command-score-contacts-energy"><a href="#TOC">Command 'score-contacts-energy'</a></h2>
+<h3 id="command-line-arguments-7"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--potential-file string * file path to input potential values
+--ignorable-max-seq-sep number maximum residue sequence separation for ignorable contacts
+--inter-atom-scores-file string file path to output inter-atom scores
+--atom-scores-file string file path to output atom scores
+--depth number neighborhood normalization depth
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-7"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of contacts (line format: 'annotation1 annotation2 conditions area')
+</code></pre>
+<h3 id="output-stream-7"><a href="#TOC">Output stream:</a></h3>
+<pre><code>global scores
+</code></pre>
+<h2 id="command-score-contacts-quality"><a href="#TOC">Command 'score-contacts-quality'</a></h2>
+<h3 id="command-line-arguments-8"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--default-mean number default mean parameter
+--default-sd number default standard deviation parameter
+--means-and-sds-file string file path to input atomic mean and sd parameters
+--mean-shift number mean shift in standard deviations
+--external-weights-file string file path to input external weights for global scoring
+--smoothing-window number window to smooth residue quality scores along sequence
+--atom-scores-file string file path to output atom scores
+--residue-scores-file string file path to output residue scores
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-8"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of atom energy descriptors
+</code></pre>
+<h3 id="output-stream-8"><a href="#TOC">Output stream:</a></h3>
+<pre><code>weighted average local score
+</code></pre>
+<h2 id="command-score-contacts-potential"><a href="#TOC">Command 'score-contacts-potential'</a></h2>
+<h3 id="command-line-arguments-9"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--input-file-list flag to read file list from stdin
+--input-contributions string file path to input contact types contributions
+--input-fixed-types string file path to input fixed types
+--input-seq-pairs-stats string file path to input sequence pairings statistics
+--potential-file string file path to output potential values
+--probabilities-file string file path to output observed and expected probabilities
+--single-areas-file string file path to output single type total areas
+--contributions-file string file path to output contact types contributions
+--multiply-areas number coefficient to multiply output areas
+--toggling-list string list of toggling subtags
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-9"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of contacts (line format: 'annotation1 annotation2 conditions area')
+</code></pre>
+<h3 id="output-stream-9"><a href="#TOC">Output stream:</a></h3>
+<pre><code>line of contact type area summaries (line format: 'annotation1 annotation2 conditions area')
+</code></pre>
+<h2 id="command-compare-contacts"><a href="#TOC">Command 'compare-contacts'</a></h2>
+<h3 id="command-line-arguments-10"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--target-contacts-file string * file path to input target contacts
+--inter-atom-scores-file string file path to output inter-atom scores
+--inter-residue-scores-file string file path to output inter-residue scores
+--atom-scores-file string file path to output atom scores
+--residue-scores-file string file path to output residue scores
+--depth number local neighborhood depth
+--smoothing-window number window to smooth residue scores along sequence
+--smoothed-scores-file string file path to output smoothed residue scores
+--ignore-residue-names flag to consider just residue numbers and ignore residue names
+--residue-level-only flag to output only residue-level results
+--detailed-output flag to enable detailed output
+--chains-renaming-file string file path to input chains renaming
+--remap-chains flag to calculate optimal chains remapping
+--remap-chains-log flag output remapping progress to stderr
+--remapped-chains-file string file path to output calculated chains remapping
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-10"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of model contacts (line format: 'annotation1 annotation2 area')
+</code></pre>
+<h3 id="output-stream-10"><a href="#TOC">Output stream:</a></h3>
+<pre><code>global scores (atom-level and residue-level)
+</code></pre>
+<h2 id="command-write-balls-to-atoms-file"><a href="#TOC">Command 'write-balls-to-atoms-file'</a></h2>
+<h3 id="command-line-arguments-11"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--pdb-output string file path to output query result in PDB format
+--pdb-output-b-factor string name of adjunct to output as B-factor in PDB format
+--pdb-output-template string file path to input template for B-factor insertions
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-11"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of balls (line format: 'annotation x y z r tags adjuncts')
+</code></pre>
+<h3 id="output-stream-11"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of balls (line format: 'annotation x y z r tags adjuncts')
+</code></pre>
+<h2 id="command-query-balls-clashes"><a href="#TOC">Command 'query-balls-clashes'</a></h2>
+<h3 id="command-line-arguments-12"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--clash-distance number clash distance threshold in angstroms, default is 3.0
+--min-seq-sep number minimum residue sequence separation, default is 2
+--init-radius-for-BSH number initial radius for bounding sphere hierarchy
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-12"><a href="#TOC">Input stream:</a></h3>
+<pre><code>list of balls (line format: 'annotation x y z r')
+</code></pre>
+<h3 id="output-stream-12"><a href="#TOC">Output stream:</a></h3>
+<pre><code>list of clashes (line format: 'annotation1 annotation2 distance min-distance-between-balls')
+</code></pre>
+<h2 id="command-expand-descriptors"><a href="#TOC">Command 'expand-descriptors'</a></h2>
+<h3 id="command-line-arguments-13"><a href="#TOC">Command line arguments:</a></h3>
+<pre><code>Name Type Description
+------------------------------- ------ ---- ------------------------------------------------------------------------
+--help flag to print usage help to stdout and exit
+</code></pre>
+<h3 id="input-stream-13"><a href="#TOC">Input stream:</a></h3>
+<pre><code>any text containing atom descriptors
+</code></pre>
+<h3 id="output-stream-13"><a href="#TOC">Output stream:</a></h3>
+<pre><code>text with each atom descriptor expanded to 'chainID resSeq iCode serial altLoc resName name'
+</code></pre>
+<h1 id="wrapper-scripts"><a href="#TOC">Wrapper scripts</a></h1>
+<h2 id="voromqa-method-script"><a href="#TOC">VoroMQA method script</a></h2>
+<p>'voronota-voromqa' script is an implementation of VoroMQA (Voronoi diagram-based Model Quality Assessment) method using Voronota. The script interface is presented below:</p>
+<pre><code>Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --output-atom-scores string output text file with atom scores
+ --output-atom-scores-pdb string output PDB file with atom scores as B-factors
+ --output-residue-scores string output text file with residue scores
+ --output-residue-scores-pdb string output PDB file with residue scores as B-factors
+ --output-residue-scores-plot string output PNG image file with residue scores plot, requires R
+ --help | -h flag to display help message and exit
+
+Advanced options:
+ --cache-dir string path to cache directory
+ --smoothing-window number residue scores smoothing window size, default is 5
+ --atoms-query string atoms query parameters to define selection
+ --contacts-query string contacts query parameters to define selection
+ --output-selected-scores string output text file with selected atom scores
+ --reference-sequence string sequence file or string for residue renumbering
+ --output-sequence-alignment string output text file with sequence alignment
+ --multiple-models flag to handle multiple models in PDB file
+
+Standard output (one line):
+ {input file path} {global score} {number of residues} {number of atoms} [ {selection score} {number of selected atoms} ]
+</code></pre>
+<h2 id="cad-score-method-script"><a href="#TOC">CAD-score method script</a></h2>
+<p>'voronota-cadscore' script is an implementation of CAD-score (Contact Area Difference score) method using Voronota. The script interface is presented below:</p>
+<pre><code>Basic options:
+ --input-target | -t string * input target structure file in PDB format
+ --input-model | -m string * input model structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --output-residue-scores string output text file with residue scores
+ --output-residue-scores-pdb-t string output target PDB file with residue scores as B-factors
+ --output-residue-scores-pdb-m string output model PDB file with residue scores as B-factors
+ --smoothing-window number residue scores smoothing window size, default is 0
+ --contacts-query string contacts query parameters
+ --contacts-query-inter-chain flag to consider only inter-chain contacts
+ --contacts-query-by-code string contacts query code, possible codes are AA, AS, SS, AM, MM, MS
+ --use-all-query-codes flag to output global scores for all query codes, one line per code
+ --cache-dir string path to cache directory
+ --output-header flag to output header before result line
+ --help | -h flag to display help message and exit
+
+Advanced options:
+ --ignore-residue-names flag to consider just residue numbers and ignore residue names
+ --enable-site-based-scoring falg to enable site-based scoring
+ --multiple-models flag to handle multiple models in PDB file
+ --remap-chains flag to automatically rearrange chain names for higher scores
+ --remap-chains-output string output file with chain names rearrangement
+ --old-regime flag to calculate areas as in pre-Voronota CAD-score
+
+Standard output (one line):
+ {target file path} {model file path} {query code} {number of residues} {global score} {target total area} {corresponding model total area}
+ [ {site-based number of residues} {site-based global score} {site-based target total area} {corresponding site-based model total area} ]
+</code></pre>
+<h2 id="contacts-calculation-convenience-script"><a href="#TOC">Contacts calculation convenience script</a></h2>
+<p>'voronota-contacts' script provides a way for calculating and querying interatomic contacts with just one command (without the need to construct a pipeline from 'voronota' calls).</p>
+<pre><code>Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --contacts-query string contacts query parameters
+ --contacts-query-additional string additional contacts query parameters
+ --cache-dir string path to cache directory
+ --sum-at-end flag to print sum of areas as the last line in output
+ --help | -h flag to display help message and exit
+
+Advanced options:
+ --output-drawing string output file with drawing script for PyMol
+ --drawing-parameters string drawing parameters
+ --wireframe-drawing flag to draw wireframe representation of contacts
+ --multiple-models flag to handle multiple models in PDB file
+
+Standard output (multiple lines):
+ {contacting atom} {contacting atom} {contact area} {distance between atoms centers} {tags} {adjunct values}
+</code></pre>
+<h2 id="volumes-calculation-convenience-script"><a href="#TOC">Volumes calculation convenience script</a></h2>
+<p>'voronota-volumes' script provides a way for calculating and querying atomic volumes with just one command (without the need to construct a pipeline from 'voronota' calls).</p>
+<pre><code>Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --cache-dir string path to cache directory
+ --sum-at-end flag to print sum of areas as the last line in output
+ --help | -h flag to display help message and exit
+
+Advanced options:
+ --atoms-query string atoms query parameters
+ --per-residue flag to output per-residue results
+ --multiple-models flag to handle multiple models in PDB file
+
+Standard output (multiple lines):
+ {name} {volume}
+</code></pre>
+</body>
+</html>
diff --git a/README.txt b/README.txt
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--- /dev/null
+++ b/README.txt
@@ -0,0 +1,792 @@
+# About Voronota
+
+The analysis of macromolecular structures often requires
+a comprehensive definition of atomic neighborhoods.
+Such a definition can be based on the Voronoi diagram of balls,
+where each ball represents an atom of some van der Waals radius.
+Voronota is a software tool for finding all the vertices
+of the Voronoi diagram of balls. Such vertices correspond to
+the centers of the empty tangent spheres defined by quadruples of balls.
+Voronota is especially suitable for processing three-dimensional
+structures of biological macromolecules such as proteins and RNA.
+
+Since version 1.2 Voronota also uses the Voronoi vertices to construct
+inter-atom contact surfaces and solvent accessible surfaces.
+Voronota provides tools to query contacts, generate contacts graphics,
+compare contacts and evaluate quality of protein structural models using contacts.
+
+Voronota is developed by Kliment Olechnovic (kliment at ibt.lt).
+
+
+# Getting the latest version
+
+Download the latest archive from the official downloads page:
+[https://bitbucket.org/kliment/voronota/downloads](https://bitbucket.org/kliment/voronota/downloads).
+
+The archive contains ready-to-use statically compiled 'voronota' program for
+64 bit Linux systems. This executable can be rebuilt from the provided
+source code to work on any modern Linux, Mac OS X or Windows operating systems.
+
+Packages in .deb or .rpm formats are currently not available. However,
+installing Voronota in Linux or Mac OS X is easy: just copy Voronota
+executable files ('voronota' program and, if needed, the wrapper scripts)
+to one of the directories listed in $PATH variable.
+
+
+# Building from source code
+
+## Using C++ compiler directly
+
+Voronota has no required external dependencies, only
+a standard-compliant C++ compiler is needed to build it.
+
+For example, "voronota" executable can be built from
+the sources in "src" directory using GNU C++ compiler:
+
+ g++ -O3 -o voronota src/*.cpp
+
+## Using make
+
+You can generate and use a makefile:
+
+ ./configure
+ make
+
+It allows to install and uninstall Voronota executables:
+
+ make install
+ make uninstall
+
+## Using CMake
+
+You can build using CMake for makefile generation.
+Starting in the directory containing "CMakeLists.txt" file,
+run the sequence of commands:
+
+ cmake ./
+ make
+
+## Enabling OpenMP
+
+To enable the usage of OpenMP for parallel processing when
+building using C++ compiler directly, add "-fopenmp" option:
+
+ g++ -O3 -fopenmp -o voronota src/*.cpp
+
+When generating a makefile with a "configure" script,
+OpenMP usage can be enabled by setting CXXFLAGS variable:
+
+ ./configure CXXFLAGS="-O3 -fopenmp"
+ make
+
+When using CMake, OpenMP usage is enabled automatically if it is possible.
+
+## Enabling MPI
+
+To enable the usage of MPI for parallel processing, you
+can use mpic++ compiler wrapper. You also need to define
+"ENABLE_MPI" macro when buiding:
+
+ mpic++ -O3 -DENABLE_MPI -o voronota ./src/*.cpp
+
+## TR1 usage switch
+
+Voronota can be built with either modern C++ compilers or
+pre-C++11 compilers that support C++ Technical Report 1 (TR1) features.
+The voronota code has preprocessor-based checks to find out
+if C++ TR1 namespace is available and needs to be used.
+If compilation fails, it may mean that these checks failed.
+To troubleshoot this, try setting the value of the "USE_TR1" macro
+to 0 (to not use TR1 and to rely on C++11 standard)
+or 1 (to use TR1) when compiling, for example:
+
+ g++ -O3 -DUSE_TR1=1 -o voronota src/*.cpp
+
+or
+
+ g++ -O3 -std=c++11 -DUSE_TR1=0 -o voronota src/*.cpp
+
+
+# Basic usage example
+
+## Computing Voronoi vertices
+
+Here is a basic example of computing Voronoi vertices
+for a structure in a PDB file:
+
+ ./voronota get-balls-from-atoms-file < input.pdb > balls.txt
+ ./voronota calculate-vertices < balls.txt > vertices.txt
+
+The first command reads a PDB file "input.pdb" and outputs a file "balls.txt"
+that contains balls corresponding to the atoms in "input.pdb"
+(by default, Voronota ignores all heteroatoms and all hydrogen atoms
+when reading PDB files: this behavior can be altered using command-line options).
+The second command reads "balls.txt" and outputs a file "vertices.txt"
+that contains a quadruples and empty tangent spheres that correspond
+to the vertices of the Voronoi diagram of the input balls.
+The formats of "balls.txt" and "vertices.txt" are described below.
+
+In "balls.txt" the line format is "x y z r # comments".
+The first four values (x, y, z, r) are atomic ball coordinates and radius.
+Comments are not needed for further calculations, they are to assist human readers.
+For example, below is a part of some possible "balls.txt":
+
+ 28.888 9.409 52.301 1.7 # 1 A 2 SER N
+ 27.638 10.125 52.516 1.9 # 2 A 2 SER CA
+ 26.499 9.639 51.644 1.75 # 3 A 2 SER C
+ 26.606 8.656 50.915 1.49 # 4 A 2 SER O
+ 27.783 11.635 52.378 1.91 # 5 A 2 SER CB
+ 27.69 12.033 51.012 1.54 # 6 A 2 SER OG
+
+In "vertices.txt" the line format is "q1 q2 q3 q4 x y z r".
+The first four numbers (q1, q2, q3, q4) are numbers
+of atomic records in "balls.txt", starting from 0.
+The remaining four values (x, y, z, r) are the coordinates and the radius of
+an empty tangent sphere of the quadruple of atoms.
+For example, below is a part of some possible "vertices.txt":
+
+ 0 1 2 3 27.761 8.691 51.553 -0.169
+ 0 1 2 23 28.275 9.804 50.131 0.588
+ 0 1 3 1438 24.793 -3.225 60.761 14.047
+ 0 1 4 5 28.785 10.604 50.721 0.283
+ 0 1 4 1453 30.018 10.901 55.386 1.908
+ 0 1 5 23 28.544 10.254 50.194 0.595
+
+## Computing inter-atom contacts
+
+Taking the "balls.txt" file described in the previous section,
+here is a basic example of computing inter-atom contacts:
+
+ ./voronota calculate-contacts < balls.txt > contacts.txt
+
+In "contacts.txt" file the line format is "b1 b2 area".
+The first two numbers (b1 and b2) are numbers of atomic records in "balls.txt", starting from 0.
+If b1 does not equal b2, then the 'area' value is the area of contact between atoms b1 and b2.
+If b1 equals b2, then the 'area' value is the solvent-accessible area of atom b1.
+For example, below is a part of some possible "contacts.txt":
+
+ 0 0 35.440
+ 0 1 15.908
+ 0 2 0.167
+ 0 3 7.025
+ 0 4 7.021
+ 0 5 0.624
+ 0 23 2.849
+ 0 25 0.008
+ 0 26 11.323
+ 0 1454 0.021
+ 1 1 16.448
+ 1 2 11.608
+ 1 3 0.327
+ 1 4 14.170
+ 1 5 0.820
+ 1 6 3.902
+ 1 23 0.081
+ 2 2 3.591
+ 2 3 11.714
+ 2 4 0.305
+ 2 5 2.019
+
+## Computing annotated inter-atom contacts
+
+Here is a basic example of computing annotated inter-atom contacts:
+
+ ./voronota get-balls-from-atoms-file --annotated < input.pdb > annotated_balls.txt
+ ./voronota calculate-contacts --annotated < annotated_balls.txt > annotated_contacts.txt
+
+In "annotated_contacts.txt" the line format is
+"annotation1 annotation2 area distance tags adjuncts [graphics]".
+The strings 'annotation1' and 'annotation2' describe contacting atoms,
+the 'area' value is the area of contact between the two atoms,
+the 'distance' value is the distance between the centers of the contacting atoms.
+If 'annotation2' contains string "solvent", then the 'area' value is
+the solvent-accessible area of the atom described by 'annotation1'.
+The remaining part of the line is used by Voronota querying
+and drawing commands that are not covered in this section.
+Below is a part of some possible "annotated_contacts.txt"
+(with text fields aligned using "column -t" command):
+
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<2>R<SER>A<CA> 15.908 1.456 . .
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<3>R<SER>A<C> 0.167 2.488 . .
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<4>R<SER>A<O> 7.025 2.774 . .
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<5>R<SER>A<CB> 7.021 2.486 . .
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<2>a<6>R<SER>A<OG> 0.624 3.159 . .
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<24>R<GLU>A<CB> 2.849 4.628 . .
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<26>R<GLU>A<CD> 0.008 4.792 . .
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<5>a<27>R<GLU>A<OE1> 11.323 3.932 . .
+ c<A>r<2>a<1>R<SER>A<N> c<A>r<194>a<1501>R<LEU>A<CD2> 0.021 5.465 . .
+ c<A>r<2>a<1>R<SER>A<N> c<solvent> 35.440 5.9 . .
+ c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<3>R<SER>A<C> 11.608 1.514 . .
+ c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<4>R<SER>A<O> 0.327 2.405 . .
+ c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<5>R<SER>A<CB> 14.170 1.523 . .
+ c<A>r<2>a<2>R<SER>A<CA> c<A>r<2>a<6>R<SER>A<OG> 0.820 2.430 . .
+ c<A>r<2>a<2>R<SER>A<CA> c<A>r<3>a<7>R<LYS>A<N> 3.902 2.371 . .
+ c<A>r<2>a<2>R<SER>A<CA> c<A>r<5>a<24>R<GLU>A<CB> 0.081 4.954 . .
+ c<A>r<2>a<2>R<SER>A<CA> c<solvent> 16.448 6.1 . .
+
+Each atomic descriptor in the above text can be transformed into a space-separated
+list (chainID resSeq iCode serial altLoc resName name) using "voronota expand-descriptors" command:
+
+ cat annotated_contacts.txt | voronota expand-descriptors | column -t > expanded_table_of_contacts.txt
+
+Below is a part of some possible "expanded_table_of_contacts.txt":
+
+ A 2 . 1 . SER N A 2 . 2 . SER CA 15.908 1.456 . .
+ A 2 . 1 . SER N A 2 . 3 . SER C 0.167 2.488 . .
+ A 2 . 1 . SER N A 2 . 4 . SER O 7.025 2.774 . .
+ A 2 . 1 . SER N A 2 . 5 . SER CB 7.021 2.486 . .
+ A 2 . 1 . SER N A 2 . 6 . SER OG 0.624 3.159 . .
+ A 2 . 1 . SER N A 5 . 24 . GLU CB 2.849 4.628 . .
+ A 2 . 1 . SER N A 5 . 26 . GLU CD 0.008 4.792 . .
+ A 2 . 1 . SER N A 5 . 27 . GLU OE1 11.323 3.932 . .
+ A 2 . 1 . SER N A 194 . 1501 . LEU CD2 0.021 5.465 . .
+ A 2 . 1 . SER N solvent . . . . . . 35.440 5.9 . .
+ A 2 . 2 . SER CA A 2 . 3 . SER C 11.608 1.514 . .
+ A 2 . 2 . SER CA A 2 . 4 . SER O 0.327 2.405 . .
+ A 2 . 2 . SER CA A 2 . 5 . SER CB 14.170 1.523 . .
+ A 2 . 2 . SER CA A 2 . 6 . SER OG 0.820 2.430 . .
+ A 2 . 2 . SER CA A 3 . 7 . LYS N 3.902 2.371 . .
+ A 2 . 2 . SER CA A 5 . 24 . GLU CB 0.081 4.954 . .
+ A 2 . 2 . SER CA solvent . . . . . . 16.448 6.1 . .
+
+## Querying annotated inter-atom contacts
+
+The "voronota query-contacts" command can be used to query and manipulate computed annotated contacts.
+For example, below is the command that selects contacts that probably correspond to salt bridges:
+
+ cat annotated_contacts.txt | voronota query-contacts --match-first 'R<ASP,GLU>&A<OD1,OD2,OE1,OE2,OXT>' --match-second 'R<ARG,HIS,LYS>&A<NH1,NH2,ND1,NE2,NZ>' --match-max-dist 4.0
+
+The "support/generate-arguments-for-query-contacts.html" file in the Voronota package
+provides a graphical interface for generating sets of arguments for
+the "voronota query-contacts" command: it serves as an interactive documentation.
+A similar interface for the "voronota query-balls" command is provided by
+the "support/generate-arguments-for-query-balls.html" file.
+
+## Getting help in command line
+
+The list of all available Voronota commands is displayed when executing Voronota without any parameters.
+
+Command help is shown when "--help" command line option is present, for example:
+
+ ./voronota calculate-vertices --help
+
+Using "--help" option without specific command results in printing help for all commands:
+
+ ./voronota --help
+
+# Command reference
+## List of all commands
+
+* get-balls-from-atoms-file
+* calculate-vertices
+* calculate-vertices-in-parallel
+* calculate-contacts
+* query-balls
+* query-contacts
+* draw-contacts
+* score-contacts-energy
+* score-contacts-quality
+* score-contacts-potential
+* compare-contacts
+* write-balls-to-atoms-file
+* query-balls-clashes
+* expand-descriptors
+
+## Command 'get-balls-from-atoms-file'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --annotated flag to enable annotated mode
+ --include-heteroatoms flag to include heteroatoms
+ --include-hydrogens flag to include hydrogen atoms
+ --multimodel-chains flag to read multiple models in PDB format and rename chains accordingly
+ --mmcif flag to input in mmCIF format
+ --radii-file string path to radii configuration file
+ --default-radius number default atomic radius
+ --only-default-radius flag to make all radii equal to the default radius
+ --hull-offset number positive offset distance enables adding artificial hull balls
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ file in PDB or mmCIF format
+
+### Output stream:
+
+ list of balls
+
+ default mode line format: 'x y z r # atomSerial chainID resSeq resName atomName altLoc iCode'
+
+ annotated mode line format: 'annotation x y z r tags adjuncts'
+
+## Command 'calculate-vertices'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --print-log flag to print log of calculations
+ --exclude-hidden-balls flag to exclude hidden input balls
+ --include-surplus-quadruples flag to include surplus quadruples
+ --link flag to output links between vertices
+ --init-radius-for-BSH number initial radius for bounding sphere hierarchy
+ --check flag to slowly check the resulting vertices (used only for testing)
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of balls (line format: 'x y z r')
+
+### Output stream:
+
+ list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')
+
+## Command 'calculate-vertices-in-parallel'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --method string * parallelization method name, variants are: 'simulated'
+ --parts number * number of parts for splitting, must be power of 2
+ --print-log flag to print log of calculations
+ --include-surplus-quadruples flag to include surplus quadruples
+ --link flag to output links between vertices
+ --init-radius-for-BSH number initial radius for bounding sphere hierarchy
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of balls (line format: 'x y z r')
+
+### Output stream:
+
+ list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')
+
+## Command 'calculate-contacts'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --annotated flag to enable annotated mode
+ --probe number probe radius
+ --exclude-hidden-balls flag to exclude hidden input balls
+ --step number curve step length
+ --projections number curve optimization depth
+ --sih-depth number spherical surface optimization depth
+ --add-mirrored flag to add mirrored contacts to non-annnotated output
+ --draw flag to output graphics for annotated contacts
+ --tag-centrality flag to tag contacts centrality
+ --tag-peripherial flag to tag peripherial contacts
+ --old-contacts-output string file path to output spherical contacts
+ --volumes-output string file path to output constrained cells volumes
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of balls
+
+ default mode line format: 'x y z r'
+
+ annotated mode line format: 'annotation x y z r tags adjuncts'
+
+### Output stream:
+
+ list of contacts
+
+ default mode line format: 'b1 b2 area'
+
+ annotated mode line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]'
+
+## Command 'query-balls'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --match string selection
+ --match-not string negative selection
+ --match-tags string tags to match
+ --match-tags-not string tags to not match
+ --match-adjuncts string adjuncts intervals to match
+ --match-adjuncts-not string adjuncts intervals to not match
+ --match-external-annotations string file path to input matchable annotations
+ --invert flag to invert selection
+ --whole-residues flag to select whole residues
+ --drop-atom-serials flag to drop atom serial numbers from input
+ --drop-altloc-indicators flag to drop alternate location indicators from input
+ --drop-tags flag to drop all tags from input
+ --drop-adjuncts flag to drop all adjuncts from input
+ --set-tags string set tags instead of filtering
+ --set-dssp-info string file path to input DSSP file
+ --set-adjuncts string set adjuncts instead of filtering
+ --set-external-adjuncts string file path to input external adjuncts
+ --set-external-adjuncts-name string name for external adjuncts
+ --rename-chains flag to rename input chains to be in interval from 'A' to 'Z'
+ --renumber-from-adjunct string adjunct name to use for input residue renumbering
+ --renumber-positively flag to increment residue numbers to make them positive
+ --reset-serials flag to reset atom serial numbers
+ --set-seq-pos-adjunct flag to set normalized sequence position adjunct
+ --set-ref-seq-num-adjunct string file path to input reference sequence
+ --ref-seq-alignment string file path to output alignment with reference
+ --seq-output string file path to output query result sequence string
+ --chains-summary-output string file path to output chains summary
+ --chains-seq-identity number sequence identity threshold for chains summary, default is 0.9
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of balls (line format: 'annotation x y z r tags adjuncts')
+
+### Output stream:
+
+ list of balls (line format: 'annotation x y z r tags adjuncts')
+
+## Command 'query-contacts'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --match-first string selection for first contacting group
+ --match-first-not string negative selection for first contacting group
+ --match-second string selection for second contacting group
+ --match-second-not string negative selection for second contacting group
+ --match-min-seq-sep number minimum residue sequence separation
+ --match-max-seq-sep number maximum residue sequence separation
+ --match-min-area number minimum contact area
+ --match-max-area number maximum contact area
+ --match-min-dist number minimum distance
+ --match-max-dist number maximum distance
+ --match-tags string tags to match
+ --match-tags-not string tags to not match
+ --match-adjuncts string adjuncts intervals to match
+ --match-adjuncts-not string adjuncts intervals to not match
+ --match-external-first string file path to input matchable annotations
+ --match-external-second string file path to input matchable annotations
+ --match-external-pairs string file path to input matchable annotation pairs
+ --no-solvent flag to not include solvent accessible areas
+ --no-same-chain flag to not include same chain contacts
+ --invert flag to invert selection
+ --drop-tags flag to drop all tags from input
+ --drop-adjuncts flag to drop all adjuncts from input
+ --set-tags string set tags instead of filtering
+ --set-hbplus-tags string file path to input HBPLUS file
+ --set-distance-bins-tags string list of distance thresholds
+ --inter-residue-hbplus-tags flag to set inter-residue H-bond tags
+ --set-adjuncts string set adjuncts instead of filtering
+ --set-external-adjuncts string file path to input external adjuncts
+ --set-external-adjuncts-name string name for external adjuncts
+ --set-external-means string file path to input external values for averaging
+ --set-external-means-name string name for external means
+ --renaming-map string file path to input atoms renaming map
+ --inter-residue flag to convert input to inter-residue contacts
+ --inter-residue-after flag to convert output to inter-residue contacts
+ --summing-exceptions string file path to input inter-residue summing exceptions annotations
+ --summarize flag to output only summary of matched contacts
+ --summarize-by-first flag to output only summary of matched contacts by first identifier
+ --preserve-graphics flag to preserve graphics in output
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')
+
+### Output stream:
+
+ list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')
+
+## Command 'draw-contacts'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --drawing-for-pymol string file path to output drawing as pymol script
+ --drawing-for-jmol string file path to output drawing as jmol script
+ --drawing-for-scenejs string file path to output drawing as scenejs script
+ --drawing-name string graphics object name for drawing output
+ --default-color string default color for drawing output, in hex format, white is 0xFFFFFF
+ --adjunct-gradient string adjunct name to use for gradient-based coloring
+ --adjunct-gradient-blue number blue adjunct gradient value
+ --adjunct-gradient-red number red adjunct gradient value
+ --adjuncts-rgb flag to use RGB color values from adjuncts
+ --random-colors flag to use random color for each drawn contact
+ --alpha number alpha opacity value for drawing output
+ --use-labels flag to use labels in drawing if possible
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')
+
+### Output stream:
+
+ list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')
+
+## Command 'score-contacts-energy'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --potential-file string * file path to input potential values
+ --ignorable-max-seq-sep number maximum residue sequence separation for ignorable contacts
+ --inter-atom-scores-file string file path to output inter-atom scores
+ --atom-scores-file string file path to output atom scores
+ --depth number neighborhood normalization depth
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of contacts (line format: 'annotation1 annotation2 conditions area')
+
+### Output stream:
+
+ global scores
+
+## Command 'score-contacts-quality'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --default-mean number default mean parameter
+ --default-sd number default standard deviation parameter
+ --means-and-sds-file string file path to input atomic mean and sd parameters
+ --mean-shift number mean shift in standard deviations
+ --external-weights-file string file path to input external weights for global scoring
+ --smoothing-window number window to smooth residue quality scores along sequence
+ --atom-scores-file string file path to output atom scores
+ --residue-scores-file string file path to output residue scores
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of atom energy descriptors
+
+### Output stream:
+
+ weighted average local score
+
+## Command 'score-contacts-potential'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --input-file-list flag to read file list from stdin
+ --input-contributions string file path to input contact types contributions
+ --input-fixed-types string file path to input fixed types
+ --input-seq-pairs-stats string file path to input sequence pairings statistics
+ --potential-file string file path to output potential values
+ --probabilities-file string file path to output observed and expected probabilities
+ --single-areas-file string file path to output single type total areas
+ --contributions-file string file path to output contact types contributions
+ --multiply-areas number coefficient to multiply output areas
+ --toggling-list string list of toggling subtags
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of contacts (line format: 'annotation1 annotation2 conditions area')
+
+### Output stream:
+
+ line of contact type area summaries (line format: 'annotation1 annotation2 conditions area')
+
+## Command 'compare-contacts'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --target-contacts-file string * file path to input target contacts
+ --inter-atom-scores-file string file path to output inter-atom scores
+ --inter-residue-scores-file string file path to output inter-residue scores
+ --atom-scores-file string file path to output atom scores
+ --residue-scores-file string file path to output residue scores
+ --depth number local neighborhood depth
+ --smoothing-window number window to smooth residue scores along sequence
+ --smoothed-scores-file string file path to output smoothed residue scores
+ --ignore-residue-names flag to consider just residue numbers and ignore residue names
+ --residue-level-only flag to output only residue-level results
+ --detailed-output flag to enable detailed output
+ --chains-renaming-file string file path to input chains renaming
+ --remap-chains flag to calculate optimal chains remapping
+ --remap-chains-log flag output remapping progress to stderr
+ --remapped-chains-file string file path to output calculated chains remapping
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of model contacts (line format: 'annotation1 annotation2 area')
+
+### Output stream:
+
+ global scores (atom-level and residue-level)
+
+## Command 'write-balls-to-atoms-file'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --pdb-output string file path to output query result in PDB format
+ --pdb-output-b-factor string name of adjunct to output as B-factor in PDB format
+ --pdb-output-template string file path to input template for B-factor insertions
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of balls (line format: 'annotation x y z r tags adjuncts')
+
+### Output stream:
+
+ list of balls (line format: 'annotation x y z r tags adjuncts')
+
+## Command 'query-balls-clashes'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --clash-distance number clash distance threshold in angstroms, default is 3.0
+ --min-seq-sep number minimum residue sequence separation, default is 2
+ --init-radius-for-BSH number initial radius for bounding sphere hierarchy
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ list of balls (line format: 'annotation x y z r')
+
+### Output stream:
+
+ list of clashes (line format: 'annotation1 annotation2 distance min-distance-between-balls')
+
+## Command 'expand-descriptors'
+
+### Command line arguments:
+
+ Name Type Description
+ ------------------------------- ------ ---- ------------------------------------------------------------------------
+ --help flag to print usage help to stdout and exit
+
+### Input stream:
+
+ any text containing atom descriptors
+
+### Output stream:
+
+ text with each atom descriptor expanded to 'chainID resSeq iCode serial altLoc resName name'
+
+# Wrapper scripts
+
+## VoroMQA method script
+
+'voronota-voromqa' script is an implementation of VoroMQA (Voronoi diagram-based Model Quality Assessment) method using Voronota.
+The script interface is presented below:
+
+ Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --output-atom-scores string output text file with atom scores
+ --output-atom-scores-pdb string output PDB file with atom scores as B-factors
+ --output-residue-scores string output text file with residue scores
+ --output-residue-scores-pdb string output PDB file with residue scores as B-factors
+ --output-residue-scores-plot string output PNG image file with residue scores plot, requires R
+ --help | -h flag to display help message and exit
+
+ Advanced options:
+ --cache-dir string path to cache directory
+ --smoothing-window number residue scores smoothing window size, default is 5
+ --atoms-query string atoms query parameters to define selection
+ --contacts-query string contacts query parameters to define selection
+ --output-selected-scores string output text file with selected atom scores
+ --reference-sequence string sequence file or string for residue renumbering
+ --output-sequence-alignment string output text file with sequence alignment
+ --multiple-models flag to handle multiple models in PDB file
+
+ Standard output (one line):
+ {input file path} {global score} {number of residues} {number of atoms} [ {selection score} {number of selected atoms} ]
+
+
+## CAD-score method script
+
+'voronota-cadscore' script is an implementation of CAD-score (Contact Area Difference score) method using Voronota.
+The script interface is presented below:
+
+ Basic options:
+ --input-target | -t string * input target structure file in PDB format
+ --input-model | -m string * input model structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --output-residue-scores string output text file with residue scores
+ --output-residue-scores-pdb-t string output target PDB file with residue scores as B-factors
+ --output-residue-scores-pdb-m string output model PDB file with residue scores as B-factors
+ --smoothing-window number residue scores smoothing window size, default is 0
+ --contacts-query string contacts query parameters
+ --contacts-query-inter-chain flag to consider only inter-chain contacts
+ --contacts-query-by-code string contacts query code, possible codes are AA, AS, SS, AM, MM, MS
+ --use-all-query-codes flag to output global scores for all query codes, one line per code
+ --cache-dir string path to cache directory
+ --output-header flag to output header before result line
+ --help | -h flag to display help message and exit
+
+ Advanced options:
+ --ignore-residue-names flag to consider just residue numbers and ignore residue names
+ --enable-site-based-scoring falg to enable site-based scoring
+ --multiple-models flag to handle multiple models in PDB file
+ --remap-chains flag to automatically rearrange chain names for higher scores
+ --remap-chains-output string output file with chain names rearrangement
+ --old-regime flag to calculate areas as in pre-Voronota CAD-score
+
+ Standard output (one line):
+ {target file path} {model file path} {query code} {number of residues} {global score} {target total area} {corresponding model total area}
+ [ {site-based number of residues} {site-based global score} {site-based target total area} {corresponding site-based model total area} ]
+
+
+## Contacts calculation convenience script
+
+'voronota-contacts' script provides a way for calculating and querying interatomic contacts with just one command (without the need to construct a pipeline from 'voronota' calls).
+
+ Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --contacts-query string contacts query parameters
+ --contacts-query-additional string additional contacts query parameters
+ --cache-dir string path to cache directory
+ --sum-at-end flag to print sum of areas as the last line in output
+ --help | -h flag to display help message and exit
+
+ Advanced options:
+ --output-drawing string output file with drawing script for PyMol
+ --drawing-parameters string drawing parameters
+ --wireframe-drawing flag to draw wireframe representation of contacts
+ --multiple-models flag to handle multiple models in PDB file
+
+ Standard output (multiple lines):
+ {contacting atom} {contacting atom} {contact area} {distance between atoms centers} {tags} {adjunct values}
+
+
+## Volumes calculation convenience script
+
+'voronota-volumes' script provides a way for calculating and querying atomic volumes with just one command (without the need to construct a pipeline from 'voronota' calls).
+
+ Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --cache-dir string path to cache directory
+ --sum-at-end flag to print sum of areas as the last line in output
+ --help | -h flag to display help message and exit
+
+ Advanced options:
+ --atoms-query string atoms query parameters
+ --per-residue flag to output per-residue results
+ --multiple-models flag to handle multiple models in PDB file
+
+ Standard output (multiple lines):
+ {name} {volume}
+
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+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_$1_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_$1_dependencies_compiler_type=none
+fi
+])
+AC_SUBST([$1DEPMODE], [depmode=$am_cv_$1_dependencies_compiler_type])
+AM_CONDITIONAL([am__fastdep$1], [
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_$1_dependencies_compiler_type" = gcc3])
+])
+
+
+# AM_SET_DEPDIR
+# -------------
+# Choose a directory name for dependency files.
+# This macro is AC_REQUIREd in _AM_DEPENDENCIES
+AC_DEFUN([AM_SET_DEPDIR],
+[AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
+])
+
+
+# AM_DEP_TRACK
+# ------------
+AC_DEFUN([AM_DEP_TRACK],
+[AC_ARG_ENABLE(dependency-tracking,
+[ --disable-dependency-tracking speeds up one-time build
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+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
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+AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
+AC_SUBST([AMDEPBACKSLASH])dnl
+_AM_SUBST_NOTMAKE([AMDEPBACKSLASH])dnl
+])
+
+# Generate code to set up dependency tracking. -*- Autoconf -*-
+
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+#serial 5
+
+# _AM_OUTPUT_DEPENDENCY_COMMANDS
+# ------------------------------
+AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
+[{
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
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+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`AS_DIRNAME("$mf")`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`AS_DIRNAME(["$file"])`
+ AS_MKDIR_P([$dirpart/$fdir])
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+])# _AM_OUTPUT_DEPENDENCY_COMMANDS
+
+
+# AM_OUTPUT_DEPENDENCY_COMMANDS
+# -----------------------------
+# This macro should only be invoked once -- use via AC_REQUIRE.
+#
+# This code is only required when automatic dependency tracking
+# is enabled. FIXME. This creates each `.P' file that we will
+# need in order to bootstrap the dependency handling code.
+AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
+[AC_CONFIG_COMMANDS([depfiles],
+ [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
+ [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
+])
+
+# Do all the work for Automake. -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
+# 2005, 2006, 2008, 2009 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 16
+
+# This macro actually does too much. Some checks are only needed if
+# your package does certain things. But this isn't really a big deal.
+
+# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
+# AM_INIT_AUTOMAKE([OPTIONS])
+# -----------------------------------------------
+# The call with PACKAGE and VERSION arguments is the old style
+# call (pre autoconf-2.50), which is being phased out. PACKAGE
+# and VERSION should now be passed to AC_INIT and removed from
+# the call to AM_INIT_AUTOMAKE.
+# We support both call styles for the transition. After
+# the next Automake release, Autoconf can make the AC_INIT
+# arguments mandatory, and then we can depend on a new Autoconf
+# release and drop the old call support.
+AC_DEFUN([AM_INIT_AUTOMAKE],
+[AC_PREREQ([2.62])dnl
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+AC_REQUIRE([AM_SET_CURRENT_AUTOMAKE_VERSION])dnl
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+if test "`cd $srcdir && pwd`" != "`pwd`"; then
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+ AC_SUBST([am__isrc], [' -I$(srcdir)'])_AM_SUBST_NOTMAKE([am__isrc])dnl
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
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+ CYGPATH_W=echo
+ fi
+fi
+AC_SUBST([CYGPATH_W])
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+# Define the identity of the package.
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+ AC_SUBST([VERSION], [$2])],
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+ AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
+ AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
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+_AM_IF_OPTION([no-define],,
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+AM_MISSING_PROG(AUTOHEADER, autoheader)
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+AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
+AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
+AC_REQUIRE([AM_PROG_MKDIR_P])dnl
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+AC_REQUIRE([AC_PROG_AWK])dnl
+AC_REQUIRE([AC_PROG_MAKE_SET])dnl
+AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+_AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
+ [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])],
+ [_AM_PROG_TAR([v7])])])
+_AM_IF_OPTION([no-dependencies],,
+[AC_PROVIDE_IFELSE([AC_PROG_CC],
+ [_AM_DEPENDENCIES(CC)],
+ [define([AC_PROG_CC],
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+AC_PROVIDE_IFELSE([AC_PROG_CXX],
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+ [define([AC_PROG_CXX],
+ defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
+AC_PROVIDE_IFELSE([AC_PROG_OBJC],
+ [_AM_DEPENDENCIES(OBJC)],
+ [define([AC_PROG_OBJC],
+ defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl
+])
+_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl
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+ [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
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+dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
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+m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
+
+
+# When config.status generates a header, we must update the stamp-h file.
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+
+# Autoconf calls _AC_AM_CONFIG_HEADER_HOOK (when defined) in the
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+
+# Copyright (C) 2001, 2003, 2005, 2008 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_INSTALL_SH
+# ------------------
+# Define $install_sh.
+AC_DEFUN([AM_PROG_INSTALL_SH],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
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+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+AC_SUBST(install_sh)])
+
+# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# Check whether the underlying file-system supports filenames
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+AC_DEFUN([AM_SET_LEADING_DOT],
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+ am__leading_dot=_
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+rmdir .tst 2>/dev/null
+AC_SUBST([am__leading_dot])])
+
+# Check to see how 'make' treats includes. -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 4
+
+# AM_MAKE_INCLUDE()
+# -----------------
+# Check to see how make treats includes.
+AC_DEFUN([AM_MAKE_INCLUDE],
+[am_make=${MAKE-make}
+cat > confinc << 'END'
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+ @echo this is the am__doit target
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+# If we don't find an include directive, just comment out the code.
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+am__include="#"
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+ _am_result=GNU
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+ case `$am_make -s -f confmf 2> /dev/null` in #(
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+ am__quote="\""
+ _am_result=BSD
+ ;;
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+fi
+AC_SUBST([am__include])
+AC_SUBST([am__quote])
+AC_MSG_RESULT([$_am_result])
+rm -f confinc confmf
+])
+
+# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
+
+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 6
+
+# AM_MISSING_PROG(NAME, PROGRAM)
+# ------------------------------
+AC_DEFUN([AM_MISSING_PROG],
+[AC_REQUIRE([AM_MISSING_HAS_RUN])
+$1=${$1-"${am_missing_run}$2"}
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+
+
+# AM_MISSING_HAS_RUN
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+ am_missing_run=
+ AC_MSG_WARN([`missing' script is too old or missing])
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+])
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+# Copyright (C) 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# AM_PROG_MKDIR_P
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+case $mkdir_p in
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+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+])
+
+# Helper functions for option handling. -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005, 2008 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 4
+
+# _AM_MANGLE_OPTION(NAME)
+# -----------------------
+AC_DEFUN([_AM_MANGLE_OPTION],
+[[_AM_OPTION_]m4_bpatsubst($1, [[^a-zA-Z0-9_]], [_])])
+
+# _AM_SET_OPTION(NAME)
+# ------------------------------
+# Set option NAME. Presently that only means defining a flag for this option.
+AC_DEFUN([_AM_SET_OPTION],
+[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
+
+# _AM_SET_OPTIONS(OPTIONS)
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+
+# Check to make sure that the build environment is sane. -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 5
+
+# AM_SANITY_CHECK
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+ AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);;
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+
+# Do `set' in a subshell so we don't clobber the current shell's
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+ set X `ls -t "$srcdir/configure" conftest.file`
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+ # If neither matched, then we have a broken ls. This can happen
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+ AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
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+ fi
+
+ test "$[2]" = conftest.file
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+ # Ok.
+ :
+else
+ AC_MSG_ERROR([newly created file is older than distributed files!
+Check your system clock])
+fi
+AC_MSG_RESULT(yes)])
+
+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_INSTALL_STRIP
+# ---------------------
+# One issue with vendor `install' (even GNU) is that you can't
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+# annoying in cross-compiling environments, where the build's strip
+# is unlikely to handle the host's binaries.
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+AC_DEFUN([AM_PROG_INSTALL_STRIP],
+[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
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+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
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+dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
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+ AC_CHECK_TOOL([STRIP], [strip], :)
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+AC_SUBST([INSTALL_STRIP_PROGRAM])])
+
+# Copyright (C) 2006, 2008 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# _AM_SUBST_NOTMAKE(VARIABLE)
+# ---------------------------
+# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
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+AC_DEFUN([_AM_SUBST_NOTMAKE])
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+# AM_SUBST_NOTMAKE(VARIABLE)
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+AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
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+# Check how to create a tarball. -*- Autoconf -*-
+
+# Copyright (C) 2004, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# _AM_PROG_TAR(FORMAT)
+# --------------------
+# Check how to create a tarball in format FORMAT.
+# FORMAT should be one of `v7', `ustar', or `pax'.
+#
+# Substitute a variable $(am__tar) that is a command
+# writing to stdout a FORMAT-tarball containing the directory
+# $tardir.
+# tardir=directory && $(am__tar) > result.tar
+#
+# Substitute a variable $(am__untar) that extract such
+# a tarball read from stdin.
+# $(am__untar) < result.tar
+AC_DEFUN([_AM_PROG_TAR],
+[# Always define AMTAR for backward compatibility.
+AM_MISSING_PROG([AMTAR], [tar])
+m4_if([$1], [v7],
+ [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
+ [m4_case([$1], [ustar],, [pax],,
+ [m4_fatal([Unknown tar format])])
+AC_MSG_CHECKING([how to create a $1 tar archive])
+# Loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
+# Do not fold the above two line into one, because Tru64 sh and
+# Solaris sh will not grok spaces in the rhs of `-'.
+for _am_tool in $_am_tools
+do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar;
+ do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
+
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
+
+ # tar/untar a dummy directory, and stop if the command works
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+done
+rm -rf conftest.dir
+
+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+AC_SUBST([am__tar])
+AC_SUBST([am__untar])
+]) # _AM_PROG_TAR
+
diff --git a/configure b/configure
new file mode 100755
index 0000000..683840d
--- /dev/null
+++ b/configure
@@ -0,0 +1,4272 @@
+#! /bin/sh
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.68 for voronota 1.18.1877.
+#
+# Report bugs to <kliment at ibt.lt>.
+#
+#
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+# Foundation, Inc.
+#
+#
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
+
+exitcode=0
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
+
+else
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
+else
+ as_have_required=no
+fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
+
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ as_found=:
+ case $as_dir in #(
+ /*)
+ for as_base in sh bash ksh sh5; do
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
+ done;;
+ esac
+ as_found=false
+done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
+IFS=$as_save_IFS
+
+
+ if test "x$CONFIG_SHELL" != x; then :
+ # We cannot yet assume a decent shell, so we have to provide a
+ # neutralization value for shells without unset; and this also
+ # works around shells that cannot unset nonexistent variables.
+ # Preserve -v and -x to the replacement shell.
+ BASH_ENV=/dev/null
+ ENV=/dev/null
+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+ export CONFIG_SHELL
+ case $- in # ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+ esac
+ exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
+fi
+
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug-autoconf at gnu.org and kliment at ibt.lt
+$0: about your system, including any error possibly output
+$0: before this message. Then install a modern shell, or
+$0: manually run the script under such a shell if you do
+$0: have one."
+ fi
+ exit 1
+fi
+fi
+fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
+
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+
+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
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+ as_fn_error $? "pwd does not report name of working directory"
+
+
+# Find the source files, if location was not specified.
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+ ac_srcdir_defaulted=yes
+ # Try the directory containing this script, then the parent directory.
+ ac_confdir=`$as_dirname -- "$as_myself" ||
+$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
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+ X"$as_myself" : 'X\(//\)$' \| \
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+$as_echo X"$as_myself" |
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+ s//\1/
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+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
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+ /^X\(\/\/\)$/{
+ s//\1/
+ q
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+ /^X\(\/\).*/{
+ s//\1/
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+ s/.*/./; q'`
+ srcdir=$ac_confdir
+ if test ! -r "$srcdir/$ac_unique_file"; then
+ srcdir=..
+ fi
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+ ac_srcdir_defaulted=no
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+if test ! -r "$srcdir/$ac_unique_file"; then
+ test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
+ as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
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+ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
+ac_abs_confdir=`(
+ cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
+ pwd)`
+# When building in place, set srcdir=.
+if test "$ac_abs_confdir" = "$ac_pwd"; then
+ srcdir=.
+fi
+# Remove unnecessary trailing slashes from srcdir.
+# Double slashes in file names in object file debugging info
+# mess up M-x gdb in Emacs.
+case $srcdir in
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+esac
+for ac_var in $ac_precious_vars; do
+ eval ac_env_${ac_var}_set=\${${ac_var}+set}
+ eval ac_env_${ac_var}_value=\$${ac_var}
+ eval ac_cv_env_${ac_var}_set=\${${ac_var}+set}
+ eval ac_cv_env_${ac_var}_value=\$${ac_var}
+done
+
+#
+# Report the --help message.
+#
+if test "$ac_init_help" = "long"; then
+ # Omit some internal or obsolete options to make the list less imposing.
+ # This message is too long to be a string in the A/UX 3.1 sh.
+ cat <<_ACEOF
+\`configure' configures voronota 1.18.1877 to adapt to many kinds of systems.
+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE. See below for descriptions of some of the useful variables.
+
+Defaults for the options are specified in brackets.
+
+Configuration:
+ -h, --help display this help and exit
+ --help=short display options specific to this package
+ --help=recursive display the short help of all the included packages
+ -V, --version display version information and exit
+ -q, --quiet, --silent do not print \`checking ...' messages
+ --cache-file=FILE cache test results in FILE [disabled]
+ -C, --config-cache alias for \`--cache-file=config.cache'
+ -n, --no-create do not create output files
+ --srcdir=DIR find the sources in DIR [configure dir or \`..']
+
+Installation directories:
+ --prefix=PREFIX install architecture-independent files in PREFIX
+ [$ac_default_prefix]
+ --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
+ [PREFIX]
+
+By default, \`make install' will install all the files in
+\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
+an installation prefix other than \`$ac_default_prefix' using \`--prefix',
+for instance \`--prefix=\$HOME'.
+
+For better control, use the options below.
+
+Fine tuning of the installation directories:
+ --bindir=DIR user executables [EPREFIX/bin]
+ --sbindir=DIR system admin executables [EPREFIX/sbin]
+ --libexecdir=DIR program executables [EPREFIX/libexec]
+ --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
+ --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
+ --localstatedir=DIR modifiable single-machine data [PREFIX/var]
+ --libdir=DIR object code libraries [EPREFIX/lib]
+ --includedir=DIR C header files [PREFIX/include]
+ --oldincludedir=DIR C header files for non-gcc [/usr/include]
+ --datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
+ --datadir=DIR read-only architecture-independent data [DATAROOTDIR]
+ --infodir=DIR info documentation [DATAROOTDIR/info]
+ --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
+ --mandir=DIR man documentation [DATAROOTDIR/man]
+ --docdir=DIR documentation root [DATAROOTDIR/doc/voronota]
+ --htmldir=DIR html documentation [DOCDIR]
+ --dvidir=DIR dvi documentation [DOCDIR]
+ --pdfdir=DIR pdf documentation [DOCDIR]
+ --psdir=DIR ps documentation [DOCDIR]
+_ACEOF
+
+ cat <<\_ACEOF
+
+Program names:
+ --program-prefix=PREFIX prepend PREFIX to installed program names
+ --program-suffix=SUFFIX append SUFFIX to installed program names
+ --program-transform-name=PROGRAM run sed PROGRAM on installed program names
+_ACEOF
+fi
+
+if test -n "$ac_init_help"; then
+ case $ac_init_help in
+ short | recursive ) echo "Configuration of voronota 1.18.1877:";;
+ esac
+ cat <<\_ACEOF
+
+Optional Features:
+ --disable-option-checking ignore unrecognized --enable/--with options
+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors
+
+Some influential environment variables:
+ CXX C++ compiler command
+ CXXFLAGS C++ compiler flags
+ LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
+ nonstandard directory <lib dir>
+ LIBS libraries to pass to the linker, e.g. -l<library>
+ CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
+ you have headers in a nonstandard directory <include dir>
+
+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
+
+Report bugs to <kliment at ibt.lt>.
+_ACEOF
+ac_status=$?
+fi
+
+if test "$ac_init_help" = "recursive"; then
+ # If there are subdirs, report their specific --help.
+ for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+ test -d "$ac_dir" ||
+ { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
+ continue
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
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+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
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+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+ cd "$ac_dir" || { ac_status=$?; continue; }
+ # Check for guested configure.
+ if test -f "$ac_srcdir/configure.gnu"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure.gnu" --help=recursive
+ elif test -f "$ac_srcdir/configure"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure" --help=recursive
+ else
+ $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+ fi || ac_status=$?
+ cd "$ac_pwd" || { ac_status=$?; break; }
+ done
+fi
+
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+ cat <<\_ACEOF
+voronota configure 1.18.1877
+generated by GNU Autoconf 2.68
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+ exit
+fi
+
+## ------------------------ ##
+## Autoconf initialization. ##
+## ------------------------ ##
+
+# ac_fn_cxx_try_compile LINENO
+# ----------------------------
+# Try to compile conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
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+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_cxx_werror_flag" ||
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+ $as_echo "$as_me: failed program was:" >&5
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+
+ ac_retval=1
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+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
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+
+} # ac_fn_cxx_try_compile
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by voronota $as_me 1.18.1877, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
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+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ $as_echo "PATH: $as_dir"
+ done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
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+ac_configure_args=
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+ *\'*)
+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
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+ case "$ac_configure_args0 " in
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+ -* ) ac_must_keep_next=true ;;
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+{ ac_configure_args0=; unset ac_configure_args0;}
+{ ac_configure_args1=; unset ac_configure_args1;}
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+# When interrupted or exit'd, cleanup temporary files, and complete
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+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
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+ {
+ echo
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+ $as_echo "## ---------------- ##
+## Cache variables. ##
+## ---------------- ##"
+ echo
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+)
+ echo
+
+ $as_echo "## ----------------- ##
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+
+$as_echo "/* confdefs.h */" > confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
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+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
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+_ACEOF
+
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+ *) ac_site_file1=./$CONFIG_SITE;;
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+ ac_site_file2=$prefix/etc/config.site
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+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
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+
+# Check that the precious variables saved in the cache have kept the same
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+am__api_version='1.11'
+
+ac_aux_dir=
+for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
+ if test -f "$ac_dir/install-sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f "$ac_dir/shtool"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if ${ac_cv_path_install+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in #((
+ ./ | .// | /[cC]/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+ done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5;;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+esac
+
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
+alias in your environment" "$LINENO" 5
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ as_fn_error $? "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+test "$program_prefix" != NONE &&
+ program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.
+# By default was `s,x,x', remove it if useless.
+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if ${ac_cv_path_mkdir+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in mkdir gmkdir; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
+ 'mkdir (GNU coreutils) '* | \
+ 'mkdir (coreutils) '* | \
+ 'mkdir (fileutils) '4.1*)
+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
+ break 3;;
+ esac
+ done
+ done
+ done
+IFS=$as_save_IFS
+
+fi
+
+ test -d ./--version && rmdir ./--version
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ MKDIR_P="$ac_cv_path_mkdir -p"
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for MKDIR_P within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ MKDIR_P="$ac_install_sh -d"
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+mkdir_p="$MKDIR_P"
+case $mkdir_p in
+ [\\/$]* | ?:[\\/]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_AWK+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='voronota'
+ VERSION='1.18.1877'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility.
+
+AMTAR=${AMTAR-"${am_missing_run}tar"}
+
+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
+
+
+
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CXX+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
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+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CXX+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
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+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
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+case "(($ac_try" in
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+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
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+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
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+$as_echo_n "checking whether the C++ compiler works... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
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+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
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+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { { ac_try="$ac_link_default"
+case "(($ac_try" in
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+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
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+# in a Makefile. We should not override ac_cv_exeext if it was cached,
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+for ac_file in $ac_files ''
+do
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+ case $ac_file in
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+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
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+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
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+ # We set ac_cv_exeext here because the later test for it is not
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+ # Even if this section looks crufty: it has the advantage of
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+ * )
+ break;;
+ esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+ ac_file=''
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+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler default output file name" >&5
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
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+
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
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+if { { ac_try="$ac_link"
+case "(($ac_try" in
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+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
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+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
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+ case $ac_file in
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+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
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+fi
+rm -f conftest conftest$ac_cv_exeext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
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+ *) ac_try_echo=$ac_try;;
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+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
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+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
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+ *) ac_try_echo=$ac_try;;
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+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
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+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
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+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C++ compiled programs.
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+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
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+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
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+if ${ac_cv_objext+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { { ac_try="$ac_compile"
+case "(($ac_try" in
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+ ac_status=$?
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+ for ac_file in conftest.o conftest.obj conftest.*; do
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+ $as_echo "$as_me: failed program was:" >&5
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+
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+as_fn_error $? "cannot compute suffix of object files: cannot compile
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+rm -f conftest.$ac_cv_objext conftest.$ac_ext
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+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
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+{
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+ choke me
+#endif
+
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+ return 0;
+}
+_ACEOF
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+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
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+int
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+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
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+ CXXFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
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+{
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+ ;
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+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
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+/* end confdefs.h. */
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+{
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+ ;
+ return 0;
+}
+_ACEOF
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+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
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+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
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+
+
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+ am__quote=
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+ ;;
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+rm -f confinc confmf
+
+# Check whether --enable-dependency-tracking was given.
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+
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+ AMDEPBACKSLASH='\'
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+ AMDEP_TRUE='#'
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+
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+
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+if ${am_cv_CXX_dependencies_compiler_type+:} false; then :
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+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
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+ # Copy depcomp to subdir because otherwise we won't find it if we're
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+ # side effect of compilation, but ICC will put the dependencies in
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+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
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+ case " $depcc " in #(
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+
+ for depmode in $am_compiler_list; do
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+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
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+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
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+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
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+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
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+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+ac_config_files="$ac_config_files Makefile"
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ if test "x$cache_file" != "x/dev/null"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ if test ! -f "$cache_file" || test -h "$cache_file"; then
+ cat confcache >"$cache_file"
+ else
+ case $cache_file in #(
+ */* | ?:*)
+ mv -f confcache "$cache_file"$$ &&
+ mv -f "$cache_file"$$ "$cache_file" ;; #(
+ *)
+ mv -f confcache "$cache_file" ;;
+ esac
+ fi
+ fi
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+# Transform confdefs.h into DEFS.
+# Protect against shell expansion while executing Makefile rules.
+# Protect against Makefile macro expansion.
+#
+# If the first sed substitution is executed (which looks for macros that
+# take arguments), then branch to the quote section. Otherwise,
+# look for a macro that doesn't take arguments.
+ac_script='
+:mline
+/\\$/{
+ N
+ s,\\\n,,
+ b mline
+}
+t clear
+:clear
+s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+b any
+:quote
+s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g
+s/\[/\\&/g
+s/\]/\\&/g
+s/\$/$$/g
+H
+:any
+${
+ g
+ s/^\n//
+ s/\n/ /g
+ p
+}
+'
+DEFS=`sed -n "$ac_script" confdefs.h`
+
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ as_fn_error $? "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+
+: "${CONFIG_STATUS=./config.status}"
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by voronota $as_me 1.18.1877, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+
+Configuration files:
+$config_files
+
+Configuration commands:
+$config_commands
+
+Report bugs to <kliment at ibt.lt>."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
+ac_cs_version="\\
+voronota config.status 1.18.1877
+configured by $0, generated by GNU Autoconf 2.68,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h | --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp= ac_tmp=
+ trap 'exit_status=$?
+ : "${ac_tmp:=$tmp}"
+ { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+ac_tmp=$tmp
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
+_ACEOF
+
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+
+ print line
+}
+
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+
+eval set X " :F $CONFIG_FILES :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$ac_tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$ac_tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+ esac
+ ac_MKDIR_P=$MKDIR_P
+ case $MKDIR_P in
+ [\\/$]* | ?:[\\/]* ) ;;
+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
+ esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+s&@MKDIR_P@&$ac_MKDIR_P&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
+ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
+ "$ac_tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&5
+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$ac_tmp/stdin"
+ case $ac_file in
+ -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
+ *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
+ esac \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+
+
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+$as_echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+ esac
+
+
+ case $ac_file$ac_mode in
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`$as_dirname -- "$mf" ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+ ;;
+
+ esac
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 0000000..24747ce
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,5 @@
+AC_INIT([voronota], [1.18.1877], [kliment at ibt.lt], [voronota])
+AM_INIT_AUTOMAKE([foreign])
+AC_PROG_CXX
+AC_CONFIG_FILES([Makefile])
+AC_OUTPUT
diff --git a/depcomp b/depcomp
new file mode 100755
index 0000000..df8eea7
--- /dev/null
+++ b/depcomp
@@ -0,0 +1,630 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
+# Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
+
+case $1 in
+ '')
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+ depmode Dependency tracking mode.
+ source Source file read by `PROGRAMS ARGS'.
+ object Object file output by `PROGRAMS ARGS'.
+ DEPDIR directory where to store dependencies.
+ depfile Dependency file to output.
+ tmpdepfile Temporary file to use when outputing dependencies.
+ libtool Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "depcomp $scriptversion"
+ exit $?
+ ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+ echo "depcomp: Variables source, object and depmode must be set" 1>&2
+ exit 1
+fi
+
+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
+depfile=${depfile-`echo "$object" |
+ sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags. We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write. Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+ # HP compiler uses -M and no extra arg.
+ gccflag=-M
+ depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
+fi
+
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u="sed s,\\\\\\\\,/,g"
+ depmode=msvisualcpp
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want. Yay! Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff. Hmm.
+## Unfortunately, FreeBSD c89 acceptance of flags depends upon
+## the command line argument order; so add the flags where they
+## appear in depend2.am. Note that the slowdown incurred here
+## affects only configure: in makefiles, %FASTDEP% shortcuts this.
+ for arg
+ do
+ case $arg in
+ -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
+ *) set fnord "$@" "$arg" ;;
+ esac
+ shift # fnord
+ shift # $arg
+ done
+ "$@"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ mv "$tmpdepfile" "$depfile"
+ ;;
+
+gcc)
+## There are various ways to get dependency output from gcc. Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+## up in a subdir. Having to rename by hand is ugly.
+## (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+## -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+## than renaming).
+ if test -z "$gccflag"; then
+ gccflag=-MD,
+ fi
+ "$@" -Wp,"$gccflag$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+ sed -e 's/^[^:]*: / /' \
+ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header). We avoid this by adding
+## dummy dependencies for each header file. Too bad gcc doesn't do
+## this for us directly.
+ tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'. On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+sgi)
+ if test "$libtool" = yes; then
+ "$@" "-Wp,-MDupdate,$tmpdepfile"
+ else
+ "$@" -MDupdate "$tmpdepfile"
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+
+ if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
+ echo "$object : \\" > "$depfile"
+
+ # Clip off the initial element (the dependent). Don't try to be
+ # clever and replace this with sed code, as IRIX sed won't handle
+ # lines with more than a fixed number of characters (4096 in
+ # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
+ # the IRIX cc adds comments like `#:fec' to the end of the
+ # dependency line.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+ tr '
+' ' ' >> "$depfile"
+ echo >> "$depfile"
+
+ # The second pass generates a dummy entry for each header file.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+aix)
+ # The C for AIX Compiler uses -M and outputs the dependencies
+ # in a .u file. In older versions, this file always lives in the
+ # current directory. Also, the AIX compiler puts `$object:' at the
+ # start of each line; $object doesn't have directory information.
+ # Version 6 uses the directory in both cases.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ if test "$libtool" = yes; then
+ tmpdepfile1=$dir$base.u
+ tmpdepfile2=$base.u
+ tmpdepfile3=$dir.libs/$base.u
+ "$@" -Wc,-M
+ else
+ tmpdepfile1=$dir$base.u
+ tmpdepfile2=$dir$base.u
+ tmpdepfile3=$dir$base.u
+ "$@" -M
+ fi
+ stat=$?
+
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ # Each line is of the form `foo.o: dependent.h'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+icc)
+ # Intel's C compiler understands `-MD -MF file'. However on
+ # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+ # ICC 7.0 will fill foo.d with something like
+ # foo.o: sub/foo.c
+ # foo.o: sub/foo.h
+ # which is wrong. We want:
+ # sub/foo.o: sub/foo.c
+ # sub/foo.o: sub/foo.h
+ # sub/foo.c:
+ # sub/foo.h:
+ # ICC 7.1 will output
+ # foo.o: sub/foo.c sub/foo.h
+ # and will wrap long lines using \ :
+ # foo.o: sub/foo.c ... \
+ # sub/foo.h ... \
+ # ...
+
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ # Each line is of the form `foo.o: dependent.h',
+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+ sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp2)
+ # The "hp" stanza above does not work with aCC (C++) and HP's ia64
+ # compilers, which have integrated preprocessors. The correct option
+ # to use with these is +Maked; it writes dependencies to a file named
+ # 'foo.d', which lands next to the object file, wherever that
+ # happens to be.
+ # Much of this is similar to the tru64 case; see comments there.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ if test "$libtool" = yes; then
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir.libs/$base.d
+ "$@" -Wc,+Maked
+ else
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir$base.d
+ "$@" +Maked
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
+ # Add `dependent.h:' lines.
+ sed -ne '2,${
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile" "$tmpdepfile2"
+ ;;
+
+tru64)
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in `foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+ if test "$libtool" = yes; then
+ # With Tru64 cc, shared objects can also be used to make a
+ # static library. This mechanism is used in libtool 1.4 series to
+ # handle both shared and static libraries in a single compilation.
+ # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+ #
+ # With libtool 1.5 this exception was removed, and libtool now
+ # generates 2 separate objects for the 2 libraries. These two
+ # compilations output dependencies in $dir.libs/$base.o.d and
+ # in $dir$base.o.d. We have to check for both files, because
+ # one of the two compilations can be disabled. We should prefer
+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+ # automatically cleaned when .libs/ is deleted, while ignoring
+ # the former would cause a distcleancheck panic.
+ tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
+ tmpdepfile2=$dir$base.o.d # libtool 1.5
+ tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
+ tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.o.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ tmpdepfile4=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+#nosideeffect)
+ # This comment above is used by automake to tell side-effect
+ # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout, regardless of -o.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ test -z "$dashmflag" && dashmflag=-M
+ # Require at least two characters before searching for `:'
+ # in the target name. This is to cope with DOS-style filenames:
+ # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+ "$@" $dashmflag |
+ sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+dashXmstdout)
+ # This case only exists to satisfy depend.m4. It is never actually
+ # run, as this mode is specially recognized in the preamble.
+ exit 1
+ ;;
+
+makedepend)
+ "$@" || exit $?
+ # Remove any Libtool call
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+ # X makedepend
+ shift
+ cleared=no eat=no
+ for arg
+ do
+ case $cleared in
+ no)
+ set ""; shift
+ cleared=yes ;;
+ esac
+ if test $eat = yes; then
+ eat=no
+ continue
+ fi
+ case "$arg" in
+ -D*|-I*)
+ set fnord "$@" "$arg"; shift ;;
+ # Strip any option that makedepend may not understand. Remove
+ # the object too, otherwise makedepend will parse it as a source file.
+ -arch)
+ eat=yes ;;
+ -*|$object)
+ ;;
+ *)
+ set fnord "$@" "$arg"; shift ;;
+ esac
+ done
+ obj_suffix=`echo "$object" | sed 's/^.*\././'`
+ touch "$tmpdepfile"
+ ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile" "$tmpdepfile".bak
+ ;;
+
+cpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ "$@" -E |
+ sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+ sed '$ s: \\$::' > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ cat < "$tmpdepfile" >> "$depfile"
+ sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvisualcpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ IFS=" "
+ for arg
+ do
+ case "$arg" in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+ set fnord "$@"
+ shift
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
+ esac
+ done
+ "$@" -E 2>/dev/null |
+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ echo " " >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvcmsys)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+none)
+ exec "$@"
+ ;;
+
+*)
+ echo "Unknown depmode $depmode" 1>&2
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/install-sh b/install-sh
new file mode 100755
index 0000000..6781b98
--- /dev/null
+++ b/install-sh
@@ -0,0 +1,520 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2009-04-28.21; # UTC
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch.
+
+nl='
+'
+IFS=" "" $nl"
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit=${DOITPROG-}
+if test -z "$doit"; then
+ doit_exec=exec
+else
+ doit_exec=$doit
+fi
+
+# Put in absolute file names if you don't have them in your path;
+# or use environment vars.
+
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
+
+posix_glob='?'
+initialize_posix_glob='
+ test "$posix_glob" != "?" || {
+ if (set -f) 2>/dev/null; then
+ posix_glob=
+ else
+ posix_glob=:
+ fi
+ }
+'
+
+posix_mkdir=
+
+# Desired mode of installed file.
+mode=0755
+
+chgrpcmd=
+chmodcmd=$chmodprog
+chowncmd=
+mvcmd=$mvprog
+rmcmd="$rmprog -f"
+stripcmd=
+
+src=
+dst=
+dir_arg=
+dst_arg=
+
+copy_on_change=false
+no_target_directory=
+
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+ or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+ --help display this help and exit.
+ --version display version info and exit.
+
+ -c (ignored)
+ -C install only if different (preserve the last data modification time)
+ -d create directories instead of installing files.
+ -g GROUP $chgrpprog installed files to GROUP.
+ -m MODE $chmodprog installed files to MODE.
+ -o USER $chownprog installed files to USER.
+ -s $stripprog installed files.
+ -t DIRECTORY install into DIRECTORY.
+ -T report an error if DSTFILE is a directory.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+ RMPROG STRIPPROG
+"
+
+while test $# -ne 0; do
+ case $1 in
+ -c) ;;
+
+ -C) copy_on_change=true;;
+
+ -d) dir_arg=true;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift;;
+
+ --help) echo "$usage"; exit $?;;
+
+ -m) mode=$2
+ case $mode in
+ *' '* | *' '* | *'
+'* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
+
+ -o) chowncmd="$chownprog $2"
+ shift;;
+
+ -s) stripcmd=$stripprog;;
+
+ -t) dst_arg=$2
+ shift;;
+
+ -T) no_target_directory=true;;
+
+ --version) echo "$0 $scriptversion"; exit $?;;
+
+ --) shift
+ break;;
+
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
+
+ *) break;;
+ esac
+ shift
+done
+
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
+ # When -d is used, all remaining arguments are directories to create.
+ # When -t is used, the destination is already specified.
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dst_arg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dst_arg"
+ shift # fnord
+ fi
+ shift # arg
+ dst_arg=$arg
+ done
+fi
+
+if test $# -eq 0; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+if test -z "$dir_arg"; then
+ trap '(exit $?); exit' 1 2 13 15
+
+ # Set umask so as not to create temps with too-generous modes.
+ # However, 'strip' requires both read and write access to temps.
+ case $mode in
+ # Optimize common cases.
+ *644) cp_umask=133;;
+ *755) cp_umask=22;;
+
+ *[0-7])
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw='% 200'
+ fi
+ cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
+ *)
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw=,u+rw
+ fi
+ cp_umask=$mode$u_plus_rw;;
+ esac
+fi
+
+for src
+do
+ # Protect names starting with `-'.
+ case $src in
+ -*) src=./$src;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ dstdir=$dst
+ test -d "$dstdir"
+ dstdir_status=$?
+ else
+
+ # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dst_arg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+
+ dst=$dst_arg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst;;
+ esac
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ if test -n "$no_target_directory"; then
+ echo "$0: $dst_arg: Is a directory" >&2
+ exit 1
+ fi
+ dstdir=$dst
+ dst=$dstdir/`basename "$src"`
+ dstdir_status=0
+ else
+ # Prefer dirname, but fall back on a substitute if dirname fails.
+ dstdir=`
+ (dirname "$dst") 2>/dev/null ||
+ expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$dst" : 'X\(//\)[^/]' \| \
+ X"$dst" : 'X\(//\)$' \| \
+ X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+ echo X"$dst" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'
+ `
+
+ test -d "$dstdir"
+ dstdir_status=$?
+ fi
+ fi
+
+ obsolete_mkdir_used=false
+
+ if test $dstdir_status != 0; then
+ case $posix_mkdir in
+ '')
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ if (umask $mkdir_umask &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writeable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/d" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
+ esac
+
+ if
+ $posix_mkdir && (
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ )
+ then :
+ else
+
+ # The umask is ridiculous, or mkdir does not conform to POSIX,
+ # or it failed possibly due to a race condition. Create the
+ # directory the slow way, step by step, checking for races as we go.
+
+ case $dstdir in
+ /*) prefix='/';;
+ -*) prefix='./';;
+ *) prefix='';;
+ esac
+
+ eval "$initialize_posix_glob"
+
+ oIFS=$IFS
+ IFS=/
+ $posix_glob set -f
+ set fnord $dstdir
+ shift
+ $posix_glob set +f
+ IFS=$oIFS
+
+ prefixes=
+
+ for d
+ do
+ test -z "$d" && continue
+
+ prefix=$prefix$d
+ if test -d "$prefix"; then
+ prefixes=
+ else
+ if $posix_mkdir; then
+ (umask=$mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+ # Don't fail if two instances are running concurrently.
+ test -d "$prefix" || exit 1
+ else
+ case $prefix in
+ *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) qprefix=$prefix;;
+ esac
+ prefixes="$prefixes '$qprefix'"
+ fi
+ fi
+ prefix=$prefix/
+ done
+
+ if test -n "$prefixes"; then
+ # Don't fail if two instances are running concurrently.
+ (umask $mkdir_umask &&
+ eval "\$doit_exec \$mkdirprog $prefixes") ||
+ test -d "$dstdir" || exit 1
+ obsolete_mkdir_used=true
+ fi
+ fi
+ fi
+
+ if test -n "$dir_arg"; then
+ { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
+ { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
+ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
+ else
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+
+ # Copy the file name to the temp name.
+ (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $cpprog $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+ { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+ { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
+
+ # If -C, don't bother to copy if it wouldn't change the file.
+ if $copy_on_change &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+
+ eval "$initialize_posix_glob" &&
+ $posix_glob set -f &&
+ set X $old && old=:$2:$4:$5:$6 &&
+ set X $new && new=:$2:$4:$5:$6 &&
+ $posix_glob set +f &&
+
+ test "$old" = "$new" &&
+ $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+ then
+ rm -f "$dsttmp"
+ else
+ # Rename the file to the real destination.
+ $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+ # The rename failed, perhaps because mv can't rename something else
+ # to itself, or perhaps because mv is so ancient that it does not
+ # support -f.
+ {
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$dst" ||
+ $doit $rmcmd -f "$dst" 2>/dev/null ||
+ { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+ { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+ } ||
+ { echo "$0: cannot unlink or rename $dst" >&2
+ (exit 1); exit 1
+ }
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dst"
+ }
+ fi || exit 1
+
+ trap '' 0
+ fi
+done
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/missing b/missing
new file mode 100755
index 0000000..28055d2
--- /dev/null
+++ b/missing
@@ -0,0 +1,376 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ autom4te touch the output file, or create a stub one
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
+Send bug reports to <bug-automake at gnu.org>."
+ exit $?
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ exit $?
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+esac
+
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+ lex*|yacc*)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ tar*)
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ exit 1
+ fi
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case $f in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te*)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison*|yacc*)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f y.tab.h; then
+ echo >y.tab.h
+ fi
+ if test ! -f y.tab.c; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex*|flex*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f lex.yy.c; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit $?
+ fi
+ ;;
+
+ makeinfo*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '
+ /^@setfilename/{
+ s/.* \([^ ]*\) *$/\1/
+ p
+ q
+ }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ tar*)
+ shift
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case $firstarg in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case $firstarg in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/radii b/radii
new file mode 100644
index 0000000..d40a1c6
--- /dev/null
+++ b/radii
@@ -0,0 +1,119 @@
+# default radii
+
+* * 1.80
+* C* 1.80
+* CL* 1.80
+* F* 1.80
+* FE* 1.80
+* N* 1.60
+* O* 1.50
+* P* 1.90
+* S* 1.90
+* ZN* 1.70
+* H* 1.30
+
+
+# protein main chain radii
+
+* C 1.75
+* CA 1.90
+* N 1.70
+* O 1.49
+
+
+# protein side chain radii
+
+ALA CB 1.92
+
+ARG CB 1.91
+ARG CD* 1.88
+ARG CG* 1.92
+ARG NE* 1.62
+ARG NH1 1.62
+ARG NH2 1.67
+
+ASN CB 1.91
+ASN CG* 1.81
+ASN ND2 1.62
+ASN OD1 1.52
+
+ASP CB 1.91
+ASP CG* 1.76
+ASP OD1 1.49
+ASP OD2 1.49
+
+CYS CB 1.91
+CYS S* 1.88
+
+GLN CB 1.91
+GLN CD* 1.81
+GLN NE2 1.62
+GLN OE1 1.52
+
+GLU CB 1.91
+GLU CD* 1.76
+GLU CG* 1.88
+GLU OE1 1.49
+GLU OE2 1.49
+
+HIS CB 1.91
+HIS CD* 1.74
+HIS CE* 1.74
+HIS ND2 1.65
+HIS NE1 1.65
+
+ILE CB 2.01
+ILE CD1 1.92
+ILE CG1 1.92
+ILE CG2 1.92
+
+LEU CB 1.91
+LEU CD1 1.92
+LEU CD2 1.92
+LEU CG* 2.01
+
+LYS CB 1.91
+LYS CD* 1.92
+LYS CE* 1.88
+LYS CG* 1.92
+LYS NZ* 1.67
+
+MET CB 1.91
+MET CG* 1.92
+MET S* 1.94
+
+PHE CB 1.91
+PHE CD* 1.82
+PHE CE* 1.82
+PHE CG* 1.74
+PHE CZ* 1.82
+
+PRO CB 1.91
+PRO CD* 1.92
+PRO CG* 1.92
+
+SER CB 1.91
+SER OG* 1.54
+
+THR CB 2.01
+THR CG2 1.92
+THR OG* 1.54
+
+TRP CB 1.91
+TRP CD* 1.82
+TRP CE* 1.82
+TRP CE2 1.74
+TRP CG* 1.74
+TRP CH* 1.82
+TRP CZ* 1.82
+TRP NE1 1.66
+
+TYR CB 1.91
+TYR CD* 1.82
+TYR CE* 1.82
+TYR CG* 1.74
+TYR OH* 1.54
+
+VAL CB 2.01
+VAL CG1 1.92
+VAL CG2 1.92
diff --git a/src/apollota/basic_operations_on_points.h b/src/apollota/basic_operations_on_points.h
new file mode 100644
index 0000000..0d1b257
--- /dev/null
+++ b/src/apollota/basic_operations_on_points.h
@@ -0,0 +1,373 @@
+#ifndef APOLLOTA_BASIC_OPERATIONS_ON_POINTS_H_
+#define APOLLOTA_BASIC_OPERATIONS_ON_POINTS_H_
+
+#include <cmath>
+
+#include "safer_comparison_of_numbers.h"
+
+namespace apollota
+{
+
+struct PODPoint
+{
+ double x;
+ double y;
+ double z;
+};
+
+template<typename OutputPointType>
+OutputPointType custom_point(const double x, const double y, const double z)
+{
+ OutputPointType result;
+ result.x=x;
+ result.y=y;
+ result.z=z;
+ return result;
+}
+
+template<typename OutputPointType, typename InputObjectType>
+OutputPointType custom_point_from_object(const InputObjectType& o)
+{
+ return custom_point<OutputPointType>(o.x, o.y, o.z);
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB>
+bool points_equal(const InputPointTypeA& a, const InputPointTypeB& b)
+{
+ return (equal(a.x, b.x) && equal(a.y, b.y) && equal(a.z, b.z));
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB>
+bool points_less(const InputPointTypeA& a, const InputPointTypeB& b)
+{
+ if(less(a.x, b.x)) { return true; }
+ else if(greater(a.x, b.x)) { return false; }
+
+ if(less(a.y, b.y)) { return true; }
+ else if(greater(a.y, b.y)) { return false; }
+
+ if(less(a.z, b.z)) { return true; }
+ else if(greater(a.z, b.z)) { return false; }
+
+ return false;
+}
+
+template<typename OutputPointType, typename InputPointType>
+OutputPointType inverted_point(const InputPointType& a)
+{
+ return custom_point<OutputPointType>(0-a.x, 0-a.y, 0-a.z);
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB>
+double squared_distance_from_point_to_point(const InputPointTypeA& a, const InputPointTypeB& b)
+{
+ const double dx=(a.x-b.x);
+ const double dy=(a.y-b.y);
+ const double dz=(a.z-b.z);
+ return (dx*dx+dy*dy+dz*dz);
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB>
+double distance_from_point_to_point(const InputPointTypeA& a, const InputPointTypeB& b)
+{
+ return sqrt(squared_distance_from_point_to_point(a, b));
+}
+
+template<typename InputPointType>
+double squared_point_module(const InputPointType& a)
+{
+ return (a.x*a.x+a.y*a.y+a.z*a.z);
+}
+
+template<typename InputPointType>
+double point_module(const InputPointType& a)
+{
+ return sqrt(squared_point_module(a));
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB>
+double dot_product(const InputPointTypeA& a, const InputPointTypeB& b)
+{
+ return (a.x*b.x+a.y*b.y+a.z*b.z);
+}
+
+template<typename OutputPointType, typename InputPointTypeA, typename InputPointTypeB>
+OutputPointType cross_product(const InputPointTypeA& a, const InputPointTypeB& b)
+{
+ return custom_point<OutputPointType>(a.y*b.z-a.z*b.y, a.z*b.x-a.x*b.z, a.x*b.y-a.y*b.x);
+}
+
+template<typename OutputPointType, typename InputPointType>
+OutputPointType point_and_number_product(const InputPointType& a, const double k)
+{
+ return custom_point<OutputPointType>(a.x*k, a.y*k, a.z*k);
+}
+
+template<typename OutputPointType, typename InputPointType>
+OutputPointType unit_point(const InputPointType& a)
+{
+ return point_and_number_product<OutputPointType>(a, 1/point_module(a));
+}
+
+template<typename OutputPointType, typename InputPointTypeA, typename InputPointTypeB>
+OutputPointType sum_of_points(const InputPointTypeA& a, const InputPointTypeB& b)
+{
+ return custom_point<OutputPointType>(a.x+b.x, a.y+b.y, a.z+b.z);
+}
+
+template<typename OutputPointType, typename InputPointTypeA, typename InputPointTypeB>
+OutputPointType sub_of_points(const InputPointTypeA& a, const InputPointTypeB& b)
+{
+ return custom_point<OutputPointType>(a.x-b.x, a.y-b.y, a.z-b.z);
+}
+
+template<typename OutputPointType, typename InputPointTypeA, typename InputPointTypeB, typename InputPointTypeC>
+OutputPointType plane_normal_from_three_points(const InputPointTypeA& a, const InputPointTypeB& b, const InputPointTypeC& c)
+{
+ return unit_point<OutputPointType>(cross_product<PODPoint>(sub_of_points<PODPoint>(b, a), sub_of_points<PODPoint>(c, a)));
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB, typename InputPointTypeC>
+double signed_distance_from_point_to_plane(const InputPointTypeA& plane_point, const InputPointTypeB& plane_normal, const InputPointTypeC& x)
+{
+ return dot_product(unit_point<PODPoint>(plane_normal), sub_of_points<PODPoint>(x, plane_point));
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB, typename InputPointTypeC>
+int halfspace_of_point(const InputPointTypeA& plane_point, const InputPointTypeB& plane_normal, const InputPointTypeC& x)
+{
+ const double sd=signed_distance_from_point_to_plane(plane_point, plane_normal, x);
+ if(sd>0)
+ {
+ return 1;
+ }
+ else if(sd<0)
+ {
+ return -1;
+ }
+ return 0;
+}
+
+template<typename OutputPointType, typename InputPointTypeA, typename InputPointTypeB, typename InputPointTypeC, typename InputPointTypeD>
+OutputPointType intersection_of_plane_and_segment(const InputPointTypeA& plane_point, const InputPointTypeB& plane_normal, const InputPointTypeC& a, const InputPointTypeD& b)
+{
+ const double da=signed_distance_from_point_to_plane(plane_point, plane_normal, a);
+ const double db=signed_distance_from_point_to_plane(plane_point, plane_normal, b);
+ if((da-db)==0)
+ {
+ return custom_point_from_object<OutputPointType>(a);
+ }
+ else
+ {
+ const double t=da/(da-db);
+ return sum_of_points<OutputPointType>(a, point_and_number_product<PODPoint>(sub_of_points<PODPoint>(b, a), t));
+ }
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB, typename InputPointTypeC, typename InputPointTypeD>
+double signed_volume_of_tetrahedron(const InputPointTypeA& a, const InputPointTypeB& b, const InputPointTypeC& c, const InputPointTypeD& d)
+{
+ return (dot_product(sub_of_points<PODPoint>(a, d), cross_product<PODPoint>(sub_of_points<PODPoint>(b, d), sub_of_points<PODPoint>(c, d)))/6);
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB, typename InputPointTypeC>
+double triangle_area(const InputPointTypeA& a, const InputPointTypeB& b, const InputPointTypeC& c)
+{
+ return (point_module(cross_product<PODPoint>(sub_of_points<PODPoint>(b, a), sub_of_points<PODPoint>(c, a)))/2.0);
+}
+
+template<typename InputPointO, typename InputPointA, typename InputPointB>
+static double min_angle(const InputPointO& o, const InputPointA& a, const InputPointB& b)
+{
+ double cos_val=dot_product(unit_point<PODPoint>(sub_of_points<PODPoint>(a, o)), unit_point<PODPoint>(sub_of_points<PODPoint>(b, o)));
+ if(cos_val<-1.0)
+ {
+ cos_val=-1.0;
+ }
+ else if(cos_val>1.0)
+ {
+ cos_val=1.0;
+ }
+ return acos(cos_val);
+}
+
+inline double pi_value()
+{
+ static const double pi=acos(-1.0);
+ return pi;
+}
+
+template<typename InputPointO, typename InputPointA, typename InputPointB, typename InputPointC>
+static double directed_angle(const InputPointO& o, const InputPointA& a, const InputPointB& b, const InputPointC& c)
+{
+ const double angle=min_angle(o, a, b);
+ const PODPoint n=cross_product<PODPoint>(unit_point<PODPoint>(sub_of_points<PODPoint>(a, o)), unit_point<PODPoint>(sub_of_points<PODPoint>(b, o)));
+ if(dot_product(sub_of_points<PODPoint>(c, o), n)>=0)
+ {
+ return angle;
+ }
+ else
+ {
+ return (pi_value()*2-angle);
+ }
+}
+
+template<typename InputSphereType, typename InputPointTypeA, typename InputPointTypeB, typename InputPointTypeC>
+double spherical_triangle_area(const InputSphereType& s, const InputPointTypeA& a, const InputPointTypeB& b, const InputPointTypeC& c)
+{
+ const double va=min_angle(a, b, c);
+ const double vb=min_angle(b, a, c);
+ const double vc=min_angle(c, a, b);
+ const PODPoint sa=sub_of_points<PODPoint>(a, s);
+ const PODPoint sb=sub_of_points<PODPoint>(b, s);
+ const PODPoint sc=sub_of_points<PODPoint>(c, s);
+ const PODPoint o=custom_point<PODPoint>(0.0, 0.0, 0.0);
+ const PODPoint nab=cross_product<PODPoint>(sa, sb);
+ const PODPoint nac=cross_product<PODPoint>(sa, sc);
+ const PODPoint nbc=cross_product<PODPoint>(sb, sc);
+ const double vpa=min_angle(o, nab, nac);
+ const double vpb=min_angle(o, inverted_point<PODPoint>(nab), nbc);
+ const double vpc=min_angle(o, inverted_point<PODPoint>(nac), inverted_point<PODPoint>(nbc));
+ const double e=(vpa+vpb+vpc)-(va+vb+vc);
+ return (e*s.r*s.r);
+}
+
+template<typename OutputPointType, typename InputPointType>
+OutputPointType any_normal_of_vector(const InputPointType& a)
+{
+ PODPoint b=custom_point_from_object<PODPoint>(a);
+ if(!equal(b.x, 0.0) && (!equal(b.y, 0.0) || !equal(b.z, 0.0)))
+ {
+ b.x=0.0-b.x;
+ return unit_point<OutputPointType>(cross_product<OutputPointType>(a, b));
+ }
+ else if(!equal(b.y, 0.0) && (!equal(b.x, 0.0) || !equal(b.z, 0.0)))
+ {
+ b.y=0.0-b.y;
+ return unit_point<OutputPointType>(cross_product<OutputPointType>(a, b));
+ }
+ else if(!equal(b.x, 0.0))
+ {
+ return custom_point<OutputPointType>(0, 1, 0);
+ }
+ else
+ {
+ return custom_point<OutputPointType>(1, 0, 0);
+ }
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB, typename InputPointTypeC>
+double distance_from_point_to_line(const InputPointTypeA& p, const InputPointTypeB& start, const InputPointTypeC& end)
+{
+ const PODPoint line_vector=unit_point<PODPoint>(sub_of_points<PODPoint>(end, start));
+ const PODPoint translated_p=sub_of_points<PODPoint>(p, start);
+ const double distance_on_line=dot_product(translated_p, line_vector);
+ return sqrt(squared_point_module(translated_p)-(distance_on_line*distance_on_line));
+}
+
+template<typename OutputPointType, typename InputIterator>
+static OutputPointType mass_center(const InputIterator begin, const InputIterator end)
+{
+ PODPoint mc=custom_point<PODPoint>(0.0, 0.0, 0.0);
+ unsigned int count=0;
+ InputIterator it=begin;
+ while(it!=end)
+ {
+ mc=sum_of_points<PODPoint>(mc, *it);
+ count++;
+ ++it;
+ }
+ if(count>0)
+ {
+ mc=point_and_number_product<PODPoint>(mc, 1.0/static_cast<double>(count));
+ }
+ return custom_point_from_object<OutputPointType>(mc);
+}
+
+struct SimplePoint
+{
+ double x;
+ double y;
+ double z;
+
+ SimplePoint() : x(0), y(0), z(0)
+ {
+ }
+
+ SimplePoint(const double x, const double y, const double z) : x(x), y(y), z(z)
+ {
+ }
+
+ template<typename InputPointType>
+ explicit SimplePoint(const InputPointType& input_point) : x(input_point.x), y(input_point.y), z(input_point.z)
+ {
+ }
+
+ bool operator==(const SimplePoint& b) const
+ {
+ return points_equal(*this, b);
+ }
+
+ bool operator<(const SimplePoint& b) const
+ {
+ return points_less(*this, b);
+ }
+
+ SimplePoint operator+(const SimplePoint& b) const
+ {
+ return sum_of_points<SimplePoint>(*this, b);
+ }
+
+ SimplePoint operator-(const SimplePoint& b) const
+ {
+ return sub_of_points<SimplePoint>(*this, b);
+ }
+
+ double operator*(const SimplePoint& b) const
+ {
+ return dot_product(*this, b);
+ }
+
+ SimplePoint operator*(const double k) const
+ {
+ return point_and_number_product<SimplePoint>(*this, k);
+ }
+
+ SimplePoint operator&(const SimplePoint& b) const
+ {
+ return cross_product<SimplePoint>(*this, b);
+ }
+
+ double module() const
+ {
+ return point_module(*this);
+ }
+
+ SimplePoint unit() const
+ {
+ return unit_point<SimplePoint>(*this);
+ }
+
+ SimplePoint inverted() const
+ {
+ return inverted_point<SimplePoint>(*this);
+ }
+};
+
+template<typename T>
+inline T& operator<<(T& output, const SimplePoint& p)
+{
+ output << p.x << " " << p.y << " " << p.z;
+ return output;
+}
+
+template<typename T>
+inline T& operator>>(T& input, SimplePoint& p)
+{
+ input >> p.x >> p.y >> p.z;
+ return input;
+}
+
+}
+
+#endif /* APOLLOTA_BASIC_OPERATIONS_ON_POINTS_H_ */
diff --git a/src/apollota/basic_operations_on_spheres.h b/src/apollota/basic_operations_on_spheres.h
new file mode 100644
index 0000000..28d7b8b
--- /dev/null
+++ b/src/apollota/basic_operations_on_spheres.h
@@ -0,0 +1,222 @@
+#ifndef APOLLOTA_BASIC_OPERATIONS_ON_SPHERES_H_
+#define APOLLOTA_BASIC_OPERATIONS_ON_SPHERES_H_
+
+#include "basic_operations_on_points.h"
+
+namespace apollota
+{
+
+template<typename OutputSphereType>
+OutputSphereType custom_sphere(const double x, const double y, const double z, const double r)
+{
+ OutputSphereType result;
+ result.x=x;
+ result.y=y;
+ result.z=z;
+ result.r=r;
+ return result;
+}
+
+template<typename OutputSphereType, typename InputObjectType>
+OutputSphereType custom_sphere_from_object(const InputObjectType& o)
+{
+ return custom_sphere<OutputSphereType>(o.x, o.y, o.z, o.r);
+}
+
+template<typename OutputSphereType, typename InputPointType>
+OutputSphereType custom_sphere_from_point(const InputPointType& p, const double r)
+{
+ return custom_sphere<OutputSphereType>(p.x, p.y, p.z, r);
+}
+
+template<typename InputSphereTypeA, typename InputSphereTypeB>
+bool spheres_equal(const InputSphereTypeA& a, const InputSphereTypeB& b, const double epsilon)
+{
+ return (equal(a.x, b.x, epsilon) && equal(a.y, b.y, epsilon) && equal(a.z, b.z, epsilon) && equal(a.r, b.r, epsilon));
+}
+
+template<typename InputSphereTypeA, typename InputSphereTypeB>
+bool spheres_less(const InputSphereTypeA& a, const InputSphereTypeB& b)
+{
+ if(less(a.x, b.x)) { return true; }
+ else if(greater(a.x, b.x)) { return false; }
+
+ if(less(a.y, b.y)) { return true; }
+ else if(greater(a.y, b.y)) { return false; }
+
+ if(less(a.z, b.z)) { return true; }
+ else if(greater(a.z, b.z)) { return false; }
+
+ if(less(a.r, b.r)) { return true; }
+ else if(greater(a.r, b.r)) { return false; }
+
+ return false;
+}
+
+template<typename InputPointType, typename InputSphereType>
+double minimal_distance_from_point_to_sphere(const InputPointType& a, const InputSphereType& b)
+{
+ return (distance_from_point_to_point(a, b)-b.r);
+}
+
+template<typename InputPointType, typename InputSphereType>
+double maximal_distance_from_point_to_sphere(const InputPointType& a, const InputSphereType& b)
+{
+ return (distance_from_point_to_point(a, b)+b.r);
+}
+
+template<typename InputSphereTypeA,typename InputSphereTypeB>
+double minimal_distance_from_sphere_to_sphere(const InputSphereTypeA& a, const InputSphereTypeB& b)
+{
+ return (distance_from_point_to_point(a, b)-a.r-b.r);
+}
+
+template<typename InputSphereTypeA, typename InputSphereTypeB>
+bool sphere_intersects_sphere(const InputSphereTypeA& a, const InputSphereTypeB& b)
+{
+ return less(distance_from_point_to_point(a, b), (a.r+b.r));
+}
+
+template<typename InputSphereTypeA, typename InputSphereTypeB>
+bool sphere_intersects_sphere_with_expansion(const InputSphereTypeA& a, const InputSphereTypeB& b, const double expansion)
+{
+ return less(distance_from_point_to_point(a, b), (a.r+b.r+expansion));
+}
+
+template<typename InputSphereTypeA, typename InputSphereTypeB>
+bool sphere_touches_sphere(const InputSphereTypeA& a, const InputSphereTypeB& b)
+{
+ return equal(distance_from_point_to_point(a, b), (a.r+b.r));
+}
+
+template<typename InputSphereTypeA, typename InputSphereTypeB>
+bool sphere_contains_sphere(const InputSphereTypeA& a, const InputSphereTypeB& b)
+{
+ return (greater_or_equal(a.r, b.r) && less_or_equal(distance_from_point_to_point(a, b), (a.r-b.r)));
+}
+
+template<typename InputPointTypeA, typename InputPointTypeB, typename InputSphereTypeC>
+int halfspace_of_sphere(const InputPointTypeA& plane_point, const InputPointTypeB& plane_normal, const InputSphereTypeC& x)
+{
+ const double dc=signed_distance_from_point_to_plane(plane_point, plane_normal, x);
+ if(dc>0 && (dc-x.r>0))
+ {
+ return 1;
+ }
+ else if(dc<0 && (dc+x.r<0))
+ {
+ return -1;
+ }
+ return 0;
+}
+
+template<typename OutputSphereType, typename InputSphereTypeA, typename InputSphereTypeB>
+OutputSphereType intersection_circle_of_two_spheres(const InputSphereTypeA& a, const InputSphereTypeB& b)
+{
+ const SimplePoint ap=custom_point_from_object<SimplePoint>(a);
+ const SimplePoint bp=custom_point_from_object<SimplePoint>(b);
+ const SimplePoint cv=bp-ap;
+ const double cm=cv.module();
+ const double cos_g=(a.r*a.r+cm*cm-b.r*b.r)/(2*a.r*cm);
+ const double sin_g=sqrt(1-cos_g*cos_g);
+ return custom_sphere_from_point<OutputSphereType>(ap+(cv.unit()*(a.r*cos_g)), a.r*sin_g);
+}
+
+template<typename InputSphereType>
+bool intersect_line_segment_with_sphere(const InputSphereType& sphere, const SimplePoint& a, const SimplePoint& b, SimplePoint& c)
+{
+ if(sphere.r<=0.0)
+ {
+ return false;
+ }
+ const double d_oa=distance_from_point_to_point(a, sphere);
+ const double d_ob=distance_from_point_to_point(b, sphere);
+ if((d_oa<sphere.r && d_ob<sphere.r) || (d_oa>sphere.r && d_ob>sphere.r))
+ {
+ return false;
+ }
+ else if(d_oa>sphere.r && d_ob<sphere.r)
+ {
+ return intersect_line_segment_with_sphere(sphere, b, a, c);
+ }
+ else
+ {
+ const double angle_oac=min_angle(a, sphere, b);
+ if(equal(angle_oac, 0.0) || equal(angle_oac, pi_value()))
+ {
+ c=SimplePoint(sphere)+((b-SimplePoint(sphere)).unit()*d_ob);
+ }
+ else
+ {
+ const double k=sin(angle_oac)/sphere.r;
+ double sin_aio=k*d_oa;
+ if(sin_aio<-1.0)
+ {
+ sin_aio=-1.0;
+ }
+ else if(sin_aio>1.0)
+ {
+ sin_aio=1.0;
+ }
+ const double angle_aco=asin(sin_aio);
+ const double angle_aoc=pi_value()-(angle_oac+angle_aco);
+ const double d_ai=sin(angle_aoc)/k;
+ c=a+((b-a).unit()*d_ai);
+ }
+ return true;
+ }
+}
+
+struct SimpleSphere
+{
+ double x;
+ double y;
+ double z;
+ double r;
+
+ SimpleSphere() : x(0), y(0), z(0), r(0)
+ {
+ }
+
+ SimpleSphere(const double x, const double y, const double z, const double r) : x(x), y(y), z(z), r(r)
+ {
+ }
+
+ template<typename InputSphereType>
+ explicit SimpleSphere(const InputSphereType& input_sphere) : x(input_sphere.x), y(input_sphere.y), z(input_sphere.z), r(input_sphere.r)
+ {
+ }
+
+ template<typename InputPointType>
+ SimpleSphere(const InputPointType& input_point, const double r) : x(input_point.x), y(input_point.y), z(input_point.z), r(r)
+ {
+ }
+
+ bool operator==(const SimpleSphere& b) const
+ {
+ return spheres_equal(*this, b, default_comparison_epsilon());
+ }
+
+ bool operator<(const SimpleSphere& b) const
+ {
+ return spheres_less(*this, b);
+ }
+};
+
+template<typename T>
+inline T& operator<<(T& output, const SimpleSphere& sphere)
+{
+ output << sphere.x << " " << sphere.y << " " << sphere.z << " " << sphere.r;
+ return output;
+}
+
+template<typename T>
+inline T& operator>>(T& input, SimpleSphere& sphere)
+{
+ input >> sphere.x >> sphere.y >> sphere.z >> sphere.r;
+ return input;
+}
+
+}
+
+#endif /* APOLLOTA_BASIC_OPERATIONS_ON_SPHERES_H_ */
diff --git a/src/apollota/bounding_spheres_hierarchy.h b/src/apollota/bounding_spheres_hierarchy.h
new file mode 100644
index 0000000..38dde3f
--- /dev/null
+++ b/src/apollota/bounding_spheres_hierarchy.h
@@ -0,0 +1,343 @@
+#ifndef APOLLOTA_BOUNDING_SPHERES_HIERARCH_2_H_
+#define APOLLOTA_BOUNDING_SPHERES_HIERARCH_2_H_
+
+#include <vector>
+#include <algorithm>
+#include <limits>
+
+#include "basic_operations_on_spheres.h"
+#include "splitting_of_spheres.h"
+
+namespace apollota
+{
+
+class BoundingSpheresHierarchy
+{
+public:
+ template<typename InputSphereType>
+ BoundingSpheresHierarchy(const std::vector<InputSphereType>& input_spheres, const double initial_radius_for_spheres_bucketing, const std::size_t min_number_of_clusters) :
+ leaves_spheres_(convert_input_spheres_to_simple_spheres(input_spheres)),
+ input_radii_range_(calc_input_radii_range(leaves_spheres_)),
+ clusters_layers_(cluster_spheres_in_layers(leaves_spheres_, initial_radius_for_spheres_bucketing, min_number_of_clusters))
+ {
+ }
+
+ const std::vector<SimpleSphere>& leaves_spheres() const
+ {
+ return leaves_spheres_;
+ }
+
+ double min_input_radius() const
+ {
+ return input_radii_range_.first;
+ }
+
+ double max_input_radius() const
+ {
+ return input_radii_range_.second;
+ }
+
+ std::size_t levels() const
+ {
+ return clusters_layers_.size();
+ }
+
+ std::vector<SimpleSphere> collect_bounding_spheres(const std::size_t level) const
+ {
+ std::vector<SimpleSphere> result;
+ if(level<clusters_layers_.size())
+ {
+ result.reserve(clusters_layers_[level].size());
+ for(std::size_t i=0;i<clusters_layers_[level].size();i++)
+ {
+ result.push_back(SimpleSphere(clusters_layers_[level][i]));
+ }
+ }
+ return result;
+ }
+
+ template<typename NodeChecker, typename LeafChecker>
+ std::vector<std::size_t> search(NodeChecker& node_checker, LeafChecker& leaf_checker) const
+ {
+ std::vector<std::size_t> results;
+ if(!clusters_layers_.empty())
+ {
+ std::vector<NodeCoordinates> stack;
+ stack.reserve(clusters_layers_.back().size()+clusters_layers_.size()+1);
+ {
+ const std::size_t top_level=clusters_layers_.size()-1;
+ for(std::size_t top_id=0;top_id<clusters_layers_[top_level].size();top_id++)
+ {
+ stack.push_back(NodeCoordinates(top_level, top_id, 0));
+ }
+ }
+ while(!stack.empty())
+ {
+ const NodeCoordinates ncs=stack.back();
+ if(
+ ncs.level_id<clusters_layers_.size()
+ && ncs.cluster_id<clusters_layers_[ncs.level_id].size()
+ && ncs.child_id<clusters_layers_[ncs.level_id][ncs.cluster_id].children.size()
+ && (ncs.child_id>0 || node_checker(clusters_layers_[ncs.level_id][ncs.cluster_id]))
+ )
+ {
+ const std::vector<std::size_t>& children=clusters_layers_[ncs.level_id][ncs.cluster_id].children;
+ if(ncs.level_id==0)
+ {
+ for(std::size_t i=0;i<children.size();i++)
+ {
+ const std::size_t child=children[i];
+ const std::pair<bool, bool> status=leaf_checker(child, leaves_spheres_[child]);
+ if(status.first)
+ {
+ results.push_back(child);
+ if(status.second)
+ {
+ return results;
+ }
+ }
+ }
+ stack.pop_back();
+ }
+ else
+ {
+ stack.back().child_id++;
+ stack.push_back(NodeCoordinates(ncs.level_id-1, children[ncs.child_id], 0));
+ }
+ }
+ else
+ {
+ stack.pop_back();
+ }
+ }
+ }
+ return results;
+ }
+
+ template<typename ListType, typename FunctorType>
+ static std::vector<std::size_t> sort_objects_by_distance_to_one_of_them(const ListType& list, const std::size_t starting_id, const FunctorType& functor, const double max_distance=std::numeric_limits<double>::max())
+ {
+ std::vector<std::size_t> result;
+ if(starting_id<list.size())
+ {
+ std::vector< std::pair<double, std::size_t> > distances;
+ distances.reserve(list.size()-1);
+ for(std::size_t i=0;i<list.size();i++)
+ {
+ if(i!=starting_id)
+ {
+ const double distance=functor(list[starting_id], list[i]);
+ if(distance<=max_distance)
+ {
+ distances.push_back(std::make_pair(distance, i));
+ }
+ }
+ }
+ std::sort(distances.begin(), distances.end());
+ result.reserve(distances.size()+1);
+ result.push_back(starting_id);
+ for(std::size_t i=0;i<distances.size();i++)
+ {
+ result.push_back(distances[i].second);
+ }
+ }
+ return result;
+ }
+
+private:
+
+ class Cluster : public SimpleSphere
+ {
+ public:
+ std::vector<std::size_t> children;
+ std::vector<std::size_t> leaves_ids;
+ };
+
+ struct NodeCoordinates
+ {
+ std::size_t level_id;
+ std::size_t cluster_id;
+ std::size_t child_id;
+
+ NodeCoordinates(std::size_t level_id, std::size_t cluster_id, std::size_t child_id) :
+ level_id(level_id), cluster_id(cluster_id), child_id(child_id)
+ {
+ }
+ };
+
+ template<typename InputSphereType>
+ static std::vector<SimpleSphere> convert_input_spheres_to_simple_spheres(const std::vector<InputSphereType>& input_spheres)
+ {
+ std::vector<SimpleSphere> result;
+ result.reserve(input_spheres.size());
+ for(std::size_t i=0;i<input_spheres.size();i++)
+ {
+ result.push_back(SimpleSphere(input_spheres[i]));
+ }
+ return result;
+ }
+
+ template<typename SphereType>
+ static std::pair<double, double> calc_input_radii_range(const std::vector<SphereType>& spheres)
+ {
+ std::pair<double, double> range(0, 0);
+ if(!spheres.empty())
+ {
+ range.first=spheres.front().r;
+ range.second=spheres.front().r;
+ for(std::size_t i=1;i<spheres.size();i++)
+ {
+ range.first=std::min(range.first, spheres[i].r);
+ range.second=std::max(range.second, spheres[i].r);
+ }
+ }
+ return range;
+ }
+
+ template<typename SphereType>
+ static std::vector<SimpleSphere> select_centers_for_clusters(const std::vector<SphereType>& spheres, const double expansion)
+ {
+ std::vector<SimpleSphere> centers;
+ if(!spheres.empty())
+ {
+ std::vector<bool> allowed(spheres.size(), true);
+ const std::vector<std::size_t> global_traversal=sort_objects_by_distance_to_one_of_them(spheres, 0, maximal_distance_from_point_to_sphere<SphereType, SphereType>);
+ for(std::size_t k=0;k<spheres.size();k++)
+ {
+ const std::size_t i=global_traversal[k];
+ if(allowed[i])
+ {
+ centers.push_back(spheres[i]);
+ allowed[i]=false;
+ for(std::size_t j=0;j<spheres.size();j++)
+ {
+ if(allowed[j] && sphere_intersects_sphere_with_expansion(spheres[i], spheres[j], expansion))
+ {
+ allowed[j]=false;
+ }
+ }
+ }
+ }
+ }
+ return centers;
+ }
+
+ template<typename SphereType>
+ static std::vector<Cluster> cluster_spheres_using_centers(const std::vector<SphereType>& spheres, const std::vector<std::size_t>& selection, const std::vector<SimpleSphere>& centers)
+ {
+ std::vector<Cluster> clusters;
+ clusters.reserve(centers.size());
+ for(std::size_t i=0;i<centers.size();i++)
+ {
+ clusters.push_back(custom_sphere_from_object<Cluster>(centers[i]));
+ }
+ for(std::size_t i=0;i<selection.size();i++)
+ {
+ const SphereType& sphere=spheres[selection[i]];
+ std::size_t min_dist_id=0;
+ double min_dist_value=maximal_distance_from_point_to_sphere(clusters[min_dist_id], sphere);
+ for(std::size_t j=1;j<clusters.size();j++)
+ {
+ const double dist_value=maximal_distance_from_point_to_sphere(clusters[j], sphere);
+ if(dist_value<min_dist_value)
+ {
+ min_dist_id=j;
+ min_dist_value=dist_value;
+ }
+ }
+ Cluster& cluster=clusters[min_dist_id];
+ cluster.r=std::max(cluster.r, min_dist_value);
+ cluster.children.push_back(selection[i]);
+ }
+ std::vector<Cluster> nonempty_clusters;
+ nonempty_clusters.reserve(clusters.size());
+ for(std::size_t i=0;i<clusters.size();i++)
+ {
+ if(!clusters[i].children.empty())
+ {
+ nonempty_clusters.push_back(clusters[i]);
+ }
+ }
+ return nonempty_clusters;
+ }
+
+ template<typename SphereType>
+ static std::vector<Cluster> cluster_spheres_using_radius_expansion(const std::vector<SphereType>& spheres, const double radius_expansion)
+ {
+ const std::size_t max_part_size=10000;
+ if(spheres.size()<=max_part_size)
+ {
+ std::vector<std::size_t> selection(spheres.size(), 0);
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ selection[i]=i;
+ }
+ return cluster_spheres_using_centers(spheres, selection, select_centers_for_clusters(spheres, radius_expansion));
+ }
+ else
+ {
+ std::vector<Cluster> result;
+ const std::vector< std::vector<std::size_t> > selections=SplittingOfSpheres::split_for_size_of_part(spheres, max_part_size);
+ for(std::size_t i=0;i<selections.size();i++)
+ {
+ const std::vector<std::size_t>& selection=selections[i];
+ std::vector<SimpleSphere> selection_contents(selection.size());
+ for(std::size_t j=0;j<selection.size();j++)
+ {
+ selection_contents[j]=SimpleSphere(spheres[selection[j]]);
+ }
+ const std::vector<Cluster> partial_result=cluster_spheres_using_centers(spheres, selection, select_centers_for_clusters(selection_contents, radius_expansion));
+ result.insert(result.end(), partial_result.begin(), partial_result.end());
+ }
+ return result;
+ }
+ }
+
+ template<typename SphereType>
+ static std::vector< std::vector<Cluster> > cluster_spheres_in_layers(const std::vector<SphereType>& spheres, const double r, const std::size_t min_number_of_clusters)
+ {
+ std::vector< std::vector<Cluster> > clusters_layers;
+ {
+ std::vector<Cluster> clusters=cluster_spheres_using_radius_expansion(spheres, r);
+ for(std::size_t i=0;i<clusters.size();i++)
+ {
+ clusters[i].leaves_ids=clusters[i].children;
+ }
+ clusters_layers.push_back(clusters);
+ }
+ bool need_more=clusters_layers.back().size()>min_number_of_clusters;
+ while(need_more)
+ {
+ std::vector<Cluster> clusters=cluster_spheres_using_radius_expansion(clusters_layers.back(), 0.0);
+ if(clusters.size()<clusters_layers.back().size() && clusters.size()>min_number_of_clusters)
+ {
+ for(std::size_t i=0;i<clusters.size();i++)
+ {
+ for(std::size_t j=0;j<clusters[i].children.size();j++)
+ {
+ clusters[i].leaves_ids.insert(clusters[i].leaves_ids.end(), clusters_layers.back()[clusters[i].children[j]].leaves_ids.begin(), clusters_layers.back()[clusters[i].children[j]].leaves_ids.end());
+ }
+ clusters[i].r=0.0;
+ for(std::size_t j=0;j<clusters[i].leaves_ids.size();j++)
+ {
+ clusters[i].r=std::max(clusters[i].r, maximal_distance_from_point_to_sphere(clusters[i], spheres[clusters[i].leaves_ids[j]]));
+ }
+ }
+ clusters_layers.push_back(clusters);
+ }
+ else
+ {
+ need_more=false;
+ }
+ }
+ return clusters_layers;
+ }
+
+ std::vector<SimpleSphere> leaves_spheres_;
+ std::pair<double, double> input_radii_range_;
+ std::vector< std::vector<Cluster> > clusters_layers_;
+};
+
+}
+
+#endif /* APOLLOTA_BOUNDING_SPHERES_HIERARCH_2_H_ */
diff --git a/src/apollota/constrained_contact_contour.h b/src/apollota/constrained_contact_contour.h
new file mode 100644
index 0000000..0b8638f
--- /dev/null
+++ b/src/apollota/constrained_contact_contour.h
@@ -0,0 +1,646 @@
+#ifndef APOLLOTA_CONSTRAINED_CONTACT_CONTOUR_H_
+#define APOLLOTA_CONSTRAINED_CONTACT_CONTOUR_H_
+
+#include <vector>
+#include <list>
+
+#include "triangulation.h"
+#include "hyperboloid_between_two_spheres.h"
+#include "rotation.h"
+#include "simple_polygon_utilities.h"
+
+namespace apollota
+{
+
+class ConstrainedContactContour
+{
+public:
+ struct PointRecord
+ {
+ SimplePoint p;
+ std::size_t left_id;
+ std::size_t right_id;
+
+ PointRecord(const SimplePoint& p, const std::size_t left_id, const std::size_t right_id) : p(p), left_id(left_id), right_id(right_id)
+ {
+ }
+ };
+
+ typedef std::list<PointRecord> Contour;
+
+ struct ContourAreaDescriptor
+ {
+ std::vector<SimplePoint> outline;
+ SimplePoint center;
+ bool star_domain;
+ std::vector<Triple> simple_polygon_triangulation;
+
+ ContourAreaDescriptor() : star_domain(false)
+ {
+ }
+ };
+
+ static std::list<Contour> construct_contact_contours(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const std::set<std::size_t>& vertices_ids,
+ const std::size_t a_id,
+ const std::size_t b_id,
+ const double probe,
+ const double step,
+ const int projections)
+ {
+ std::list<Contour> result;
+ if(a_id<spheres.size() && b_id<spheres.size())
+ {
+ const SimpleSphere& a=spheres[a_id];
+ const SimpleSphere& b=spheres[b_id];
+ if(minimal_distance_from_sphere_to_sphere(a, b)<(probe*2.0))
+ {
+ const std::multimap<double, std::size_t> neighbor_ids=collect_pair_neighbors_with_distances(a, spheres, collect_pair_neighbors_from_pair_vertices(a_id, b_id, vertices_vector, vertices_ids));
+ const Contour initial_contour=construct_circular_contour(a, b, a_id, vertices_vector, vertices_ids, probe, step);
+ if(!initial_contour.empty())
+ {
+ result.push_back(initial_contour);
+ if(!vertices_ids.empty())
+ {
+ const SimpleSphere bounding_sphere_of_vertices_centers=construct_bounding_sphere_of_vertices_centers(vertices_vector, vertices_ids, step);
+ for(std::multimap<double, std::size_t>::const_iterator it=neighbor_ids.begin();it!=neighbor_ids.end();++it)
+ {
+ const std::size_t c_id=it->second;
+ if(c_id<spheres.size())
+ {
+ const SimpleSphere& c=spheres[c_id];
+ std::list<Contour>::iterator jt=result.begin();
+ while(jt!=result.end())
+ {
+ Contour& contour=(*jt);
+ std::list<Contour> segments;
+ if(cut_and_split_contour(a, c, c_id, contour, segments))
+ {
+ if(!contour.empty())
+ {
+ mend_contour(a, b, c, c_id, step, projections, contour);
+ if(check_contour_intersects_sphere(bounding_sphere_of_vertices_centers, contour))
+ {
+ ++jt;
+ }
+ else
+ {
+ jt=result.erase(jt);
+ }
+ }
+ else
+ {
+ if(!segments.empty())
+ {
+ for(std::list<Contour>::iterator st=segments.begin();st!=segments.end();++st)
+ {
+ mend_contour(a, b, c, c_id, step, projections, (*st));
+ }
+ filter_contours_intersecting_sphere(bounding_sphere_of_vertices_centers, segments);
+ if(!segments.empty())
+ {
+ result.splice(jt, segments);
+ }
+ }
+ jt=result.erase(jt);
+ }
+ }
+ else
+ {
+ ++jt;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static std::list<Contour> collect_subcontours_from_contour(const Contour& contour)
+ {
+ std::list<Contour> result;
+ Contour::const_iterator start_it=contour.begin();
+ while(start_it!=contour.end() && start_it->left_id==start_it->right_id)
+ {
+ ++start_it;
+ }
+ if(start_it==contour.end())
+ {
+ result.push_back(contour);
+ }
+ else
+ {
+ Contour::const_iterator it=start_it;
+ result.push_back(Contour());
+ result.back().push_back(*it);
+ it=get_right_iterator(contour, it);
+ while(it!=start_it)
+ {
+ if(it->left_id!=it->right_id)
+ {
+ result.back().push_back(*it);
+ result.push_back(Contour());
+ }
+ result.back().push_back(*it);
+ it=get_right_iterator(contour, it);
+ }
+ result.back().push_back(*it);
+ }
+ return result;
+ }
+
+ static ContourAreaDescriptor construct_contour_area_descriptor(const Contour& contour, const SimpleSphere& sphere1, const SimpleSphere& sphere2, const bool check_and_handle_non_star_domain)
+ {
+ ContourAreaDescriptor d;
+ d.outline=collect_points_from_contour(contour);
+ if(!d.outline.empty())
+ {
+ d.center=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(mass_center<SimplePoint>(d.outline.begin(), d.outline.end()), sphere1, sphere2);
+ if(check_and_handle_non_star_domain)
+ {
+ d.star_domain=check_star_domain(d.outline, d.center);
+ if(!d.star_domain)
+ {
+ d.simple_polygon_triangulation=SimplePolygonUtilities::triangulate_simple_polygon(d.outline, sub_of_points<SimplePoint>(sphere1, sphere2)).triangulation;
+ }
+ }
+ else
+ {
+ d.star_domain=true;
+ }
+ }
+ return d;
+ }
+
+private:
+ static std::set<std::size_t> collect_pair_neighbors_from_pair_vertices(
+ const std::size_t a_id,
+ const std::size_t b_id,
+ const Triangulation::VerticesVector& vertices_vector,
+ const std::set<std::size_t>& vertices_ids)
+ {
+ std::set<std::size_t> neighbors_ids;
+ for(std::set<std::size_t>::const_iterator it=vertices_ids.begin();it!=vertices_ids.end();++it)
+ {
+ const std::size_t vertex_id=(*it);
+ if(vertex_id<vertices_vector.size())
+ {
+ const Quadruple& quadruple=vertices_vector[vertex_id].first;
+ for(int i=0;i<4;i++)
+ {
+ const std::size_t neighbor_id=quadruple.get(i);
+ if(neighbor_id!=a_id && neighbor_id!=b_id)
+ {
+ neighbors_ids.insert(neighbor_id);
+ }
+ }
+ }
+ }
+ return neighbors_ids;
+ }
+
+ static std::multimap<double, std::size_t> collect_pair_neighbors_with_distances(
+ const SimpleSphere& a,
+ const std::vector<SimpleSphere>& spheres,
+ const std::set<std::size_t>& neighbor_ids)
+ {
+ std::multimap<double, std::size_t> result;
+ for(std::set<std::size_t>::const_iterator it=neighbor_ids.begin();it!=neighbor_ids.end();++it)
+ {
+ const std::size_t c_id=(*it);
+ if(c_id<spheres.size())
+ {
+ const SimpleSphere& c=spheres[c_id];
+ result.insert(std::make_pair(minimal_distance_from_sphere_to_sphere(a, c), c_id));
+ }
+ }
+ return result;
+ }
+
+ static bool check_if_radiuses_of_vertices_are_below_probe(
+ const Triangulation::VerticesVector& vertices_vector,
+ const std::set<std::size_t>& vertices_ids,
+ const double probe)
+ {
+ for(std::set<std::size_t>::const_iterator it=vertices_ids.begin();it!=vertices_ids.end();++it)
+ {
+ if(vertices_vector[(*it)].second.r>=probe)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ static SimpleSphere construct_bounding_sphere_of_vertices_centers(
+ const Triangulation::VerticesVector& vertices_vector,
+ const std::set<std::size_t>& vertices_ids,
+ const double radius_extension)
+ {
+ if(!vertices_ids.empty())
+ {
+ SimplePoint mc;
+ for(std::set<std::size_t>::const_iterator it=vertices_ids.begin();it!=vertices_ids.end();++it)
+ {
+ mc=mc+SimplePoint(vertices_vector[(*it)].second);
+ }
+ mc=mc*(1.0/static_cast<double>(vertices_ids.size()));
+ SimpleSphere result(mc, 0.0);
+ for(std::set<std::size_t>::const_iterator it=vertices_ids.begin();it!=vertices_ids.end();++it)
+ {
+ result.r=std::max(result.r, distance_from_point_to_point(result, vertices_vector[(*it)].second));
+ }
+ result.r+=radius_extension;
+ return result;
+ }
+ else
+ {
+ return SimpleSphere();
+ }
+ }
+
+ static Contour construct_circular_contour(
+ const SimpleSphere& a,
+ const SimpleSphere& b,
+ const std::size_t a_id,
+ const Triangulation::VerticesVector& vertices_vector,
+ const std::set<std::size_t>& vertices_ids,
+ const double probe,
+ const double step)
+ {
+ Contour result;
+ const SimpleSphere a_expanded=custom_sphere_from_point<SimpleSphere>(a, a.r+probe);
+ const SimpleSphere b_expanded=custom_sphere_from_point<SimpleSphere>(b, b.r+probe);
+ if(sphere_intersects_sphere(a_expanded, b_expanded))
+ {
+ const SimplePoint axis=sub_of_points<SimplePoint>(b, a).unit();
+ if(vertices_ids.size()>1 && check_if_radiuses_of_vertices_are_below_probe(vertices_vector, vertices_ids, probe))
+ {
+ construct_circular_contour_from_base_and_axis(a_id, construct_bounding_sphere_of_vertices_centers(vertices_vector, vertices_ids, step), axis, step, result);
+ for(Contour::iterator it=result.begin();it!=result.end();++it)
+ {
+ it->p=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(it->p, a, b);
+ }
+ }
+ else
+ {
+ construct_circular_contour_from_base_and_axis(a_id, intersection_circle_of_two_spheres<SimpleSphere>(a_expanded, b_expanded), axis, step, result);
+ }
+ }
+ return result;
+ }
+
+ static void construct_circular_contour_from_base_and_axis(
+ const std::size_t a_id,
+ const SimpleSphere& base,
+ const SimplePoint& axis,
+ const double step,
+ Contour& result)
+ {
+ Rotation rotation(axis, 0);
+ const SimplePoint first_point=any_normal_of_vector<SimplePoint>(rotation.axis)*base.r;
+ const double angle_step=std::max(std::min(360*(step/(2*pi_value()*base.r)), 60.0), 5.0);
+ result.push_back(PointRecord(sum_of_points<SimplePoint>(base, first_point), a_id, a_id));
+ for(rotation.angle=angle_step;rotation.angle<360;rotation.angle+=angle_step)
+ {
+ result.push_back(PointRecord(sum_of_points<SimplePoint>(base, rotation.rotate<SimplePoint>(first_point)), a_id, a_id));
+ }
+ }
+
+ static bool cut_and_split_contour(
+ const SimpleSphere& a,
+ const SimpleSphere& c,
+ const std::size_t c_id,
+ Contour& contour,
+ std::list<Contour>& segments)
+ {
+ const std::size_t outsiders_count=mark_contour(a, c, c_id, contour);
+ if(outsiders_count>0)
+ {
+ if(outsiders_count<contour.size())
+ {
+ std::list<Contour::iterator> cuts;
+ const int cuts_count=cut_contour(a, c, c_id, contour, cuts);
+ if(cuts_count>0 && cuts_count%2==0)
+ {
+ if(cuts_count>2)
+ {
+ order_cuts(cuts);
+ split_contour(contour, cuts, segments);
+ }
+ }
+ }
+ else
+ {
+ contour.clear();
+ }
+ return true;
+ }
+ return false;
+ }
+
+ static std::size_t mark_contour(
+ const SimpleSphere& a,
+ const SimpleSphere& c,
+ const std::size_t c_id,
+ Contour& contour)
+ {
+ std::size_t outsiders_count=0;
+ for(Contour::iterator it=contour.begin();it!=contour.end();++it)
+ {
+ if(minimal_distance_from_point_to_sphere(it->p, c)<minimal_distance_from_point_to_sphere(it->p, a))
+ {
+ it->left_id=c_id;
+ it->right_id=c_id;
+ outsiders_count++;
+ }
+ }
+ return outsiders_count;
+ }
+
+ static std::size_t cut_contour(
+ const SimpleSphere& a,
+ const SimpleSphere& c,
+ const std::size_t c_id,
+ Contour& contour,
+ std::list<Contour::iterator>& cuts)
+ {
+ std::size_t cuts_count=0;
+ Contour::iterator it=contour.begin();
+ while(it!=contour.end())
+ {
+ if(it->left_id==c_id && it->right_id==c_id)
+ {
+ const Contour::iterator left_it=get_left_iterator(contour, it);
+ const Contour::iterator right_it=get_right_iterator(contour, it);
+
+ if(left_it->right_id!=c_id)
+ {
+ const SimplePoint& p0=it->p;
+ const SimplePoint& p1=left_it->p;
+ const double l=HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(p0, p1, a, c);
+ cuts.push_back(contour.insert(it, PointRecord(p0+((p1-p0).unit()*l), left_it->right_id, it->left_id)));
+ cuts_count++;
+ }
+
+ if(right_it->left_id!=c_id)
+ {
+ const SimplePoint& p0=it->p;
+ const SimplePoint& p1=right_it->p;
+ const double l=HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(p0, p1, a, c);
+ cuts.push_back(contour.insert(right_it, PointRecord(p0+((p1-p0).unit()*l), it->right_id, right_it->left_id)));
+ cuts_count++;
+ }
+
+ it=contour.erase(it);
+ }
+ else
+ {
+ ++it;
+ }
+ }
+ return cuts_count;
+ }
+
+ static void order_cuts(std::list<Contour::iterator>& cuts)
+ {
+ double sums[2]={0.0, 0.0};
+ for(int i=0;i<2;i++)
+ {
+ if(i==1)
+ {
+ shift_list(cuts, false);
+ }
+ std::list<Contour::iterator>::const_iterator it=cuts.begin();
+ while(it!=cuts.end())
+ {
+ std::list<Contour::iterator>::const_iterator next=it;
+ ++next;
+ if(next!=cuts.end())
+ {
+ sums[i]+=distance_from_point_to_point((*it)->p, (*next)->p);
+ it=next;
+ ++it;
+ }
+ else
+ {
+ it=cuts.end();
+ }
+ }
+ }
+ if(sums[0]<sums[1])
+ {
+ shift_list(cuts, true);
+ }
+ }
+
+ static std::size_t split_contour(
+ Contour& contour,
+ const std::list<Contour::iterator>& ordered_cuts,
+ std::list<Contour>& segments)
+ {
+ std::size_t segments_count=0;
+ std::list<Contour::iterator>::const_iterator it=ordered_cuts.begin();
+ while(it!=ordered_cuts.end())
+ {
+ std::list<Contour::iterator>::const_iterator next=it;
+ ++next;
+ if(next!=ordered_cuts.end())
+ {
+ if((*next)!=get_right_iterator(contour, (*it)))
+ {
+ segments_count++;
+ Contour segment;
+ Contour::iterator jt=(*it);
+ do
+ {
+ segment.push_back(*jt);
+ jt=get_right_iterator(contour, jt);
+ }
+ while(jt!=(*next));
+ segments.push_back(segment);
+ }
+ it=next;
+ ++it;
+ }
+ else
+ {
+ it=ordered_cuts.end();
+ }
+ }
+ if(segments_count>0)
+ {
+ contour.clear();
+ }
+ return segments_count;
+ }
+
+ static void mend_contour(
+ const SimpleSphere& a,
+ const SimpleSphere& b,
+ const SimpleSphere& c,
+ const std::size_t c_id,
+ const double step,
+ const int projections,
+ Contour& contour)
+ {
+ Contour::iterator it=contour.begin();
+ while(it!=contour.end())
+ {
+ if(it->left_id!=c_id && it->right_id==c_id)
+ {
+ const Contour::iterator jt=get_right_iterator(contour, it);
+ if(jt->left_id==c_id)
+ {
+ SimplePoint& p0=it->p;
+ SimplePoint& p1=jt->p;
+ for(int e=0;e<projections;e++)
+ {
+ p0=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p0, b, c);
+ p0=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p0, a, c);
+ p0=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p0, a, b);
+ p1=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p1, b, c);
+ p1=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p1, a, c);
+ p1=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p1, a, b);
+ }
+ const double distance=distance_from_point_to_point(p0, p1);
+ if(distance>step)
+ {
+ const int leap_distance=static_cast<int>(floor(distance/step+0.5));
+ const double leap_size=distance/static_cast<double>(leap_distance);
+ const SimplePoint direction=(p1-p0).unit();
+ for(int leap=1;leap<leap_distance;leap++)
+ {
+ SimplePoint p=p0+(direction*(leap_size*static_cast<double>(leap)));
+ for(int e=0;e<projections;e++)
+ {
+ p=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p, b, c);
+ p=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p, a, c);
+ p=HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(p, a, b);
+ }
+ contour.insert(jt, PointRecord(p, c_id, c_id));
+ }
+ }
+ }
+ }
+ ++it;
+ }
+ }
+
+ static bool check_contour_intersects_sphere(const SimpleSphere& shell, const Contour& contour)
+ {
+ for(Contour::const_iterator it=contour.begin();it!=contour.end();++it)
+ {
+ if(distance_from_point_to_point(shell, it->p)<=shell.r)
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ static void filter_contours_intersecting_sphere(const SimpleSphere& shell, std::list<Contour>& contours)
+ {
+ std::list<Contour>::iterator it=contours.begin();
+ while(it!=contours.end())
+ {
+ if(!check_contour_intersects_sphere(shell, (*it)))
+ {
+ it=contours.erase(it);
+ }
+ else
+ {
+ ++it;
+ }
+ }
+ }
+
+ template<typename List, typename Iterator>
+ static Iterator get_left_iterator(List& container, const Iterator& iterator)
+ {
+ Iterator left_it=iterator;
+ if(left_it==container.begin())
+ {
+ left_it=container.end();
+ }
+ --left_it;
+ return left_it;
+ }
+
+ template<typename List, typename Iterator>
+ static Iterator get_right_iterator(List& container, const Iterator& iterator)
+ {
+ Iterator right_it=iterator;
+ ++right_it;
+ if(right_it==container.end())
+ {
+ right_it=container.begin();
+ }
+ return right_it;
+ }
+
+ template<typename List>
+ static void shift_list(List& list, const bool reverse)
+ {
+ if(!reverse)
+ {
+ list.push_front(*list.rbegin());
+ list.pop_back();
+ }
+ else
+ {
+ list.push_back(*list.begin());
+ list.pop_front();
+ }
+ }
+
+ static std::vector<SimplePoint> collect_points_from_contour(const Contour& contour)
+ {
+ std::vector<SimplePoint> result;
+ if(!contour.empty())
+ {
+ result.reserve(contour.size());
+ for(Contour::const_iterator jt=contour.begin();jt!=contour.end();++jt)
+ {
+ result.push_back(jt->p);
+ }
+ }
+ return result;
+ }
+
+ static bool check_star_domain(const std::vector<SimplePoint>& outline, const SimplePoint& center)
+ {
+ bool star_domain=(outline.size()>2);
+ for(std::size_t i0=0;i0<outline.size() && star_domain;i0++)
+ {
+ std::size_t i1=(i0+1);
+ std::size_t i2=(i0+2);
+ if(i1>=outline.size())
+ {
+ i1=0;
+ i2=1;
+ }
+ if(i2>=outline.size())
+ {
+ i2=0;
+ }
+ const SimplePoint v0=(outline[i0]-center).unit();
+ const SimplePoint v1=(outline[i1]-center).unit();
+ const SimplePoint v2=(outline[i2]-center).unit();
+ if(dot_product(v0, v1)<dot_product(v0, v2))
+ {
+ star_domain=false;
+ }
+ }
+ return star_domain;
+ }
+};
+
+}
+
+#endif /* APOLLOTA_CONSTRAINED_CONTACT_CONTOUR_H_ */
diff --git a/src/apollota/constrained_contact_remainder.h b/src/apollota/constrained_contact_remainder.h
new file mode 100644
index 0000000..c0abc45
--- /dev/null
+++ b/src/apollota/constrained_contact_remainder.h
@@ -0,0 +1,218 @@
+#ifndef APOLLOTA_CONSTRAINED_CONTACT_REMAINDER_H_
+#define APOLLOTA_CONSTRAINED_CONTACT_REMAINDER_H_
+
+#include "triangulation.h"
+#include "subdivided_icosahedron.h"
+
+namespace apollota
+{
+
+class ConstrainedContactRemainder
+{
+public:
+ struct TriangleRecord
+ {
+ SimplePoint p[3];
+ int s[3];
+
+ TriangleRecord(const SimplePoint& a, const SimplePoint& b, const SimplePoint& c,
+ const int sa, const int sb, const int sc)
+ {
+ p[0]=a;
+ p[1]=b;
+ p[2]=c;
+ s[0]=sa;
+ s[1]=sb;
+ s[2]=sc;
+ }
+ };
+
+ typedef std::list<TriangleRecord> Remainder;
+
+ static Remainder construct_contact_remainder(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const std::set<std::size_t>& vertices_ids,
+ const std::size_t a_id,
+ const double probe,
+ const SubdividedIcosahedron& raw_sih)
+ {
+ Remainder result;
+ if(a_id<spheres.size() && check_remainder_possible(vertices_vector, vertices_ids, probe))
+ {
+ const SimpleSphere& a=spheres[a_id];
+ const std::multimap<double, std::size_t> neighbor_ids=collect_neighbors_with_distances(a, spheres, collect_neighbors_from_vertices(a_id, vertices_vector, vertices_ids));
+ if(!neighbor_ids.empty())
+ {
+ const SimpleSphere a_expanded=SimpleSphere(a, a.r+probe);
+ result=init_remainder(a_expanded, raw_sih);
+ for(std::multimap<double, std::size_t>::const_iterator it=neighbor_ids.begin();it!=neighbor_ids.end();++it)
+ {
+ const std::size_t c_id=it->second;
+ if(c_id<spheres.size())
+ {
+ const SimpleSphere& c=spheres[c_id];
+ const SimpleSphere c_expanded=SimpleSphere(c, c.r+probe);
+ cut_contact_remainder(c_expanded, std::make_pair(10, a_expanded), result);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+private:
+ static void cut_contact_remainder(const SimpleSphere& sphere, const std::pair<int, SimpleSphere>& projection_parameters, Remainder& remainder)
+ {
+ int marks[3]={0, 0, 0};
+ Remainder::iterator it=remainder.begin();
+ while(it!=remainder.end())
+ {
+ for(int i=0;i<3;i++)
+ {
+ marks[i]=distance_from_point_to_point(it->p[i], sphere)<sphere.r ? 1 : 0;
+ }
+ int marks_sum=marks[0]+marks[1]+marks[2];
+ if(marks_sum==3)
+ {
+ it=remainder.erase(it);
+ }
+ else if(marks_sum==2)
+ {
+ int s0=(marks[0]==0 ? 0 : (marks[1]==0 ? 1 : 2));
+ int s1=(s0==0 ? 1 : 0);
+ int s2=(s0==2 ? 1 : 2);
+ SimplePoint c01;
+ SimplePoint c02;
+ if(intersect_line_segment_with_sphere(sphere, it->p[s0], it->p[s1], c01) && intersect_line_segment_with_sphere(sphere, it->p[s0], it->p[s2], c02))
+ {
+ if(projection_parameters.first>0)
+ {
+ c01=project_point_on_spheres(projection_parameters.second, sphere, c01, projection_parameters.first);
+ c02=project_point_on_spheres(projection_parameters.second, sphere, c02, projection_parameters.first);
+ }
+ remainder.insert(it, TriangleRecord(it->p[s0], c01, c02, it->s[s0], 1, 1));
+ it=remainder.erase(it);
+ }
+ }
+ else if(marks_sum==1)
+ {
+ int s0=(marks[0]==1 ? 0 : (marks[1]==1 ? 1 : 2));
+ int s1=(s0==0 ? 1 : 0);
+ int s2=(s0==2 ? 1 : 2);
+ SimplePoint c01;
+ SimplePoint c02;
+ if(intersect_line_segment_with_sphere(sphere, it->p[s0], it->p[s1], c01) && intersect_line_segment_with_sphere(sphere, it->p[s0], it->p[s2], c02))
+ {
+ if(projection_parameters.first>0)
+ {
+ c01=project_point_on_spheres(projection_parameters.second, sphere, c01, projection_parameters.first);
+ c02=project_point_on_spheres(projection_parameters.second, sphere, c02, projection_parameters.first);
+ }
+ remainder.insert(it, TriangleRecord(it->p[s1], c01, c02, it->s[s1], 1, 1));
+ remainder.insert(it, TriangleRecord(it->p[s1], c02, it->p[s2], it->s[s1], 1, it->s[s2]));
+ it=remainder.erase(it);
+ }
+ }
+ else
+ {
+ ++it;
+ }
+ }
+ }
+
+ static bool check_remainder_possible(
+ const Triangulation::VerticesVector& vertices_vector,
+ const std::set<std::size_t>& vertices_ids,
+ const double probe)
+ {
+ for(std::set<std::size_t>::const_iterator it=vertices_ids.begin();it!=vertices_ids.end();++it)
+ {
+ const std::size_t vertex_id=(*it);
+ if(vertex_id<vertices_vector.size() && vertices_vector[vertex_id].second.r>probe)
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ static std::set<std::size_t> collect_neighbors_from_vertices(
+ const std::size_t a_id,
+ const Triangulation::VerticesVector& vertices_vector,
+ const std::set<std::size_t>& vertices_ids)
+ {
+ std::set<std::size_t> neighbors_ids;
+ for(std::set<std::size_t>::const_iterator it=vertices_ids.begin();it!=vertices_ids.end();++it)
+ {
+ const std::size_t vertex_id=(*it);
+ if(vertex_id<vertices_vector.size())
+ {
+ const Quadruple& quadruple=vertices_vector[vertex_id].first;
+ for(int i=0;i<4;i++)
+ {
+ const std::size_t neighbor_id=quadruple.get(i);
+ if(neighbor_id!=a_id)
+ {
+ neighbors_ids.insert(neighbor_id);
+ }
+ }
+ }
+ }
+ return neighbors_ids;
+ }
+
+ static std::multimap<double, std::size_t> collect_neighbors_with_distances(
+ const SimpleSphere& a,
+ const std::vector<SimpleSphere>& spheres,
+ const std::set<std::size_t>& neighbor_ids)
+ {
+ std::multimap<double, std::size_t> result;
+ for(std::set<std::size_t>::const_iterator it=neighbor_ids.begin();it!=neighbor_ids.end();++it)
+ {
+ const std::size_t c_id=(*it);
+ if(c_id<spheres.size())
+ {
+ const SimpleSphere& c=spheres[c_id];
+ result.insert(std::make_pair(minimal_distance_from_sphere_to_sphere(a, c), c_id));
+ }
+ }
+ return result;
+ }
+
+ static Remainder init_remainder(
+ const SimpleSphere& sphere,
+ const SubdividedIcosahedron& raw_sih)
+ {
+ Remainder result;
+ SubdividedIcosahedron sih=raw_sih;
+ sih.fit_into_sphere(sphere, sphere.r);
+ for(std::size_t i=0;i<sih.triples().size();i++)
+ {
+ const Triple& t=sih.triples()[i];
+ result.push_back(TriangleRecord(sih.vertices()[t.get(0)], sih.vertices()[t.get(1)], sih.vertices()[t.get(2)], 0, 0, 0));
+ }
+ return result;
+ }
+
+ static SimplePoint project_point_on_sphere(const SimpleSphere& sphere, const SimplePoint& p)
+ {
+ const SimplePoint s(sphere);
+ return (s+((p-s).unit()*sphere.r));
+ }
+
+ static SimplePoint project_point_on_spheres(const SimpleSphere& sphere_a, const SimpleSphere& sphere_b, const SimplePoint& p, const int times)
+ {
+ SimplePoint result=p;
+ for(int i=0;i<times;i++)
+ {
+ result=project_point_on_sphere(sphere_a, result);
+ result=project_point_on_sphere(sphere_b, result);
+ }
+ return result;
+ }
+};
+
+}
+
+#endif /* APOLLOTA_CONSTRAINED_CONTACT_REMAINDER_H_ */
diff --git a/src/apollota/constrained_contacts_construction.h b/src/apollota/constrained_contacts_construction.h
new file mode 100644
index 0000000..d51afce
--- /dev/null
+++ b/src/apollota/constrained_contacts_construction.h
@@ -0,0 +1,419 @@
+#ifndef APOLLOTA_CONSTRAINED_CONTACTS_CONSTRUCTION_H_
+#define APOLLOTA_CONSTRAINED_CONTACTS_CONSTRUCTION_H_
+
+#include <deque>
+
+#include "../compatability_macros.h"
+
+#include "constrained_contact_contour.h"
+#include "constrained_contact_remainder.h"
+#include "triangulation_queries.h"
+
+namespace apollota
+{
+
+class ConstrainedContactsConstruction
+{
+public:
+ static std::map<Pair, double> construct_contacts(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const double probe,
+ const double step,
+ const int projections,
+ const std::set<std::size_t>& mock_solvent_ids,
+ std::pair< bool, std::map<std::size_t, double> >& volumes_bundle)
+ {
+ std::map<Pair, double> result;
+
+ const TriangulationQueries::PairsMap pairs_vertices=TriangulationQueries::collect_pairs_vertices_map_from_vertices_vector(vertices_vector);
+ for(TriangulationQueries::PairsMap::const_iterator pairs_vertices_it=pairs_vertices.begin();pairs_vertices_it!=pairs_vertices.end();++pairs_vertices_it)
+ {
+ const std::size_t a=pairs_vertices_it->first.get(0);
+ const std::size_t b=pairs_vertices_it->first.get(1);
+ const bool a_is_not_mock_solvent=(mock_solvent_ids.count(a)==0);
+ const bool b_is_not_mock_solvent=(mock_solvent_ids.count(b)==0);
+ if((a_is_not_mock_solvent || b_is_not_mock_solvent) && minimal_distance_from_sphere_to_sphere(spheres[a], spheres[b])<(probe*2))
+ {
+ double sum=0.0;
+ const std::list<ConstrainedContactContour::Contour> contours=ConstrainedContactContour::construct_contact_contours(spheres, vertices_vector, pairs_vertices_it->second, a, b, probe, step, projections);
+ for(std::list<ConstrainedContactContour::Contour>::const_iterator contours_it=contours.begin();contours_it!=contours.end();++contours_it)
+ {
+ const ConstrainedContactContour::Contour& contour=(*contours_it);
+ if(!contour.empty())
+ {
+ const ConstrainedContactContour::ContourAreaDescriptor d=ConstrainedContactContour::construct_contour_area_descriptor(contour, spheres[a], spheres[b], false);
+ if(d.star_domain || d.simple_polygon_triangulation.empty())
+ {
+ for(std::size_t i=0;i<d.outline.size();i++)
+ {
+ const std::size_t second_index=((i+1<d.outline.size()) ? (i+1) : 0);
+ sum+=triangle_area(d.center, d.outline[i], d.outline[second_index]);
+ if(volumes_bundle.first)
+ {
+ if(a_is_not_mock_solvent)
+ {
+ volumes_bundle.second[a]+=fabs(signed_volume_of_tetrahedron(spheres[a], d.center, d.outline[i], d.outline[second_index]));
+ }
+ if(b_is_not_mock_solvent)
+ {
+ volumes_bundle.second[b]+=fabs(signed_volume_of_tetrahedron(spheres[b], d.center, d.outline[i], d.outline[second_index]));
+ }
+ }
+ }
+ }
+ else
+ {
+ for(std::size_t i=0;i<d.simple_polygon_triangulation.size();i++)
+ {
+ const Triple& t=d.simple_polygon_triangulation[i];
+ sum+=triangle_area(d.outline[t.get(0)], d.outline[t.get(1)], d.outline[t.get(2)]);
+ if(volumes_bundle.first)
+ {
+ if(a_is_not_mock_solvent)
+ {
+ volumes_bundle.second[a]+=fabs(signed_volume_of_tetrahedron(spheres[a], d.outline[t.get(0)], d.outline[t.get(1)], d.outline[t.get(2)]));
+ }
+ if(b_is_not_mock_solvent)
+ {
+ volumes_bundle.second[b]+=fabs(signed_volume_of_tetrahedron(spheres[b], d.outline[t.get(0)], d.outline[t.get(1)], d.outline[t.get(2)]));
+ }
+ }
+ }
+ }
+ }
+ }
+ if(sum>0.0)
+ {
+ result[Pair(a,b)]=sum;
+ }
+ }
+ }
+
+ return result;
+ }
+
+ static std::map<std::size_t, double> construct_contact_remainders(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const double probe,
+ const int sih_depth,
+ std::pair< bool, std::map<std::size_t, double> >& volumes_bundle)
+ {
+ std::map<std::size_t, double> result;
+
+ SubdividedIcosahedron sih(sih_depth);
+ const TriangulationQueries::IDsMap ids_vertices=TriangulationQueries::collect_vertices_map_from_vertices_vector(vertices_vector);
+ for(TriangulationQueries::IDsMap::const_iterator ids_vertices_it=ids_vertices.begin();ids_vertices_it!=ids_vertices.end();++ids_vertices_it)
+ {
+ const std::size_t a=ids_vertices_it->first;
+ const ConstrainedContactRemainder::Remainder remainder=ConstrainedContactRemainder::construct_contact_remainder(spheres, vertices_vector, ids_vertices_it->second, a, probe, sih);
+ if(!remainder.empty())
+ {
+ const SimpleSphere surface_sphere(spheres[a], spheres[a].r+probe);
+ double sum=0.0;
+ for(ConstrainedContactRemainder::Remainder::const_iterator remainder_it=remainder.begin();remainder_it!=remainder.end();++remainder_it)
+ {
+ sum+=spherical_triangle_area(surface_sphere, remainder_it->p[0], remainder_it->p[1], remainder_it->p[2]);
+ }
+ if(sum>0.0)
+ {
+ result[a]=sum;
+ if(volumes_bundle.first)
+ {
+ volumes_bundle.second[a]+=((sum*surface_sphere.r)/3.0);
+ }
+ }
+ }
+ }
+
+ return result;
+ }
+
+ template<typename ContactRemainderDescriptor>
+ static std::map< int, std::map<std::size_t, ContactRemainderDescriptor> > construct_groups_of_contact_remainders(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const double probe,
+ const double step,
+ const int projections,
+ const std::size_t sih_depth,
+ const bool exclude_external_remainders)
+ {
+ std::map< int, std::map<std::size_t, ContactRemainderDescriptor> > result;
+
+ std::vector< std::pair<Pair, ConstrainedContactContour::Contour> > surface_contours_vector;
+ std::vector<int> surface_contours_vector_marks;
+ construct_surface_contours(spheres, vertices_vector, probe, step, projections, surface_contours_vector, surface_contours_vector_marks);
+
+ const std::set<int> external_groups_set=
+ select_external_contours_groups(spheres, mark_spheres_by_connected_components(spheres, vertices_vector, probe), surface_contours_vector, surface_contours_vector_marks);
+
+ std::vector< std::map<int, std::list<std::size_t> > > spheres_exposures(spheres.size());
+ for(std::size_t i=0;i<surface_contours_vector.size();i++)
+ {
+ const std::size_t a=surface_contours_vector[i].first.get(0);
+ const std::size_t b=surface_contours_vector[i].first.get(1);
+ int group_id=surface_contours_vector_marks[i];
+ if(external_groups_set.count(group_id))
+ {
+ group_id=0-group_id;
+ }
+ if(group_id>0 || !exclude_external_remainders)
+ {
+ spheres_exposures[a][group_id].push_back(i);
+ spheres_exposures[b][group_id].push_back(i);
+ }
+ }
+
+ const SubdividedIcosahedron sih(sih_depth);
+ const TriangulationQueries::IDsMap ids_vertices=TriangulationQueries::collect_vertices_map_from_vertices_vector(vertices_vector);
+
+ for(std::size_t sphere_id=0;sphere_id<spheres_exposures.size();sphere_id++)
+ {
+ if(!spheres_exposures[sphere_id].empty())
+ {
+ TriangulationQueries::IDsMap::const_iterator ids_vertices_it=ids_vertices.find(sphere_id);
+ if(ids_vertices_it!=ids_vertices.end())
+ {
+ const ConstrainedContactRemainder::Remainder full_remainder=ConstrainedContactRemainder::construct_contact_remainder(spheres, vertices_vector, ids_vertices_it->second, sphere_id, probe, sih);
+ if(!full_remainder.empty())
+ {
+ const std::map<int, std::list<std::size_t> >& sphere_exposure=spheres_exposures[sphere_id];
+ if(sphere_exposure.size()==1)
+ {
+ result[sphere_exposure.begin()->first][sphere_id].feed(full_remainder);
+ }
+ else
+ {
+ std::map<int, ConstrainedContactRemainder::Remainder> split_remainders;
+ for(ConstrainedContactRemainder::Remainder::const_iterator full_remainder_it=full_remainder.begin();full_remainder_it!=full_remainder.end();++full_remainder_it)
+ {
+ const SimplePoint p=(full_remainder_it->p[0]+full_remainder_it->p[1]+full_remainder_it->p[2])*(1.0/3.0);
+ std::pair<double, int> minimal_distance_to_group(std::numeric_limits<double>::max(), 0);
+ for(std::map<int, std::list<std::size_t> >::const_iterator sphere_exposure_it=sphere_exposure.begin();sphere_exposure_it!=sphere_exposure.end();++sphere_exposure_it)
+ {
+ const int group_id=sphere_exposure_it->first;
+ const std::list<std::size_t>& contours_ids=sphere_exposure_it->second;
+ for(std::list<std::size_t>::const_iterator contours_ids_it=contours_ids.begin();contours_ids_it!=contours_ids.end();++contours_ids_it)
+ {
+ const ConstrainedContactContour::Contour& contour=surface_contours_vector[*contours_ids_it].second;
+ for(ConstrainedContactContour::Contour::const_iterator contour_it=contour.begin();contour_it!=contour.end();++contour_it)
+ {
+ minimal_distance_to_group=std::min(minimal_distance_to_group, std::make_pair(distance_from_point_to_point(p, contour_it->p), group_id));
+ }
+ }
+ }
+ split_remainders[minimal_distance_to_group.second].push_back(*full_remainder_it);
+ }
+ for(std::map<int, ConstrainedContactRemainder::Remainder>::const_iterator split_remainders_it=split_remainders.begin();split_remainders_it!=split_remainders.end();++split_remainders_it)
+ {
+ if(split_remainders_it->first!=0)
+ {
+ result[split_remainders_it->first][sphere_id].feed(split_remainders_it->second);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return result;
+ }
+
+ static std::vector<int> mark_spheres_by_connected_components(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const double probe)
+ {
+ const std::vector< std::vector<std::size_t> > graph=
+ TriangulationQueries::collect_ids_graph_from_ids_map(
+ TriangulationQueries::collect_neighbors_map_from_quadruples_map(vertices_vector), spheres.size());
+
+ std::vector<int> marks(spheres.size(), 0);
+
+ int groups_count=0;
+ for(std::size_t i=0;i<graph.size();i++)
+ {
+ if(marks[i]==0)
+ {
+ groups_count++;
+ std::deque<std::size_t> stack;
+ marks[i]=groups_count;
+ stack.push_back(i);
+ while(!stack.empty())
+ {
+ const std::size_t a=stack.back();
+ stack.pop_back();
+ for(std::size_t e=0;e<graph[a].size();e++)
+ {
+ const std::size_t b=graph[a][e];
+ if(marks[b]==0 && minimal_distance_from_sphere_to_sphere(spheres[a], spheres[b])<(2*probe))
+ {
+ marks[b]=groups_count;
+ stack.push_back(b);
+ }
+ }
+ }
+ }
+ }
+
+ return marks;
+ }
+
+ static int construct_surface_contours(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const double probe,
+ const double step,
+ const int projections,
+ std::vector< std::pair<Pair, ConstrainedContactContour::Contour> >& surface_contours_vector,
+ std::vector<int>& marks)
+ {
+#if USE_TR1 > 0
+typedef std::tr1::unordered_map< Pair, std::list<std::size_t>, Pair::HashFunctor > PairsIDsMap;
+#else
+typedef std::unordered_map< Pair, std::list<std::size_t>, Pair::HashFunctor > PairsIDsMap;
+#endif
+
+ const TriangulationQueries::PairsMap pairs_vertices=TriangulationQueries::collect_pairs_vertices_map_from_vertices_vector(vertices_vector);
+ PairsIDsMap pairs_surface_contours_map;
+ surface_contours_vector.clear();
+ for(TriangulationQueries::PairsMap::const_iterator it=pairs_vertices.begin();it!=pairs_vertices.end();++it)
+ {
+ const std::size_t a=it->first.get(0);
+ const std::size_t b=it->first.get(1);
+ if(minimal_distance_from_sphere_to_sphere(spheres[a], spheres[b])<(probe*2))
+ {
+ const std::set<std::size_t>& pair_vertices_list=it->second;
+ bool has_surface=false;
+ for(std::set<std::size_t>::const_iterator list_it=pair_vertices_list.begin();list_it!=pair_vertices_list.end() && !has_surface;++list_it)
+ {
+ has_surface=vertices_vector[*list_it].second.r>=probe;
+ }
+ if(has_surface)
+ {
+ const std::list<ConstrainedContactContour::Contour> contours=ConstrainedContactContour::construct_contact_contours(spheres, vertices_vector, pair_vertices_list, a, b, probe, step, projections);
+ for(std::list<ConstrainedContactContour::Contour>::const_iterator contours_it=contours.begin();contours_it!=contours.end();++contours_it)
+ {
+ const ConstrainedContactContour::Contour& contour=(*contours_it);
+ const std::list<ConstrainedContactContour::Contour> subcontours=ConstrainedContactContour::collect_subcontours_from_contour(contour);
+ for(std::list<ConstrainedContactContour::Contour>::const_iterator subcontours_it=subcontours.begin();subcontours_it!=subcontours.end();++subcontours_it)
+ {
+ const ConstrainedContactContour::Contour& subcontour=(*subcontours_it);
+ if(!subcontour.empty() && subcontour.front().right_id==a && subcontour.front().left_id!=a)
+ {
+ pairs_surface_contours_map[it->first].push_back(surface_contours_vector.size());
+ surface_contours_vector.push_back(std::make_pair(it->first, subcontour));
+ }
+ }
+ }
+ }
+ }
+ }
+ marks.clear();
+ marks.resize(surface_contours_vector.size(), 0);
+ int groups_count=0;
+ for(std::size_t i=0;i<marks.size();i++)
+ {
+ if(marks[i]==0)
+ {
+ groups_count++;
+ std::deque<std::size_t> stack;
+ marks[i]=groups_count;
+ stack.push_back(i);
+ while(!stack.empty())
+ {
+ const std::size_t j=stack.back();
+ stack.pop_back();
+ const std::size_t a=surface_contours_vector[j].first.get(0);
+ const std::size_t b=surface_contours_vector[j].first.get(1);
+ const ConstrainedContactContour::Contour& contour=surface_contours_vector[j].second;
+ const std::size_t c[2]={contour.front().left_id, contour.back().right_id};
+ const Pair related_pairs[4]={Pair(a, c[0]), Pair(a, c[1]), Pair(b, c[0]), Pair(b, c[1])};
+ for(int e=0;e<4;e++)
+ {
+ const Pair& related_pair=related_pairs[e];
+ PairsIDsMap::const_iterator it=pairs_surface_contours_map.find(related_pair);
+ if(it!=pairs_surface_contours_map.end())
+ {
+ const std::list<std::size_t>& related_contours_ids=it->second;
+ if(!related_contours_ids.empty())
+ {
+ std::pair<double, std::size_t> real_related_contour(std::numeric_limits<double>::max(), j);
+ for(std::list<std::size_t>::const_iterator jt=related_contours_ids.begin();jt!=related_contours_ids.end();++jt)
+ {
+ const std::size_t related_contour_id=(*jt);
+ const ConstrainedContactContour::Contour& related_contour=surface_contours_vector[related_contour_id].second;
+ double shortest_dist=distance_from_point_to_point(contour.front().p, related_contour.front().p);
+ shortest_dist=std::min(shortest_dist, distance_from_point_to_point(contour.front().p, related_contour.back().p));
+ shortest_dist=std::min(shortest_dist, distance_from_point_to_point(contour.back().p, related_contour.front().p));
+ shortest_dist=std::min(shortest_dist, distance_from_point_to_point(contour.back().p, related_contour.back().p));
+ real_related_contour=std::min(real_related_contour, std::make_pair(shortest_dist, related_contour_id));
+ }
+ if(marks[real_related_contour.second]==0)
+ {
+ marks[real_related_contour.second]=groups_count;
+ stack.push_back(real_related_contour.second);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return groups_count;
+ }
+
+private:
+ static std::set<int> select_external_contours_groups(
+ const std::vector<SimpleSphere>& spheres,
+ const std::vector<int>& spheres_marks,
+ const std::vector< std::pair<Pair, ConstrainedContactContour::Contour> >& surface_contours_vector,
+ const std::vector<int>& surface_contours_vector_marks)
+ {
+ std::set<int> result;
+ if(!spheres.empty() && spheres.size()==spheres_marks.size() && surface_contours_vector.size()==surface_contours_vector_marks.size())
+ {
+ SimplePoint mc;
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ mc=mc+SimplePoint(spheres[i]);
+ }
+ mc=mc*(1.0/static_cast<double>(spheres.size()));
+
+ std::map< int, std::pair<double, int> > max_map;
+ for(std::size_t i=0;i<surface_contours_vector.size();i++)
+ {
+ const int sphere_mark=spheres_marks[surface_contours_vector[i].first.get(0)];
+ std::map< int, std::pair<double, int> >::iterator val_it=max_map.find(sphere_mark);
+ if(val_it==max_map.end())
+ {
+ val_it=max_map.insert(std::make_pair(sphere_mark, std::make_pair(0.0, 0))).first;
+ }
+ const ConstrainedContactContour::Contour& contour=surface_contours_vector[i].second;
+ const int group_id=surface_contours_vector_marks[i];
+ for(ConstrainedContactContour::Contour::const_iterator it=contour.begin();it!=contour.end();++it)
+ {
+ const double dist=distance_from_point_to_point(it->p, mc);
+ if(dist>(val_it->second.first))
+ {
+ val_it->second.first=dist;
+ val_it->second.second=group_id;
+ }
+ }
+ }
+
+ for(std::map< int, std::pair<double, int> >::const_iterator it=max_map.begin();it!=max_map.end();++it)
+ {
+ result.insert(it->second.second);
+ }
+ }
+ return result;
+ }
+};
+
+}
+
+#endif /* APOLLOTA_CONSTRAINED_CONTACTS_CONSTRUCTION_H_ */
diff --git a/src/apollota/constrained_contacts_utilities.h b/src/apollota/constrained_contacts_utilities.h
new file mode 100644
index 0000000..08f97ae
--- /dev/null
+++ b/src/apollota/constrained_contacts_utilities.h
@@ -0,0 +1,152 @@
+#ifndef APOLLOTA_CONSTRAINED_CONTACT_UTILITIES_H_
+#define APOLLOTA_CONSTRAINED_CONTACT_UTILITIES_H_
+
+#include "constrained_contacts_construction.h"
+
+namespace apollota
+{
+
+
+template<typename OpenGLPrinter>
+std::string draw_inter_atom_contact(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const TriangulationQueries::PairsMap& pairs_vertices,
+ const std::size_t a_id,
+ const std::size_t b_id,
+ const double probe,
+ const double step,
+ const int projections)
+{
+ OpenGLPrinter opengl_printer;
+ if(a_id<spheres.size() && b_id<spheres.size())
+ {
+ TriangulationQueries::PairsMap::const_iterator pairs_vertices_it=pairs_vertices.find(Pair(a_id, b_id));
+ if(pairs_vertices_it!=pairs_vertices.end())
+ {
+ const std::list<ConstrainedContactContour::Contour> contours=ConstrainedContactContour::construct_contact_contours(
+ spheres, vertices_vector, pairs_vertices_it->second, a_id, b_id, probe, step, projections);
+ for(std::list<ConstrainedContactContour::Contour>::const_iterator contours_it=contours.begin();contours_it!=contours.end();++contours_it)
+ {
+ const ConstrainedContactContour::ContourAreaDescriptor d=ConstrainedContactContour::construct_contour_area_descriptor(*contours_it, spheres[a_id], spheres[b_id], false);
+ const SimplePoint normal=sub_of_points<SimplePoint>(spheres[b_id], spheres[a_id]).unit();
+ if(d.star_domain || d.simple_polygon_triangulation.empty())
+ {
+ opengl_printer.add_triangle_fan(d.center, d.outline, normal);
+ }
+ else
+ {
+ std::vector<SimplePoint> strip_vertices(3);
+ std::vector<SimplePoint> strip_normals(3, normal);
+ for(std::size_t i=0;i<d.simple_polygon_triangulation.size();i++)
+ {
+ const Triple& t=d.simple_polygon_triangulation[i];
+ strip_vertices[0]=d.outline[t.get(0)];
+ strip_vertices[1]=d.outline[t.get(1)];
+ strip_vertices[2]=d.outline[t.get(2)];
+ opengl_printer.add_triangle_strip(strip_vertices, strip_normals);
+ }
+ }
+ }
+ }
+ }
+ return opengl_printer.str();
+}
+
+template<typename OpenGLPrinter>
+std::string draw_solvent_contact(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const TriangulationQueries::IDsMap& ids_vertices,
+ const std::size_t a_id,
+ const double probe,
+ const SubdividedIcosahedron& sih)
+{
+ OpenGLPrinter opengl_printer;
+ if(a_id<spheres.size())
+ {
+ TriangulationQueries::IDsMap::const_iterator ids_vertices_it=ids_vertices.find(a_id);
+ if(ids_vertices_it!=ids_vertices.end())
+ {
+ const ConstrainedContactRemainder::Remainder remainder=ConstrainedContactRemainder::construct_contact_remainder(
+ spheres, vertices_vector, ids_vertices_it->second, a_id, probe, sih);
+ for(ConstrainedContactRemainder::Remainder::const_iterator remainder_it=remainder.begin();remainder_it!=remainder.end();++remainder_it)
+ {
+ std::vector<SimplePoint> ts(3);
+ std::vector<SimplePoint> ns(3);
+ for(int i=0;i<3;i++)
+ {
+ ts[i]=remainder_it->p[i];
+ ns[i]=sub_of_points<SimplePoint>(ts[i], spheres[a_id]).unit();
+ }
+ opengl_printer.add_triangle_strip(ts, ns);
+ }
+ }
+ }
+ return opengl_printer.str();
+}
+
+bool check_inter_atom_contact_centrality(
+ const std::vector<SimpleSphere>& spheres,
+ const TriangulationQueries::PairsMap& pairs_neighbors,
+ const std::size_t a_id,
+ const std::size_t b_id)
+{
+ if(a_id<spheres.size() && b_id<spheres.size())
+ {
+ TriangulationQueries::PairsMap::const_iterator pairs_neighbors_it=pairs_neighbors.find(Pair(a_id, b_id));
+ if(pairs_neighbors_it!=pairs_neighbors.end())
+ {
+ const std::set<std::size_t>& neighbors=pairs_neighbors_it->second;
+ if(!neighbors.empty())
+ {
+ const SimplePoint pa(spheres[a_id]);
+ const SimplePoint pb(spheres[b_id]);
+ const double ra=spheres[a_id].r;
+ const double rb=spheres[b_id].r;
+ const double distance_to_a_or_b=((distance_from_point_to_point(pa, pb)-ra-rb)*0.5);
+ const SimplePoint p=(pa+((pb-pa).unit()*(ra+distance_to_a_or_b)));
+ for(std::set<std::size_t>::const_iterator neighbors_it=neighbors.begin();neighbors_it!=neighbors.end();++neighbors_it)
+ {
+ const std::size_t c_id=(*neighbors_it);
+ if(c_id<spheres.size() && minimal_distance_from_point_to_sphere(p, spheres[c_id])<distance_to_a_or_b)
+ {
+ return false;
+ }
+ }
+ }
+ }
+ }
+ return true;
+}
+
+bool check_inter_atom_contact_peripherial(
+ const std::vector<SimpleSphere>& spheres,
+ const Triangulation::VerticesVector& vertices_vector,
+ const TriangulationQueries::PairsMap& pairs_vertices,
+ const std::size_t a_id,
+ const std::size_t b_id,
+ const double probe)
+{
+ if(a_id<spheres.size() && b_id<spheres.size())
+ {
+ TriangulationQueries::PairsMap::const_iterator pairs_vertices_it=pairs_vertices.find(Pair(a_id, b_id));
+ if(pairs_vertices_it!=pairs_vertices.end())
+ {
+ const std::set<std::size_t>& vertices_ids=pairs_vertices_it->second;
+ for(std::set<std::size_t>::const_iterator vertices_ids_it=vertices_ids.begin();vertices_ids_it!=vertices_ids.end();++vertices_ids_it)
+ {
+ const std::size_t vertex_id=(*vertices_ids_it);
+ if(vertex_id<vertices_vector.size() && vertices_vector[vertex_id].second.r>probe)
+ {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+}
+
+}
+
+#endif /* APOLLOTA_CONSTRAINED_CONTACT_UTILITIES_H_ */
diff --git a/src/apollota/hyperboloid_between_two_spheres.h b/src/apollota/hyperboloid_between_two_spheres.h
new file mode 100644
index 0000000..774773e
--- /dev/null
+++ b/src/apollota/hyperboloid_between_two_spheres.h
@@ -0,0 +1,118 @@
+#ifndef APOLLOTA_HYPERBOLOID_BETWEEN_TWO_SPHERES_H_
+#define APOLLOTA_HYPERBOLOID_BETWEEN_TWO_SPHERES_H_
+
+#include "basic_operations_on_points.h"
+
+namespace apollota
+{
+
+class HyperboloidBetweenTwoSpheres
+{
+public:
+ template<typename SphereType>
+ static inline SimplePoint project_point_on_hyperboloid(const SimplePoint& p, const SphereType& s1, const SphereType& s2)
+ {
+ if(s1.r>s2.r)
+ {
+ return project_point_on_hyperboloid(p, s2, s1);
+ }
+ else
+ {
+ const SimplePoint dv=(custom_point_from_object<SimplePoint>(s1)-custom_point_from_object<SimplePoint>(s2))*(0.5);
+ const SimplePoint dv_unit=dv.unit();
+ const SimplePoint c=custom_point_from_object<SimplePoint>(s2)+dv;
+ const SimplePoint cp=p-c;
+ const double lz=dv_unit*cp;
+ const double lx=sqrt(std::max(squared_point_module(cp)-(lz*lz), 0.0));
+ const double z=project_point_on_simple_hyperboloid(lx, 0, dv.module(), s1.r, s2.r);
+ return ((p-(dv_unit*lz))+(dv_unit*z));
+ }
+ }
+
+ template<typename SphereType>
+ static inline double intersect_vector_with_hyperboloid(const SimplePoint& a, const SimplePoint& b, const SphereType& s1, const SphereType& s2)
+ {
+ if(s1.r>s2.r)
+ {
+ return intersect_vector_with_hyperboloid(a, b, s2, s1);
+ }
+ else
+ {
+ const SimplePoint dv=(custom_point_from_object<SimplePoint>(s1)-custom_point_from_object<SimplePoint>(s2))*(0.5);
+ const SimplePoint c=custom_point_from_object<SimplePoint>(s2)+dv;
+
+ const SimplePoint ca=a-c;
+ const double maz=dv.unit()*ca;
+ const SimplePoint cax=(a-(dv.unit()*maz))-c;
+ const double max=cax.unit()*ca;
+ const double may=0;
+
+ const SimplePoint cb=b-c;
+ const double mbz=dv.unit()*cb;
+ const double mbx=cax.unit()*cb;
+ const double mby=sqrt(std::max(squared_point_module(cb)-mbz*mbz-mbx*mbx, 0.0));
+
+ return intersect_vector_with_simple_hyperboloid(SimplePoint(max, may, maz), SimplePoint(mbx, mby, mbz), dv.module(), s1.r, s2.r);
+ }
+ }
+
+private:
+ static inline double project_point_on_simple_hyperboloid(const double x, const double y, const double d, const double r1, const double r2)
+ {
+ if(r1>r2)
+ {
+ return project_point_on_simple_hyperboloid(x, y, d, r2, r1);
+ }
+ else
+ {
+ const double r=r2-r1;
+ return 2*r*sqrt(std::max((0-r*r+4*d*d)*(4*x*x+4*y*y+4*d*d-r*r), 0.0))/(0-4*r*r+16*d*d);
+ }
+ }
+
+ static inline double intersect_vector_with_simple_hyperboloid(const SimplePoint& a, const SimplePoint& b, const double d, const double r1, const double r2)
+ {
+ if(r1>r2)
+ {
+ return intersect_vector_with_simple_hyperboloid(a, b, d, r2, r1);
+ }
+ else
+ {
+ const double r=r2-r1;
+ SimplePoint ab=(b-a);
+ SimplePoint v=ab.unit();
+ const double k=(4*r*r/((0-4*r*r+16*d*d)*(0-4*r*r+16*d*d))) * (0-r*r+4*d*d) * 4;
+ const double m=(4*d*d-r*r)*k/4;
+
+ const double x0=a.x;
+ const double y0=a.y;
+ const double z0=a.z;
+ const double vx=v.x;
+ const double vy=v.y;
+ const double vz=v.z;
+
+ const double t1 = (sqrt((k*vy*vy+k*vx*vx)*z0*z0+(-2*k*vy*vz*y0-2*k*vx*vz*x0)*z0+(k*vz*vz-k*k*vx*vx)*y0*y0+2*k*k*vx*vy*x0*y0+(k*vz*vz-k*k*vy*vy)*x0*x0+m*vz*vz-k*m*vy*vy-k*m*vx*vx)-vz*z0+k*vy*y0+k*vx*x0)/(vz*vz-k*vy*vy-k*vx*vx);
+
+ const double t2 = -(sqrt((k*vy*vy+k*vx*vx)*z0*z0+(-2*k*vy*vz*y0-2*k*vx*vz*x0)*z0+(k*vz*vz-k*k*vx*vx)*y0*y0+2*k*k*vx*vy*x0*y0+(k*vz*vz-k*k*vy*vy)*x0*x0+m*vz*vz-k*m*vy*vy-k*m*vx*vx)+vz*z0-k*vy*y0-k*vx*x0)/(vz*vz-k*vy*vy-k*vx*vx);
+
+ const SimplePoint tp1=a+(v*t1);
+ const SimplePoint tp2=a+(v*t2);
+ if(greater(t1, 0) && less(t1, ab.module()) && equal(tp1.z, sqrt(k*tp1.x*tp1.x+k*tp1.y*tp1.y+m), 0.000001))
+ {
+ return t1;
+ }
+ else if(greater(t2, 0) && less(t2, ab.module()) && equal(tp2.z, sqrt(k*tp2.x*tp2.x+k*tp2.y*tp2.y+m), 0.000001))
+ {
+ return t2;
+ }
+ else
+ {
+ return 0;
+ }
+ }
+ }
+};
+
+}
+
+#endif /* APOLLOTA_HYPERBOLOID_BETWEEN_TWO_SPHERES_H_ */
diff --git a/src/apollota/polar_sorting.h b/src/apollota/polar_sorting.h
new file mode 100644
index 0000000..ff13265
--- /dev/null
+++ b/src/apollota/polar_sorting.h
@@ -0,0 +1,86 @@
+#ifndef APOLLOTA_POLAR_SORTING_H_
+#define APOLLOTA_POLAR_SORTING_H_
+
+#include <algorithm>
+
+#include "basic_operations_on_points.h"
+
+namespace apollota
+{
+
+class PolarSorting
+{
+public:
+ template<typename CenterPointType, typename AxisPointType, typename RandomAccessIteratorType>
+ static void sort(const CenterPointType& center, const AxisPointType& axis, RandomAccessIteratorType first, RandomAccessIteratorType last)
+ {
+ std::sort(first, last, Less(center, axis));
+ }
+
+ template<typename CenterPointType, typename AxisPointType, typename RandomAccessIteratorType>
+ static void sort_mapping(const CenterPointType& center, const AxisPointType& axis, RandomAccessIteratorType first, RandomAccessIteratorType last)
+ {
+ std::sort(first, last, LessForPairs(Less(center, axis)));
+ }
+
+private:
+ class Less
+ {
+ public:
+ template<typename CenterPointType, typename AxisPointType>
+ Less(const CenterPointType& center, const AxisPointType& axis) :
+ center(custom_point_from_object<PODPoint>(center)),
+ axis(unit_point<PODPoint>(axis)),
+ normal(any_normal_of_vector<PODPoint>(axis))
+ {
+ }
+
+ template<typename PointType>
+ bool operator()(const PointType& a, const PointType& b) const
+ {
+ return (calc_angle_with_normal(a)<calc_angle_with_normal(b));
+ }
+
+ private:
+ PODPoint center;
+ PODPoint axis;
+ PODPoint normal;
+
+ template<typename PointType>
+ double calc_angle_with_normal(const PointType& a) const
+ {
+ const PODPoint ap=sub_of_points<PODPoint>(a, point_and_number_product<PODPoint>(axis, signed_distance_from_point_to_plane(center, axis, a)));
+ return directed_angle(center, sum_of_points<PODPoint>(center, normal), ap, sum_of_points<PODPoint>(center, axis));
+ }
+ };
+
+ struct LessForPairs
+ {
+ Less less;
+
+ LessForPairs(const Less& less) : less(less)
+ {
+ }
+
+ template<typename PairType>
+ bool operator()(const PairType& a, const PairType& b) const
+ {
+ if(less(a.first, b.first))
+ {
+ return true;
+ }
+ else if(less(b.first, a.first))
+ {
+ return false;
+ }
+ else
+ {
+ return (a.second<b.second);
+ }
+ }
+ };
+};
+
+}
+
+#endif /* APOLLOTA_POLAR_SORTING_H_ */
diff --git a/src/apollota/polynomial_curves.h b/src/apollota/polynomial_curves.h
new file mode 100644
index 0000000..84f7bda
--- /dev/null
+++ b/src/apollota/polynomial_curves.h
@@ -0,0 +1,310 @@
+#ifndef APOLLOTA_POLYNOMIAL_CURVES_H_
+#define APOLLOTA_POLYNOMIAL_CURVES_H_
+
+#include <vector>
+#include <list>
+
+#include "basic_operations_on_points.h"
+
+namespace apollota
+{
+
+inline std::vector<SimplePoint> interpolate_using_cubic_hermite_spline(
+ const SimplePoint& a,
+ const SimplePoint& b,
+ const SimplePoint& c,
+ const SimplePoint& d,
+ const double k,
+ const int steps)
+{
+ std::vector<SimplePoint> result(steps+1);
+ const double step=1.0/static_cast<double>(steps);
+ const SimplePoint mb=(c-a)*k;
+ const SimplePoint mc=(d-b)*k;
+ for(int i=0;i<=steps;i++)
+ {
+ const double t=(i<steps ? static_cast<double>(i)*step : 1.0);
+ const double h00=(2*t*t*t)-(3*t*t)+1;
+ const double h10=(t*t*t)-(2*t*t)+t;
+ const double h01=0-(2*t*t*t)+(3*t*t);
+ const double h11=(t*t*t)-(t*t);
+ result[i]=((b*h00)+(mb*h10)+(c*h01)+(mc*h11));
+ }
+ return result;
+}
+
+inline double binomial_coefficient(const unsigned long n, const unsigned long k)
+{
+ if(k==0 || k==n)
+ {
+ return 1.0;
+ }
+ else if(k==1)
+ {
+ return static_cast<double>(n);
+ }
+ else if(k>n)
+ {
+ return 0.0;
+ }
+ else if((n-k)<k)
+ {
+ return binomial_coefficient(n, n-k);
+ }
+ else
+ {
+ double result=1.0;
+ for(unsigned long i=1;i<=k;i++)
+ {
+ result*=static_cast<double>(n-k+i)/static_cast<double>(i);
+ }
+ return result;
+ }
+}
+
+inline double bernstein_polynomial(const unsigned long n, const unsigned long k, const double t)
+{
+ if(k>n)
+ {
+ return 0.0;
+ }
+ else
+ {
+ return (binomial_coefficient(n, k)*pow(t, k)*pow(1-t, n-k));
+ }
+}
+
+inline SimplePoint bezier_curve_point(const std::vector<SimplePoint>& controls, const double t)
+{
+ SimplePoint result;
+ for(std::size_t i=0;i<controls.size();i++)
+ {
+ result=result+(controls[i]*bernstein_polynomial(controls.size()-1, i, t));
+ }
+ return result;
+}
+
+inline SimplePoint bezier_curve_point_de_casteljau(const std::vector<SimplePoint>& controls, const double t)
+{
+ static std::vector<SimplePoint> buffer(4);
+ if(buffer.size()<controls.size())
+ {
+ buffer.resize(controls.size());
+ }
+ for(std::size_t i=0;i<controls.size();i++)
+ {
+ buffer[i]=controls[i];
+ }
+ for(std::size_t j=0;j+1<controls.size();j++)
+ {
+ for(std::size_t i=0;i+1<(controls.size()-j);i++)
+ {
+ buffer[i]=(buffer[i]*(1-t))+(buffer[i+1]*t);
+ }
+ }
+ return buffer.at(0);
+}
+
+inline std::vector<SimplePoint> bezier_curve_points(const std::vector<SimplePoint>& controls, const unsigned int n, const bool de_casteljau=true)
+{
+ std::vector<SimplePoint> result(n+1);
+ for(std::size_t i=0;i<(n+1);i++)
+ {
+ const double t=static_cast<double>(i)/static_cast<double>(n);
+ result[i]=(de_casteljau ? bezier_curve_point_de_casteljau(controls, t) : bezier_curve_point(controls, t));
+ }
+ return result;
+}
+
+inline SimplePoint rational_bezier_curve_point(const std::vector<SimplePoint>& controls, const std::vector<double>& weights, const double t)
+{
+ const std::size_t size=std::min(controls.size(), weights.size());
+ SimplePoint numerator;
+ double denominator=0.0;
+ for(std::size_t i=0;i<size;i++)
+ {
+ numerator=numerator+(controls[i]*(bernstein_polynomial(size-1, i, t)*weights[i]));
+ denominator+=(bernstein_polynomial(size-1, i, t)*weights[i]);
+ }
+ return (numerator*(1.0/denominator));
+}
+
+
+inline SimplePoint rational_bezier_curve_point_de_casteljau(const std::vector<SimplePoint>& controls, const std::vector<double>& weights, const double t)
+{
+ const std::size_t size=std::min(controls.size(), weights.size());
+ static std::vector<SimplePoint> buffer_of_points(4);
+ static std::vector<double> buffer_of_weights(4);
+ if(buffer_of_points.size()<size)
+ {
+ buffer_of_points.resize(size);
+ }
+ if(buffer_of_weights.size()<size)
+ {
+ buffer_of_weights.resize(size);
+ }
+ for(std::size_t i=0;i<size;i++)
+ {
+ buffer_of_points[i]=controls[i];
+ buffer_of_weights[i]=weights[i];
+ }
+ for(std::size_t j=0;j+1<size;j++)
+ {
+ for(std::size_t i=0;i+1<(size-j);i++)
+ {
+ const double w=(buffer_of_weights[i]*(1-t))+(buffer_of_weights[i+1]*t);
+ buffer_of_points[i]=(buffer_of_points[i]*((1-t)*(buffer_of_weights[i]/w)))+(buffer_of_points[i+1]*(t*(buffer_of_weights[i+1]/w)));
+ buffer_of_weights[i]=w;
+ }
+ }
+ return buffer_of_points.at(0);
+}
+
+inline std::vector<SimplePoint> rational_bezier_curve_points(const std::vector<SimplePoint>& controls, const std::vector<double>& weights, const unsigned int n, const bool de_casteljau=true)
+{
+ std::vector<SimplePoint> result(n+1);
+ for(std::size_t i=0;i<(n+1);i++)
+ {
+ const double t=static_cast<double>(i)/static_cast<double>(n);
+ result[i]=(de_casteljau ? rational_bezier_curve_point_de_casteljau(controls, weights, t) : rational_bezier_curve_point(controls, weights, t));
+ }
+ return result;
+}
+
+inline std::vector<SimplePoint> bezier_curve_using_explicit_de_casteljau_subdivision(const std::vector<SimplePoint>& controls, const int depth)
+{
+ const std::size_t dimensions=controls.size();
+ std::list<SimplePoint> approximation(controls.begin(), controls.end());
+ std::vector< std::list<SimplePoint>::iterator > subcontrols(dimensions);
+ for(int level=0;level<depth;level++)
+ {
+ std::list<SimplePoint>::iterator it=approximation.begin();
+ while(it!=approximation.end())
+ {
+ if(it!=approximation.begin())
+ {
+ --it;
+ }
+ for(std::size_t i=0;i<dimensions;i++)
+ {
+ subcontrols[i]=it;
+ ++it;
+ }
+ for(std::size_t j=0;j+1<dimensions;j++)
+ {
+ for(std::size_t i=0;i+1<(dimensions-j);i++)
+ {
+ const SimplePoint p=((*(subcontrols[i]))*0.5)+((*(subcontrols[i+1]))*0.5);
+ std::list<SimplePoint>::iterator p_it=approximation.insert(subcontrols[i+1], p);
+ if(i+2<(dimensions-j))
+ {
+ approximation.erase(subcontrols[i+1]);
+ }
+ subcontrols[i]=p_it;
+ }
+ }
+ }
+ }
+ return std::vector<SimplePoint>(approximation.begin(), approximation.end());
+}
+
+inline std::vector<SimplePoint> rational_bezier_curve_using_explicit_de_casteljau_subdivision(const std::vector<SimplePoint>& controls, const std::vector<double>& weights, const int depth)
+{
+ typedef std::pair<SimplePoint, double> WeightedPoint;
+ const std::size_t dimensions=std::min(controls.size(), weights.size());
+ std::list<WeightedPoint> approximation;
+ for(std::size_t i=0;i<dimensions;i++)
+ {
+ approximation.push_back(WeightedPoint(controls[i], weights[i]));
+ }
+ std::vector< std::list<WeightedPoint>::iterator > subcontrols(dimensions);
+ for(int level=0;level<depth;level++)
+ {
+ std::list<WeightedPoint>::iterator it=approximation.begin();
+ while(it!=approximation.end())
+ {
+ if(it!=approximation.begin())
+ {
+ --it;
+ }
+ for(std::size_t i=0;i<dimensions;i++)
+ {
+ subcontrols[i]=it;
+ ++it;
+ }
+ for(std::size_t j=0;j+1<dimensions;j++)
+ {
+ for(std::size_t i=0;i+1<(dimensions-j);i++)
+ {
+ const double w=((subcontrols[i]->second)*0.5)+((subcontrols[i+1]->second)*0.5);
+ const SimplePoint p=((subcontrols[i]->first)*(0.5*((subcontrols[i]->second)/w)))+((subcontrols[i+1]->first)*(0.5*((subcontrols[i+1]->second)/w)));
+ std::list<WeightedPoint>::iterator wp_it=approximation.insert(subcontrols[i+1], WeightedPoint(p, w));
+ if(i+2<(dimensions-j))
+ {
+ approximation.erase(subcontrols[i+1]);
+ }
+ subcontrols[i]=wp_it;
+ }
+ }
+ }
+ }
+ std::vector<SimplePoint> result;
+ result.reserve(approximation.size());
+ for(std::list<WeightedPoint>::const_iterator it=approximation.begin();it!=approximation.end();++it)
+ {
+ result.push_back(it->first);
+ }
+ return result;
+}
+
+template<typename ControlPointsList>
+inline ControlPointsList transform_points_to_increase_bezier_curve_degree(const ControlPointsList& controls)
+{
+ const std::size_t n=controls.size();
+ if(n>1)
+ {
+ ControlPointsList new_controls;
+ std::size_t i=0;
+ for(typename ControlPointsList::const_iterator it=controls.begin();it!=controls.end();++it)
+ {
+ if(it==controls.begin())
+ {
+ new_controls.push_back(*it);
+ }
+ else
+ {
+ typename ControlPointsList::const_iterator prev_it=it;
+ --prev_it;
+ new_controls.push_back(((*prev_it)*(static_cast<double>(i)/static_cast<double>(n)))+((*it)*(1.0-static_cast<double>(i)/static_cast<double>(n))));
+ }
+ i++;
+ }
+ new_controls.push_back(controls.back());
+ return new_controls;
+ }
+ else
+ {
+ return controls;
+ }
+}
+
+inline SimplePoint barycentric_coordinates(const SimplePoint& a, const SimplePoint& b, const SimplePoint& c, const SimplePoint& p)
+{
+ const SimplePoint v0=(b-a);
+ const SimplePoint v1=(c-a);
+ const SimplePoint v2=(p-a);
+ const double d00=(v0*v0);
+ const double d01=(v0*v1);
+ const double d11=(v1*v1);
+ const double d20=(v2*v0);
+ const double d21=(v2*v1);
+ const double denom=(d00*d11-d01*d01);
+ const double v=(d11*d20-d01*d21)/denom;
+ const double w=(d00*d21-d01*d20)/denom;
+ const double u=1.0-v-w;
+ return SimplePoint(u, v, w);
+}
+
+}
+
+#endif /* APOLLOTA_POLYNOMIAL_CURVES_H_ */
diff --git a/src/apollota/rolling_topology.h b/src/apollota/rolling_topology.h
new file mode 100644
index 0000000..310aa0a
--- /dev/null
+++ b/src/apollota/rolling_topology.h
@@ -0,0 +1,227 @@
+#ifndef APOLLOTA_ROLLING_TOPOLOGY_H_
+#define APOLLOTA_ROLLING_TOPOLOGY_H_
+
+#include <list>
+#include <vector>
+#include <set>
+
+#include "tangent_sphere_of_three_spheres.h"
+#include "polar_sorting.h"
+#include "rotation.h"
+
+namespace apollota
+{
+
+class RollingTopology
+{
+public:
+ struct RollingPoint
+ {
+ std::size_t generator;
+ SimpleSphere tangent;
+ };
+
+ struct RollingStrip
+ {
+ RollingPoint start;
+ RollingPoint end;
+ };
+
+ struct RollingDescriptor
+ {
+ std::size_t a_id;
+ std::size_t b_id;
+ bool possible;
+ SimpleSphere circle;
+ SimplePoint axis;
+ bool detached;
+ std::set<std::size_t> generators;
+ std::list<RollingStrip> strips;
+ std::vector<SimplePoint> breaks;
+ };
+
+ static inline RollingDescriptor calculate_rolling_descriptor(
+ const std::vector<SimpleSphere>& spheres,
+ const std::size_t a_id,
+ const std::size_t b_id,
+ const std::set<std::size_t>& neighbor_ids,
+ const std::set<std::size_t>& a_neighbor_ids,
+ const std::set<std::size_t>& b_neighbor_ids,
+ const double probe)
+ {
+ RollingDescriptor result;
+ result.a_id=a_id;
+ result.b_id=b_id;
+ const SimpleSphere& a=spheres[a_id];
+ const SimpleSphere& b=spheres[b_id];
+ result.possible=sphere_intersects_sphere_with_expansion(a, b, probe*2);
+ if(result.possible)
+ {
+ result.circle=intersection_circle_of_two_spheres<SimpleSphere>(SimpleSphere(a, a.r+probe), SimpleSphere(b, b.r+probe));
+ result.axis=sub_of_points<SimplePoint>(a, b).unit();
+ if(result.circle.r<probe)
+ {
+ result.breaks.resize(2);
+ const double dl=sqrt((probe*probe)-(result.circle.r*result.circle.r));
+ result.breaks[0]=sum_of_points<SimplePoint>(result.circle, point_and_number_product<PODPoint>(result.axis, dl));
+ result.breaks[1]=sum_of_points<SimplePoint>(result.circle, point_and_number_product<PODPoint>(result.axis, 0.0-dl));
+ }
+ result.detached=true;
+ for(std::set<std::size_t>::const_iterator c_id_it=neighbor_ids.begin();c_id_it!=neighbor_ids.end() && result.detached;++c_id_it)
+ {
+ const SimpleSphere expanded_c(spheres[*c_id_it], spheres[*c_id_it].r+probe);
+ const double distance_to_circle_plane=signed_distance_from_point_to_plane(result.circle, result.axis, expanded_c);
+ if(fabs(distance_to_circle_plane)<expanded_c.r)
+ {
+ const SimpleSphere projected_c(SimplePoint(expanded_c)-(result.axis*distance_to_circle_plane), sqrt((expanded_c.r*expanded_c.r)-(distance_to_circle_plane*distance_to_circle_plane)));
+ if(sphere_intersects_sphere(result.circle, projected_c))
+ {
+ result.detached=false;
+ }
+ }
+ }
+ if(!result.detached)
+ {
+ std::list<RollingPoint> rolling_points;
+ for(std::set<std::size_t>::const_iterator c_id_it=neighbor_ids.begin();c_id_it!=neighbor_ids.end();++c_id_it)
+ {
+ const std::vector<SimpleSphere> tangents=TangentSphereOfThreeSpheres::calculate(a, b, spheres[*c_id_it], probe);
+ if(tangents.size()==2)
+ {
+ const double allowed_tangent_error=0.00001;
+ for(std::vector<SimpleSphere>::const_iterator tangent_it=tangents.begin();tangent_it!=tangents.end();++tangent_it)
+ {
+ bool tangent_empty=true;
+ for(std::set<std::size_t>::const_iterator d_id_it=neighbor_ids.begin();d_id_it!=neighbor_ids.end() && tangent_empty;++d_id_it)
+ {
+ if(d_id_it!=c_id_it)
+ {
+ tangent_empty=!sphere_intersects_sphere_with_expansion((*tangent_it), spheres[*d_id_it], 0.0-allowed_tangent_error);
+ }
+ }
+ for(std::set<std::size_t>::const_iterator d_id_it=a_neighbor_ids.begin();d_id_it!=a_neighbor_ids.end() && tangent_empty;++d_id_it)
+ {
+ if(d_id_it!=c_id_it && (*d_id_it)!=a_id && (*d_id_it)!=b_id)
+ {
+ tangent_empty=!sphere_intersects_sphere_with_expansion((*tangent_it), spheres[*d_id_it], 0.0-allowed_tangent_error);
+ }
+ }
+ for(std::set<std::size_t>::const_iterator d_id_it=b_neighbor_ids.begin();d_id_it!=b_neighbor_ids.end() && tangent_empty;++d_id_it)
+ {
+ if(d_id_it!=c_id_it && (*d_id_it)!=a_id && (*d_id_it)!=b_id)
+ {
+ tangent_empty=!sphere_intersects_sphere_with_expansion((*tangent_it), spheres[*d_id_it], 0.0-allowed_tangent_error);
+ }
+ }
+ if(tangent_empty)
+ {
+ result.generators.insert(*c_id_it);
+ RollingPoint rolling_point;
+ rolling_point.tangent=(*tangent_it);
+ rolling_point.generator=(*c_id_it);
+ rolling_points.push_back(rolling_point);
+ }
+ }
+ }
+ }
+ if(rolling_points.size()>=2 && rolling_points.size()%2==0)
+ {
+ std::vector< std::pair<SimpleSphere, std::pair<bool, std::size_t> > > circular_mapping;
+ {
+ circular_mapping.reserve(rolling_points.size()*2);
+ for(std::set<std::size_t>::const_iterator c_id_it=result.generators.begin();c_id_it!=result.generators.end();++c_id_it)
+ {
+ circular_mapping.push_back(std::make_pair(spheres[*c_id_it], std::make_pair(false, (*c_id_it))));
+ }
+ for(std::list<RollingPoint>::const_iterator rolling_point_it=rolling_points.begin();rolling_point_it!=rolling_points.end();++rolling_point_it)
+ {
+ circular_mapping.push_back(std::make_pair(rolling_point_it->tangent, std::make_pair(true, rolling_point_it->generator)));
+ }
+ }
+ PolarSorting::sort_mapping(result.circle, result.axis, circular_mapping.begin(), circular_mapping.end());
+ for(std::size_t i=0;i<circular_mapping.size();i++)
+ {
+ const std::size_t j=((i+1<circular_mapping.size()) ? (i+1) : 0);
+ if(circular_mapping[i].second.first && circular_mapping[j].second.first)
+ {
+ RollingStrip rolling_strip;
+ rolling_strip.start.tangent=circular_mapping[i].first;
+ rolling_strip.start.generator=circular_mapping[i].second.second;
+ rolling_strip.end.tangent=circular_mapping[j].first;
+ rolling_strip.end.generator=circular_mapping[j].second.second;
+ result.strips.push_back(rolling_strip);
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static std::vector<SimplePoint> construct_rolling_circle_approximation(const RollingDescriptor& rolling_descriptor, const double angle_step)
+ {
+ return construct_circular_arc_approximation_from_axis_and_start(
+ SimplePoint(rolling_descriptor.circle),
+ rolling_descriptor.axis,
+ any_normal_of_vector<SimplePoint>(rolling_descriptor.axis)*rolling_descriptor.circle.r,
+ pi_value()*2,
+ angle_step);
+ }
+
+ static std::vector<SimplePoint> construct_rolling_strip_approximation(const RollingDescriptor& rolling_descriptor, const RollingStrip& rolling_strip, const double angle_step)
+ {
+ const SimplePoint base(rolling_descriptor.circle);
+ const SimplePoint start_vector=(SimplePoint(rolling_strip.start.tangent)-base);
+ const SimplePoint end_vector=(SimplePoint(rolling_strip.end.tangent)-base);
+ const double angle=directed_angle(SimplePoint(0, 0, 0), start_vector, end_vector, rolling_descriptor.axis);
+ return construct_circular_arc_approximation_from_axis_and_start(
+ base,
+ rolling_descriptor.axis,
+ start_vector,
+ angle,
+ angle_step);
+ }
+
+ static std::vector<SimplePoint> construct_circular_arc_approximation_from_start_and_end(const SimplePoint& center, const SimplePoint& start_vector, const SimplePoint& end_vector, const double angle_step)
+ {
+ const double angle=min_angle(SimplePoint(0, 0, 0), start_vector, end_vector);
+ const int steps=static_cast<int>(floor(angle/angle_step)+1.0);
+ return construct_circular_arc_approximation_from_start_and_end(center, start_vector, end_vector, steps);
+ }
+
+ static std::vector<SimplePoint> construct_circular_arc_approximation_from_start_and_end(const SimplePoint& base, const SimplePoint& start_vector, const SimplePoint& end_vector, const int steps)
+ {
+ SimplePoint axis=(start_vector&end_vector).unit();
+ double angle=directed_angle(SimplePoint(0, 0, 0), start_vector, end_vector, axis);
+ if(angle>pi_value())
+ {
+ axis=axis.inverted();
+ angle=(pi_value()*2-angle);
+ }
+ return construct_circular_arc_approximation_from_axis_and_start(base, axis, start_vector, angle, steps);
+ }
+
+ static std::vector<SimplePoint> construct_circular_arc_approximation_from_axis_and_start(const SimplePoint& base, const SimplePoint& axis, const SimplePoint& start_vector, const double angle, const double angle_step)
+ {
+ const int steps=static_cast<int>(floor(angle/angle_step)+1.0);
+ return construct_circular_arc_approximation_from_axis_and_start(base, axis, start_vector, angle, steps);
+ }
+
+ static std::vector<SimplePoint> construct_circular_arc_approximation_from_axis_and_start(const SimplePoint& base, const SimplePoint& axis, const SimplePoint& start_vector, const double angle, const int steps)
+ {
+ std::vector<SimplePoint> result;
+ Rotation rotation(axis, 0, true);
+ const double adjusted_angle_step=angle/static_cast<double>(steps);
+ result.reserve(steps+1);
+ for(int i=0;i<=steps;i++)
+ {
+ rotation.angle=adjusted_angle_step*static_cast<double>(i);
+ result.push_back(base+rotation.rotate<SimplePoint>(start_vector));
+ }
+ return result;
+ }
+};
+
+}
+
+#endif /* APOLLOTA_ROLLING_TOPOLOGY_H_ */
diff --git a/src/apollota/rotation.h b/src/apollota/rotation.h
new file mode 100644
index 0000000..a079361
--- /dev/null
+++ b/src/apollota/rotation.h
@@ -0,0 +1,79 @@
+#ifndef APOLLOTA_ROTATION_H_
+#define APOLLOTA_ROTATION_H_
+
+#include "basic_operations_on_points.h"
+
+namespace apollota
+{
+
+class Rotation
+{
+public:
+ SimplePoint axis;
+ double angle;
+ bool angle_in_radians;
+
+ template<typename InputPointType>
+ Rotation(const InputPointType& axis, const double angle) : axis(axis), angle(angle), angle_in_radians(false)
+ {
+ }
+
+ template<typename InputPointType>
+ Rotation(const InputPointType& axis, const double angle, const bool angle_in_radians) : axis(axis), angle(angle), angle_in_radians(angle_in_radians)
+ {
+ }
+
+ template<typename OutputPointType, typename InputPointType>
+ OutputPointType rotate(const InputPointType& p) const
+ {
+ if(axis.module()>0)
+ {
+ const double radians_angle_half=(angle_in_radians ? (angle*0.5) : (angle*pi_value()/360.0));
+ const Quaternion q1=quaternion_from_value_and_point(cos(radians_angle_half), axis.unit()*sin(radians_angle_half));
+ const Quaternion q2=quaternion_from_value_and_point(0, p);
+ const Quaternion q3=((q1*q2)*(!q1));
+ return custom_point<OutputPointType>(q3.b, q3.c, q3.d);
+ }
+ else
+ {
+ return custom_point_from_object<OutputPointType>(p);
+ }
+ }
+
+private:
+ struct Quaternion
+ {
+ double a;
+ double b;
+ double c;
+ double d;
+
+ Quaternion(const double a, const double b, const double c, const double d) : a(a), b(b), c(c), d(d)
+ {
+ }
+
+ Quaternion operator*(const Quaternion& q) const
+ {
+ return Quaternion(
+ a*q.a - b*q.b - c*q.c - d*q.d,
+ a*q.b + b*q.a + c*q.d - d*q.c,
+ a*q.c - b*q.d + c*q.a + d*q.b,
+ a*q.d + b*q.c - c*q.b + d*q.a);
+ }
+
+ Quaternion operator!() const
+ {
+ return Quaternion(a, 0-b, 0-c, 0-d);
+ }
+ };
+
+ template<typename InputPointType>
+ static Quaternion quaternion_from_value_and_point(const double a, const InputPointType& p)
+ {
+ return Quaternion(a, p.x, p.y, p.z);
+ }
+};
+
+}
+
+#endif /* APOLLOTA_ROTATION_H_ */
diff --git a/src/apollota/safer_comparison_of_numbers.h b/src/apollota/safer_comparison_of_numbers.h
new file mode 100644
index 0000000..08e1049
--- /dev/null
+++ b/src/apollota/safer_comparison_of_numbers.h
@@ -0,0 +1,45 @@
+#ifndef APOLLOTA_SAFE_COMPARISON_OF_NUMBERS_H_
+#define APOLLOTA_SAFE_COMPARISON_OF_NUMBERS_H_
+
+namespace apollota
+{
+
+inline double default_comparison_epsilon()
+{
+ static double e=0.0000000001;
+ return e;
+}
+
+inline bool equal(const double a, const double b, const double e)
+{
+ return (((a-b)<=e) && ((b-a)<=e));
+}
+
+inline bool equal(const double a, const double b)
+{
+ return equal(a, b, default_comparison_epsilon());
+}
+
+inline bool less(const double a, const double b)
+{
+ return ((a+default_comparison_epsilon())<b);
+}
+
+inline bool greater(const double a, const double b)
+{
+ return ((a-default_comparison_epsilon())>b);
+}
+
+inline bool less_or_equal(const double a, const double b)
+{
+ return (less(a, b) || equal(a, b));
+}
+
+inline bool greater_or_equal(const double a, const double b)
+{
+ return (greater(a, b) || equal(a, b));
+}
+
+}
+
+#endif /* APOLLOTA_SAFE_COMPARISON_OF_NUMBERS_H_ */
diff --git a/src/apollota/safer_quadratic_equation_root.h b/src/apollota/safer_quadratic_equation_root.h
new file mode 100644
index 0000000..3885ffc
--- /dev/null
+++ b/src/apollota/safer_quadratic_equation_root.h
@@ -0,0 +1,57 @@
+#ifndef APOLLOTA_SAFE_QUADRATIC_EQUATION_ROOT_H_
+#define APOLLOTA_SAFE_QUADRATIC_EQUATION_ROOT_H_
+
+#include "safer_summation.h"
+
+namespace apollota
+{
+
+inline bool check_if_quadratic_equation_is_solvable(const double a, const double b)
+{
+ return (a>0.0 || a<0.0 || b>0.0 || b<0.0);
+}
+
+template<typename ResultsContainer>
+inline bool solve_quadratic_equation(const double a, const double b, const double c, ResultsContainer& roots)
+{
+ if(check_if_quadratic_equation_is_solvable(a, b))
+ {
+ if(a>0.0 || a<0.0)
+ {
+ const double D = safer_sum(b*b, -4*a*c);
+ if(D>=0.0)
+ {
+ if(D==0.0)
+ {
+ roots.push_back((-b)/(2*a));
+ }
+ else
+ {
+ if(b>0.0 || b<0.0)
+ {
+ const double b_sign=(b>0.0 ? 1.0 : -1.0);
+ const double q=-(0.5*safer_sum(b, b_sign*sqrt(D)));
+ roots.push_back(q/a);
+ roots.push_back(c/q);
+ }
+ else
+ {
+ roots.push_back((-sqrt(D))/(2*a));
+ roots.push_back((+sqrt(D))/(2*a));
+ }
+ }
+ return true;
+ }
+ }
+ else if(b>0.0 || b<0.0)
+ {
+ roots.push_back((-c)/b);
+ return true;
+ }
+ }
+ return false;
+}
+
+}
+
+#endif /* APOLLOTA_SAFE_QUADRATIC_EQUATION_ROOT_H_ */
diff --git a/src/apollota/safer_summation.h b/src/apollota/safer_summation.h
new file mode 100644
index 0000000..8ac1b8d
--- /dev/null
+++ b/src/apollota/safer_summation.h
@@ -0,0 +1,116 @@
+#ifndef APOLLOTA_SAFE_SUMMATION_H_
+#define APOLLOTA_SAFE_SUMMATION_H_
+
+namespace apollota
+{
+
+inline double safer_sum(const double v0, const double v1)
+{
+ double sum=0.0;
+ double c=0.0;
+ double y;
+ double t;
+
+ y=v0-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v1-c;
+ sum=sum+y;
+
+ return sum;
+}
+
+inline double safer_sum(const double v0, const double v1, const double v2)
+{
+ double sum=0.0;
+ double c=0.0;
+ double y;
+ double t;
+
+ y=v0-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v1-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v2-c;
+ sum=sum+y;
+
+ return sum;
+}
+
+inline double safer_sum(const double v0, const double v1, const double v2, const double v3)
+{
+ double sum=0.0;
+ double c=0.0;
+ double y;
+ double t;
+
+ y=v0-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v1-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v2-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v3-c;
+ sum=sum+y;
+
+ return sum;
+}
+
+inline double safer_sum(const double v0, const double v1, const double v2, const double v3, const double v4, const double v5)
+{
+ double sum=0.0;
+ double c=0.0;
+ double y;
+ double t;
+
+ y=v0-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v1-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v2-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v3-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v4-c;
+ t=sum+y;
+ c=(t-sum)-y;
+ sum=t;
+
+ y=v5-c;
+ sum=sum+y;
+
+ return sum;
+}
+
+}
+
+#endif /* APOLLOTA_SAFE_SUMMATION_H_ */
diff --git a/src/apollota/search_for_spherical_collisions.h b/src/apollota/search_for_spherical_collisions.h
new file mode 100644
index 0000000..5e5c1d2
--- /dev/null
+++ b/src/apollota/search_for_spherical_collisions.h
@@ -0,0 +1,104 @@
+#ifndef APOLLOTA_SEARCH_FOR_SPHERICAL_COLLISIONS_H_
+#define APOLLOTA_SEARCH_FOR_SPHERICAL_COLLISIONS_H_
+
+#include <set>
+
+#include "bounding_spheres_hierarchy.h"
+
+namespace apollota
+{
+
+class SearchForSphericalCollisions
+{
+public:
+ static std::vector<std::size_t> find_collisions(const BoundingSpheresHierarchy& bsh, const SimpleSphere& target, const bool one_hit_is_enough)
+ {
+ NodeCheckerForCollisions node_checker(target);
+ LeafCheckerForCollisions leaf_checker(target, one_hit_is_enough);
+ return bsh.search(node_checker, leaf_checker);
+ }
+
+ static std::vector<std::size_t> find_all_collisions(const BoundingSpheresHierarchy& bsh, const SimpleSphere& target)
+ {
+ return find_collisions(bsh, target, false);
+ }
+
+ static std::vector<std::size_t> find_any_collision(const BoundingSpheresHierarchy& bsh, const SimpleSphere& target)
+ {
+ return find_collisions(bsh, target, true);
+ }
+
+ static std::set<std::size_t> find_all_hidden_spheres(const BoundingSpheresHierarchy& bsh)
+ {
+ std::set<std::size_t> result;
+ for(std::size_t i=0;i<bsh.leaves_spheres().size();i++)
+ {
+ std::vector<std::size_t> candidates=find_all_collisions(bsh, custom_sphere_from_object<SimpleSphere>(bsh.leaves_spheres()[i]));
+ for(std::size_t j=0;j<candidates.size();j++)
+ {
+ if(i!=candidates[j])
+ {
+ const bool i_contains_candidate_j=sphere_contains_sphere(bsh.leaves_spheres()[i], bsh.leaves_spheres()[candidates[j]]);
+ const bool candidate_j_contains_i=sphere_contains_sphere(bsh.leaves_spheres()[candidates[j]], bsh.leaves_spheres()[i]);
+ if(i_contains_candidate_j && candidate_j_contains_i)
+ {
+ if(i<candidates[j])
+ {
+ result.insert(candidates[j]);
+ }
+ else
+ {
+ result.insert(i);
+ }
+ }
+ else if(i_contains_candidate_j)
+ {
+ result.insert(candidates[j]);
+ }
+ else if(candidate_j_contains_i)
+ {
+ result.insert(i);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+private:
+ struct NodeCheckerForCollisions
+ {
+ const SimpleSphere& target;
+
+ explicit NodeCheckerForCollisions(const SimpleSphere& target) : target(target) {}
+
+ bool operator()(const SimpleSphere& sphere) const
+ {
+ return sphere_intersects_sphere(sphere, target);
+ }
+ };
+
+ struct LeafCheckerForCollisions
+ {
+ const SimpleSphere& target;
+ const bool one_hit_is_enough;
+
+ explicit LeafCheckerForCollisions(const SimpleSphere& target) : target(target), one_hit_is_enough(true) {}
+
+ LeafCheckerForCollisions(const SimpleSphere& target, const bool one_hit_is_enough) : target(target), one_hit_is_enough(one_hit_is_enough) {}
+
+ template<typename Sphere>
+ std::pair<bool, bool> operator()(const std::size_t /*id*/, const Sphere& sphere) const
+ {
+ if(sphere_intersects_sphere(sphere, target))
+ {
+ return std::make_pair(true, one_hit_is_enough);
+ }
+ return std::make_pair(false, false);
+ }
+ };
+};
+
+}
+
+#endif /* APOLLOTA_SEARCH_FOR_SPHERICAL_COLLISIONS_H_ */
diff --git a/src/apollota/simple_polygon_utilities.h b/src/apollota/simple_polygon_utilities.h
new file mode 100644
index 0000000..0473d40
--- /dev/null
+++ b/src/apollota/simple_polygon_utilities.h
@@ -0,0 +1,262 @@
+#ifndef APOLLOTA_SIMPLE_POLYGON_UTILITIES_H_
+#define APOLLOTA_SIMPLE_POLYGON_UTILITIES_H_
+
+#include <list>
+#include <set>
+
+#include "basic_operations_on_points.h"
+#include "tuple.h"
+
+namespace apollota
+{
+
+class SimplePolygonUtilities
+{
+public:
+ struct ConvexityInfo
+ {
+ std::vector<SimplePoint> points;
+ std::vector<double> convexity;
+ SimplePoint normal;
+ };
+
+ struct TriangulationInfo
+ {
+ ConvexityInfo convexity_info;
+ std::vector<Triple> triangulation;
+ };
+
+ static ConvexityInfo calc_polygon_convexity(const std::vector<SimplePoint>& points, const SimplePoint& normal)
+ {
+ ConvexityInfo result;
+ if(points.size()<3)
+ {
+ return result;
+ }
+ result.normal=normal.unit();
+ result.points=flatten_points(points, result.normal);
+ result.convexity.reserve(result.points.size());
+ for(std::vector<SimplePoint>::const_iterator it=result.points.begin();it!=result.points.end();++it)
+ {
+ const double v=calc_convexity(
+ result.normal,
+ *get_prev_iter_in_cycle<std::vector<SimplePoint>::const_iterator>(result.points.begin(), result.points.end(), it),
+ *it,
+ *get_next_iter_in_cycle<std::vector<SimplePoint>::const_iterator>(result.points.begin(), result.points.end(), it));
+ result.convexity.push_back(v);
+ }
+ std::size_t max_dist_id=0;
+ {
+ double max_dist=distance_from_point_to_point(result.points[0], result.points[max_dist_id]);
+ for(std::size_t i=0;i<result.points.size();i++)
+ {
+ const double dist=distance_from_point_to_point(result.points[0], result.points[i]);
+ if(dist>max_dist)
+ {
+ max_dist_id=i;
+ max_dist=dist;
+ }
+ }
+ }
+ if(result.convexity[max_dist_id]<0.0)
+ {
+ result.normal=result.normal.inverted();
+ for(std::size_t i=0;i<result.convexity.size();i++)
+ {
+ result.convexity[i]=(0.0-result.convexity[i]);
+ }
+ }
+ return result;
+ }
+
+ static TriangulationInfo triangulate_simple_polygon(const std::vector<SimplePoint>& points, const SimplePoint& normal)
+ {
+ TriangulationInfo result;
+ if(points.size()<3)
+ {
+ return result;
+ }
+ result.convexity_info=calc_polygon_convexity(points, normal);
+ if(result.convexity_info.convexity.size()!=points.size())
+ {
+ return result;
+ }
+
+ const std::vector<SimplePoint>& polygon_points=result.convexity_info.points;
+ const SimplePoint& polygon_normal=result.convexity_info.normal;
+ std::vector<double> polygon_convexity_vector=result.convexity_info.convexity;
+ std::list<std::size_t> polygon_ids;
+ for(std::size_t i=0;i<polygon_points.size();i++)
+ {
+ polygon_ids.push_back(i);
+ }
+ std::set<std::size_t> polygon_concave_set;
+ for(std::size_t i=0;i<polygon_convexity_vector.size();i++)
+ {
+ if(polygon_convexity_vector[i]<=0.0)
+ {
+ polygon_concave_set.insert(i);
+ }
+ }
+
+ std::vector< std::pair<double, std::list<std::size_t>::iterator> > current_convex_ids;
+ current_convex_ids.reserve(polygon_convexity_vector.size());
+ bool triangulation_ended=false;
+ while(!triangulation_ended)
+ {
+ current_convex_ids.clear();
+ for(std::list<std::size_t>::iterator it=polygon_ids.begin();it!=polygon_ids.end();++it)
+ {
+ if(polygon_convexity_vector[*it]>0.0)
+ {
+ current_convex_ids.push_back(std::make_pair(polygon_convexity_vector[*it], it));
+ }
+ }
+ if(current_convex_ids.size()<=3)
+ {
+ if(current_convex_ids.size()==3)
+ {
+ result.triangulation.push_back(Triple(*(current_convex_ids[0].second), *(current_convex_ids[1].second), *(current_convex_ids[2].second)));
+ }
+ triangulation_ended=true;
+ }
+ else
+ {
+ std::sort(current_convex_ids.begin(), current_convex_ids.end(), custom_pair_comparison<double, std::list<std::size_t>::iterator>());
+ bool ear_found=false;
+ for(std::vector< std::pair<double, std::list<std::size_t>::iterator> >::const_iterator current_convex_ids_it=current_convex_ids.begin();current_convex_ids_it!=current_convex_ids.end() && !ear_found;++current_convex_ids_it)
+ {
+ std::list<std::size_t>::iterator it=current_convex_ids_it->second;
+ std::list<std::size_t>::iterator prev_it=get_prev_iter_in_cycle<std::list<std::size_t>::iterator>(polygon_ids.begin(), polygon_ids.end(), it);
+ std::list<std::size_t>::iterator next_it=get_next_iter_in_cycle<std::list<std::size_t>::iterator>(polygon_ids.begin(), polygon_ids.end(), it);
+ bool triangle_is_empty=true;
+ for(std::set<std::size_t>::const_iterator concave_it=polygon_concave_set.begin();concave_it!=polygon_concave_set.end() && triangle_is_empty;++concave_it)
+ {
+ triangle_is_empty=!check_point_in_triangle(polygon_points[*prev_it], polygon_points[*it], polygon_points[*next_it], polygon_points[*concave_it]);
+ }
+ if(triangle_is_empty)
+ {
+ ear_found=true;
+ result.triangulation.push_back(Triple(*prev_it, *it, *next_it));
+ polygon_ids.erase(it);
+ polygon_concave_set.erase(*it);
+ std::list<std::size_t>::iterator prev_prev_it=get_prev_iter_in_cycle<std::list<std::size_t>::iterator>(polygon_ids.begin(), polygon_ids.end(), prev_it);
+ std::list<std::size_t>::iterator next_next_it=get_next_iter_in_cycle<std::list<std::size_t>::iterator>(polygon_ids.begin(), polygon_ids.end(), next_it);
+ polygon_convexity_vector[*prev_it]=calc_convexity(polygon_normal, polygon_points[*prev_prev_it], polygon_points[*prev_it], polygon_points[*next_it]);
+ polygon_convexity_vector[*next_it]=calc_convexity(polygon_normal, polygon_points[*prev_it], polygon_points[*next_it], polygon_points[*next_next_it]);
+ if(polygon_convexity_vector[*prev_it]<=0.0)
+ {
+ polygon_concave_set.insert(*prev_it);
+ }
+ else
+ {
+ polygon_concave_set.erase(*prev_it);
+ }
+ if(polygon_convexity_vector[*next_it]<=0.0)
+ {
+ polygon_concave_set.insert(*next_it);
+ }
+ else
+ {
+ polygon_concave_set.erase(*next_it);
+ }
+ }
+ }
+ triangulation_ended=!ear_found;
+ }
+ }
+
+ if(result.triangulation.size()!=(result.convexity_info.points.size()-2))
+ {
+ result.triangulation.clear();
+ }
+ else
+ {
+ std::set<std::size_t> included_vertices;
+ for(std::size_t i=0;i<result.triangulation.size();i++)
+ {
+ const apollota::Triple& t=result.triangulation[i];
+ included_vertices.insert(t.get(0));
+ included_vertices.insert(t.get(1));
+ included_vertices.insert(t.get(2));
+ }
+ if(included_vertices.size()!=result.convexity_info.points.size())
+ {
+ result.triangulation.clear();
+ }
+ }
+
+ return result;
+ }
+
+private:
+ static std::vector<SimplePoint> flatten_points(const std::vector<SimplePoint>& points, const SimplePoint& normal)
+ {
+ std::vector<SimplePoint> result(points.size());
+ for(std::size_t i=0;i<points.size();i++)
+ {
+ const double dist_to_plane=(points[i]-points[0])*normal;
+ result[i]=(points[i]-(normal*dist_to_plane));
+ }
+ return result;
+ }
+
+ template<typename Iter>
+ static Iter get_prev_iter_in_cycle(Iter begin, Iter end, Iter it)
+ {
+ Iter result=it;
+ if(result==begin)
+ {
+ result=end;
+ }
+ --result;
+ return result;
+ }
+
+ template<typename Iter>
+ static Iter get_next_iter_in_cycle(Iter begin, Iter end, Iter it)
+ {
+ Iter result=it;
+ ++result;
+ if(result==end)
+ {
+ result=begin;
+ }
+ return result;
+ }
+
+ static double calc_convexity(const SimplePoint& normal, const SimplePoint& a, const SimplePoint& b, const SimplePoint& c)
+ {
+ const bool convex=((((b-a)&(c-b))*normal)>=0.0);
+ return (min_angle(b, a, c)*(convex ? 1.0 : -1.0));
+ }
+
+ static bool check_point_between_rays(const SimplePoint& o, const SimplePoint& a, const SimplePoint& b, const SimplePoint& p)
+ {
+ const SimplePoint oa=(a-o).unit();
+ const SimplePoint ob=(b-o).unit();
+ const SimplePoint op=(p-o).unit();
+ const double cos_aob=oa*ob;
+ const double cos_aop=oa*op;
+ const double cos_pob=op*ob;
+ return (cos_aop>cos_aob && cos_pob>cos_aob);
+ }
+
+ static bool check_point_in_triangle(const SimplePoint& a, const SimplePoint& b, const SimplePoint& c, const SimplePoint& p)
+ {
+ return (check_point_between_rays(a, b, c, p) && check_point_between_rays(b, a, c, p));
+ }
+
+ template<typename T1, typename T2>
+ struct custom_pair_comparison
+ {
+ bool operator()(const std::pair<T1, T2>& a, const std::pair<T1, T2>& b)
+ {
+ return (a.first<b.first);
+ }
+ };
+};
+
+}
+
+#endif /* APOLLOTA_SIMPLE_POLYGON_UTILITIES_H_ */
diff --git a/src/apollota/spheres_boundary_construction.h b/src/apollota/spheres_boundary_construction.h
new file mode 100644
index 0000000..60c9fba
--- /dev/null
+++ b/src/apollota/spheres_boundary_construction.h
@@ -0,0 +1,48 @@
+#ifndef APOLLOTA_SPHERES_BOUNDARY_CONSTRUCTION_H_
+#define APOLLOTA_SPHERES_BOUNDARY_CONSTRUCTION_H_
+
+#include <vector>
+#include <limits>
+
+#include "basic_operations_on_spheres.h"
+
+namespace apollota
+{
+
+inline std::vector<SimpleSphere> construct_artificial_boundary(const std::vector<SimpleSphere>& spheres, const double coordinate_shift)
+{
+ std::vector<SimpleSphere> result;
+ if(!spheres.empty())
+ {
+ SimpleSphere a(std::numeric_limits<double>::max(), std::numeric_limits<double>::max(), std::numeric_limits<double>::max(), std::numeric_limits<double>::max());
+ SimpleSphere b(std::numeric_limits<double>::min(), std::numeric_limits<double>::min(), std::numeric_limits<double>::min(), std::numeric_limits<double>::min());
+ for(std::vector<SimpleSphere>::const_iterator it=spheres.begin();it!=spheres.end();++it)
+ {
+ a.x=std::min(a.x, it->x);
+ a.y=std::min(a.y, it->y);
+ a.z=std::min(a.z, it->z);
+ a.r=std::min(a.r, it->r);
+ b.x=std::max(b.x, it->x);
+ b.y=std::max(b.y, it->y);
+ b.z=std::max(b.z, it->z);
+ b.r=std::max(b.r, it->r);
+ }
+ const double r=std::max(b.r, 0.0);
+ const double shift=std::max(coordinate_shift, 0.0)+(r*2.0)+1.0;
+ const double shift_more=shift+1.0;
+ result.reserve(8);
+ result.push_back(SimpleSphere(a.x-shift_more, a.y-shift_more, a.z-shift_more, r));
+ result.push_back(SimpleSphere(a.x-shift, a.y-shift, b.z+shift, r));
+ result.push_back(SimpleSphere(a.x-shift, b.y+shift, a.z-shift, r));
+ result.push_back(SimpleSphere(a.x-shift, b.y+shift, b.z+shift, r));
+ result.push_back(SimpleSphere(b.x+shift, a.y-shift, a.z-shift, r));
+ result.push_back(SimpleSphere(b.x+shift, a.y-shift, b.z+shift, r));
+ result.push_back(SimpleSphere(b.x+shift, b.y+shift, a.z-shift, r));
+ result.push_back(SimpleSphere(b.x+shift_more, b.y+shift_more, b.z+shift_more, r));
+ }
+ return result;
+}
+
+}
+
+#endif /* APOLLOTA_SPHERES_BOUNDARY_CONSTRUCTION_H_ */
diff --git a/src/apollota/spherical_contacts_construction.h b/src/apollota/spherical_contacts_construction.h
new file mode 100644
index 0000000..70ae6f4
--- /dev/null
+++ b/src/apollota/spherical_contacts_construction.h
@@ -0,0 +1,124 @@
+#ifndef APOLLOTA_SPHERICAL_CONTACTS_CONSTRUCTION_H_
+#define APOLLOTA_SPHERICAL_CONTACTS_CONSTRUCTION_H_
+
+#include "triangulation_queries.h"
+#include "subdivided_icosahedron.h"
+
+namespace apollota
+{
+
+class SphericalContactsConstruction
+{
+public:
+ struct Result
+ {
+ std::map<std::size_t, double> areas;
+
+ void add(const std::size_t id, const SimplePoint& a, const SimplePoint& b, const SimplePoint& c)
+ {
+ areas[id]+=triangle_area(a, b, c);
+ }
+ };
+
+ SphericalContactsConstruction(const std::size_t subdivision_depth) : sih_(subdivision_depth)
+ {
+ }
+
+ Result construct_contacts(
+ const double probe_radius,
+ const std::vector<SimpleSphere>& spheres,
+ std::size_t self_id,
+ const std::vector<size_t>& neighbours) const
+ {
+ Result result;
+ if(self_id<spheres.size())
+ {
+ SubdividedIcosahedron sih=sih_;
+ sih.fit_into_sphere(spheres[self_id], spheres[self_id].r+probe_radius);
+ std::vector<std::size_t> influences(sih.vertices().size());
+ for(std::size_t i=0;i<influences.size();i++)
+ {
+ double min_distance=minimal_distance_from_point_to_sphere(sih.vertices().at(i), spheres.at(self_id));
+ influences[i]=self_id;
+ for(std::size_t j=0;j<neighbours.size();j++)
+ {
+ double distance=minimal_distance_from_point_to_sphere(sih.vertices().at(i), spheres.at(neighbours[j]));
+ if(distance<min_distance)
+ {
+ min_distance=distance;
+ influences[i]=neighbours[j];
+ }
+ }
+ }
+ for(std::size_t e=0;e<sih.triples().size();e++)
+ {
+ const Triple& triple=sih.triples()[e];
+ const std::size_t a=triple.get(0);
+ const std::size_t b=triple.get(1);
+ const std::size_t c=triple.get(2);
+ if(influences[a]==influences[b] && influences[a]==influences[c])
+ {
+ result.add(influences[a], sih.vertices()[a], sih.vertices()[b], sih.vertices()[c]);
+ }
+ else if(influences[a]!=influences[b] && influences[a]!=influences[c] && influences[b]!=influences[c])
+ {
+ const SimplePoint& pa=sih.vertices()[a];
+ const SimplePoint& pb=sih.vertices()[b];
+ const SimplePoint& pc=sih.vertices()[c];
+
+ const SimplePoint a_b_border=pa+((pb-pa).unit()*HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(pa, pb, spheres[influences[a]], spheres[influences[b]]));
+ const SimplePoint a_c_border=pa+((pc-pa).unit()*HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(pa, pc, spheres[influences[a]], spheres[influences[c]]));
+ const SimplePoint b_c_border=pb+((pc-pb).unit()*HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(pb, pc, spheres[influences[b]], spheres[influences[c]]));
+
+ const SimplePoint middle=(a_b_border+a_c_border+b_c_border)*(1.0/3.0);
+
+ result.add(influences[a], pa, a_b_border, a_c_border);
+ result.add(influences[a], middle, a_b_border, a_c_border);
+
+ result.add(influences[b], pb, a_b_border, b_c_border);
+ result.add(influences[b], middle, a_b_border, b_c_border);
+
+ result.add(influences[c], pc, a_c_border, b_c_border);
+ result.add(influences[c], middle, a_c_border, b_c_border);
+ }
+ else
+ {
+ std::size_t s=a;
+ std::size_t d1=b;
+ std::size_t d2=c;
+ if(influences[b]!=influences[a] && influences[b]!=influences[c])
+ {
+ s=b;
+ d1=a;
+ d2=c;
+ }
+ else if(influences[c]!=influences[a] && influences[c]!=influences[b])
+ {
+ s=c;
+ d1=a;
+ d2=b;
+ }
+
+ const SimplePoint& ps=sih.vertices()[s];
+ const SimplePoint& pd1=sih.vertices()[d1];
+ const SimplePoint& pd2=sih.vertices()[d2];
+
+ const SimplePoint s_d1_border=ps+((pd1-ps).unit()*HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(ps, pd1, spheres[influences[s]], spheres[influences[d1]]));
+ const SimplePoint s_d2_border=ps+((pd2-ps).unit()*HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(ps, pd2, spheres[influences[s]], spheres[influences[d2]]));
+
+ result.add(influences[s], ps, s_d1_border, s_d2_border);
+ result.add(influences[d1], pd1, s_d1_border, s_d2_border);
+ result.add(influences[d2], pd2, pd1, s_d2_border);
+ }
+ }
+ }
+ return result;
+ }
+
+private:
+ SubdividedIcosahedron sih_;
+};
+
+}
+
+#endif /* APOLLOTA_SPHERICAL_CONTACTS_CONSTRUCTION_H_ */
diff --git a/src/apollota/splitting_of_spheres.h b/src/apollota/splitting_of_spheres.h
new file mode 100644
index 0000000..3ab863a
--- /dev/null
+++ b/src/apollota/splitting_of_spheres.h
@@ -0,0 +1,119 @@
+#ifndef APOLLOTA_SPLITTING_OF_SPHERES_H_
+#define APOLLOTA_SPLITTING_OF_SPHERES_H_
+
+#include <vector>
+#include <algorithm>
+
+namespace apollota
+{
+
+class SplittingOfSpheres
+{
+public:
+ template<typename SphereType>
+ static std::vector< std::vector<std::size_t> > split_for_number_of_parts(const std::vector<SphereType>& spheres, const std::size_t number_of_parts)
+ {
+ return binary_split(spheres, estimate_splitting_depth_by_number_of_parts(number_of_parts));
+ }
+
+ template<typename SphereType>
+ static std::vector< std::vector<std::size_t> > split_for_size_of_part(const std::vector<SphereType>& spheres, const std::size_t size_of_part)
+ {
+ return binary_split(spheres, estimate_splitting_depth_by_number_of_parts(spheres.size()/size_of_part));
+ }
+
+private:
+ template<typename PointType>
+ static std::vector< std::vector<std::size_t> > binary_split(const std::vector<PointType>& points, const unsigned int depth)
+ {
+ std::vector<std::size_t> ids(points.size());
+ for(std::size_t i=0;i<points.size();i++)
+ {
+ ids[i]=i;
+ }
+ std::vector< std::vector<std::size_t> > result(1, ids);
+ for(unsigned int k=0;k<depth;k++)
+ {
+ std::vector< std::vector<std::size_t> > updated_result;
+ for(std::size_t i=0;i<result.size();i++)
+ {
+ const std::vector< std::vector<std::size_t> > addition=split_by_median(points, result[i], k);
+ updated_result.insert(updated_result.end(), addition.begin(), addition.end());
+ }
+ result=updated_result;
+ }
+ return result;
+ }
+
+ template<typename PointType>
+ static double coord(const PointType& p, const unsigned int k)
+ {
+ const unsigned int d=k%3;
+ return (d==0 ? p.x : (d==1 ? p.y : p.z));
+ }
+
+ template<typename PointType>
+ static std::vector< std::vector<std::size_t> > split_by_median(const std::vector<PointType>& points, const std::vector<std::size_t>& ids, const unsigned int k)
+ {
+ return split_by_middle(order_for_median(points, ids, k));
+ }
+
+ template<typename PointType>
+ static std::vector<std::size_t> order_for_median(const std::vector<PointType>& points, const std::vector<std::size_t>& ids, const unsigned int k)
+ {
+ if(ids.size()<=1)
+ {
+ return ids;
+ }
+ else
+ {
+ std::vector< std::pair<double, std::size_t> > coord_positions(ids.size());
+ for(std::size_t i=0;i<ids.size();i++)
+ {
+ coord_positions[i].first=coord(points[ids[i]], k);
+ coord_positions[i].second=ids[i];
+ }
+ std::nth_element(coord_positions.begin(), (coord_positions.begin()+(coord_positions.size()/2)), coord_positions.end());
+ std::vector<std::size_t> result(ids.size());
+ for(std::size_t i=0;i<ids.size();i++)
+ {
+ result[i]=coord_positions[i].second;
+ }
+ return result;
+ }
+ }
+
+ static std::vector< std::vector<std::size_t> > split_by_middle(const std::vector<std::size_t>& ids)
+ {
+ if(ids.empty())
+ {
+ return std::vector< std::vector<std::size_t> >();
+ }
+ if(ids.size()==1)
+ {
+ return std::vector< std::vector<std::size_t> >(1, ids);
+ }
+ else
+ {
+ std::vector< std::vector<std::size_t> > result(2);
+ std::vector<std::size_t>::const_iterator middle_it=(ids.begin()+(ids.size()/2));
+ result[0].insert(result[0].end(), ids.begin(), middle_it);
+ result[1].insert(result[1].end(), middle_it, ids.end());
+ return result;
+ }
+ }
+
+ static unsigned int estimate_splitting_depth_by_number_of_parts(const unsigned long number_of_parts)
+ {
+ unsigned int depth=0;
+ while(((1UL << depth)<number_of_parts) && (depth<16))
+ {
+ depth++;
+ }
+ return depth;
+ }
+};
+
+}
+
+#endif /* APOLLOTA_SPLITTING_OF_SPHERES_H_ */
diff --git a/src/apollota/subdivided_icosahedron.h b/src/apollota/subdivided_icosahedron.h
new file mode 100644
index 0000000..5392d43
--- /dev/null
+++ b/src/apollota/subdivided_icosahedron.h
@@ -0,0 +1,189 @@
+#ifndef APOLLOTA_SUBDIVIDED_ICOSAHEDRON_H_
+#define APOLLOTA_SUBDIVIDED_ICOSAHEDRON_H_
+
+#include "../compatability_macros.h"
+
+#if USE_TR1 > 0
+#include <tr1/unordered_map>
+#else
+#include <unordered_map>
+#endif
+
+#include "basic_operations_on_points.h"
+#include "tuple.h"
+
+namespace apollota
+{
+
+class SubdividedIcosahedron
+{
+public:
+ explicit SubdividedIcosahedron(const int depth) : fitted_into_sphere_(false), center_(0, 0, 0), radius_(1.0)
+ {
+ const double t=(1+sqrt(5.0))/2.0;
+
+ vertices_.push_back(SimplePoint( t, 1, 0).unit());
+ vertices_.push_back(SimplePoint(-t, 1, 0).unit());
+ vertices_.push_back(SimplePoint( t,-1, 0).unit());
+ vertices_.push_back(SimplePoint(-t,-1, 0).unit());
+ vertices_.push_back(SimplePoint( 1, 0, t).unit());
+ vertices_.push_back(SimplePoint( 1, 0,-t).unit());
+ vertices_.push_back(SimplePoint(-1, 0, t).unit());
+ vertices_.push_back(SimplePoint(-1, 0,-t).unit());
+ vertices_.push_back(SimplePoint( 0, t, 1).unit());
+ vertices_.push_back(SimplePoint( 0,-t, 1).unit());
+ vertices_.push_back(SimplePoint( 0, t,-1).unit());
+ vertices_.push_back(SimplePoint( 0,-t,-1).unit());
+
+ triples_.push_back(Triple(0, 8, 4));
+ triples_.push_back(Triple(1, 10, 7));
+ triples_.push_back(Triple(2, 9, 11));
+ triples_.push_back(Triple(7, 3, 1));
+ triples_.push_back(Triple(0, 5, 10));
+ triples_.push_back(Triple(3, 9, 6));
+ triples_.push_back(Triple(3, 11, 9));
+ triples_.push_back(Triple(8, 6, 4));
+ triples_.push_back(Triple(2, 4, 9));
+ triples_.push_back(Triple(3, 7, 11));
+ triples_.push_back(Triple(4, 2, 0));
+ triples_.push_back(Triple(9, 4, 6));
+ triples_.push_back(Triple(2, 11, 5));
+ triples_.push_back(Triple(0, 10, 8));
+ triples_.push_back(Triple(5, 0, 2));
+ triples_.push_back(Triple(10, 5, 7));
+ triples_.push_back(Triple(1, 6, 8));
+ triples_.push_back(Triple(1, 8, 10));
+ triples_.push_back(Triple(6, 1, 3));
+ triples_.push_back(Triple(11, 7, 5));
+
+ history_of_growth_.push_back(std::make_pair(vertices_.size(), triples_.size()));
+
+ for(int i=0;i<depth;i++)
+ {
+ grow();
+ }
+ }
+
+ void grow(const std::size_t selected_vertex_id, bool fit_into_current_sphere)
+ {
+#if USE_TR1 > 0
+typedef std::tr1::unordered_map<Pair, std::size_t, Pair::HashFunctor> PairsMap;
+#else
+typedef std::unordered_map<Pair, std::size_t, Pair::HashFunctor> PairsMap;
+#endif
+
+ const bool valid_selected_vertex_id=(selected_vertex_id<vertices_.size());
+ PairsMap pairs_vertices;
+ std::vector<Triple> new_triples;
+ if(!valid_selected_vertex_id)
+ {
+ new_triples.reserve(triples_.size()*4);
+ }
+ std::size_t middle_point_ids[3]={0, 0, 0};
+ for(std::size_t i=0;i<triples_.size();i++)
+ {
+ const Triple& triple=triples_[i];
+ if(!valid_selected_vertex_id || triple.contains(selected_vertex_id))
+ {
+ for(int j=0;j<3;j++)
+ {
+ const Pair pair=triple.exclude(j);
+ PairsMap::const_iterator it=pairs_vertices.find(pair);
+ if(it==pairs_vertices.end())
+ {
+ middle_point_ids[j]=vertices_.size();
+ vertices_.push_back(((vertices_[pair.get(0)]+vertices_[pair.get(1)])*(0.5)).unit());
+ if(fit_into_current_sphere && fitted_into_sphere_)
+ {
+ vertices_.back()=(center_+((vertices_.back()-center_).unit()*radius_));
+ }
+ pairs_vertices[pair]=middle_point_ids[j];
+ }
+ else
+ {
+ middle_point_ids[j]=it->second;
+ }
+ }
+ new_triples.push_back(Triple(triple.get(0), middle_point_ids[1], middle_point_ids[2]));
+ new_triples.push_back(Triple(triple.get(1), middle_point_ids[0], middle_point_ids[2]));
+ new_triples.push_back(Triple(triple.get(2), middle_point_ids[0], middle_point_ids[1]));
+ new_triples.push_back(Triple(middle_point_ids[0], middle_point_ids[1], middle_point_ids[2]));
+ }
+ }
+ triples_=new_triples;
+ history_of_growth_.push_back(std::make_pair(vertices_.size(), triples_.size()));
+ }
+
+ void grow()
+ {
+ grow(vertices_.size(), false);
+ }
+
+ double calc_max_edge_length() const
+ {
+ double max_length=0.0;
+ for(std::size_t i=0;i<triples_.size();i++)
+ {
+ const Triple& t=triples_[i];
+ max_length=std::max(max_length, distance_from_point_to_point(vertices_[t.get(0)], vertices_[t.get(1)]));
+ max_length=std::max(max_length, distance_from_point_to_point(vertices_[t.get(0)], vertices_[t.get(2)]));
+ max_length=std::max(max_length, distance_from_point_to_point(vertices_[t.get(1)], vertices_[t.get(2)]));
+ }
+ return max_length;
+ }
+
+ template<typename PointType>
+ void fit_into_sphere(const PointType& center, const double radius)
+ {
+ const SimplePoint new_center=custom_point_from_object<SimplePoint>(center);
+ for(std::size_t i=0;i<vertices_.size();i++)
+ {
+ vertices_[i]=new_center+((vertices_[i]-center_).unit()*radius);
+ }
+ fitted_into_sphere_=true;
+ center_=new_center;
+ radius_=radius;
+ }
+
+ bool fitted_into_sphere() const
+ {
+ return fitted_into_sphere_;
+ }
+
+ const SimplePoint center() const
+ {
+ return center_;
+ }
+
+ double radius() const
+ {
+ return radius_;
+ }
+
+ const std::vector<SimplePoint>& vertices() const
+ {
+ return vertices_;
+ }
+
+ const std::vector<Triple>& triples() const
+ {
+ return triples_;
+ }
+
+ const std::vector< std::pair<std::size_t, std::size_t> > history_of_growth() const
+ {
+ return history_of_growth_;
+ }
+
+private:
+ bool fitted_into_sphere_;
+ SimplePoint center_;
+ double radius_;
+ std::vector<SimplePoint> vertices_;
+ std::vector<Triple> triples_;
+ std::vector< std::pair<std::size_t, std::size_t> > history_of_growth_;
+};
+
+}
+
+#endif /* APOLLOTA_SUBDIVIDED_ICOSAHEDRON_H_ */
diff --git a/src/apollota/tangent_plane_of_three_spheres.h b/src/apollota/tangent_plane_of_three_spheres.h
new file mode 100644
index 0000000..b77bbee
--- /dev/null
+++ b/src/apollota/tangent_plane_of_three_spheres.h
@@ -0,0 +1,134 @@
+#ifndef APOLLOTA_TANGENT_PLANE_OF_THREE_SPHERES_H_
+#define APOLLOTA_TANGENT_PLANE_OF_THREE_SPHERES_H_
+
+#include <vector>
+#include <algorithm>
+
+#include "basic_operations_on_spheres.h"
+#include "rotation.h"
+#include "safer_quadratic_equation_root.h"
+#include "safer_summation.h"
+
+namespace apollota
+{
+
+class TangentPlaneOfThreeSpheres
+{
+public:
+ template<typename InputSphereTypeA, typename InputSphereTypeB, typename InputSphereTypeC>
+ static inline std::vector< std::pair<SimplePoint, SimplePoint> > calculate(const InputSphereTypeA& a, const InputSphereTypeB& b, const InputSphereTypeC& c)
+ {
+ const std::vector<SimplePoint> normals=calculate_tangent_planes_normals(a, b, c);
+ std::vector< std::pair<SimplePoint, SimplePoint> > planes;
+ for(std::size_t i=0;i<normals.size();i++)
+ {
+ planes.push_back(std::make_pair((custom_point_from_object<SimplePoint>(a)+(normals[i]*(a.r+default_comparison_epsilon()))), normals[i]));
+ }
+ return planes;
+ }
+
+private:
+ template<typename InputSphereTypeA, typename InputSphereTypeB, typename InputSphereTypeC, typename InputPointType>
+ static inline bool check_tangent_plane(const InputSphereTypeA& s1, const InputSphereTypeB& s2, const InputSphereTypeC& s3, const InputPointType& tangent_plane_normal)
+ {
+ const SimplePoint sp1=custom_point_from_object<SimplePoint>(s1);
+ const SimplePoint sp2=custom_point_from_object<SimplePoint>(s2);
+ const SimplePoint sp3=custom_point_from_object<SimplePoint>(s3);
+ const SimplePoint t=custom_point_from_object<SimplePoint>(tangent_plane_normal);
+ return (equal( (((sp2+t*s2.r)-(sp1+t*s1.r)) * t), 0 ) &&
+ equal( (((sp3+t*s3.r)-(sp1+t*s1.r)) * t), 0 ));
+ }
+
+ template<typename InputSphereTypeA, typename InputSphereTypeB, typename InputSphereTypeC>
+ static inline std::vector<SimplePoint> calculate_tangent_planes_normals(const InputSphereTypeA& sm, const InputSphereTypeB& s1, const InputSphereTypeC& s2)
+ {
+ {
+ const double min_r=std::min(sm.r, std::min(s1.r, s2.r));
+ if(sm.r!=min_r)
+ {
+ if(s1.r==min_r) return calculate_tangent_planes_normals(s1, sm, s2);
+ if(s2.r==min_r) return calculate_tangent_planes_normals(s2, sm, s1);
+ }
+ }
+
+ const unsigned int rotation_steps=2;
+ const SimplePoint rotation_axis(1.0, 1.0, 1.0);
+ const double rotation_step_angle=30.0;
+
+ for(unsigned int rotation_step=0;rotation_step<=rotation_steps;rotation_step++)
+ {
+ SimpleSphere ts1(s1.x-sm.x, s1.y-sm.y, s1.z-sm.z, s1.r-sm.r);
+ SimpleSphere ts2(s2.x-sm.x, s2.y-sm.y, s2.z-sm.z, s2.r-sm.r);
+
+ if(rotation_step>0)
+ {
+ const Rotation rotation(rotation_axis, rotation_step_angle*static_cast<double>(rotation_step));
+ ts1=SimpleSphere(rotation.rotate<SimplePoint>(ts1), ts1.r);
+ ts2=SimpleSphere(rotation.rotate<SimplePoint>(ts2), ts2.r);
+ }
+
+ const double x1=ts1.x;
+ const double y1=ts1.y;
+ const double z1=ts1.z;
+ const double r1=ts1.r;
+
+ const double x2=ts2.x;
+ const double y2=ts2.y;
+ const double z2=ts2.z;
+ const double r2=ts2.r;
+
+ const double ad=0-x1;
+ if(ad>0.0 || ad<0.0)
+ {
+ const double a0=r1/ad;
+ const double ay=y1/ad;
+ const double az=z1/ad;
+
+ const double bd=-safer_sum(y2, ay*x2);
+ if(bd>0.0 || bd<0.0)
+ {
+ const double b0=safer_sum(r2, a0*x2)/bd;
+ const double bz=safer_sum(z2, az*x2)/bd;
+
+ const double c0=safer_sum(a0, ay*b0);
+ const double cz=safer_sum(ay*bz, az);
+
+ const double a=safer_sum(1, cz*cz, bz*bz);
+ const double b=safer_sum(2*c0*cz, 2*b0*bz);
+
+ if(check_if_quadratic_equation_is_solvable(a, b))
+ {
+ const double c=safer_sum(c0*c0, b0*b0, -1.0);
+ std::vector<SimplePoint> results;
+ std::vector<double> zs;
+ if(solve_quadratic_equation(a, b, c, zs))
+ {
+ results.reserve(zs.size());
+ for(std::size_t i=0;i<zs.size();i++)
+ {
+ const double z=zs[i];
+ SimplePoint candidate(safer_sum(c0, z*cz), safer_sum(b0, z*bz), z);
+ if(rotation_step>0)
+ {
+ const Rotation rotation(rotation_axis, (-rotation_step_angle)*static_cast<double>(rotation_step));
+ candidate=rotation.rotate<SimplePoint>(candidate);
+ }
+ if(check_tangent_plane(sm, s1, s2, candidate))
+ {
+ results.push_back(candidate);
+ }
+ }
+ }
+ return results;
+ }
+ }
+ }
+ }
+
+ return std::vector<SimplePoint>();
+ }
+};
+
+}
+
+#endif /* APOLLOTA_TANGENT_PLANE_OF_THREE_SPHERES_H_ */
diff --git a/src/apollota/tangent_sphere_of_four_spheres.h b/src/apollota/tangent_sphere_of_four_spheres.h
new file mode 100644
index 0000000..298c21f
--- /dev/null
+++ b/src/apollota/tangent_sphere_of_four_spheres.h
@@ -0,0 +1,170 @@
+#ifndef APOLLOTA_TANGENT_SPHERE_OF_FOUR_SPHERES_H_
+#define APOLLOTA_TANGENT_SPHERE_OF_FOUR_SPHERES_H_
+
+#include <vector>
+
+#include "basic_operations_on_spheres.h"
+#include "rotation.h"
+#include "safer_quadratic_equation_root.h"
+#include "safer_summation.h"
+
+namespace apollota
+{
+
+class TangentSphereOfFourSpheres
+{
+public:
+ template<typename InputSphereTypeA, typename InputSphereTypeB, typename InputSphereTypeC, typename InputSphereTypeD>
+ static inline std::vector<SimpleSphere> calculate(const InputSphereTypeA& sm, const InputSphereTypeB& s1, const InputSphereTypeC& s2, const InputSphereTypeD& s3)
+ {
+ {
+ const double min_r=std::min(sm.r, std::min(s1.r, std::min(s2.r, s3.r)));
+ if(sm.r!=min_r)
+ {
+ if(s1.r==min_r) return calculate(s1, sm, s2, s3);
+ if(s2.r==min_r) return calculate(s2, sm, s1, s3);
+ if(s3.r==min_r) return calculate(s3, sm, s1, s2);
+ }
+ }
+
+ SimpleSphere usm(sm);
+ for(int i=0;i<3 && equal(fabs(signed_volume_of_tetrahedron(usm, s1, s2, s3)), 0.0);i++)
+ {
+ const double allowed_shift=std::max(default_comparison_epsilon(), 0.00001);
+ usm=SimpleSphere(sm);
+ if(i%3==0) usm.x+=allowed_shift;
+ else if(i%3==1) usm.y+=allowed_shift;
+ else usm.z+=allowed_shift;
+ }
+
+ const unsigned int rotation_steps=2;
+ const SimplePoint rotation_axis(1.0, 1.0, 1.0);
+ const double rotation_step_angle=30.0;
+
+ for(unsigned int rotation_step=0;rotation_step<=rotation_steps;rotation_step++)
+ {
+ SimpleSphere ts1(s1.x-usm.x, s1.y-usm.y, s1.z-usm.z, s1.r-usm.r);
+ SimpleSphere ts2(s2.x-usm.x, s2.y-usm.y, s2.z-usm.z, s2.r-usm.r);
+ SimpleSphere ts3(s3.x-usm.x, s3.y-usm.y, s3.z-usm.z, s3.r-usm.r);
+
+ if(rotation_step>0)
+ {
+ const Rotation rotation(rotation_axis, rotation_step_angle*static_cast<double>(rotation_step));
+ ts1=SimpleSphere(rotation.rotate<SimplePoint>(ts1), ts1.r);
+ ts2=SimpleSphere(rotation.rotate<SimplePoint>(ts2), ts2.r);
+ ts3=SimpleSphere(rotation.rotate<SimplePoint>(ts3), ts3.r);
+ }
+
+ const double x1=ts1.x;
+ const double y1=ts1.y;
+ const double z1=ts1.z;
+ const double r1=ts1.r;
+
+ const double x2=ts2.x;
+ const double y2=ts2.y;
+ const double z2=ts2.z;
+ const double r2=ts2.r;
+
+ const double x3=ts3.x;
+ const double y3=ts3.y;
+ const double z3=ts3.z;
+ const double r3=ts3.r;
+
+ const double a1=2*x1;
+ const double b1=2*y1;
+ const double c1=2*z1;
+ const double d1=2*r1;
+ const double o1=safer_sum(r1*r1, -x1*x1, -y1*y1, -z1*z1);
+
+ const double a2=2*x2;
+ const double b2=2*y2;
+ const double c2=2*z2;
+ const double d2=2*r2;
+ const double o2=safer_sum(r2*r2, -x2*x2, -y2*y2, -z2*z2);
+
+ const double a3=2*x3;
+ const double b3=2*y3;
+ const double c3=2*z3;
+ const double d3=2*r3;
+ const double o3=safer_sum(r3*r3, -x3*x3, -y3*y3, -z3*z3);
+
+ const double w = safer_sum(a1*b3*c2, -a1*b2*c3, b1*a2*c3, -b1*a3*c2, c1*a3*b2, -c1*a2*b3);
+
+ if(w>0.0 || w<0.0)
+ {
+ const double u1 = -safer_sum( b1*c3*d2, -b1*c2*d3, c1*b2*d3, -c1*b3*d2, d1*b3*c2, -d1*b2*c3 ) / w;
+ const double v1 = -safer_sum( b1*c3*o2, -b1*c2*o3, c1*b2*o3, -c1*b3*o2, o1*b3*c2, -o1*b2*c3 ) / w;
+
+ const double u2 = safer_sum( a1*c3*d2, -a1*c2*d3, c1*a2*d3, -c1*a3*d2, d1*a3*c2, -d1*a2*c3 ) / w;
+ const double v2 = safer_sum( a1*c3*o2, -a1*c2*o3, c1*a2*o3, -c1*a3*o2, o1*a3*c2, -o1*a2*c3 ) / w;
+
+ const double u3 = -safer_sum( a1*b3*d2, -a1*b2*d3, b1*a2*d3, -b1*a3*d2, d1*a3*b2, -d1*a2*b3 ) / w;
+ const double v3 = -safer_sum( a1*b3*o2, -a1*b2*o3, b1*a2*o3, -b1*a3*o2, o1*a3*b2, -o1*a2*b3 ) / w;
+
+ const double a = safer_sum(u1*u1, u2*u2, u3*u3, -1.0);
+ const double b = safer_sum(2*u1*v1, 2*u2*v2, 2*u3*v3);
+
+ if(check_if_quadratic_equation_is_solvable(a, b))
+ {
+ const double c = safer_sum(v1*v1, v2*v2, v3*v3);
+ std::vector<SimpleSphere> results;
+ std::vector<double> radiuses;
+ if(solve_quadratic_equation(a, b, c, radiuses))
+ {
+ results.reserve(radiuses.size());
+ for(std::size_t i=0;i<radiuses.size();i++)
+ {
+ const double r=radiuses[i];
+ if(r>=0.0)
+ {
+ SimpleSphere candidate(safer_sum(u1*r, v1), safer_sum(u2*r, v2), safer_sum(u3*r, v3), r);
+ if(rotation_step>0)
+ {
+ const Rotation rotation(rotation_axis, (0.0-rotation_step_angle)*static_cast<double>(rotation_step));
+ candidate=SimpleSphere(rotation.rotate<SimplePoint>(candidate), candidate.r);
+ }
+ candidate.x+=usm.x;
+ candidate.y+=usm.y;
+ candidate.z+=usm.z;
+ candidate.r-=usm.r;
+ std::pair<double, double> error_estimate=calculate_tangent_sphere_radius_error_estimate(sm, s1, s2, s3, candidate);
+ if(error_estimate.first<0.0)
+ {
+ candidate.r+=error_estimate.first;
+ error_estimate=calculate_tangent_sphere_radius_error_estimate(sm, s1, s2, s3, candidate);
+ }
+ if(std::max(fabs(error_estimate.first), fabs(error_estimate.second))<tangent_spheres_max_allowed_error())
+ {
+ results.push_back(candidate);
+ }
+ }
+ }
+ }
+ return results;
+ }
+ }
+ }
+
+ return std::vector<SimpleSphere>();
+ }
+
+private:
+ template<typename InputSphereTypeA, typename InputSphereTypeB, typename InputSphereTypeC, typename InputSphereTypeD, typename InputSphereTypeE>
+ static inline std::pair<double, double> calculate_tangent_sphere_radius_error_estimate(const InputSphereTypeA& s1, const InputSphereTypeB& s2, const InputSphereTypeC& s3, const InputSphereTypeD& s4, const InputSphereTypeE& tangent)
+ {
+ const double d1=minimal_distance_from_sphere_to_sphere(tangent, s1);
+ const double d2=minimal_distance_from_sphere_to_sphere(tangent, s2);
+ const double d3=minimal_distance_from_sphere_to_sphere(tangent, s3);
+ const double d4=minimal_distance_from_sphere_to_sphere(tangent, s4);
+ return std::make_pair(std::min(std::min(d1, d2), std::min(d3, d4)), std::max(std::max(d1, d2), std::max(d3, d4)));
+ }
+
+ inline static double tangent_spheres_max_allowed_error()
+ {
+ return std::max(default_comparison_epsilon(), 0.001);
+ }
+};
+
+}
+
+#endif /* APOLLOTA_TANGENT_SPHERE_OF_FOUR_SPHERES_H_ */
diff --git a/src/apollota/tangent_sphere_of_three_spheres.h b/src/apollota/tangent_sphere_of_three_spheres.h
new file mode 100644
index 0000000..bc38c7f
--- /dev/null
+++ b/src/apollota/tangent_sphere_of_three_spheres.h
@@ -0,0 +1,223 @@
+#ifndef APOLLOTA_TANGENT_SPHERE_OF_THREE_SPHERES_H_
+#define APOLLOTA_TANGENT_SPHERE_OF_THREE_SPHERES_H_
+
+#include <vector>
+
+#include "basic_operations_on_spheres.h"
+#include "rotation.h"
+#include "safer_quadratic_equation_root.h"
+
+namespace apollota
+{
+
+class TangentSphereOfThreeSpheres
+{
+public:
+ template<typename InputSphereTypeA, typename InputSphereTypeB, typename InputSphereTypeC>
+ static inline std::vector<SimpleSphere> calculate(const InputSphereTypeA& sm, const InputSphereTypeB& s1, const InputSphereTypeC& s2)
+ {
+ {
+ const double min_r=std::min(sm.r, std::min(s1.r, s2.r));
+ if(sm.r!=min_r)
+ {
+ if(s1.r==min_r) return calculate(s1, sm, s2);
+ if(s2.r==min_r) return calculate(s2, sm, s1);
+ }
+ }
+
+ const double x1=distance_from_point_to_point(sm, s1);
+ const double y1=0;
+ const double r1=s1.r-sm.r;
+
+ const double x2=dot_product(sub_of_points<SimplePoint>(s1, sm).unit(), sub_of_points<PODPoint>(s2, sm));
+ const double y2=sqrt(squared_point_module(sub_of_points<PODPoint>(s2, sm))-x2*x2);
+ const double r2=s2.r-sm.r;
+
+ const double a1=2*x1;
+ const double b1=2*y1;
+ const double d1=2*r1;
+ const double o1=(r1*r1-x1*x1-y1*y1);
+
+ const double a2=2*x2;
+ const double b2=2*y2;
+ const double d2=2*r2;
+ const double o2=(r2*r2-x2*x2-y2*y2);
+
+ const double w = a2*b1-a1*b2;
+
+ const double u1 = (b2*d1-b1*d2) / w;
+ const double v1 = (b2*o1-b1*o2) / w;
+
+ const double u2 = -(a2*d1-a1*d2) / w;
+ const double v2 = -(a2*o1-a1*o2) / w;
+
+ const double a = u1*u1+u2*u2-1;
+ const double b = 2*(u1*v1+u2*v2);
+
+ std::vector<SimpleSphere> results;
+
+ if(check_if_quadratic_equation_is_solvable(a, b))
+ {
+ const double c = v1*v1+v2*v2;
+ std::vector<double> radiuses;
+ if(solve_quadratic_equation(a, b, c, radiuses))
+ {
+ results.reserve(radiuses.size());
+ for(std::size_t i=0;i<radiuses.size();i++)
+ {
+ const double r=radiuses[i];
+ if(r>0)
+ {
+ const double virtual_x=u1*r+v1;
+ const double virtual_y=u2*r+v2;
+ const double real_l1_offset=virtual_y*x2/y2;
+ const double real_l1=virtual_x-real_l1_offset;
+ const double real_l2=sqrt(real_l1_offset*real_l1_offset+virtual_y*virtual_y);
+ for(int sign_id=0;sign_id<2;sign_id++)
+ {
+ const double signed_real_l2=real_l2*(sign_id==0 ? 1.0 : -1.0);
+ SimpleSphere candidate(SimplePoint(sm)+(sub_of_points<SimplePoint>(s1, sm).unit()*real_l1)+(sub_of_points<SimplePoint>(s2, sm).unit()*signed_real_l2), (r-sm.r));
+ if((results.empty() || !(candidate==results.back())) && less(fabs(signed_volume_of_tetrahedron(sm, s1, s2, candidate)), tangent_spheres_max_allowed_error()))
+ {
+ std::pair<double, double> error_estimate=calculate_tangent_sphere_radius_error_estimate(sm, s1, s2, candidate);
+ if(error_estimate.first<0.0)
+ {
+ candidate.r+=error_estimate.first;
+ error_estimate=calculate_tangent_sphere_radius_error_estimate(sm, s1, s2, candidate);
+ }
+ if(std::max(fabs(error_estimate.first), fabs(error_estimate.second))<tangent_spheres_max_allowed_error())
+ {
+ results.push_back(candidate);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return results;
+ }
+
+ template<typename InputSphereTypeA, typename InputSphereTypeB, typename InputSphereTypeC>
+ static inline std::vector<SimpleSphere> calculate(const InputSphereTypeA& sm, const InputSphereTypeB& s1, const InputSphereTypeC& s2, const double custom_tangent_sphere_radius)
+ {
+ {
+ const double min_r=std::min(sm.r, std::min(s1.r, s2.r));
+ if(sm.r!=min_r)
+ {
+ if(s1.r==min_r) return calculate(s1, sm, s2, custom_tangent_sphere_radius);
+ if(s2.r==min_r) return calculate(s2, sm, s1, custom_tangent_sphere_radius);
+ }
+ }
+
+ const double r=custom_tangent_sphere_radius+sm.r;
+
+ const unsigned int rotation_steps=2;
+ const SimplePoint rotation_axis(1.0, 1.0, 1.0);
+ const double rotation_step_angle=30.0;
+
+ for(unsigned int rotation_step=0;rotation_step<=rotation_steps;rotation_step++)
+ {
+ SimpleSphere ts1(s1.x-sm.x, s1.y-sm.y, s1.z-sm.z, s1.r-sm.r);
+ SimpleSphere ts2(s2.x-sm.x, s2.y-sm.y, s2.z-sm.z, s2.r-sm.r);
+
+ if(rotation_step>0)
+ {
+ const Rotation rotation(rotation_axis, rotation_step_angle*static_cast<double>(rotation_step));
+ ts1=SimpleSphere(rotation.rotate<SimplePoint>(ts1), ts1.r);
+ ts2=SimpleSphere(rotation.rotate<SimplePoint>(ts2), ts2.r);
+ }
+
+ const double x1=ts1.x;
+ const double y1=ts1.y;
+ const double z1=ts1.z;
+ const double r1=ts1.r;
+
+ const double x2=ts2.x;
+ const double y2=ts2.y;
+ const double z2=ts2.z;
+ const double r2=ts2.r;
+
+ const double a1=2*x1;
+ const double b1=2*y1;
+ const double c1=2*z1;
+ const double o1=(r+r1)*(r+r1)-(r*r)-(x1*x1+y1*y1+z1*z1);
+
+ const double a2=2*x2;
+ const double b2=2*y2;
+ const double c2=2*z2;
+ const double o2=(r+r2)*(r+r2)-(r*r)-(x2*x2+y2*y2+z2*z2);
+
+ const double w1=(a1*b2-a2*b1);
+ const double w2=(b1*a2-b2*a1);
+
+ if((w1>0.0 || w1<0.0) && (w2>0.0 || w2<0.0))
+ {
+ const double ux=(c2*b1-c1*b2)/w1;
+ const double vx=(o2*b1-o1*b2)/w1;
+
+ const double uy=(c2*a1-c1*a2)/w2;
+ const double vy=(o2*a1-o1*a2)/w2;
+
+ const double a=(ux*ux+uy*uy+1);
+ const double b=2*(ux*vx+uy*vy);
+
+ if(check_if_quadratic_equation_is_solvable(a, b))
+ {
+ const double c=(vx*vx+vy*vy-r*r);
+ std::vector<SimpleSphere> results;
+ std::vector<double> zs;
+ if(solve_quadratic_equation(a, b, c, zs))
+ {
+ results.reserve(zs.size());
+ for(std::size_t i=0;i<zs.size();i++)
+ {
+ const double z=zs[i];
+ SimpleSphere candidate((ux*z+vx), (uy*z+vy), z, r);
+ if(rotation_step>0)
+ {
+ const Rotation rotation(rotation_axis, (0.0-rotation_step_angle)*static_cast<double>(rotation_step));
+ candidate=SimpleSphere(rotation.rotate<SimplePoint>(candidate), candidate.r);
+ }
+ candidate.x+=sm.x;
+ candidate.y+=sm.y;
+ candidate.z+=sm.z;
+ candidate.r-=sm.r;
+ if(equal(candidate.r, custom_tangent_sphere_radius))
+ {
+ const std::pair<double, double> error_estimate=calculate_tangent_sphere_radius_error_estimate(sm, s1, s2, candidate);
+ if(std::max(fabs(error_estimate.first), fabs(error_estimate.second))<tangent_spheres_max_allowed_error())
+ {
+ results.push_back(candidate);
+ }
+ }
+ }
+ return results;
+ }
+ }
+ }
+ }
+
+ return std::vector<SimpleSphere>();
+ }
+
+private:
+ template<typename InputSphereTypeA, typename InputSphereTypeB, typename InputSphereTypeC, typename InputSphereTypeD>
+ static inline std::pair<double, double> calculate_tangent_sphere_radius_error_estimate(const InputSphereTypeA& s1, const InputSphereTypeB& s2, const InputSphereTypeC& s3, const InputSphereTypeD& tangent)
+ {
+ const double d1=minimal_distance_from_sphere_to_sphere(tangent, s1);
+ const double d2=minimal_distance_from_sphere_to_sphere(tangent, s2);
+ const double d3=minimal_distance_from_sphere_to_sphere(tangent, s3);
+ return std::make_pair(std::min(std::min(d1, d2), d3), std::max(std::max(d1, d2), d3));
+ }
+
+ inline static double tangent_spheres_max_allowed_error()
+ {
+ return std::max(default_comparison_epsilon(), 0.001);
+ }
+};
+
+}
+
+#endif /* APOLLOTA_TANGENT_SPHERE_OF_THREE_SPHERES_H_ */
diff --git a/src/apollota/triangulation.h b/src/apollota/triangulation.h
new file mode 100644
index 0000000..5dba58c
--- /dev/null
+++ b/src/apollota/triangulation.h
@@ -0,0 +1,1265 @@
+#ifndef APOLLOTA_TRIANGULATION_H_
+#define APOLLOTA_TRIANGULATION_H_
+
+#include <limits>
+#include <vector>
+#include <map>
+#include <set>
+
+#include "../compatability_macros.h"
+
+#if USE_TR1 > 0
+#include <tr1/unordered_map>
+#include <tr1/unordered_set>
+#else
+#include <unordered_map>
+#include <unordered_set>
+#endif
+
+#include "tuple.h"
+#include "search_for_spherical_collisions.h"
+#include "tangent_plane_of_three_spheres.h"
+#include "tangent_sphere_of_four_spheres.h"
+#include "tangent_sphere_of_three_spheres.h"
+
+namespace apollota
+{
+
+static const std::size_t npos=static_cast<std::size_t>(-1);
+
+class Triangulation
+{
+public:
+
+#if USE_TR1 > 0
+typedef std::tr1::unordered_map<Quadruple, std::vector<SimpleSphere>, Quadruple::HashFunctor> QuadruplesMap;
+#else
+typedef std::unordered_map<Quadruple, std::vector<SimpleSphere>, Quadruple::HashFunctor> QuadruplesMap;
+#endif
+
+ typedef std::vector< std::pair<Quadruple, SimpleSphere> > VerticesVector;
+ typedef std::vector< std::vector<std::size_t> > VerticesGraph;
+
+ struct QuadruplesSearchLog
+ {
+ std::size_t added_quadruples;
+ std::size_t added_tangent_spheres;
+ std::size_t processed_faces;
+ std::size_t encountered_difficult_faces;
+ std::size_t produced_faces;
+ std::size_t updated_faces;
+ std::size_t encountered_triples_repetitions;
+ std::size_t performed_iterations_for_finding_first_faces;
+ };
+
+ struct SurplusQuadruplesSearchLog
+ {
+ std::size_t surplus_quadruples;
+ std::size_t surplus_tangent_spheres;
+ };
+
+ struct Result
+ {
+ QuadruplesMap quadruples_map;
+ QuadruplesSearchLog quadruples_search_log;
+ SurplusQuadruplesSearchLog surplus_quadruples_search_log;
+ std::set<std::size_t> excluded_hidden_spheres_ids;
+ std::set<std::size_t> ignored_spheres_ids;
+
+ Result() : quadruples_search_log(), surplus_quadruples_search_log()
+ {
+ }
+ };
+
+ static Result construct_result(
+ const std::vector<SimpleSphere>& spheres,
+ const double initial_radius_for_spheres_bucketing,
+ const bool exclude_hidden_spheres,
+ const bool include_surplus_valid_quadruples)
+ {
+ Result result;
+
+ {
+ BoundingSpheresHierarchy bsh(spheres, initial_radius_for_spheres_bucketing, 1);
+
+ std::vector<std::size_t> refined_spheres_backward_mapping;
+ if(exclude_hidden_spheres)
+ {
+ result.excluded_hidden_spheres_ids=SearchForSphericalCollisions::find_all_hidden_spheres(bsh);
+ if(!result.excluded_hidden_spheres_ids.empty())
+ {
+ std::vector<SimpleSphere> refined_spheres;
+ const std::size_t refined_spheres_count=bsh.leaves_spheres().size()-result.excluded_hidden_spheres_ids.size();
+ refined_spheres.reserve(refined_spheres_count);
+ refined_spheres_backward_mapping.reserve(refined_spheres_count);
+ for(std::size_t i=0;i<bsh.leaves_spheres().size();i++)
+ {
+ if(result.excluded_hidden_spheres_ids.count(i)==0)
+ {
+ refined_spheres.push_back(bsh.leaves_spheres()[i]);
+ refined_spheres_backward_mapping.push_back(i);
+ }
+ }
+ bsh=BoundingSpheresHierarchy(refined_spheres, initial_radius_for_spheres_bucketing, 1);
+ }
+ }
+
+ result.quadruples_search_log=find_valid_quadruples(bsh, std::vector<int>(bsh.leaves_spheres().size(), 1), result.quadruples_map);
+ if(include_surplus_valid_quadruples)
+ {
+ result.surplus_quadruples_search_log=find_surplus_valid_quadruples(bsh, result.quadruples_map);
+ }
+
+ if(!refined_spheres_backward_mapping.empty())
+ {
+ result.quadruples_map=renumber_quadruples_map(result.quadruples_map, refined_spheres_backward_mapping);
+ }
+ }
+
+ result.ignored_spheres_ids=collect_ignored_spheres_ids(std::vector<int>(spheres.size(), 1), result.quadruples_map);
+
+ return result;
+ }
+
+ template<typename AdmittanceSet>
+ static Result construct_result_for_admittance_set(
+ const BoundingSpheresHierarchy& bsh,
+ const AdmittanceSet& admittance_set,
+ const bool include_surplus_valid_quadruples)
+ {
+ Result result;
+ std::vector<int> admittance(bsh.leaves_spheres().size(), 0);
+ bool admittance_filled=false;
+ for(typename AdmittanceSet::const_iterator it=admittance_set.begin();it!=admittance_set.end();++it)
+ {
+ const std::size_t id=(*it);
+ if(id<admittance.size())
+ {
+ admittance[id]=1;
+ admittance_filled=true;
+ }
+ }
+ if(admittance_filled)
+ {
+ result.quadruples_search_log=find_valid_quadruples(bsh, admittance, result.quadruples_map);
+ if(include_surplus_valid_quadruples)
+ {
+ result.surplus_quadruples_search_log=find_surplus_valid_quadruples(bsh, result.quadruples_map);
+ }
+ result.ignored_spheres_ids=collect_ignored_spheres_ids(admittance, result.quadruples_map);
+ }
+ return result;
+ }
+
+ static void merge_quadruples_maps(const QuadruplesMap& source_quadruples_map, QuadruplesMap& destination_quadruples_map)
+ {
+ for(QuadruplesMap::const_iterator it=source_quadruples_map.begin();it!=source_quadruples_map.end();++it)
+ {
+ const Quadruple& quadruple=it->first;
+ const std::vector<SimpleSphere>& tangent_spheres=it->second;
+ for(std::size_t i=0;i<tangent_spheres.size();i++)
+ {
+ augment_quadruples_map(quadruple, tangent_spheres[i], destination_quadruples_map);
+ }
+ }
+ }
+
+ static VerticesVector collect_vertices_vector_from_quadruples_map(const QuadruplesMap& quadruples_map)
+ {
+ typedef std::multimap<QuadruplesMap::key_type, QuadruplesMap::mapped_type> QuadruplesOrderedMultimap;
+ QuadruplesOrderedMultimap quadruples_ordered_multimap;
+ for(QuadruplesMap::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ quadruples_ordered_multimap.insert(*it);
+ }
+ VerticesVector vertices_vector;
+ vertices_vector.reserve(count_tangent_spheres_in_quadruples_map(quadruples_map));
+ for(QuadruplesOrderedMultimap::const_iterator it=quadruples_ordered_multimap.begin();it!=quadruples_ordered_multimap.end();++it)
+ {
+ const std::vector<SimpleSphere>& tangent_spheres=it->second;
+ if(tangent_spheres.size()==1)
+ {
+ vertices_vector.push_back(std::make_pair(it->first, tangent_spheres.front()));
+ }
+ else if(tangent_spheres.size()==2)
+ {
+ const SimpleSphere& a=tangent_spheres.front();
+ const SimpleSphere& b=tangent_spheres.back();
+ if(std::make_pair(a.r, std::make_pair(a.x, std::make_pair(a.y, a.z)))<std::make_pair(b.r, std::make_pair(b.x, std::make_pair(b.y, b.z))))
+ {
+ vertices_vector.push_back(std::make_pair(it->first, a));
+ vertices_vector.push_back(std::make_pair(it->first, b));
+ }
+ else
+ {
+ vertices_vector.push_back(std::make_pair(it->first, b));
+ vertices_vector.push_back(std::make_pair(it->first, a));
+ }
+ }
+ }
+ return vertices_vector;
+ }
+
+ static std::size_t count_tangent_spheres_in_quadruples_map(const QuadruplesMap& quadruples_map)
+ {
+ std::size_t sum=0;
+ for(QuadruplesMap::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ sum+=it->second.size();
+ }
+ return sum;
+ }
+
+ template<typename SphereType>
+ static bool check_quadruples_map(const std::vector<SphereType>& spheres, const QuadruplesMap& quadruples_map)
+ {
+ for(typename QuadruplesMap::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ const QuadruplesMap::key_type& q=it->first;
+ const QuadruplesMap::mapped_type& ts=it->second;
+ if(q.has_repetetions() || ts.empty() || ts.size()>2)
+ {
+ return false;
+ }
+ for(std::size_t i=0;i<ts.size();i++)
+ {
+ const SimpleSphere& t=ts[i];
+ for(std::size_t j=0;j<spheres.size();j++)
+ {
+ if(sphere_intersects_sphere(t, spheres[j]))
+ {
+ return false;
+ }
+ }
+ }
+ }
+ return true;
+ }
+
+ static VerticesGraph construct_vertices_graph(const std::vector<SimpleSphere>& spheres, const QuadruplesMap& quadruples_map)
+ {
+#if USE_TR1 > 0
+typedef std::tr1::unordered_map<Triple, std::vector<std::size_t>, Triple::HashFunctor> TriplesVerticesMap;
+#else
+typedef std::unordered_map<Triple, std::vector<std::size_t>, Triple::HashFunctor> TriplesVerticesMap;
+#endif
+
+ const VerticesVector valid_vertices_vector=collect_vertices_vector_from_quadruples_map(quadruples_map);
+ const VerticesVector invalid_vertices_vector=collect_vertices_vector_from_quadruples_map(collect_invalid_tangent_spheres_of_valid_quadruples(spheres, quadruples_map));
+ VerticesVector all_vertices_vector=valid_vertices_vector;
+ all_vertices_vector.insert(all_vertices_vector.end(), invalid_vertices_vector.begin(), invalid_vertices_vector.end());
+
+ TriplesVerticesMap triples_vertices_map;
+ for(std::size_t i=0;i<all_vertices_vector.size();i++)
+ {
+ const Quadruple& q=all_vertices_vector[i].first;
+ for(int j=0;j<4;j++)
+ {
+ triples_vertices_map[q.exclude(j)].push_back(i);
+ }
+ }
+
+ VerticesGraph vertices_graph(valid_vertices_vector.size(), std::vector<std::size_t>(4, npos));
+ for(TriplesVerticesMap::const_iterator it=triples_vertices_map.begin();it!=triples_vertices_map.end();++it)
+ {
+ update_vertices_graph(spheres, all_vertices_vector, it->first, it->second, vertices_graph);
+ }
+
+ return vertices_graph;
+ }
+
+private:
+ class Face
+ {
+ public:
+ Face(const std::vector<SimpleSphere>& spheres, const Triple& abc_ids, const double min_sphere_radius) :
+ spheres_(&spheres),
+ abc_ids_(abc_ids),
+ a_sphere_(&(spheres_->at(abc_ids_.get(0)))),
+ b_sphere_(&(spheres_->at(abc_ids_.get(1)))),
+ c_sphere_(&(spheres_->at(abc_ids_.get(2)))),
+ tangent_planes_(TangentPlaneOfThreeSpheres::calculate((*a_sphere_), (*b_sphere_), (*c_sphere_))),
+ can_have_d_(tangent_planes_.size()==2),
+ can_have_e_(!can_have_d_ || greater(a_sphere_->r, min_sphere_radius) || greater(b_sphere_->r, min_sphere_radius) || greater(c_sphere_->r, min_sphere_radius))
+ {
+ if(can_have_d_)
+ {
+ d_ids_and_tangent_spheres_.resize(2, std::pair<std::size_t, SimpleSphere>(npos, SimpleSphere()));
+ init_central_planes();
+ init_middle_region_approximation();
+ }
+ else
+ {
+ tangent_planes_.clear();
+ }
+ }
+
+ const Triple& abc_ids() const
+ {
+ return abc_ids_;
+ }
+
+ bool can_have_d() const
+ {
+ return can_have_d_;
+ }
+
+ template<typename InputSphereType>
+ bool sphere_may_contain_candidate_for_d(const InputSphereType& input_sphere, const std::size_t d_number) const
+ {
+ return (
+ can_have_d_
+ && (d_number<2)
+ && (halfspace_of_sphere(tangent_planes_[d_number].first, tangent_planes_[d_number].second, input_sphere)>=0)
+ );
+ }
+
+ std::pair<bool, SimpleSphere> check_candidate_for_d(const std::size_t d_id, const std::size_t d_number) const
+ {
+ if(
+ can_have_d_
+ && (d_id!=npos)
+ && (d_number<2)
+ && (d_id!=d_ids_and_tangent_spheres_[d_number].first)
+ && (!abc_ids_.contains(d_id))
+ && (halfspace_of_sphere(tangent_planes_[d_number].first, tangent_planes_[d_number].second, spheres_->at(d_id))>=0)
+ )
+ {
+ const std::vector<SimpleSphere> tangent_spheres=TangentSphereOfFourSpheres::calculate((*a_sphere_), (*b_sphere_), (*c_sphere_), spheres_->at(d_id));
+ if(!tangent_spheres.empty())
+ {
+ std::size_t i=0;
+ if(tangent_spheres.size()==2)
+ {
+ const double hs0=halfspace_of_point(central_planes_[d_number].first, central_planes_[d_number].second, tangent_spheres[0]);
+ const double hs1=halfspace_of_point(central_planes_[d_number].first, central_planes_[d_number].second, tangent_spheres[1]);
+ if(hs0==1 && hs1==-1)
+ {
+ i=0;
+ }
+ else if(hs0==-1 && hs1==1)
+ {
+ i=1;
+ }
+ else if(hs0==-1 && hs1==-1)
+ {
+ i=(tangent_spheres[0].r<tangent_spheres[1].r ? 0 : 1);
+ }
+ else if(hs0==1 && hs1==1)
+ {
+ i=(tangent_spheres[0].r>tangent_spheres[1].r ? 0 : 1);
+ }
+ }
+ const SimpleSphere& tangent_sphere=tangent_spheres[i];
+ if(!sphere_intersects_recorded_sphere(d_ids_and_tangent_spheres_, tangent_sphere) && !sphere_intersects_recorded_sphere(e_ids_and_tangent_spheres_, tangent_sphere))
+ {
+ return std::make_pair(true, tangent_sphere);
+ }
+ }
+ }
+ return std::make_pair(false, SimpleSphere());
+ }
+
+ void set_d(const std::size_t d_id, const std::size_t d_number, const SimpleSphere& tangent_sphere)
+ {
+ if(can_have_d_ && d_number<2 && d_ids_and_tangent_spheres_[d_number].first!=d_id)
+ {
+ d_ids_and_tangent_spheres_[d_number]=std::make_pair(d_id, tangent_sphere);
+ }
+ }
+
+ void set_d_with_d_number_selection(const std::size_t d_id, const SimpleSphere& tangent_sphere)
+ {
+ if(can_have_d_)
+ {
+ const int h0=halfspace_of_sphere(tangent_planes_[0].first, tangent_planes_[0].second, spheres_->at(d_id));
+ const int h1=halfspace_of_sphere(tangent_planes_[1].first, tangent_planes_[1].second, spheres_->at(d_id));
+ if(h0>=0 && h1==-1 && (halfspace_of_sphere(tangent_planes_[0].first, tangent_planes_[0].second, spheres_->at(d_id))>=0))
+ {
+ set_d(d_id, 0, tangent_sphere);
+ }
+ else if(h0==-1 && h1>=0 && (halfspace_of_sphere(tangent_planes_[1].first, tangent_planes_[1].second, spheres_->at(d_id))>=0))
+ {
+ set_d(d_id, 1, tangent_sphere);
+ }
+ }
+ }
+
+ void unset_d(const std::size_t d_number)
+ {
+ if(can_have_d_ && d_number<2)
+ {
+ d_ids_and_tangent_spheres_[d_number]=std::make_pair(npos, SimpleSphere());
+ }
+ }
+
+ bool has_d(const std::size_t d_number) const
+ {
+ return (can_have_d_ && d_number<2 && d_ids_and_tangent_spheres_[d_number].first!=npos);
+ }
+
+ std::size_t get_d_id(const std::size_t d_number) const
+ {
+ return ((can_have_d_ && d_number<2) ? d_ids_and_tangent_spheres_[d_number].first : npos);
+ }
+
+ const SimpleSphere get_d_tangent_sphere(const std::size_t d_number) const
+ {
+ return ((can_have_d_ && d_number<2) ? d_ids_and_tangent_spheres_[d_number].second : SimpleSphere());
+ }
+
+ bool can_have_e() const
+ {
+ return can_have_e_;
+ }
+
+ void update_middle_region_approximation()
+ {
+ if(can_have_e_ && can_have_d_ && d_ids_and_tangent_spheres_[0].first!=npos && d_ids_and_tangent_spheres_[1].first!=npos)
+ {
+ const std::vector<SimpleSphere> disk0=TangentSphereOfThreeSpheres::calculate(
+ SimpleSphere(SimplePoint(*a_sphere_)+(sub_of_points<SimplePoint>(d_ids_and_tangent_spheres_[0].second, *a_sphere_).unit()*a_sphere_->r), 0),
+ SimpleSphere(SimplePoint(*b_sphere_)+(sub_of_points<SimplePoint>(d_ids_and_tangent_spheres_[0].second, *b_sphere_).unit()*b_sphere_->r), 0),
+ SimpleSphere(SimplePoint(*c_sphere_)+(sub_of_points<SimplePoint>(d_ids_and_tangent_spheres_[0].second, *c_sphere_).unit()*c_sphere_->r), 0));
+ if(disk0.size()==1)
+ {
+ const std::vector<SimpleSphere> disk1=TangentSphereOfThreeSpheres::calculate(
+ SimpleSphere(SimplePoint(*a_sphere_)+(sub_of_points<SimplePoint>(d_ids_and_tangent_spheres_[1].second, *a_sphere_).unit()*a_sphere_->r), 0),
+ SimpleSphere(SimplePoint(*b_sphere_)+(sub_of_points<SimplePoint>(d_ids_and_tangent_spheres_[1].second, *b_sphere_).unit()*b_sphere_->r), 0),
+ SimpleSphere(SimplePoint(*c_sphere_)+(sub_of_points<SimplePoint>(d_ids_and_tangent_spheres_[1].second, *c_sphere_).unit()*c_sphere_->r), 0));
+ if(disk1.size()==1)
+ {
+ const SimplePoint center(sum_of_points<SimplePoint>(disk0.front(), disk1.front())*0.5);
+ middle_region_approximation_sphere_.first=true;
+ middle_region_approximation_sphere_.second=SimpleSphere(center, std::max(distance_from_point_to_point(center, disk0.front())+disk0.front().r, distance_from_point_to_point(center, disk1.front())+disk1.front().r));
+ }
+ }
+ }
+ }
+
+ template<typename InputSphereType>
+ bool sphere_may_contain_candidate_for_e(const InputSphereType& input_sphere) const
+ {
+ return (
+ can_have_e_
+ && (!can_have_d_ || !middle_region_approximation_sphere_.first || sphere_intersects_sphere(middle_region_approximation_sphere_.second, input_sphere))
+ && (!can_have_d_ || d_ids_and_tangent_spheres_[0].first==npos || d_ids_and_tangent_spheres_[1].first==npos
+ || (distance_from_point_to_line(input_sphere, d_ids_and_tangent_spheres_[0].second, d_ids_and_tangent_spheres_[1].second)<(input_sphere.r+std::max(d_ids_and_tangent_spheres_[0].second.r, d_ids_and_tangent_spheres_[1].second.r)))
+ || (can_have_negative_tangent_spheres_ && sphere_intersects_sphere(input_sphere, *a_sphere_) && sphere_intersects_sphere(input_sphere, *b_sphere_) && sphere_intersects_sphere(input_sphere, *c_sphere_)))
+ && (!can_have_d_ || (halfspace_of_sphere(tangent_planes_[0].first, tangent_planes_[0].second, input_sphere)<=0 && halfspace_of_sphere(tangent_planes_[1].first, tangent_planes_[1].second, input_sphere)<=0))
+ );
+ }
+
+ std::vector<SimpleSphere> check_candidate_for_e(const std::size_t e_id) const
+ {
+ if(
+ can_have_e_
+ && (e_id!=npos)
+ && (!abc_ids_.contains(e_id))
+ && (!can_have_d_ || (e_id!=d_ids_and_tangent_spheres_[0].first && e_id!=d_ids_and_tangent_spheres_[1].first))
+ && (!can_have_d_ || !middle_region_approximation_sphere_.first || sphere_intersects_sphere(middle_region_approximation_sphere_.second, spheres_->at(e_id)))
+ && (!can_have_d_ || (halfspace_of_sphere(tangent_planes_[0].first, tangent_planes_[0].second, spheres_->at(e_id))==-1 && halfspace_of_sphere(tangent_planes_[1].first, tangent_planes_[1].second, spheres_->at(e_id))==-1))
+ )
+ {
+ const std::vector<SimpleSphere> tangent_spheres=TangentSphereOfFourSpheres::calculate((*a_sphere_), (*b_sphere_), (*c_sphere_), spheres_->at(e_id));
+ std::vector<SimpleSphere> valid_tangent_spheres;
+ for(std::size_t i=0;i<tangent_spheres.size();i++)
+ {
+ const SimpleSphere& tangent_sphere=tangent_spheres[i];
+ if(!sphere_intersects_recorded_sphere(d_ids_and_tangent_spheres_, tangent_sphere) && !sphere_intersects_recorded_sphere(e_ids_and_tangent_spheres_, tangent_sphere))
+ {
+ valid_tangent_spheres.push_back(tangent_sphere);
+ }
+ }
+ return valid_tangent_spheres;
+ }
+ return std::vector<SimpleSphere>();
+ }
+
+ void add_e(const std::size_t e_id, const SimpleSphere& tangent_sphere)
+ {
+ if(can_have_e_ && e_id!=npos)
+ {
+ e_ids_and_tangent_spheres_.push_back(std::make_pair(e_id, tangent_sphere));
+ }
+ }
+
+ void unset_e()
+ {
+ e_ids_and_tangent_spheres_.clear();
+ }
+
+ bool has_e() const
+ {
+ return (!e_ids_and_tangent_spheres_.empty());
+ }
+
+ const std::vector< std::pair<std::size_t, SimpleSphere> >& get_e_ids_and_tangent_spheres() const
+ {
+ return e_ids_and_tangent_spheres_;
+ }
+
+ std::vector< std::pair<Quadruple, SimpleSphere> > produce_quadruples(const bool with_d0, const bool with_d1, const bool with_e) const
+ {
+ std::vector< std::pair<Quadruple, SimpleSphere> > quadruples_with_tangent_spheres;
+ const std::vector< std::pair<std::size_t, SimpleSphere> > recorded_ids_and_tangent_spheres=collect_all_recorded_ids_and_tangent_spheres(with_d0, with_d1, with_e);
+ for(std::size_t i=0;i<recorded_ids_and_tangent_spheres.size();i++)
+ {
+ quadruples_with_tangent_spheres.push_back(std::make_pair(Quadruple(abc_ids_, recorded_ids_and_tangent_spheres[i].first), recorded_ids_and_tangent_spheres[i].second));
+ }
+ return quadruples_with_tangent_spheres;
+ }
+
+ std::vector< std::pair<Triple, std::pair<std::size_t, SimpleSphere> > > produce_prefaces(const bool with_d0, const bool with_d1, const bool with_e) const
+ {
+ std::vector< std::pair<Triple, std::pair<std::size_t, SimpleSphere> > > produced_prefaces;
+ const std::vector< std::pair<std::size_t, SimpleSphere> > recorded_ids_and_tangent_spheres=collect_all_recorded_ids_and_tangent_spheres(with_d0, with_d1, with_e);
+ for(int j=0;j<3;j++)
+ {
+ for(std::size_t i=0;i<recorded_ids_and_tangent_spheres.size();i++)
+ {
+ produced_prefaces.push_back(std::make_pair(Triple(abc_ids_.exclude(j), recorded_ids_and_tangent_spheres[i].first), std::make_pair(abc_ids_.get(j), recorded_ids_and_tangent_spheres[i].second)));
+ }
+ }
+ return produced_prefaces;
+ }
+
+ private:
+ void init_central_planes()
+ {
+ central_planes_.clear();
+ if(can_have_d_)
+ {
+ central_planes_.resize(2);
+ const SimplePoint centeral_plane_normal=plane_normal_from_three_points<SimplePoint>((*a_sphere_), (*b_sphere_), (*c_sphere_));
+ const bool consistent_orientation=(halfspace_of_point((*a_sphere_), centeral_plane_normal, (tangent_planes_[0].first+tangent_planes_[0].second))==1);
+ central_planes_[0]=std::make_pair(SimplePoint(*a_sphere_), consistent_orientation ? centeral_plane_normal : centeral_plane_normal.inverted());
+ central_planes_[1]=std::make_pair(SimplePoint(*a_sphere_), consistent_orientation ? centeral_plane_normal.inverted() : centeral_plane_normal);
+ }
+ }
+
+ void init_middle_region_approximation()
+ {
+ can_have_negative_tangent_spheres_=(sphere_intersects_sphere(*a_sphere_, *b_sphere_) && sphere_intersects_sphere(*a_sphere_, *c_sphere_) && sphere_intersects_sphere(*b_sphere_, *c_sphere_));
+ middle_region_approximation_sphere_.first=false;
+ if(can_have_e_ && can_have_d_)
+ {
+ const std::vector<SimpleSphere> disk0=TangentSphereOfThreeSpheres::calculate(
+ SimpleSphere(SimplePoint(*a_sphere_)+(tangent_planes_[0].second*(a_sphere_->r)), 0),
+ SimpleSphere(SimplePoint(*b_sphere_)+(tangent_planes_[0].second*(b_sphere_->r)), 0),
+ SimpleSphere(SimplePoint(*c_sphere_)+(tangent_planes_[0].second*(c_sphere_->r)), 0));
+ if(disk0.size()==1)
+ {
+ const std::vector<SimpleSphere> disk1=TangentSphereOfThreeSpheres::calculate(
+ SimpleSphere(SimplePoint(*a_sphere_)+(tangent_planes_[1].second*(a_sphere_->r)), 0),
+ SimpleSphere(SimplePoint(*b_sphere_)+(tangent_planes_[1].second*(b_sphere_->r)), 0),
+ SimpleSphere(SimplePoint(*c_sphere_)+(tangent_planes_[1].second*(c_sphere_->r)), 0));
+ if(disk1.size()==1)
+ {
+ const SimplePoint center(sum_of_points<SimplePoint>(disk0.front(), disk1.front())*0.5);
+ middle_region_approximation_sphere_.first=true;
+ middle_region_approximation_sphere_.second=SimpleSphere(center, std::max(distance_from_point_to_point(center, disk0.front())+disk0.front().r, distance_from_point_to_point(center, disk1.front())+disk1.front().r));
+ }
+ }
+ }
+ }
+
+ std::vector< std::pair<std::size_t, SimpleSphere> > collect_all_recorded_ids_and_tangent_spheres(const bool with_d0, const bool with_d1, const bool with_e) const
+ {
+ std::vector< std::pair<std::size_t, SimpleSphere> > recorded_ids_and_tangent_spheres;
+ recorded_ids_and_tangent_spheres.reserve(d_ids_and_tangent_spheres_.size()+e_ids_and_tangent_spheres_.size());
+ if(can_have_d_ && with_d0 && d_ids_and_tangent_spheres_[0].first!=npos)
+ {
+ recorded_ids_and_tangent_spheres.push_back(d_ids_and_tangent_spheres_[0]);
+ }
+ if(can_have_d_ && with_d1 && d_ids_and_tangent_spheres_[1].first!=npos)
+ {
+ recorded_ids_and_tangent_spheres.push_back(d_ids_and_tangent_spheres_[1]);
+ }
+ if(can_have_e_ && with_e && !e_ids_and_tangent_spheres_.empty())
+ {
+ recorded_ids_and_tangent_spheres.insert(recorded_ids_and_tangent_spheres.end(), e_ids_and_tangent_spheres_.begin(), e_ids_and_tangent_spheres_.end());
+ }
+ return recorded_ids_and_tangent_spheres;
+ }
+
+ template<typename InputSphereType>
+ bool sphere_intersects_recorded_sphere(const std::vector< std::pair<std::size_t, SimpleSphere> >& recorded_ids_and_tangent_spheres, const InputSphereType& input_sphere) const
+ {
+ for(std::size_t i=0;i<recorded_ids_and_tangent_spheres.size();i++)
+ {
+ if(recorded_ids_and_tangent_spheres[i].first!=npos && sphere_intersects_sphere(input_sphere, spheres_->at(recorded_ids_and_tangent_spheres[i].first)))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ const std::vector<SimpleSphere>* spheres_;
+ Triple abc_ids_;
+ const SimpleSphere* a_sphere_;
+ const SimpleSphere* b_sphere_;
+ const SimpleSphere* c_sphere_;
+ std::vector< std::pair<SimplePoint, SimplePoint> > tangent_planes_;
+ std::vector< std::pair<std::size_t, SimpleSphere> > d_ids_and_tangent_spheres_;
+ std::vector< std::pair<std::size_t, SimpleSphere> > e_ids_and_tangent_spheres_;
+ bool can_have_d_;
+ bool can_have_e_;
+ std::vector< std::pair<SimplePoint, SimplePoint> > central_planes_;
+ bool can_have_negative_tangent_spheres_;
+ std::pair<bool, SimpleSphere> middle_region_approximation_sphere_;
+ };
+
+ class SearchForAnyDOfFace
+ {
+ public:
+ static bool find_any_d(const BoundingSpheresHierarchy& bsh, Face& face, const std::size_t d_number)
+ {
+ if(!face.has_d(d_number))
+ {
+ NodeCheckerForAnyD node_checker(face, d_number);
+ LeafCheckerForAnyD leaf_checker(face, d_number);
+ node_checker.constrain();
+ bsh.search(node_checker, leaf_checker);
+ if(node_checker.constrained && !face.has_d(d_number))
+ {
+ node_checker.unconstrain();
+ bsh.search(node_checker, leaf_checker);
+ }
+ return face.has_d(d_number);
+ }
+ return false;
+ }
+
+ private:
+ struct NodeCheckerForAnyD
+ {
+ const Face& face;
+ const std::size_t d_number;
+ bool constrained;
+ SimpleSphere constraint_sphere;
+
+ NodeCheckerForAnyD(const Face& target, const std::size_t d_number) : face(target), d_number(d_number), constrained(false)
+ {
+ }
+
+ bool constrain()
+ {
+ if(face.has_d(d_number==0 ? 1 : 0))
+ {
+ constraint_sphere=face.get_d_tangent_sphere(d_number==0 ? 1 : 0);
+ constrained=true;
+ }
+ else
+ {
+ constrained=false;
+ }
+ return constrained;
+ }
+
+ void unconstrain()
+ {
+ constrained=false;
+ }
+
+ bool operator()(const SimpleSphere& sphere) const
+ {
+ return (!constrained || sphere_intersects_sphere(constraint_sphere, sphere)) && face.sphere_may_contain_candidate_for_d(sphere, d_number);
+ }
+ };
+
+ struct LeafCheckerForAnyD
+ {
+ Face& face;
+ const std::size_t d_number;
+
+ LeafCheckerForAnyD(Face& target, const std::size_t d_number) : face(target), d_number(d_number)
+ {
+ }
+
+ std::pair<bool, bool> operator()(const std::size_t id, const SimpleSphere&)
+ {
+ const std::pair<bool, SimpleSphere> check_result=face.check_candidate_for_d(id, d_number);
+ if(check_result.first)
+ {
+ face.set_d(id, d_number, check_result.second);
+ return std::make_pair(true, true);
+ }
+ return std::make_pair(false, false);
+ }
+ };
+ };
+
+ class SearchForValidDOfFace
+ {
+ public:
+ static bool find_valid_d(const BoundingSpheresHierarchy& bsh, Face& face, const std::size_t d_number)
+ {
+ if(face.has_d(d_number))
+ {
+ NodeCheckerForValidD node_checker(face, d_number);
+ LeafCheckerForValidD leaf_checker(face, d_number);
+ while(face.has_d(d_number))
+ {
+ const std::vector<std::size_t> results=bsh.search(node_checker, leaf_checker);
+ if(results.empty())
+ {
+ return true;
+ }
+ else if(face.get_d_id(d_number)!=results.back())
+ {
+ face.unset_d(d_number);
+ }
+ }
+ }
+ return false;
+ }
+
+ private:
+ struct NodeCheckerForValidD
+ {
+ const Face& face;
+ const std::size_t d_number;
+
+ NodeCheckerForValidD(const Face& target, const std::size_t d_number) : face(target), d_number(d_number)
+ {
+ }
+
+ bool operator()(const SimpleSphere& sphere) const
+ {
+ return (face.has_d(d_number) && sphere_intersects_sphere(sphere, face.get_d_tangent_sphere(d_number)));
+ }
+ };
+
+ struct LeafCheckerForValidD
+ {
+#if USE_TR1 > 0
+typedef std::tr1::unordered_set<std::size_t> SafetyMonitor;
+#else
+typedef std::unordered_set<std::size_t> SafetyMonitor;
+#endif
+
+ Face& face;
+ const std::size_t d_number;
+ SafetyMonitor safety_monitor;
+
+ LeafCheckerForValidD(Face& target, const std::size_t d_number) : face(target), d_number(d_number)
+ {
+ }
+
+ std::pair<bool, bool> operator()(const std::size_t id, const SimpleSphere& sphere)
+ {
+ if(face.has_d(d_number) && sphere_intersects_sphere(sphere, face.get_d_tangent_sphere(d_number)))
+ {
+ const std::pair<bool, SimpleSphere> check_result=face.check_candidate_for_d(id, d_number);
+ if(check_result.first && safety_monitor.count(id)==0)
+ {
+ face.set_d(id, d_number, check_result.second);
+ safety_monitor.insert(id);
+ return std::make_pair(true, true);
+ }
+ else
+ {
+ return std::make_pair(true, false);
+ }
+ }
+ return std::make_pair(false, false);
+ }
+ };
+ };
+
+ class SearchForValidEOfFace
+ {
+ public:
+ static bool find_valid_e(const BoundingSpheresHierarchy& bsh, Face& face)
+ {
+ face.update_middle_region_approximation();
+ NodeCheckerForValidE node_checker(face);
+ LeafCheckerForValidE leaf_checker(face, bsh);
+ return !bsh.search(node_checker, leaf_checker).empty();
+ }
+
+ private:
+ struct NodeCheckerForValidE
+ {
+ const Face& face;
+
+ explicit NodeCheckerForValidE(const Face& target) : face(target)
+ {
+ }
+
+ bool operator()(const SimpleSphere& sphere) const
+ {
+ return face.sphere_may_contain_candidate_for_e(sphere);
+ }
+ };
+
+ struct LeafCheckerForValidE
+ {
+ Face& face;
+ const BoundingSpheresHierarchy& bsh;
+
+ LeafCheckerForValidE(Face& target, const BoundingSpheresHierarchy& bsh) : face(target), bsh(bsh)
+ {
+ }
+
+ std::pair<bool, bool> operator()(const std::size_t id, const SimpleSphere&)
+ {
+ const std::vector<SimpleSphere> check_result=face.check_candidate_for_e(id);
+ bool e_added=false;
+ for(std::size_t i=0;i<check_result.size();i++)
+ {
+ if(SearchForSphericalCollisions::find_any_collision(bsh, check_result[i]).empty())
+ {
+ face.add_e(id, check_result[i]);
+ e_added=true;
+ }
+ }
+ return std::make_pair(e_added, false);
+ }
+ };
+ };
+
+ static std::size_t select_starting_sphere_for_finding_first_valid_faces(const BoundingSpheresHierarchy& bsh, const std::vector<int>& admittance)
+ {
+ const std::vector<SimpleSphere>& spheres=bsh.leaves_spheres();
+ if(spheres.empty() || admittance.size()!=spheres.size())
+ {
+ return 0;
+ }
+ SimplePoint center(0.0, 0.0, 0.0);
+ int count=0;
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ if(admittance[i]>0)
+ {
+ center=center+SimplePoint(spheres[i]);
+ count++;
+ }
+ }
+ if(count==0)
+ {
+ return 0;
+ }
+ center=center*(1/static_cast<double>(count));
+ std::size_t result=0;
+ double result_distance=std::numeric_limits<double>::max();
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ if(admittance[i]>0)
+ {
+ const double i_distance=distance_from_point_to_point(center, spheres[i]);
+ if(i_distance<result_distance)
+ {
+ result=i;
+ result_distance=i_distance;
+ }
+ }
+ }
+ return result;
+ }
+
+ static std::vector<Face> find_first_valid_faces(
+ const BoundingSpheresHierarchy& bsh,
+ const std::vector<int>& admittance,
+ const std::size_t starting_sphere_id,
+ std::size_t& iterations_count,
+ const bool fix_starting_sphere_id,
+ const bool allow_quadruples_with_two_tangent_spheres,
+ const std::size_t max_size_of_traversal=std::numeric_limits<std::size_t>::max())
+ {
+ const std::vector<SimpleSphere>& spheres=bsh.leaves_spheres();
+ std::vector<Face> result;
+ if(spheres.size()>=4 && starting_sphere_id<spheres.size() && admittance.size()==spheres.size())
+ {
+ const std::vector<std::size_t> traversal=BoundingSpheresHierarchy::sort_objects_by_distance_to_one_of_them(spheres, starting_sphere_id, minimal_distance_from_sphere_to_sphere<SimpleSphere, SimpleSphere>);
+ for(std::size_t d=3;d<std::min(traversal.size(), max_size_of_traversal);d++)
+ {
+ for(std::size_t a=0;a<(fix_starting_sphere_id ? 1 : d);a++)
+ {
+ for(std::size_t b=a+1;b<d;b++)
+ {
+ for(std::size_t c=b+1;c<d;c++)
+ {
+ iterations_count++;
+ if(admittance[traversal[a]]>0 || admittance[traversal[b]]>0 || admittance[traversal[c]]>0)
+ {
+ const Triple triple(traversal[a], traversal[b], traversal[c]);
+ const Quadruple quadruple(triple, traversal[d]);
+ const std::vector<SimpleSphere> tangents=TangentSphereOfFourSpheres::calculate(spheres[quadruple.get(0)], spheres[quadruple.get(1)], spheres[quadruple.get(2)], spheres[quadruple.get(3)]);
+ if(
+ (tangents.size()==1 && SearchForSphericalCollisions::find_any_collision(bsh, tangents.front()).empty())
+ || (allow_quadruples_with_two_tangent_spheres && tangents.size()==2 && (SearchForSphericalCollisions::find_any_collision(bsh, tangents.front()).empty() || SearchForSphericalCollisions::find_any_collision(bsh, tangents.back()).empty()))
+ )
+ {
+ result.push_back(Face(bsh.leaves_spheres(), triple, bsh.min_input_radius()));
+ return result;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static std::pair<bool, bool> augment_quadruples_map(const Quadruple& quadruple, const SimpleSphere& quadruple_tangent_sphere, QuadruplesMap& quadruples_map)
+ {
+ bool quadruple_added=false;
+ bool quadruple_tangent_sphere_added=false;
+ QuadruplesMap::iterator qm_it=quadruples_map.find(quadruple);
+ if(qm_it==quadruples_map.end())
+ {
+ quadruples_map[quadruple].push_back(quadruple_tangent_sphere);
+ quadruple_added=true;
+ quadruple_tangent_sphere_added=true;
+ }
+ else
+ {
+ std::vector<SimpleSphere>& quadruple_tangent_spheres_list=qm_it->second;
+ if(quadruple_tangent_spheres_list.size()==1 && !spheres_equal(quadruple_tangent_spheres_list.front(), quadruple_tangent_sphere, tangent_spheres_equality_epsilon()))
+ {
+ quadruple_tangent_spheres_list.push_back(quadruple_tangent_sphere);
+ quadruple_tangent_sphere_added=true;
+ }
+ }
+ return std::make_pair(quadruple_added, quadruple_tangent_sphere_added);
+ }
+
+ static QuadruplesSearchLog find_valid_quadruples(const BoundingSpheresHierarchy& bsh, const std::vector<int>& admittance, QuadruplesMap& quadruples_map)
+ {
+#if USE_TR1 > 0
+typedef std::tr1::unordered_map<Triple, std::size_t, Triple::HashFunctor> TriplesMap;
+typedef std::tr1::unordered_set<Triple, Triple::HashFunctor> TriplesSet;
+#else
+typedef std::unordered_map<Triple, std::size_t, Triple::HashFunctor> TriplesMap;
+typedef std::unordered_set<Triple, Triple::HashFunctor> TriplesSet;
+#endif
+
+ QuadruplesSearchLog log=QuadruplesSearchLog();
+
+ std::vector<Face> stack=find_first_valid_faces(bsh, admittance, select_starting_sphere_for_finding_first_valid_faces(bsh, admittance), log.performed_iterations_for_finding_first_faces, false, true);
+ TriplesSet processed_triples_set;
+ std::vector<int> spheres_usage_mapping(bsh.leaves_spheres().size(), 0);
+ std::set<std::size_t> ignorable_spheres_ids;
+
+ do
+ {
+ TriplesMap stack_map;
+ for(std::size_t i=0;i<stack.size();i++)
+ {
+ stack_map[stack[i].abc_ids()]=i;
+ }
+ while(!stack.empty())
+ {
+ Face face=stack.back();
+ stack.pop_back();
+ stack_map.erase(face.abc_ids());
+ processed_triples_set.insert(face.abc_ids());
+ log.processed_faces++;
+ if(!face.can_have_d())
+ {
+ log.encountered_difficult_faces++;
+ }
+ const bool found_d0=face.can_have_d() && !face.has_d(0) && SearchForAnyDOfFace::find_any_d(bsh, face, 0) && SearchForValidDOfFace::find_valid_d(bsh, face, 0);
+ const bool found_d1=face.can_have_d() && !face.has_d(1) && SearchForAnyDOfFace::find_any_d(bsh, face, 1) && SearchForValidDOfFace::find_valid_d(bsh, face, 1);
+ const bool found_e=face.can_have_e() && SearchForValidEOfFace::find_valid_e(bsh, face);
+ if(found_d0 || found_d1 || found_e)
+ {
+ {
+ const std::vector< std::pair<Quadruple, SimpleSphere> > additional_quadruples=face.produce_quadruples(found_d0, found_d1, found_e);
+ for(std::size_t i=0;i<additional_quadruples.size();i++)
+ {
+ const std::pair<bool, bool> augmention_status=augment_quadruples_map(additional_quadruples[i].first, additional_quadruples[i].second, quadruples_map);
+ log.added_quadruples+=(augmention_status.first ? 1 : 0);
+ log.added_tangent_spheres+=(augmention_status.second ? 1 : 0);
+ }
+ }
+ {
+ const std::vector< std::pair<Triple, std::pair<std::size_t, SimpleSphere> > > produced_prefaces=face.produce_prefaces(found_d0, found_d1, found_e);
+ for(std::size_t i=0;i<produced_prefaces.size();i++)
+ {
+ const std::pair<Triple, std::pair<std::size_t, SimpleSphere> >& produced_preface=produced_prefaces[i];
+ if(admittance[produced_preface.first.get(0)]>0 || admittance[produced_preface.first.get(1)]>0 || admittance[produced_preface.first.get(2)]>0)
+ {
+ if(processed_triples_set.count(produced_preface.first)==0)
+ {
+ TriplesMap::const_iterator sm_it=stack_map.find(produced_preface.first);
+ if(sm_it==stack_map.end())
+ {
+ stack_map[produced_preface.first]=stack.size();
+ stack.push_back(Face(bsh.leaves_spheres(), produced_preface.first, bsh.min_input_radius()));
+ stack.back().set_d_with_d_number_selection(produced_preface.second.first, produced_preface.second.second);
+ log.produced_faces++;
+ }
+ else
+ {
+ stack.at(sm_it->second).set_d_with_d_number_selection(produced_preface.second.first, produced_preface.second.second);
+ log.updated_faces++;
+ }
+ }
+ else
+ {
+ log.encountered_triples_repetitions++;
+ }
+ }
+ }
+ }
+ }
+ if(face.has_d(0) || face.has_d(1) || face.has_e())
+ {
+ for(int j=0;j<3;j++)
+ {
+ if(face.abc_ids().get(j)<spheres_usage_mapping.size())
+ {
+ spheres_usage_mapping[face.abc_ids().get(j)]=1;
+ }
+ }
+ }
+ }
+ for(std::size_t i=0;i<spheres_usage_mapping.size() && stack.empty();i++)
+ {
+ if(spheres_usage_mapping[i]==0 && admittance[i]>0 && ignorable_spheres_ids.count(i)==0)
+ {
+ stack=find_first_valid_faces(bsh, admittance, i, log.performed_iterations_for_finding_first_faces, true, true, 25);
+ ignorable_spheres_ids.insert(i);
+ }
+ }
+ }
+ while(!stack.empty());
+
+ return log;
+ }
+
+ static SurplusQuadruplesSearchLog find_surplus_valid_quadruples(const BoundingSpheresHierarchy& bsh, QuadruplesMap& quadruples_map)
+ {
+ SurplusQuadruplesSearchLog log=SurplusQuadruplesSearchLog();
+ std::vector< std::pair<Quadruple, SimpleSphere> > surplus_candidates;
+ for(QuadruplesMap::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ const std::vector<SimpleSphere>& tangent_spheres=it->second;
+ for(std::size_t i=0;i<tangent_spheres.size();i++)
+ {
+ const SimpleSphere& tangent_sphere=tangent_spheres[i];
+ const SimpleSphere expanded_tangent_sphere(tangent_sphere, tangent_sphere.r+tangent_spheres_equality_epsilon());
+ const std::vector<std::size_t> expanded_collisions=SearchForSphericalCollisions::find_all_collisions(bsh, expanded_tangent_sphere);
+ std::vector<std::size_t> refined_collisions;
+ for(std::size_t j=0;j<expanded_collisions.size();j++)
+ {
+ if(sphere_touches_sphere(tangent_sphere, bsh.leaves_spheres().at(expanded_collisions[j])))
+ {
+ refined_collisions.push_back(expanded_collisions[j]);
+ }
+ }
+ if(refined_collisions.size()>4)
+ {
+ for(std::size_t a=0;a<refined_collisions.size();a++)
+ {
+ for(std::size_t b=a+1;b<refined_collisions.size();b++)
+ {
+ for(std::size_t c=b+1;c<refined_collisions.size();c++)
+ {
+ for(std::size_t d=c+1;d<refined_collisions.size();d++)
+ {
+ surplus_candidates.push_back(std::make_pair(Quadruple(refined_collisions[a], refined_collisions[b], refined_collisions[c], refined_collisions[d]), tangent_sphere));
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ for(std::size_t i=0;i<surplus_candidates.size();i++)
+ {
+ const std::pair<bool, bool> augmention_status=augment_quadruples_map(surplus_candidates[i].first, surplus_candidates[i].second, quadruples_map);
+ log.surplus_quadruples+=(augmention_status.first ? 1 : 0);
+ log.surplus_tangent_spheres+=(augmention_status.second ? 1 : 0);
+ }
+ return log;
+ }
+
+ static QuadruplesMap renumber_quadruples_map(const QuadruplesMap& quadruples_map, const std::vector<std::size_t>& mapping)
+ {
+ QuadruplesMap renumbered_quadruples_map;
+ for(QuadruplesMap::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ const Quadruple& q=it->first;
+ if(q.get(3)<mapping.size())
+ {
+ const Quadruple mq(mapping[q.get(0)], mapping[q.get(1)], mapping[q.get(2)], mapping[q.get(3)]);
+ if(mq.get(3)!=npos)
+ {
+ renumbered_quadruples_map[mq]=it->second;
+ }
+ }
+ }
+ return renumbered_quadruples_map;
+ }
+
+ static std::set<std::size_t> collect_ignored_spheres_ids(const std::vector<int>& admittance, const QuadruplesMap& quadruples_map)
+ {
+ std::set<std::size_t> ignored_spheres_ids;
+ std::vector<int> spheres_inclusion_map(admittance.size(), 0);
+ for(QuadruplesMap::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ const Quadruple& q=it->first;
+ for(int i=0;i<4;i++)
+ {
+ if(q.get(i)<spheres_inclusion_map.size())
+ {
+ spheres_inclusion_map[q.get(i)]=1;
+ }
+ }
+ }
+ for(std::size_t i=0;i<spheres_inclusion_map.size();i++)
+ {
+ if(spheres_inclusion_map[i]==0 && admittance[i]>0)
+ {
+ ignored_spheres_ids.insert(i);
+ }
+ }
+ return ignored_spheres_ids;
+ }
+
+ inline static double tangent_spheres_equality_epsilon()
+ {
+ return std::max(default_comparison_epsilon(), 0.001);
+ }
+
+ static QuadruplesMap collect_invalid_tangent_spheres_of_valid_quadruples(const std::vector<SimpleSphere>& spheres, const QuadruplesMap& quadruples_map)
+ {
+ QuadruplesMap result;
+ for(QuadruplesMap::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ const Quadruple& q=it->first;
+ const std::vector<SimpleSphere>& valid_tangent_spheres=it->second;
+ if(valid_tangent_spheres.size()==1 && q.get(0)<spheres.size() && q.get(1)<spheres.size() && q.get(2)<spheres.size() && q.get(3)<spheres.size())
+ {
+ const std::vector<SimpleSphere> all_tangent_spheres=TangentSphereOfFourSpheres::calculate(spheres[q.get(0)], spheres[q.get(1)], spheres[q.get(2)], spheres[q.get(3)]);
+ if(all_tangent_spheres.size()==2)
+ {
+ if(!spheres_equal(valid_tangent_spheres.front(), all_tangent_spheres[0], tangent_spheres_equality_epsilon()))
+ {
+ result[q].push_back(all_tangent_spheres[0]);
+ }
+ else if(!spheres_equal(valid_tangent_spheres.front(), all_tangent_spheres[1], tangent_spheres_equality_epsilon()))
+ {
+ result[q].push_back(all_tangent_spheres[1]);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static void update_vertices_graph(
+ const std::vector<SimpleSphere>& spheres,
+ const VerticesVector& all_vertices_vector,
+ const Triple& triple,
+ const std::size_t vi,
+ const std::size_t vj,
+ const bool lonely_pair,
+ VerticesGraph& vertices_graph)
+ {
+ if(vi<vertices_graph.size() && vj<vertices_graph.size())
+ {
+ const Quadruple& qi=all_vertices_vector[vi].first;
+ const Quadruple& qj=all_vertices_vector[vj].first;
+ if(qi==qj)
+ {
+ const int number_of_subtriple=qi.number_of_subtuple(triple);
+ if(number_of_subtriple>=0)
+ {
+ const std::size_t common_sphere_id=qi.get(number_of_subtriple);
+ if(common_sphere_id<spheres.size())
+ {
+ const std::vector< std::pair<SimplePoint, SimplePoint> > tangent_planes=TangentPlaneOfThreeSpheres::calculate(spheres[triple.get(0)], spheres[triple.get(1)], spheres[triple.get(2)]);
+ if(tangent_planes.size()!=2 ? lonely_pair : (halfspace_of_sphere(tangent_planes[0].first, tangent_planes[0].second, spheres[common_sphere_id])>=0 && halfspace_of_sphere(tangent_planes[1].first, tangent_planes[1].second, spheres[common_sphere_id])>=0))
+ {
+ vertices_graph[vi][number_of_subtriple]=vj;
+ vertices_graph[vj][number_of_subtriple]=vi;
+ }
+ }
+ }
+ }
+ else
+ {
+ const int number_of_subtriple_for_vi=qi.number_of_subtuple(triple);
+ const int number_of_subtriple_for_vj=qj.number_of_subtuple(triple);
+ if(number_of_subtriple_for_vi>=0 && number_of_subtriple_for_vj>=0)
+ {
+ vertices_graph[vi][number_of_subtriple_for_vi]=vj;
+ vertices_graph[vj][number_of_subtriple_for_vj]=vi;
+ }
+ }
+ }
+ }
+
+
+ static void update_vertices_graph(
+ const std::vector<SimpleSphere>& spheres,
+ const VerticesVector& all_vertices_vector,
+ const Triple& triple,
+ const std::vector<std::size_t>& triple_vertices_ids,
+ VerticesGraph& vertices_graph)
+ {
+ const std::vector<std::size_t>& v=triple_vertices_ids;
+ if(v.size()>1)
+ {
+ if(v.size()==2)
+ {
+ update_vertices_graph(spheres, all_vertices_vector, triple, v[0], v[1], true, vertices_graph);
+ }
+ else
+ {
+ const double r0=spheres[triple.get(0)].r;
+ const double r1=spheres[triple.get(1)].r;
+ const double r2=spheres[triple.get(2)].r;
+ const SimpleSphere& o=spheres[triple.get((r0<=r1 && r0<=r2) ? 0 : ((r1<=r0 && r1<=r2) ? 1 : 2))];
+ for(std::size_t i=0;i<v.size();i++)
+ {
+ const std::size_t vi=v[i];
+ if(vi<vertices_graph.size())
+ {
+ std::vector< std::pair<double, std::size_t> > v_candidates;
+ v_candidates.reserve(v.size()-1);
+ for(std::size_t j=0;j<v.size();j++)
+ {
+ const std::size_t vj=v[j];
+ if(vj!=vi)
+ {
+ const double angle=min_angle(o, all_vertices_vector[vi].second, all_vertices_vector[vj].second);
+ v_candidates.push_back(std::make_pair(angle, vj));
+ }
+ }
+ if(!v_candidates.empty())
+ {
+ std::sort(v_candidates.begin(), v_candidates.end());
+ std::vector<std::size_t> v_sel(1, v_candidates[0].second);
+ for(std::size_t j=1;j<v_candidates.size() && v_sel.size()==1;j++)
+ {
+ const std::size_t vj=v_candidates[j].second;
+ const double angle_with_vi=min_angle(o, all_vertices_vector[vi].second, all_vertices_vector[vj].second);
+ const double angle_with_v_sel0=min_angle(o, all_vertices_vector[v_sel[0]].second, all_vertices_vector[vj].second);
+ if(angle_with_vi<angle_with_v_sel0)
+ {
+ v_sel.push_back(vj);
+ }
+ }
+ for(std::size_t j=0;j<v_sel.size();j++)
+ {
+ update_vertices_graph(spheres, all_vertices_vector, triple, vi, v_sel[j], false, vertices_graph);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+};
+
+}
+
+#endif /* APOLLOTA_TRIANGULATION_H_ */
diff --git a/src/apollota/triangulation_output.h b/src/apollota/triangulation_output.h
new file mode 100644
index 0000000..eb4d4d1
--- /dev/null
+++ b/src/apollota/triangulation_output.h
@@ -0,0 +1,77 @@
+#ifndef APOLLOTA_TRIANGULATION_OUTPUT_H_
+#define APOLLOTA_TRIANGULATION_OUTPUT_H_
+
+#include <iostream>
+
+#include "triangulation.h"
+
+namespace apollota
+{
+
+class TriangulationOutput
+{
+public:
+ static void print_status(const Triangulation::Result& tr, std::ostream& output)
+ {
+ output << "quadruples " << tr.quadruples_map.size() << "\n";
+ output << "tangent_spheres " << Triangulation::count_tangent_spheres_in_quadruples_map(tr.quadruples_map) << "\n";
+ output << "processed_triples " << tr.quadruples_search_log.processed_faces << "\n";
+ output << "loose_triples " << tr.quadruples_search_log.encountered_difficult_faces << "\n";
+ output << "first_iterations " << tr.quadruples_search_log.performed_iterations_for_finding_first_faces << "\n";
+ output << "surplus_tangent_spheres " << tr.surplus_quadruples_search_log.surplus_tangent_spheres << "\n";
+ output << "excluded_hidden_balls " << tr.excluded_hidden_spheres_ids.size() << "\n";
+ output << "ignored_balls " << tr.ignored_spheres_ids.size();
+ for(std::set<std::size_t>::const_iterator it=tr.ignored_spheres_ids.begin();it!=tr.ignored_spheres_ids.end();++it)
+ {
+ output << (it==tr.ignored_spheres_ids.begin() ? ":" : ",") << (*it);
+ }
+ output << "\n";
+ }
+
+ static void print_vertices_vector(const Triangulation::VerticesVector& vertices_vector, std::ostream& output)
+ {
+ output.precision(std::numeric_limits<double>::digits10);
+ output << std::fixed;
+ for(Triangulation::VerticesVector::const_iterator it=vertices_vector.begin();it!=vertices_vector.end();++it)
+ {
+ const Quadruple& quadruple=it->first;
+ const SimpleSphere& tangent_sphere=it->second;
+ output << quadruple.get(0) << " " << quadruple.get(1) << " " << quadruple.get(2) << " " << quadruple.get(3) << " ";
+ output << tangent_sphere.x << " " << tangent_sphere.y << " " << tangent_sphere.z << " " << tangent_sphere.r << "\n";
+ }
+ }
+
+ static void print_vertices_vector_with_vertices_graph(const Triangulation::VerticesVector& vertices_vector, const Triangulation::VerticesGraph& vertices_graph, std::ostream& output)
+ {
+ if(vertices_vector.size()==vertices_graph.size())
+ {
+ output.precision(std::numeric_limits<double>::digits10);
+ output << std::fixed;
+ for(std::size_t i=0;i<vertices_vector.size();i++)
+ {
+ const Quadruple& quadruple=vertices_vector[i].first;
+ const SimpleSphere& tangent_sphere=vertices_vector[i].second;
+ const std::vector<std::size_t> links=vertices_graph[i];
+ output << quadruple.get(0) << " " << quadruple.get(1) << " " << quadruple.get(2) << " " << quadruple.get(3) << " ";
+ output << tangent_sphere.x << " " << tangent_sphere.y << " " << tangent_sphere.z << " " << tangent_sphere.r << " ";
+ for(std::size_t j=0;j<links.size();j++)
+ {
+ if(links[j]==npos)
+ {
+ output << "-1";
+ }
+ else
+ {
+ output << links[j];
+ }
+ output << (j+1<links.size() ? " " : "\n");
+ }
+ }
+ }
+ }
+
+};
+
+}
+
+#endif /* APOLLOTA_TRIANGULATION_OUTPUT_H_ */
diff --git a/src/apollota/triangulation_queries.h b/src/apollota/triangulation_queries.h
new file mode 100644
index 0000000..a0523ea
--- /dev/null
+++ b/src/apollota/triangulation_queries.h
@@ -0,0 +1,132 @@
+#ifndef APOLLOTA_TRIANGULATION_QUERIES_H_
+#define APOLLOTA_TRIANGULATION_QUERIES_H_
+
+#include "../compatability_macros.h"
+
+#include "triangulation.h"
+
+namespace apollota
+{
+
+class TriangulationQueries
+{
+public:
+
+#if USE_TR1 > 0
+typedef std::tr1::unordered_map<std::size_t, std::set<std::size_t> > IDsMap;
+typedef std::tr1::unordered_map<Pair, std::set<std::size_t>, Pair::HashFunctor> PairsMap;
+typedef std::tr1::unordered_map<Triple, std::set<std::size_t>, Triple::HashFunctor> TriplesMap;
+#else
+typedef std::unordered_map<std::size_t, std::set<std::size_t> > IDsMap;
+typedef std::unordered_map<Pair, std::set<std::size_t>, Pair::HashFunctor> PairsMap;
+typedef std::unordered_map<Triple, std::set<std::size_t>, Triple::HashFunctor> TriplesMap;
+#endif
+
+ typedef std::vector< std::vector<std::size_t> > IDsGraph;
+
+ template<typename QuadruplesMapType>
+ static IDsMap collect_neighbors_map_from_quadruples_map(const QuadruplesMapType& quadruples_map)
+ {
+ IDsMap neighbors_map;
+ for(typename QuadruplesMapType::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ const Quadruple& quadruple=it->first;
+ for(int a=0;a<4;a++)
+ {
+ for(int b=a+1;b<4;b++)
+ {
+ neighbors_map[quadruple.get(a)].insert(quadruple.get(b));
+ neighbors_map[quadruple.get(b)].insert(quadruple.get(a));
+ }
+ }
+ }
+ return neighbors_map;
+ }
+
+ static IDsGraph collect_ids_graph_from_ids_map(const IDsMap& neighbors_map, const std::size_t number_of_vertices)
+ {
+ IDsGraph neighbors_graph(number_of_vertices);
+ for(IDsMap::const_iterator it=neighbors_map.begin();it!=neighbors_map.end();++it)
+ {
+ if((it->first)<neighbors_graph.size())
+ {
+ neighbors_graph[it->first].insert(neighbors_graph[it->first].end(), it->second.begin(), it->second.end());
+ }
+ }
+ return neighbors_graph;
+ }
+
+ static IDsMap collect_vertices_map_from_vertices_vector(const Triangulation::VerticesVector& vertices_vector)
+ {
+ IDsMap ids_vertices_map;
+ for(std::size_t i=0;i<vertices_vector.size();i++)
+ {
+ const Quadruple& quadruple=vertices_vector[i].first;
+ for(int a=0;a<4;a++)
+ {
+ ids_vertices_map[quadruple.get(a)].insert(i);
+ }
+ }
+ return ids_vertices_map;
+ }
+
+ static PairsMap collect_pairs_vertices_map_from_vertices_vector(const Triangulation::VerticesVector& vertices_vector)
+ {
+ PairsMap pairs_vertices_map;
+ for(std::size_t i=0;i<vertices_vector.size();i++)
+ {
+ const Quadruple& quadruple=vertices_vector[i].first;
+ for(int a=0;a<4;a++)
+ {
+ for(int b=a+1;b<4;b++)
+ {
+ pairs_vertices_map[Pair(quadruple.get(a), quadruple.get(b))].insert(i);
+ }
+ }
+ }
+ return pairs_vertices_map;
+ }
+
+ static TriplesMap collect_triples_vertices_map_from_vertices_vector(const Triangulation::VerticesVector& vertices_vector)
+ {
+ TriplesMap triples_vertices_map;
+ for(std::size_t i=0;i<vertices_vector.size();i++)
+ {
+ const Quadruple& quadruple=vertices_vector[i].first;
+ for(int a=0;a<4;a++)
+ {
+ triples_vertices_map[quadruple.exclude(a)].insert(i);
+ }
+ }
+ return triples_vertices_map;
+ }
+
+ template<typename QuadruplesMapType>
+ static PairsMap collect_pairs_neighbors_map_from_quadruples_map(const QuadruplesMapType& quadruples_map)
+ {
+ PairsMap pairs_neighbors_map;
+ for(typename QuadruplesMapType::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ const Quadruple& quadruple=it->first;
+ for(int a=0;a<4;a++)
+ {
+ for(int b=a+1;b<4;b++)
+ {
+ const Pair p(quadruple.get(a), quadruple.get(b));
+ for(int c=0;c<4;c++)
+ {
+ if(c!=a && c!=b)
+ {
+ pairs_neighbors_map[p].insert(quadruple.get(c));
+ }
+ }
+ }
+ }
+ }
+ return pairs_neighbors_map;
+ }
+};
+
+}
+
+#endif /* APOLLOTA_TRIANGULATION_QUERIES_H_ */
diff --git a/src/apollota/tuple.h b/src/apollota/tuple.h
new file mode 100644
index 0000000..d2bee42
--- /dev/null
+++ b/src/apollota/tuple.h
@@ -0,0 +1,202 @@
+#ifndef APOLLOTA_TUPLE_H_
+#define APOLLOTA_TUPLE_H_
+
+#include <vector>
+#include <algorithm>
+
+namespace apollota
+{
+
+template<unsigned int N>
+class Tuple
+{
+public:
+ struct HashFunctor
+ {
+ std::size_t operator()(const Tuple& t) const
+ {
+ return t.hash_value();
+ }
+ };
+
+ Tuple()
+ {
+ for(unsigned int i=0;i<N;i++)
+ {
+ v_[i]=0;
+ }
+ }
+
+ explicit Tuple(const std::vector<std::size_t>& values)
+ {
+ for(unsigned int i=0;i<N && i<values.size();i++)
+ {
+ v_[i]=values[i];
+ }
+ sort();
+ }
+
+ Tuple(const Tuple<N-1>& shorter, const std::size_t tail)
+ {
+ for(unsigned int i=0;i<(N-1);i++)
+ {
+ v_[i]=shorter.get(i);
+ }
+ v_[N-1]=tail;
+ sort();
+ }
+
+ Tuple(const std::size_t a, const std::size_t b)
+ {
+ if(0<N) v_[0]=a;
+ if(1<N) v_[1]=b;
+ sort();
+ }
+
+ Tuple(const std::size_t a, const std::size_t b, const std::size_t c)
+ {
+ if(0<N) v_[0]=a;
+ if(1<N) v_[1]=b;
+ if(2<N) v_[2]=c;
+ sort();
+ }
+
+ Tuple(const std::size_t a, const std::size_t b, const std::size_t c, const std::size_t d)
+ {
+ if(0<N) v_[0]=a;
+ if(1<N) v_[1]=b;
+ if(2<N) v_[2]=c;
+ if(3<N) v_[3]=d;
+ sort();
+ }
+
+ unsigned int size() const
+ {
+ return N;
+ }
+
+ std::size_t get(unsigned int i) const
+ {
+ return v_[i];
+ }
+
+ bool contains(std::size_t x) const
+ {
+ for(unsigned int i=0;i<N;i++)
+ {
+ if(get(i)==x)
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ Tuple<N-1> exclude(unsigned int i) const
+ {
+ std::vector<std::size_t> values;
+ values.reserve(N-1);
+ for(unsigned int j=0;j<N;j++)
+ {
+ if(j!=i)
+ {
+ values.push_back(get(j));
+ }
+ }
+ return Tuple<N-1>(values);
+ }
+
+ int number_of_subtuple(const Tuple<N-1>& subtuple) const
+ {
+ for(unsigned int i=0;i<N;i++)
+ {
+ if((!subtuple.contains(get(i))) && (subtuple==exclude(i)))
+ {
+ return static_cast<int>(i);
+ }
+ }
+ return -1;
+ }
+
+ bool has_repetetions() const
+ {
+ for(unsigned int i=0;i+1<N;i++)
+ {
+ if(v_[i]==v_[i+1])
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ std::pair<std::size_t, std::size_t> get_min_max() const
+ {
+ std::pair<std::size_t, std::size_t> result(v_[0], v_[0]);
+ for(unsigned int i=1;i<N;i++)
+ {
+ result.first=std::min(result.first, v_[i]);
+ result.second=std::max(result.second, v_[i]);
+ }
+ return result;
+ }
+
+ std::size_t hash_value() const
+ {
+ std::size_t h=0;
+ for(unsigned int i=0;i<N;i++)
+ {
+ h += get(i);
+ h += (h << 10);
+ h ^= (h >> 6);
+ }
+ h += (h << 3);
+ h ^= (h >> 11);
+ h += (h << 15);
+ return h;
+ }
+
+ bool operator==(const Tuple& t) const
+ {
+ for(unsigned int i=0;i<N;i++)
+ {
+ if(get(i)!=t.get(i))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ bool operator<(const Tuple& t) const
+ {
+ for(unsigned int i=0;i<N;i++)
+ {
+ if(get(i)<t.get(i))
+ {
+ return true;
+ }
+ else if(get(i)>t.get(i))
+ {
+ return false;
+ }
+ }
+ return false;
+ }
+
+private:
+ void sort()
+ {
+ std::sort(v_, v_+N);
+ }
+
+ std::size_t v_[N];
+};
+
+typedef Tuple<2> Pair;
+typedef Tuple<3> Triple;
+typedef Tuple<4> Quadruple;
+
+}
+
+#endif /* APOLLOTA_TUPLE_H_ */
diff --git a/src/auxiliaries/atom_radius_assigner.h b/src/auxiliaries/atom_radius_assigner.h
new file mode 100644
index 0000000..f374b56
--- /dev/null
+++ b/src/auxiliaries/atom_radius_assigner.h
@@ -0,0 +1,93 @@
+#ifndef AUXILIARIES_ATOM_RADIUS_ASSIGNER_H_
+#define AUXILIARIES_ATOM_RADIUS_ASSIGNER_H_
+
+#include <string>
+#include <map>
+#include <vector>
+#include <iostream>
+
+namespace auxiliaries
+{
+
+class AtomRadiusAssigner
+{
+public:
+ explicit AtomRadiusAssigner(const double default_radius) : default_radius(default_radius)
+ {
+ }
+
+ bool add_radius_by_descriptor(const std::string& resName_pattern, const std::string& name_pattern, const double radius)
+ {
+ if(!resName_pattern.empty() && !name_pattern.empty())
+ {
+ radii_by_descriptors[Descriptor(resName_pattern, name_pattern)]=radius;
+ return true;
+ }
+ return false;
+ }
+
+ double get_atom_radius(const std::string& resName, const std::string& name) const
+ {
+ std::vector<std::string> ordered_resName_patterns;
+ ordered_resName_patterns.push_back(resName);
+ ordered_resName_patterns.push_back("*");
+
+ std::vector<std::string> ordered_name_patterns;
+ ordered_name_patterns.push_back(name);
+ for(std::size_t i=0;i<name.size();i++)
+ {
+ ordered_name_patterns.push_back(name.substr(0, name.size()-i)+"*");
+ }
+ ordered_name_patterns.push_back("*");
+
+ for(std::size_t i=0;i<ordered_resName_patterns.size();i++)
+ {
+ for(std::size_t j=0;j<ordered_name_patterns.size();j++)
+ {
+ std::map<Descriptor, double>::const_iterator it=radii_by_descriptors.find(Descriptor(ordered_resName_patterns[i], ordered_name_patterns[j]));
+ if(it!=radii_by_descriptors.end())
+ {
+ return it->second;
+ }
+ }
+ }
+ return default_radius;
+ }
+
+ static bool add_descriptor_and_radius_from_stream_to_atom_radius_assigner(std::istream& input, AtomRadiusAssigner& atom_radius_assigner)
+ {
+ std::string resName;
+ std::string name;
+ double radius=0.0;
+ input >> resName >> name >> radius;
+ if(!input.fail())
+ {
+ atom_radius_assigner.add_radius_by_descriptor(resName, name, radius);
+ return true;
+ }
+ return false;
+ }
+
+private:
+ struct Descriptor
+ {
+ std::string resName_pattern;
+ std::string name_pattern;
+
+ Descriptor(const std::string& resName_pattern, const std::string& name_pattern) : resName_pattern(resName_pattern), name_pattern(name_pattern)
+ {
+ }
+
+ bool operator<(const Descriptor& d) const
+ {
+ return ( resName_pattern<d.resName_pattern || (resName_pattern==d.resName_pattern && (name_pattern<d.name_pattern)) );
+ }
+ };
+
+ double default_radius;
+ std::map<Descriptor, double> radii_by_descriptors;
+};
+
+}
+
+#endif /* AUXILIARIES_ATOM_RADIUS_ASSIGNER_H_ */
diff --git a/src/auxiliaries/atoms_io.h b/src/auxiliaries/atoms_io.h
new file mode 100644
index 0000000..c532da0
--- /dev/null
+++ b/src/auxiliaries/atoms_io.h
@@ -0,0 +1,629 @@
+#ifndef AUXILIARIES_ATOMS_IO_H_
+#define AUXILIARIES_ATOMS_IO_H_
+
+#include <iostream>
+#include <string>
+#include <sstream>
+#include <stdexcept>
+#include <vector>
+#include <map>
+#include <iomanip>
+
+namespace auxiliaries
+{
+
+class AtomsIO
+{
+public:
+ struct AtomRecord
+ {
+ std::string record_name;
+ int serial;
+ std::string name;
+ std::string altLoc;
+ std::string resName;
+ std::string chainID;
+ int resSeq;
+ std::string iCode;
+ double x;
+ double y;
+ double z;
+ double occupancy;
+ double tempFactor;
+ std::string element;
+
+ bool serial_valid;
+ bool resSeq_valid;
+ bool x_valid;
+ bool y_valid;
+ bool z_valid;
+ bool occupancy_valid;
+ bool tempFactor_valid;
+ };
+
+ class PDBReader
+ {
+ public:
+ struct Data
+ {
+ std::vector<AtomRecord> atom_records;
+ std::vector<std::string> all_lines;
+ std::vector<std::size_t> map_of_atom_records_to_all_lines;
+
+ bool valid() const
+ {
+ if(atom_records.empty() || all_lines.size()<atom_records.size() || map_of_atom_records_to_all_lines.size()!=atom_records.size())
+ {
+ return false;
+ }
+ for(std::size_t i=0;i<map_of_atom_records_to_all_lines.size();i++)
+ {
+ if(map_of_atom_records_to_all_lines[i]>=all_lines.size())
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+ };
+
+ static Data read_data_from_file_stream(
+ std::istream& file_stream,
+ const bool include_heteroatoms,
+ const bool include_hydrogens,
+ const bool handle_multiple_models,
+ const bool store_lines)
+ {
+ Data data;
+ int model_num=1;
+ bool end_reached=false;
+ while(file_stream.good() && (!end_reached || store_lines))
+ {
+ std::string line;
+ std::getline(file_stream, line);
+ if(store_lines)
+ {
+ data.all_lines.push_back(line);
+ }
+ if(!end_reached)
+ {
+ const std::string record_name=substring_of_columned_line(line, 1, 6);
+ if(record_name=="ATOM" || record_name=="HETATM")
+ {
+ AtomRecord record=read_atom_record_from_line(line);
+ if(check_atom_record_acceptability(record, include_heteroatoms, include_hydrogens))
+ {
+ if(check_atom_record_validity(record))
+ {
+ if(handle_multiple_models && model_num>1)
+ {
+ std::ostringstream chainID_output;
+ chainID_output << record.chainID << model_num;
+ record.chainID=chainID_output.str();
+ }
+ data.atom_records.push_back(record);
+ if(store_lines)
+ {
+ data.map_of_atom_records_to_all_lines.push_back(!data.all_lines.empty() ? (data.all_lines.size()-1) : 0);
+ }
+ }
+ else
+ {
+ std::cerr << "Invalid atom record in line: " << line << "\n";
+ }
+ }
+ }
+ else if(record_name=="ENDMDL")
+ {
+ model_num++;
+ if(!handle_multiple_models)
+ {
+ end_reached=true;
+ }
+ }
+ else if(record_name=="END")
+ {
+ end_reached=true;
+ }
+ }
+ }
+ return data;
+ }
+
+ private:
+ static AtomRecord read_atom_record_from_line(const std::string& pdb_file_line)
+ {
+ AtomRecord record=AtomRecord();
+ record.record_name=substring_of_columned_line(pdb_file_line, 1, 6);
+ record.serial=convert_string<int>(substring_of_columned_line(pdb_file_line, 7, 11), record.serial_valid);
+ record.name=substring_of_columned_line(pdb_file_line, 13, 16);
+ record.altLoc=fix_undefined_string(substring_of_columned_line(pdb_file_line, 17, 17));
+ record.resName=fix_undefined_string(substring_of_columned_line(pdb_file_line, 18, 20));
+ record.chainID=fix_undefined_string(substring_of_columned_line(pdb_file_line, 22, 22));
+ record.resSeq=convert_string<int>(substring_of_columned_line(pdb_file_line, 23, 26), record.resSeq_valid);
+ record.iCode=fix_undefined_string(substring_of_columned_line(pdb_file_line, 27, 27));
+ record.x=convert_string<double>(substring_of_columned_line(pdb_file_line, 31, 38), record.x_valid);
+ record.y=convert_string<double>(substring_of_columned_line(pdb_file_line, 39, 46), record.y_valid);
+ record.z=convert_string<double>(substring_of_columned_line(pdb_file_line, 47, 54), record.z_valid);
+ record.occupancy=convert_string<double>(substring_of_columned_line(pdb_file_line, 55, 60), record.occupancy_valid);
+ record.tempFactor=convert_string<double>(substring_of_columned_line(pdb_file_line, 61, 66), record.tempFactor_valid);
+ record.element=fix_undefined_string(substring_of_columned_line(pdb_file_line, 77, 78));
+ normalize_numbered_atom_name(record.name);
+ return record;
+ }
+ };
+
+ class PDBWriter
+ {
+ public:
+ static std::string write_atom_record_in_line(const AtomRecord& atom_record)
+ {
+ std::string line(80, ' ');
+ insert_string_to_columned_line(atom_record.record_name, 1, 6, false, line);
+ if(atom_record.serial_valid)
+ {
+ insert_string_to_columned_line(convert_int_to_string(atom_record.serial), 7, 11, true, line);
+ }
+ insert_string_to_columned_line(atom_record.name, (atom_record.name.size()>3 ? 13 : 14), 16, false, line);
+ insert_string_to_columned_line(atom_record.altLoc, 17, 17, false, line);
+ insert_string_to_columned_line(atom_record.resName, 18, 20, false, line);
+ insert_string_to_columned_line(atom_record.chainID.substr(0, 1), 22, 22, false, line);
+ if(atom_record.resSeq_valid)
+ {
+ insert_string_to_columned_line(convert_int_to_string(atom_record.resSeq), 23, 26, true, line);
+ }
+ insert_string_to_columned_line(atom_record.iCode, 27, 27, false, line);
+ if(atom_record.x_valid)
+ {
+ insert_string_to_columned_line(convert_double_to_string(atom_record.x, 3), 31, 38, true, line);
+ }
+ if(atom_record.y_valid)
+ {
+ insert_string_to_columned_line(convert_double_to_string(atom_record.y, 3), 39, 46, true, line);
+ }
+ if(atom_record.z_valid)
+ {
+ insert_string_to_columned_line(convert_double_to_string(atom_record.z, 3), 47, 54, true, line);
+ }
+ if(atom_record.occupancy_valid)
+ {
+ insert_string_to_columned_line(convert_double_to_string(atom_record.occupancy, 2), 55, 60, true, line);
+ }
+ if(atom_record.tempFactor_valid)
+ {
+ insert_string_to_columned_line(convert_double_to_string(atom_record.tempFactor, 2), 61, 66, true, line);
+ }
+ insert_string_to_columned_line(atom_record.element, 77, 78, true, line);
+ return line;
+ }
+
+ static std::string write_temperature_factor_to_line(const std::string& line, const bool tempFactor_valid, const double tempFactor)
+ {
+ std::string updated_line=line;
+ if(updated_line.size()<80)
+ {
+ updated_line.resize(80, ' ');
+ }
+ insert_string_to_columned_line((tempFactor_valid ? convert_double_to_string(tempFactor, 2) : std::string()), 61, 66, true, updated_line);
+ return updated_line;
+ }
+
+ private:
+ static std::string convert_int_to_string(const int value)
+ {
+ std::ostringstream output;
+ output << value;
+ return output.str();
+ }
+
+ static std::string convert_double_to_string(const double value, const int precision)
+ {
+ std::ostringstream output;
+ output << std::fixed << std::setprecision(precision) << value;
+ return output.str();
+ }
+
+ static bool insert_string_to_columned_line(const std::string& str, const std::size_t start, const std::size_t end, const bool shift_right, std::string& line)
+ {
+ if(start>=1 && start<=end && end<=line.size())
+ {
+ const std::size_t interval_length=(end-start)+1;
+ if(str.size()<=interval_length)
+ {
+ const std::string addition(interval_length-str.size(), ' ');
+ line.replace(start-1, interval_length, (shift_right ? addition+str : str+addition));
+ return true;
+ }
+ }
+ return false;
+ }
+ };
+
+ class MMCIFReader
+ {
+ public:
+ struct Data
+ {
+ std::vector<AtomRecord> atom_records;
+ };
+
+ static Data read_data_from_file_stream(std::istream& file_stream, const bool include_heteroatoms, const bool include_hydrogens)
+ {
+ const std::string atom_site_prefix="_atom_site.";
+ Data data;
+ while(file_stream.good())
+ {
+ std::string token;
+ bool token_status=read_uncommented_token_from_mmcif_file_stream(file_stream, token);
+ if(token_status && token=="loop_")
+ {
+ std::vector<std::string> header;
+ token_status=read_uncommented_token_from_mmcif_file_stream(file_stream, token);
+ while(token_status && token.compare(0, atom_site_prefix.size(), atom_site_prefix)==0)
+ {
+ header.push_back(token);
+ token_status=read_uncommented_token_from_mmcif_file_stream(file_stream, token);
+ }
+ if(!header.empty())
+ {
+ std::map<std::string, std::size_t> header_map;
+ for(std::size_t i=0;i<header.size();i++)
+ {
+ header_map[header[i]]=i;
+ }
+ if(header_map.size()==header.size())
+ {
+ std::vector<std::string> values;
+ while(token_status && token.find("_")==std::string::npos)
+ {
+ values.push_back(token);
+ token_status=read_uncommented_token_from_mmcif_file_stream(file_stream, token);
+ }
+ if(!values.empty() && ((values.size()%header.size())==0))
+ {
+ data.atom_records.reserve(values.size()/header.size());
+ const std::string first_model_id=get_value_from_table_row(header_map, values.begin(), "_atom_site.pdbx_PDB_model_num");
+ for(std::size_t i=0;i<values.size();i+=header.size())
+ {
+ if(get_value_from_table_row(header_map, (values.begin()+i), "_atom_site.pdbx_PDB_model_num")==first_model_id)
+ {
+ const AtomRecord record=read_atom_record_from_table_row(header_map, (values.begin()+i));
+ if(check_atom_record_acceptability(record, include_heteroatoms, include_hydrogens))
+ {
+ if(check_atom_record_validity(record))
+ {
+ data.atom_records.push_back(record);
+ }
+ else
+ {
+ std::cerr << "Invalid atom record in row:";
+ for(std::size_t j=0;j<header.size();j++)
+ {
+ std::cerr << " " << header[j] << "=" << values[i+j];
+ }
+ std::cerr << "\n";
+ }
+ }
+ }
+ }
+ return data;
+ }
+ else
+ {
+ throw std::runtime_error("Invalid '_atom_site' loop in mmCIF input stream.");
+ }
+ }
+ else
+ {
+ throw std::runtime_error("Duplicate key in '_atom_site' loop in mmCIF input stream.");
+ }
+ }
+ }
+ }
+ return data;
+ }
+
+ private:
+ static bool read_uncommented_token_from_mmcif_file_stream(std::istream& file_stream, std::string& token)
+ {
+ do
+ {
+ file_stream >> token;
+ if(file_stream.fail())
+ {
+ return false;
+ }
+ else if(token.find("#")==std::string::npos)
+ {
+ return true;
+ }
+ else if(file_stream.good())
+ {
+ std::getline(file_stream, token);
+ }
+ }
+ while(file_stream.good());
+ return false;
+ }
+
+ static std::string get_value_from_table_row(const std::map<std::string, std::size_t>& header_map, const std::vector<std::string>::const_iterator& values_iter, const std::string& name)
+ {
+ std::map<std::string, std::size_t>::const_iterator it=header_map.find(name);
+ if(it!=header_map.end() && it->second<header_map.size())
+ {
+ return (*(values_iter+it->second));
+ }
+ else
+ {
+ return std::string();
+ }
+ }
+
+ static AtomRecord read_atom_record_from_table_row(const std::map<std::string, std::size_t>& header_map, const std::vector<std::string>::const_iterator& values_iter)
+ {
+ AtomRecord record=AtomRecord();
+ record.record_name=get_value_from_table_row(header_map, values_iter, "_atom_site.group_PDB");
+ record.serial=convert_string<int>(get_value_from_table_row(header_map, values_iter, "_atom_site.id"), record.serial_valid);
+ record.name=get_value_from_table_row(header_map, values_iter, "_atom_site.auth_atom_id");
+ record.altLoc=fix_undefined_string(get_value_from_table_row(header_map, values_iter, "_atom_site.label_alt_id"));
+ record.resName=fix_undefined_string(get_value_from_table_row(header_map, values_iter, "_atom_site.auth_comp_id"));
+ record.chainID=fix_undefined_string(get_value_from_table_row(header_map, values_iter, "_atom_site.auth_asym_id"));
+ record.resSeq=convert_string<int>(get_value_from_table_row(header_map, values_iter, "_atom_site.auth_seq_id"), record.resSeq_valid);
+ record.iCode=fix_undefined_string(get_value_from_table_row(header_map, values_iter, "_atom_site.pdbx_PDB_ins_code"));
+ record.x=convert_string<double>(get_value_from_table_row(header_map, values_iter, "_atom_site.Cartn_x"), record.x_valid);
+ record.y=convert_string<double>(get_value_from_table_row(header_map, values_iter, "_atom_site.Cartn_y"), record.y_valid);
+ record.z=convert_string<double>(get_value_from_table_row(header_map, values_iter, "_atom_site.Cartn_z"), record.z_valid);
+ record.occupancy=convert_string<double>(get_value_from_table_row(header_map, values_iter, "_atom_site.occupancy"), record.occupancy_valid);
+ record.tempFactor=convert_string<double>(get_value_from_table_row(header_map, values_iter, "_atom_site.B_iso_or_equiv"), record.tempFactor_valid);
+ record.element=fix_undefined_string(get_value_from_table_row(header_map, values_iter, "_atom_site.type_symbol"));
+ normalize_numbered_atom_name(record.name);
+ return record;
+ }
+ };
+
+ class DSSPReader
+ {
+ public:
+ struct DSSPRecord
+ {
+ std::string chainID;
+ int resSeq;
+ std::string iCode;
+ std::string resNameShort;
+ std::string resSSE;
+ double anglePhi;
+ double anglePsi;
+
+ bool resSeq_valid;
+ bool anglePhi_valid;
+ bool anglePsi_valid;
+ };
+
+ struct Data
+ {
+ std::vector<DSSPRecord> dssp_records;
+ };
+
+ static Data read_data_from_file_stream(std::istream& file_stream)
+ {
+ const std::string header_prefix=" # RESIDUE AA STRUCTURE";
+ Data data;
+ bool records_started=false;
+ while(file_stream.good())
+ {
+ std::string line;
+ std::getline(file_stream, line);
+ if(!line.empty())
+ {
+ if(!records_started)
+ {
+ if(line.compare(0, header_prefix.size(), header_prefix)==0)
+ {
+ records_started=true;
+ }
+ }
+ else
+ {
+ const std::string resNameShort=fix_undefined_string(substring_of_columned_line(line, 14, 14));
+ if(!resNameShort.empty() && resNameShort!="!")
+ {
+ const DSSPRecord record=read_dssp_record_from_line(line);
+ if(record.resSeq_valid && record.anglePhi_valid && record.anglePsi_valid)
+ {
+ data.dssp_records.push_back(record);
+ }
+ else
+ {
+ std::cerr << "Invalid DSSP record in line: " << line << "\n";
+ }
+ }
+ }
+ }
+ }
+ return data;
+ }
+
+ private:
+ static DSSPRecord read_dssp_record_from_line(const std::string& dssp_file_line)
+ {
+ DSSPRecord record=DSSPRecord();
+ record.chainID=fix_undefined_string(substring_of_columned_line(dssp_file_line, 12, 12));
+ record.resSeq=convert_string<int>(substring_of_columned_line(dssp_file_line, 6, 10), record.resSeq_valid);
+ record.iCode=fix_undefined_string(substring_of_columned_line(dssp_file_line, 11, 11));
+ record.resNameShort=fix_undefined_string(substring_of_columned_line(dssp_file_line, 14, 14));
+ record.resSSE=fix_undefined_string(substring_of_columned_line(dssp_file_line, 17, 17));
+ record.anglePhi=convert_string<double>(substring_of_columned_line(dssp_file_line, 104, 109), record.anglePhi_valid);
+ record.anglePsi=convert_string<double>(substring_of_columned_line(dssp_file_line, 110, 115), record.anglePsi_valid);
+ return record;
+ }
+ };
+
+ class HBPlusReader
+ {
+ public:
+ struct ShortAtomDescriptor
+ {
+ std::string chainID;
+ int resSeq;
+ std::string iCode;
+ std::string resName;
+ std::string name;
+
+ bool resSeq_valid;
+ };
+
+ struct HBPlusRecord
+ {
+ ShortAtomDescriptor first;
+ ShortAtomDescriptor second;
+ };
+
+ struct Data
+ {
+ std::vector<HBPlusRecord> hbplus_records;
+ };
+
+ static Data read_data_from_file_stream(std::istream& file_stream)
+ {
+ Data data;
+ int line_number=0;
+ while(file_stream.good())
+ {
+ std::string line;
+ std::getline(file_stream, line);
+ line_number++;
+ if(line_number>=9 && !line.empty())
+ {
+ const HBPlusRecord record=read_hbplus_record_from_line(line);
+ if(record.first.resSeq_valid && record.second.resSeq_valid)
+ {
+ data.hbplus_records.push_back(record);
+ }
+ else
+ {
+ std::cerr << "Invalid HBPlus record in line: " << line << "\n";
+ }
+ }
+ }
+ return data;
+ }
+
+ private:
+ static ShortAtomDescriptor read_short_atom_descriptor_from_line(const std::string& hbplus_file_line, const bool second)
+ {
+ const int offset=(second ? 14 : 0);
+ ShortAtomDescriptor d=ShortAtomDescriptor();
+ d.chainID=fix_undefined_string(fix_undefined_dash_string(substring_of_columned_line(hbplus_file_line, 1+offset, 1+offset)));
+ d.resSeq=convert_string_to_resSeq(substring_of_columned_line(hbplus_file_line, 2+offset, 5+offset), d.resSeq_valid);
+ d.iCode=fix_undefined_string(fix_undefined_dash_string(substring_of_columned_line(hbplus_file_line, 6+offset, 6+offset)));
+ d.resName=substring_of_columned_line(hbplus_file_line, 7+offset, 9+offset);
+ d.name=substring_of_columned_line(hbplus_file_line, 10+offset, 14+offset);
+ return d;
+ }
+
+ static HBPlusRecord read_hbplus_record_from_line(const std::string& hbplus_file_line)
+ {
+ HBPlusRecord record=HBPlusRecord();
+ record.first=read_short_atom_descriptor_from_line(hbplus_file_line, false);
+ record.second=read_short_atom_descriptor_from_line(hbplus_file_line, true);
+ return record;
+ }
+
+ static int convert_string_to_resSeq(const std::string& str, bool& valid)
+ {
+ std::string refined_str;
+ bool number_started=false;
+ for(std::size_t i=0;i<str.size();i++)
+ {
+ if(str[i]=='0')
+ {
+ if(number_started || i+1==str.size())
+ {
+ refined_str.push_back(str[i]);
+ }
+ }
+ else
+ {
+ number_started=true;
+ refined_str.push_back(str[i]);
+ }
+ }
+ return convert_string<int>(refined_str, valid);
+ }
+
+ static std::string fix_undefined_dash_string(const std::string& str)
+ {
+ return (str=="-" ? std::string() : str);
+ }
+ };
+
+private:
+ static bool check_atom_record_validity(const AtomRecord& record)
+ {
+ return (record.serial_valid &&
+ record.resSeq_valid &&
+ record.x_valid &&
+ record.y_valid &&
+ record.z_valid &&
+ !record.record_name.empty() &&
+ !record.name.empty());
+ }
+
+ static bool check_atom_record_acceptability(const AtomRecord& record, const bool include_heteroatoms, const bool include_hydrogens)
+ {
+ return ((record.record_name=="ATOM" || (include_heteroatoms && record.record_name=="HETATM")) &&
+ (record.altLoc.empty() || record.altLoc=="A" || record.altLoc==".") &&
+ (include_hydrogens || record.name.find("H")!=0) &&
+ (include_hydrogens || (record.element!="H" && record.element!="D")) &&
+ record.resName!="HOH");
+ }
+
+ template<typename T>
+ static T convert_string(const std::string& str, bool& valid)
+ {
+ T value=T();
+ if(str.empty())
+ {
+ valid=false;
+ }
+ else
+ {
+ std::istringstream input(str);
+ input >> value;
+ valid=!input.fail();
+ }
+ return value;
+ }
+
+ static std::string fix_undefined_string(const std::string& str)
+ {
+ return ((str=="." || str=="?") ? std::string() : str);
+ }
+
+ static void normalize_numbered_atom_name(std::string& name)
+ {
+ if(name.find_first_of("123456789")==0)
+ {
+ std::size_t first_letter_pos=name.find_first_not_of("0123456789");
+ if(first_letter_pos!=std::string::npos)
+ {
+ name=(name.substr(first_letter_pos)+name.substr(0, first_letter_pos));
+ }
+ }
+ }
+
+ static std::string substring_of_columned_line(const std::string& line, const int start, const int end)
+ {
+ std::string extraction;
+ int line_length=static_cast<int>(line.size());
+ for(int i=start-1;i<end && i<line_length && i>=0;i++)
+ {
+ if(line[i]!=32) { extraction.push_back(line[i]); }
+ }
+ return extraction;
+ }
+};
+
+}
+
+#endif /* AUXILIARIES_ATOMS_IO_H_ */
diff --git a/src/auxiliaries/chain_residue_atom_descriptor.h b/src/auxiliaries/chain_residue_atom_descriptor.h
new file mode 100644
index 0000000..b8e59ab
--- /dev/null
+++ b/src/auxiliaries/chain_residue_atom_descriptor.h
@@ -0,0 +1,664 @@
+#ifndef AUXILIARIES_CHAIN_RESIDUE_ATOM_DESCRIPTOR_H_
+#define AUXILIARIES_CHAIN_RESIDUE_ATOM_DESCRIPTOR_H_
+
+#include <string>
+#include <sstream>
+#include <limits>
+#include <stdexcept>
+#include <cstdlib>
+#include <vector>
+#include <set>
+#include <map>
+#include <cmath>
+
+namespace auxiliaries
+{
+
+class ChainResidueAtomDescriptor
+{
+public:
+ int serial;
+ std::string chainID;
+ int resSeq;
+ std::string resName;
+ std::string name;
+ std::string altLoc;
+ std::string iCode;
+
+ ChainResidueAtomDescriptor() : serial(null_num()), resSeq(null_num())
+ {
+ }
+
+ explicit ChainResidueAtomDescriptor(const std::string& chainID) : serial(null_num()), chainID(chainID), resSeq(null_num())
+ {
+ }
+
+ ChainResidueAtomDescriptor(
+ const int serial,
+ const std::string& chainID,
+ const int resSeq,
+ const std::string& resName,
+ const std::string& name,
+ const std::string& altLoc,
+ const std::string& iCode) :
+ serial(serial),
+ chainID(chainID),
+ resSeq(resSeq),
+ resName(resName),
+ name(name),
+ altLoc(altLoc),
+ iCode(iCode)
+ {
+ }
+
+ static int null_num()
+ {
+ return std::numeric_limits<int>::min();
+ }
+
+ static const ChainResidueAtomDescriptor& solvent()
+ {
+ static const ChainResidueAtomDescriptor v("solvent");
+ return v;
+ }
+
+ static const ChainResidueAtomDescriptor& any()
+ {
+ static const ChainResidueAtomDescriptor v("any");
+ return v;
+ }
+
+ static std::string from_str(const std::string& input_str, ChainResidueAtomDescriptor& output_descriptor)
+ {
+ static const MarkerNaming mn;
+ ChainResidueAtomDescriptor v;
+ std::string refined_input_str=input_str;
+ {
+ char last_bracket='?';
+ for(std::size_t i=0;i<refined_input_str.size();i++)
+ {
+ char& s=refined_input_str[i];
+ if(s==vend || s==vbegin)
+ {
+ if(s==last_bracket)
+ {
+ return (std::string("Invalid bracketing in descriptor string '")+input_str+"'.");
+ }
+ last_bracket=s;
+ s=' ';
+ }
+ }
+ if(last_bracket!=vend)
+ {
+ return (std::string("Incomplete bracketing in descriptor string '")+input_str+"'.");
+ }
+ }
+ std::istringstream input(refined_input_str);
+ std::vector<std::string> markers;
+ while(input.good())
+ {
+ std::string marker;
+ input >> marker;
+ if(!marker.empty())
+ {
+ if(marker==mn.chainID)
+ {
+ input >> v.chainID;
+ }
+ else if(marker==mn.resSeq)
+ {
+ input >> v.resSeq;
+ }
+ else if(marker==mn.iCode)
+ {
+ input >> v.iCode;
+ }
+ else if(marker==mn.serial)
+ {
+ input >> v.serial;
+ }
+ else if(marker==mn.altLoc)
+ {
+ input >> v.altLoc;
+ }
+ else if(marker==mn.resName)
+ {
+ input >> v.resName;
+ }
+ else if(marker==mn.name)
+ {
+ input >> v.name;
+ }
+ else
+ {
+ return (std::string("Unrecognized marker '")+marker+"' in descriptor string '"+input_str+"'.");
+ }
+ if(input.fail())
+ {
+ return (std::string("Unreadable marker '")+marker+"' value in descriptor string '"+input_str+"'.");
+ }
+ markers.push_back(marker);
+ }
+ }
+ if(!(v.valid() && v.str(markers)==input_str))
+ {
+ return (std::string("Invalid descriptor string '")+input_str+"'.");
+ }
+ output_descriptor=v;
+ return std::string();
+ }
+
+ static ChainResidueAtomDescriptor from_str(const std::string& input_str)
+ {
+ ChainResidueAtomDescriptor v;
+ const std::string error_msg=from_str(input_str, v);
+ if(!error_msg.empty())
+ {
+ throw std::runtime_error(error_msg);
+ }
+ return v;
+ }
+
+ static bool match_with_member_selection_string(const ChainResidueAtomDescriptor& crad, const std::string& input_str)
+ {
+ static const MarkerNaming mn;
+ const char vsep=',';
+ const char vinterval=':';
+ std::ostringstream control_output;
+ bool matched=false;
+ std::string refined_input_str=input_str;
+ for(std::size_t i=0;i<refined_input_str.size();i++)
+ {
+ char& s=refined_input_str[i];
+ if(s==vend || s==vbegin || s==vsep)
+ {
+ s=' ';
+ }
+ }
+ std::istringstream input(refined_input_str);
+ std::string marker;
+ input >> marker;
+ if(!input.fail() && mn.valid(marker))
+ {
+ control_output << marker << vbegin;
+ bool need_sep=false;
+ while(input.good())
+ {
+ std::string token;
+ input >> token;
+ if(!input.fail() && !token.empty())
+ {
+ if(need_sep) { control_output << vsep; } else { need_sep=true; }
+ if(marker==mn.resSeq || marker==mn.serial)
+ {
+ std::size_t pinterval=token.find(vinterval);
+ if(pinterval!=std::string::npos)
+ {
+ token[pinterval]=' ';
+ std::istringstream token_input(token);
+ std::pair<int, int> value(0, 0);
+ token_input >> value.first >> value.second;
+ if(!token_input.fail() && value.first<=value.second)
+ {
+ control_output << value.first << vinterval << value.second;
+ if(marker==mn.resSeq) { matched=matched || (crad.resSeq>=value.first && crad.resSeq<=value.second); }
+ else if(marker==mn.serial) { matched=matched || (crad.serial>=value.first && crad.serial<=value.second); }
+ }
+ }
+ else
+ {
+ std::istringstream token_input(token);
+ int value=0;
+ token_input >> value;
+ if(!token_input.fail())
+ {
+ control_output << value;
+ if(marker==mn.resSeq) { matched=matched || (crad.resSeq==value); }
+ else if(marker==mn.serial) { matched=matched || (crad.serial==value); }
+ }
+ }
+ }
+ else
+ {
+ control_output << token;
+ if(marker==mn.chainID) { matched=matched || (crad.chainID==token); }
+ else if(marker==mn.iCode) { matched=matched || (crad.iCode==token); }
+ else if(marker==mn.altLoc) { matched=matched || (crad.altLoc==token); }
+ else if(marker==mn.resName) { matched=matched || (crad.resName==token); }
+ else if(marker==mn.name) { matched=matched || (crad.name==token); }
+ }
+ }
+ }
+ control_output << vend;
+ }
+ const std::string control_output_str=control_output.str();
+ if(control_output_str.empty() || control_output_str!=input_str)
+ {
+ throw std::runtime_error(std::string("Invalid selection string '")+input_str+"'.");
+ }
+ return matched;
+ }
+
+ static bool match_with_sequence_separation_interval(const ChainResidueAtomDescriptor& a, const ChainResidueAtomDescriptor& b, const int min_sep, const int max_sep, const bool uncheckable_result)
+ {
+ if(!(min_sep==null_num() && max_sep==null_num()) && a.resSeq!=null_num() && b.resSeq!=null_num() && a.chainID==b.chainID)
+ {
+ int sep=abs(a.resSeq-b.resSeq);
+ if(sep==0 && !(a.iCode.empty() && b.iCode.empty()) && a.iCode!=b.iCode)
+ {
+ if(!a.iCode.empty() && !b.iCode.empty())
+ {
+ sep=abs(static_cast<int>(a.iCode[0])-static_cast<int>(b.iCode[1]));
+ }
+ else
+ {
+ sep=1;
+ }
+ }
+ return ((min_sep==null_num() || sep>=min_sep) && (max_sep==null_num() || sep<=max_sep));
+ }
+ else if(max_sep!=null_num() && a.chainID!=b.chainID)
+ {
+ return false;
+ }
+ return uncheckable_result;
+ }
+
+ bool valid() const
+ {
+ return ((!chainID.empty() || resSeq!=null_num() || !resName.empty() || serial!=null_num() || !name.empty()) &&
+ !(resSeq==null_num() && !iCode.empty()));
+ }
+
+ ChainResidueAtomDescriptor without_some_info(const bool no_serial, const bool no_name, const bool no_resSeq, const bool no_resName) const
+ {
+ ChainResidueAtomDescriptor v=(*this);
+ if(no_serial)
+ {
+ v.serial=null_num();
+ }
+ if(no_name)
+ {
+ v.name.clear();
+ }
+ if(no_resSeq)
+ {
+ v.resSeq=null_num();
+ }
+ if(no_resName)
+ {
+ v.resName.clear();
+ }
+ return v;
+ }
+
+ ChainResidueAtomDescriptor without_atom() const
+ {
+ return without_some_info(true, true, false, false);
+ }
+
+ ChainResidueAtomDescriptor without_numbering() const
+ {
+ if((*this)==solvent())
+ {
+ return (*this);
+ }
+ else
+ {
+ ChainResidueAtomDescriptor v;
+ v.resName=resName;
+ v.name=name;
+ return v;
+ }
+ }
+
+ bool contains(const ChainResidueAtomDescriptor& v) const
+ {
+ return (valid() && v.valid() &&
+ (v.serial==null_num() || v.serial==serial) &&
+ (v.chainID.empty() || v.chainID==chainID) &&
+ (v.resSeq==null_num() || v.resSeq==resSeq) &&
+ (v.resName.empty() || v.resName==resName) &&
+ (v.name.empty() || v.name==name) &&
+ (v.altLoc.empty() || v.altLoc==altLoc) &&
+ (v.iCode.empty() || v.iCode==iCode));
+ }
+
+ bool operator==(const ChainResidueAtomDescriptor& v) const
+ {
+ return (serial==v.serial && resSeq==v.resSeq && chainID==v.chainID && iCode==v.iCode && altLoc==v.altLoc && resName==v.resName && name==v.name);
+ }
+
+ bool operator!=(const ChainResidueAtomDescriptor& v) const
+ {
+ return (!((*this)==v));
+ }
+
+ bool operator<(const ChainResidueAtomDescriptor& v) const
+ {
+ if(chainID<v.chainID) { return true; }
+ else if(chainID==v.chainID)
+ {
+ if(resSeq<v.resSeq) { return true; }
+ else if(resSeq==v.resSeq)
+ {
+ if(iCode<v.iCode) { return true; }
+ else if(iCode==v.iCode)
+ {
+ if(serial<v.serial) { return true; }
+ else if(serial==v.serial)
+ {
+ if(altLoc<v.altLoc) { return true; }
+ else if(altLoc==v.altLoc)
+ {
+ if(resName<v.resName) { return true; }
+ else if(resName==v.resName)
+ {
+ return (name<v.name);
+ }
+ }
+ }
+ }
+ }
+ }
+ return false;
+ }
+
+ std::string str() const
+ {
+ static const MarkerNaming mn;
+ static const std::string markers_array[7]={mn.chainID, mn.resSeq, mn.iCode, mn.serial, mn.altLoc, mn.resName, mn.name};
+ static const std::vector<std::string> markers(markers_array, markers_array+7);
+ return str(markers);
+ }
+
+private:
+ struct MarkerNaming
+ {
+ std::string serial;
+ std::string chainID;
+ std::string resSeq;
+ std::string resName;
+ std::string name;
+ std::string altLoc;
+ std::string iCode;
+
+ MarkerNaming() :
+ serial("a"),
+ chainID("c"),
+ resSeq("r"),
+ resName("R"),
+ name("A"),
+ altLoc("l"),
+ iCode("i")
+ {
+ }
+
+ bool valid(const std::string& marker_name) const
+ {
+ return (marker_name==serial
+ || marker_name==chainID
+ || marker_name==resSeq
+ || marker_name==resName
+ || marker_name==name
+ || marker_name==altLoc
+ || marker_name==iCode);
+ }
+ };
+
+ static const char vbegin='<';
+ static const char vend='>';
+
+ std::string str(const std::vector<std::string>& markers) const
+ {
+ const MarkerNaming mn;
+ std::ostringstream output;
+ for(std::size_t i=0;i<markers.size();i++)
+ {
+ const std::string& m=markers[i];
+ if(m==mn.chainID && !chainID.empty())
+ {
+ output << mn.chainID << vbegin << chainID << vend;
+ }
+ else if(m==mn.resSeq && resSeq!=null_num())
+ {
+ output << mn.resSeq << vbegin << resSeq << vend;
+ }
+ else if(m==mn.iCode && !iCode.empty())
+ {
+ output << mn.iCode << vbegin << iCode << vend;
+ }
+ else if(m==mn.serial && serial!=null_num())
+ {
+ output << mn.serial << vbegin << serial << vend;
+ }
+ else if(m==mn.altLoc && !altLoc.empty())
+ {
+ output << mn.altLoc << vbegin << altLoc << vend;
+ }
+ else if(m==mn.resName && !resName.empty())
+ {
+ output << mn.resName << vbegin << resName << vend;
+ }
+ else if(m==mn.name && !name.empty())
+ {
+ output << mn.name << vbegin << name << vend;
+ }
+ }
+ return output.str();
+ }
+};
+
+inline std::ostream& operator<<(std::ostream& output, const ChainResidueAtomDescriptor& descriptor)
+{
+ output << descriptor.str();
+ return output;
+}
+
+inline std::istream& operator>>(std::istream& input, ChainResidueAtomDescriptor& descriptor)
+{
+ std::string str;
+ input >> str;
+ descriptor=ChainResidueAtomDescriptor::from_str(str);
+ if(!descriptor.valid())
+ {
+ input.setstate(std::ios::failbit);
+ }
+ return input;
+}
+
+class ChainResidueAtomDescriptorsPair
+{
+public:
+ ChainResidueAtomDescriptor a;
+ ChainResidueAtomDescriptor b;
+ bool reversed_display;
+
+ ChainResidueAtomDescriptorsPair() : reversed_display(false)
+ {
+ }
+
+ ChainResidueAtomDescriptorsPair(const ChainResidueAtomDescriptor& a, const ChainResidueAtomDescriptor& b) : a(a<b ? a : b), b(a<b ? b : a), reversed_display(false)
+ {
+ }
+
+ ChainResidueAtomDescriptorsPair(const ChainResidueAtomDescriptor& a, const ChainResidueAtomDescriptor& b, const bool reversed_display) : a(a<b ? a : b), b(a<b ? b : a), reversed_display(reversed_display)
+ {
+ }
+
+ bool operator==(const ChainResidueAtomDescriptorsPair& v) const
+ {
+ return (a==v.a && b==v.b);
+ }
+
+ bool operator<(const ChainResidueAtomDescriptorsPair& v) const
+ {
+ return ((a<v.a) || (a==v.a && b<v.b));
+ }
+
+ bool contains(const ChainResidueAtomDescriptor& v) const
+ {
+ return (a==v || b==v);
+ }
+};
+
+inline std::ostream& operator<<(std::ostream& output, const ChainResidueAtomDescriptorsPair& descriptors_pair)
+{
+ if(descriptors_pair.reversed_display)
+ {
+ output << descriptors_pair.b << " " << descriptors_pair.a;
+ }
+ else
+ {
+ output << descriptors_pair.a << " " << descriptors_pair.b;
+ }
+ return output;
+}
+
+inline std::istream& operator>>(std::istream& input, ChainResidueAtomDescriptorsPair& descriptors_pair)
+{
+ ChainResidueAtomDescriptor a;
+ ChainResidueAtomDescriptor b;
+ input >> a >> b;
+ descriptors_pair=ChainResidueAtomDescriptorsPair(a, b);
+ return input;
+}
+
+class ChainResidueAtomDescriptorsGraphOperations
+{
+public:
+ template<typename T>
+ static std::map<ChainResidueAtomDescriptor, T> accumulate_mapped_values_by_graph_neighbors(
+ const std::map< ChainResidueAtomDescriptorsPair, T >& map_of_pair_descriptors,
+ const int depth)
+ {
+ return construct_map_of_single_descriptors(map_of_pair_descriptors, construct_graph(map_of_pair_descriptors, depth));
+ }
+
+private:
+ template<typename T>
+ static std::map< ChainResidueAtomDescriptor, std::set<ChainResidueAtomDescriptor> > construct_graph(
+ const std::map<ChainResidueAtomDescriptorsPair, T>& map_of_pair_descriptors,
+ const int depth)
+ {
+ typedef ChainResidueAtomDescriptor CRAD;
+ std::map< CRAD, std::set<CRAD> > graph;
+ if(depth>0)
+ {
+ for(typename std::map<ChainResidueAtomDescriptorsPair, T>::const_iterator it=map_of_pair_descriptors.begin();it!=map_of_pair_descriptors.end();++it)
+ {
+ const ChainResidueAtomDescriptorsPair& crads=it->first;
+ if(!(crads.a==crads.b || crads.a==CRAD::solvent() || crads.b==CRAD::solvent()))
+ {
+ graph[crads.a].insert(crads.b);
+ graph[crads.b].insert(crads.a);
+ }
+ }
+ for(int i=1;i<depth;i++)
+ {
+ std::map< CRAD, std::set<CRAD> > expanded_graph=graph;
+ for(std::map< CRAD, std::set<CRAD> >::const_iterator graph_it=graph.begin();graph_it!=graph.end();++graph_it)
+ {
+ const CRAD& center=graph_it->first;
+ const std::set<CRAD>& neighbors=graph_it->second;
+ std::set<CRAD>& expandable_neighbors=expanded_graph[center];
+ for(std::set<CRAD>::const_iterator neighbors_it=neighbors.begin();neighbors_it!=neighbors.end();++neighbors_it)
+ {
+ const std::set<CRAD>& neighbor_neighbors=graph[*neighbors_it];
+ expandable_neighbors.insert(neighbor_neighbors.begin(), neighbor_neighbors.end());
+ }
+ expandable_neighbors.erase(center);
+ }
+ graph=expanded_graph;
+ }
+ }
+ return graph;
+ }
+
+ template<typename T>
+ static std::map<ChainResidueAtomDescriptor, T> construct_map_of_single_descriptors(
+ const std::map< ChainResidueAtomDescriptorsPair, T >& map_of_pair_descriptors,
+ const std::map< ChainResidueAtomDescriptor, std::set<ChainResidueAtomDescriptor> >& graph)
+ {
+ typedef ChainResidueAtomDescriptor CRAD;
+ std::map<CRAD, T> map_of_single_descriptors;
+ for(typename std::map<ChainResidueAtomDescriptorsPair, T>::const_iterator it=map_of_pair_descriptors.begin();it!=map_of_pair_descriptors.end();++it)
+ {
+ const ChainResidueAtomDescriptorsPair& crads=it->first;
+ std::set<CRAD> related_crads;
+ if(crads.a!=CRAD::solvent())
+ {
+ related_crads.insert(crads.a);
+ }
+ if(crads.b!=CRAD::solvent())
+ {
+ related_crads.insert(crads.b);
+ }
+ {
+ const std::map< CRAD, std::set<CRAD> >::const_iterator graph_it=graph.find(crads.a);
+ if(graph_it!=graph.end())
+ {
+ const std::set<CRAD>& related_crads1=graph_it->second;
+ related_crads.insert(related_crads1.begin(), related_crads1.end());
+ }
+ }
+ {
+ const std::map< CRAD, std::set<CRAD> >::const_iterator graph_it=graph.find(crads.b);
+ if(graph_it!=graph.end())
+ {
+ const std::set<CRAD>& related_crads2=graph_it->second;
+ related_crads.insert(related_crads2.begin(), related_crads2.end());
+ }
+ }
+ for(std::set<CRAD>::const_iterator jt=related_crads.begin();jt!=related_crads.end();++jt)
+ {
+ map_of_single_descriptors[*jt].add(it->second);
+ }
+ }
+ return map_of_single_descriptors;
+ }
+};
+
+class ChainResidueAtomDescriptorsSequenceOperations
+{
+public:
+ static std::map<ChainResidueAtomDescriptor, double> smooth_residue_scores_along_sequence(const std::map<ChainResidueAtomDescriptor, double>& raw_scores, const unsigned int window)
+ {
+ if(window>0)
+ {
+ std::vector< std::pair<ChainResidueAtomDescriptor, double> > v(raw_scores.size());
+ std::copy(raw_scores.begin(), raw_scores.end(), v.begin());
+ std::vector< std::pair<ChainResidueAtomDescriptor, double> > sv=v;
+ for(std::size_t i=0;i<v.size();i++)
+ {
+ const int start=std::max(0, (static_cast<int>(i)-static_cast<int>(window)));
+ const int end=std::min(static_cast<int>(v.size())-1, (static_cast<int>(i)+static_cast<int>(window)));
+ double sum_of_weighted_values=0.0;
+ double sum_of_weights=0.0;
+ for(int j=start;j<=end;j++)
+ {
+ if(v[i].first.chainID==v[j].first.chainID)
+ {
+ double ndist=fabs(static_cast<double>(static_cast<int>(i)-j))/static_cast<double>(window);
+ double weight=(1.0-(ndist*ndist));
+ sum_of_weights+=weight;
+ sum_of_weighted_values+=v[j].second*weight;
+ }
+ }
+ if(sum_of_weights>0.0)
+ {
+ sv[i].second=(sum_of_weighted_values/sum_of_weights);
+ }
+ }
+ return std::map<ChainResidueAtomDescriptor, double>(sv.begin(), sv.end());
+ }
+ else
+ {
+ return raw_scores;
+ }
+ }
+};
+
+}
+
+#endif /* AUXILIARIES_CHAIN_RESIDUE_ATOM_DESCRIPTOR_H_ */
diff --git a/src/auxiliaries/io_utilities.h b/src/auxiliaries/io_utilities.h
new file mode 100644
index 0000000..4a43d78
--- /dev/null
+++ b/src/auxiliaries/io_utilities.h
@@ -0,0 +1,336 @@
+#ifndef AUXILIARIES_IO_UTILITIES__H_
+#define AUXILIARIES_IO_UTILITIES__H_
+
+#include <iostream>
+#include <sstream>
+#include <fstream>
+#include <stdexcept>
+
+#include "../compatability_macros.h"
+
+#if USE_TR1 > 0
+#include <tr1/type_traits>
+#else
+#include <type_traits>
+#endif
+
+namespace auxiliaries
+{
+
+class IOUtilities
+{
+public:
+ bool tail_line_delimiter;
+ char line_delimiter;
+ char internal_separator;
+
+ IOUtilities() : tail_line_delimiter(true), line_delimiter('\n'), internal_separator(' ')
+ {
+ }
+
+ explicit IOUtilities(const char line_delimiter) : tail_line_delimiter(false), line_delimiter(line_delimiter), internal_separator(' ')
+ {
+ }
+
+ IOUtilities(const char line_delimiter, const char internal_separator) : tail_line_delimiter(false), line_delimiter(line_delimiter), internal_separator(internal_separator)
+ {
+ }
+
+ IOUtilities(const bool tail_line_delimiter, const char line_delimiter, const char internal_separator) : tail_line_delimiter(tail_line_delimiter), line_delimiter(line_delimiter), internal_separator(internal_separator)
+ {
+ }
+
+ template<typename LineReader, typename Container>
+ void read_lines_to_container(
+ std::istream& input,
+ LineReader line_reader,
+ Container& container) const
+ {
+ std::size_t line_num=0;
+ while(input.good())
+ {
+ std::string line;
+ std::getline(input, line, line_delimiter);
+ if(!line.empty())
+ {
+ {
+ const std::size_t comments_pos=line.find("#", 0);
+ if(comments_pos!=std::string::npos)
+ {
+ line=line.substr(0, comments_pos);
+ }
+ }
+ if(!line.empty())
+ {
+ for(std::size_t i=0;i<line.size();i++)
+ {
+ if(line[i]==internal_separator)
+ {
+ line[i]=' ';
+ }
+ }
+ std::istringstream line_input(line);
+ if(!line_reader(line_input, container))
+ {
+ throw std::runtime_error(std::string("Failed to read line '")+line+"'.");
+ }
+ line_num++;
+ }
+ }
+ }
+ }
+
+ template<typename LineReader, typename Container>
+ void read_file_lines_to_container(
+ const std::string& filename,
+ LineReader line_reader,
+ Container& container) const
+ {
+ if(!filename.empty())
+ {
+ std::ifstream finput(filename.c_str(), std::ios::in);
+ if(finput.good())
+ {
+ read_lines_to_container(finput, line_reader, container);
+ }
+ }
+ }
+
+ template<typename LineReader, typename Container>
+ void read_string_lines_to_container(
+ const std::string& str,
+ LineReader line_reader,
+ Container& container) const
+ {
+ if(!str.empty())
+ {
+ std::istringstream input(str);
+ read_lines_to_container(input, line_reader, container);
+ }
+ }
+
+ template<typename Container, typename ElementWriter>
+ void write_container(
+ const Container& container,
+ ElementWriter element_writer,
+ std::ostream& output) const
+ {
+ for(typename Container::const_iterator it=container.begin();it!=container.end() && output.good();++it)
+ {
+ if(it!=container.begin())
+ {
+ output << line_delimiter;
+ }
+ element_writer(*it, output);
+ }
+ if(tail_line_delimiter && !container.empty())
+ {
+ output << line_delimiter;
+ }
+ }
+
+ template<typename Container, typename ElementWriter>
+ void write_container_to_file(
+ const Container& container,
+ ElementWriter element_writer,
+ const std::string& filename) const
+ {
+ if(!filename.empty())
+ {
+ std::ofstream foutput(filename.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ write_container(container, element_writer, foutput);
+ }
+ }
+ }
+
+ template<typename Container, typename ElementWriter>
+ std::string write_container_to_string(
+ const Container& container,
+ ElementWriter element_writer) const
+ {
+ std::ostringstream output;
+ write_container(container, element_writer, output);
+ return output.str();
+ }
+
+ template<typename Container>
+ void read_lines_to_set(std::istream& input, Container& container) const
+ {
+ read_lines_to_container(input, read_line_to_set<Container>, container);
+ }
+
+ template<typename Container>
+ Container read_lines_to_set(std::istream& input) const
+ {
+ Container container;
+ read_lines_to_set(input, container);
+ return container;
+ }
+
+ template<typename Container>
+ void read_file_lines_to_set(const std::string& filename, Container& container) const
+ {
+ read_file_lines_to_container(filename, read_line_to_set<Container>, container);
+ }
+
+ template<typename Container>
+ Container read_file_lines_to_set(const std::string& filename) const
+ {
+ Container container;
+ read_file_lines_to_set(filename, container);
+ return container;
+ }
+
+ template<typename Container>
+ void read_string_lines_to_set(const std::string& str, Container& container) const
+ {
+ read_string_lines_to_container(str, read_line_to_set<Container>, container);
+ }
+
+ template<typename Container>
+ Container read_string_lines_to_set(const std::string& str) const
+ {
+ Container container;
+ read_string_lines_to_set(str, container);
+ return container;
+ }
+
+ template<typename Container>
+ void write_set(const Container& container, std::ostream& output) const
+ {
+ write_container(container, write_set_element<Container>, output);
+ }
+
+ template<typename Container>
+ void write_set_to_file(const Container& container, const std::string& filename) const
+ {
+ write_container_to_file(container, write_set_element<Container>, filename);
+ }
+
+ template<typename Container>
+ std::string write_set_to_string(const Container& container) const
+ {
+ return write_container_to_string(container, write_set_element<Container>);
+ }
+
+ template<typename Container>
+ void read_lines_to_map(std::istream& input, Container& container) const
+ {
+ read_lines_to_container(input, read_line_to_map<Container>, container);
+ }
+
+ template<typename Container>
+ Container read_lines_to_map(std::istream& input) const
+ {
+ Container container;
+ read_lines_to_map(input, container);
+ return container;
+ }
+
+ template<typename Container>
+ void read_file_lines_to_map(const std::string& filename, Container& container) const
+ {
+ read_file_lines_to_container(filename, read_line_to_map<Container>, container);
+ }
+
+ template<typename Container>
+ Container read_file_lines_to_map(const std::string& filename) const
+ {
+ Container container;
+ read_file_lines_to_map(filename, container);
+ return container;
+ }
+
+ template<typename Container>
+ void read_string_lines_to_map(const std::string& str, Container& container) const
+ {
+ read_string_lines_to_container(str, read_line_to_map<Container>, container);
+ }
+
+ template<typename Container>
+ Container read_string_lines_to_map(const std::string& str) const
+ {
+ Container container;
+ read_string_lines_to_map(str, container);
+ return container;
+ }
+
+
+ template<typename Container>
+ void write_map(const Container& container, std::ostream& output) const
+ {
+ write_container(container, write_map_element<Container>(internal_separator), output);
+ }
+
+ template<typename Container>
+ void write_map_to_file(const Container& container, const std::string& filename) const
+ {
+ write_container_to_file(container, write_map_element<Container>(internal_separator), filename);
+ }
+
+ template<typename Container>
+ std::string write_map_to_string(const Container& container) const
+ {
+ return write_container_to_string(container, write_map_element<Container>(internal_separator));
+ }
+
+private:
+ template<typename Container>
+ static inline bool read_line_to_set(std::istream& input, Container& container)
+ {
+ typename Container::value_type value;
+ input >> value;
+ if(input.fail())
+ {
+ return false;
+ }
+ container.insert(container.end(), value);
+ return true;
+ }
+
+ template<typename Container>
+ static inline void write_set_element(const typename Container::value_type& value, std::ostream& output)
+ {
+ output << value;
+ }
+
+ template<typename Container>
+ static inline bool read_line_to_map(std::istream& input, Container& container)
+ {
+#if USE_TR1 > 0
+typename std::tr1::remove_const<typename Container::value_type::first_type>::type key;
+#else
+typename std::remove_const<typename Container::value_type::first_type>::type key;
+#endif
+
+ typename Container::value_type::second_type value;
+ input >> key >> value;
+ if(input.fail())
+ {
+ return false;
+ }
+ container.insert(container.end(), std::make_pair(key, value));
+ return true;
+ }
+
+ template<typename Container>
+ struct write_map_element
+ {
+ char pair_separator;
+
+ explicit write_map_element(const char pair_separator) : pair_separator(pair_separator)
+ {
+ }
+
+ inline void operator()(const typename Container::value_type& value, std::ostream& output)
+ {
+ output << value.first << pair_separator << value.second;
+ }
+ };
+};
+
+}
+
+#endif /* AUXILIARIES_IO_UTILITIES__H_ */
diff --git a/src/auxiliaries/opengl_printer.h b/src/auxiliaries/opengl_printer.h
new file mode 100644
index 0000000..321d513
--- /dev/null
+++ b/src/auxiliaries/opengl_printer.h
@@ -0,0 +1,817 @@
+#ifndef AUXILIARIES_OPENGL_PRINTER_H_
+#define AUXILIARIES_OPENGL_PRINTER_H_
+
+#include <iostream>
+#include <sstream>
+#include <string>
+#include <vector>
+#include <limits>
+
+namespace auxiliaries
+{
+
+class OpenGLPrinter
+{
+public:
+ OpenGLPrinter()
+ {
+ }
+
+ void add(const std::string& str)
+ {
+ string_stream_ << " " << str;
+ }
+
+ void add_alpha(const double alpha)
+ {
+ string_stream_ << object_typer_.alpha << " " << alpha << " ";
+ }
+
+ void add_color(const unsigned int rgb)
+ {
+ string_stream_ << object_typer_.color << " ";
+ write_color_to_stream(Color(rgb), string_stream_);
+ }
+
+ void add_color(const double r, const double g, const double b)
+ {
+ string_stream_ << object_typer_.color << " ";
+ write_color_to_stream(Color(r, g, b), string_stream_);
+ }
+
+ void add_color_from_blue_white_red_gradient(const double value)
+ {
+ string_stream_ << object_typer_.color << " ";
+ write_color_to_stream(Color::from_blue_white_red_gradient(value), string_stream_);
+ }
+
+ void add_color_from_rainbow_gradient(const double value)
+ {
+ string_stream_ << object_typer_.color << " ";
+ write_color_to_stream(Color::from_rainbow_gradient(value), string_stream_);
+ }
+
+ template<typename SphereType>
+ void add_sphere(const SphereType& sphere)
+ {
+ string_stream_ << object_typer_.sphere << " ";
+ write_point_to_stream(sphere, string_stream_);
+ string_stream_.precision(3);
+ string_stream_ << std::fixed << sphere.r << " ";
+ }
+
+ template<typename PointType>
+ void add_triangle_strip(const std::vector<PointType>& vertices, const std::vector<PointType>& normals)
+ {
+ if(!vertices.empty() && vertices.size()==normals.size())
+ {
+ string_stream_ << object_typer_.tstrip << " ";
+ write_points_vector_to_stream(vertices, string_stream_);
+ write_points_vector_to_stream(normals, string_stream_);
+ }
+ }
+
+ template<typename PointType>
+ void add_triangle_fan(const std::vector<PointType>& vertices, const std::vector<PointType>& normals)
+ {
+ if(!vertices.empty() && vertices.size()==normals.size())
+ {
+ string_stream_ << object_typer_.tfan << " ";
+ write_points_vector_to_stream(vertices, string_stream_);
+ write_points_vector_to_stream(normals, string_stream_);
+ }
+ }
+
+ template<typename PointType>
+ void add_line_strip(const std::vector<PointType>& vertices)
+ {
+ if(!vertices.empty())
+ {
+ string_stream_ << object_typer_.lstrip << " ";
+ write_points_vector_to_stream(vertices, string_stream_);
+ }
+ }
+
+ template<typename PointType>
+ void add_line_strip(const PointType& a, const PointType& b)
+ {
+ std::vector<PointType> vertices(2);
+ vertices[0]=a;
+ vertices[1]=b;
+ add_line_strip(vertices);
+ }
+
+ template<typename PointType>
+ void add_line_loop(const std::vector<PointType>& vertices)
+ {
+ if(!vertices.empty())
+ {
+ string_stream_ << object_typer_.lloop << " ";
+ write_points_vector_to_stream(vertices, string_stream_);
+ }
+ }
+
+ template<typename PointType>
+ void add_triangle_fan(const PointType& center, const std::vector<PointType>& vertices, const PointType& normal)
+ {
+ if(!vertices.empty())
+ {
+ string_stream_ << object_typer_.tfanc << " ";
+ write_point_to_stream(center, string_stream_);
+ write_point_to_stream(normal, string_stream_);
+ write_points_vector_to_stream(vertices, string_stream_);
+ }
+ }
+
+ void add_label(const std::string& label)
+ {
+ string_stream_ << object_typer_.label << " " << remove_unsafe_characters_in_string(label) << " ";
+ }
+
+ std::string str() const
+ {
+ return string_stream_.str();
+ }
+
+ void print_pymol_script(const std::string& obj_name, const bool two_sided_lighting, std::ostream& output) const
+ {
+ std::istringstream input(str());
+ if(!input.good())
+ {
+ return;
+ }
+ const std::string sep=", ";
+ const std::string bigsep=",\n";
+ output << "from pymol.cgo import *\n";
+ output << "from pymol import cmd\n";
+ output << obj_name << " = [";
+ while(input.good())
+ {
+ std::string type_str;
+ input >> type_str;
+ const ObjectTypeMarker type(type_str, object_typer_);
+ if(type.alpha)
+ {
+ double alpha=1.0;
+ input >> alpha;
+ output << "ALPHA, " << alpha << bigsep;
+ }
+ else if(type.color)
+ {
+ write_color_to_stream(read_color_from_stream(input), true, "COLOR, ", sep, bigsep, output);
+ }
+ else if(type.tstrip || type.tfan || type.tfanc)
+ {
+ std::vector<PlainPoint> vertices;
+ std::vector<PlainPoint> normals;
+ if(read_strip_or_fan_from_stream(type.tstrip, type.tfan, type.tfanc, input, vertices, normals))
+ {
+ output << (type.tstrip ? "BEGIN, TRIANGLE_STRIP" : "BEGIN, TRIANGLE_FAN") << bigsep;
+ for(std::size_t i=0;i<vertices.size();i++)
+ {
+ write_point_to_stream(normals[i], "NORMAL, ", sep, bigsep, output);
+ write_point_to_stream(vertices[i], "VERTEX, ", sep, bigsep, output);
+ }
+ output << "END" << bigsep;
+ }
+ }
+ else if(type.lstrip || type.lloop)
+ {
+ const std::vector<PlainPoint> vertices=read_points_vector_from_stream(input);
+ if(!vertices.empty())
+ {
+ output << (type.lstrip ? "BEGIN, LINE_STRIP" : "BEGIN, LINE_LOOP") << bigsep;
+ for(std::size_t i=0;i<vertices.size();i++)
+ {
+ write_point_to_stream(vertices[i], "VERTEX, ", sep, bigsep, output);
+ }
+ output << "END" << bigsep;
+ }
+ }
+ else if(type.sphere)
+ {
+ const PlainPoint c=read_point_from_stream(input);
+ double r;
+ input >> r;
+ write_point_to_stream(c, "SPHERE, ", sep, sep, output);
+ output << r << bigsep;
+ }
+ }
+ output << "]\n";
+ output << "cmd.load_cgo(" << obj_name << ", '" << obj_name << "')\n";
+ output << "cmd.set('two_sided_lighting', '" << (two_sided_lighting ? "on" : "off") << "')\n";
+ }
+
+ void print_jmol_script(const std::string& obj_name, std::ostream& output) const
+ {
+ std::istringstream input(str());
+ if(!input.good())
+ {
+ return;
+ }
+ double alpha=1.0;
+ Color color(0xFFFFFF);
+ std::vector<PlainPoint> global_vertices;
+ std::vector<PlainTriple> global_triples;
+ while(input.good())
+ {
+ std::string type_str;
+ input >> type_str;
+ const ObjectTypeMarker type(type_str, object_typer_);
+ if(type.alpha || type.color)
+ {
+ print_jmol_polygon(global_vertices, global_triples, color, alpha, obj_name, output);
+ if(type.alpha)
+ {
+ input >> alpha;
+ alpha=(1.0-alpha);
+ }
+ else if(type.color)
+ {
+ color=read_color_from_stream(input);
+ }
+ }
+ else if(type.tstrip || type.tfan || type.tfanc)
+ {
+ std::vector<PlainPoint> vertices;
+ std::vector<PlainPoint> normals;
+ if(read_strip_or_fan_from_stream(type.tstrip, type.tfan, type.tfanc, input, vertices, normals))
+ {
+ const std::size_t offset=global_vertices.size();
+ global_vertices.insert(global_vertices.end(), vertices.begin(), vertices.end());
+ for(std::size_t i=0;(i+2)<vertices.size();i++)
+ {
+ global_triples.push_back(PlainTriple(offset+(type.tstrip ? i : 0), offset+(i+1), offset+(i+2)));
+ }
+ }
+ }
+ }
+ print_jmol_polygon(global_vertices, global_triples, color, alpha, obj_name, output);
+ }
+
+ void print_scenejs_script(const std::string& obj_name, const bool fit, std::ostream& output) const
+ {
+ std::istringstream input(str());
+ if(!input.good())
+ {
+ return;
+ }
+ std::ostringstream body_output;
+ Color color(0xFFFFFF);
+ std::string label="undefined";
+ std::vector<PlainPoint> global_vertices;
+ std::vector<PlainPoint> global_normals;
+ std::vector<PlainTriple> global_triples;
+ std::vector< std::pair<PlainPoint, double> > global_spheres;
+ BoundingBox bounding_box;
+ while(input.good())
+ {
+ std::string type_str;
+ input >> type_str;
+ const ObjectTypeMarker type(type_str, object_typer_);
+ if(type.color || type.label)
+ {
+ print_scenejs_polygon(global_vertices, global_normals, global_triples, color, label, body_output);
+ if(type.color)
+ {
+ color=read_color_from_stream(input);
+ }
+ else if(type.label)
+ {
+ input >> label;
+ }
+ }
+ else if(type.tstrip || type.tfan || type.tfanc)
+ {
+ std::vector<PlainPoint> vertices;
+ std::vector<PlainPoint> normals;
+ if(read_strip_or_fan_from_stream(type.tstrip, type.tfan, type.tfanc, input, vertices, normals) && vertices.size()==normals.size())
+ {
+ const std::size_t offset=global_vertices.size();
+ global_vertices.insert(global_vertices.end(), vertices.begin(), vertices.end());
+ global_normals.insert(global_normals.end(), normals.begin(), normals.end());
+ for(std::size_t i=0;(i+2)<vertices.size();i++)
+ {
+ global_triples.push_back(PlainTriple(offset+(type.tstrip ? i : 0), offset+(i+1), offset+(i+2)));
+ }
+ for(std::size_t i=0;i<vertices.size();i++)
+ {
+ bounding_box.update(vertices[i]);
+ }
+ }
+ }
+ else if(type.sphere)
+ {
+ const PlainPoint c=read_point_from_stream(input);
+ double r;
+ input >> r;
+ global_spheres.push_back(std::make_pair(c, r));
+ bounding_box.update(c);
+ print_scenejs_spheres(global_spheres, color, label, body_output);
+ }
+ }
+ print_scenejs_polygon(global_vertices, global_normals, global_triples, color, label, body_output);
+ {
+ output.precision(3);
+ output << "var " << obj_name << "={nodes:[\n" << body_output.str() << "]\n};\n";
+ if(fit)
+ {
+ const std::pair<PlainPoint, double> transformation=bounding_box.calc_normal_transformation();
+ output << "var " << obj_name << "_view={type:\"scale\",x:" << std::fixed << transformation.second << ",y:" << transformation.second << ",z:" << transformation.second << ",\n";
+ {
+ output << "nodes:[{type:\"translate\",x:" << std::fixed << transformation.first.x << ",y:" << transformation.first.y << ",z:" << transformation.first.z << ",\n";
+ {
+ output << "nodes:[{\n";
+ {
+ output << "id:\"" << obj_name << "_view\"";
+ }
+ output << "\n}]\n";
+ }
+ output << "}]\n";
+ }
+ output << "};\n";
+ }
+ }
+ }
+
+private:
+ struct ObjectTyper
+ {
+ std::string alpha;
+ std::string color;
+ std::string label;
+ std::string tstrip;
+ std::string tfan;
+ std::string tfanc;
+ std::string lstrip;
+ std::string lloop;
+ std::string sphere;
+
+ ObjectTyper() :
+ alpha("_alpha"),
+ color("_color"),
+ label("_label"),
+ tstrip("_tstrip"),
+ tfan("_tfan"),
+ tfanc("_tfanc"),
+ lstrip("_lstrip"),
+ lloop("_lloop"),
+ sphere("_sphere")
+ {
+ }
+ };
+
+ struct ObjectTypeMarker
+ {
+ bool alpha;
+ bool color;
+ bool label;
+ bool tstrip;
+ bool tfan;
+ bool tfanc;
+ bool lstrip;
+ bool lloop;
+ bool sphere;
+
+ ObjectTypeMarker(const std::string& type_str, const ObjectTyper& object_typer) :
+ alpha(type_str==object_typer.alpha),
+ color(type_str==object_typer.color),
+ label(type_str==object_typer.label),
+ tstrip(type_str==object_typer.tstrip),
+ tfan(type_str==object_typer.tfan),
+ tfanc(type_str==object_typer.tfanc),
+ lstrip(type_str==object_typer.lstrip),
+ lloop(type_str==object_typer.lloop),
+ sphere(type_str==object_typer.sphere)
+ {
+ }
+ };
+
+ struct PlainPoint
+ {
+ double x;
+ double y;
+ double z;
+
+ PlainPoint() : x(0), y(0), z(0)
+ {
+ }
+
+ PlainPoint(const double x, const double y, const double z) : x(x), y(y), z(z)
+ {
+ }
+ };
+
+ struct PlainTriple
+ {
+ std::size_t a;
+ std::size_t b;
+ std::size_t c;
+
+ PlainTriple() : a(0), b(0), c(0)
+ {
+ }
+
+ PlainTriple(const std::size_t a, const std::size_t b, const std::size_t c) : a(a), b(b), c(c)
+ {
+ }
+ };
+
+ struct Color
+ {
+ unsigned int r;
+ unsigned int g;
+ unsigned int b;
+
+ Color() : r(0), g(0), b(0)
+ {
+ }
+
+ explicit Color(const unsigned int rgb) : r((rgb&0xFF0000) >> 16), g((rgb&0x00FF00) >> 8), b(rgb&0x0000FF)
+ {
+ }
+
+ Color(const double r, const double g, const double b) : r(color_component_from_ratio(r)), g(color_component_from_ratio(g)), b(color_component_from_ratio(b))
+ {
+ }
+
+ static unsigned int color_component_from_ratio(const double r)
+ {
+ return static_cast<unsigned int>(std::min(std::max(r*255.0, 0.0), 255.0));
+ }
+
+ static Color from_blue_white_red_gradient(const double value)
+ {
+ Color color;
+ if(value<0)
+ {
+ color.b=255;
+ }
+ else if(value>1)
+ {
+ color.r=255;
+ }
+ else if(value<=0.5)
+ {
+ color.b=255;
+ color.r=static_cast<unsigned char>(255*(value/0.5));
+ color.g=color.r;
+ }
+ else if(value>0.5)
+ {
+ color.r=255;
+ color.b=static_cast<unsigned char>(255*(1-(value-0.5)/0.5));
+ color.g=color.b;
+ }
+ return color;
+ }
+
+ static Color from_rainbow_gradient(const double value)
+ {
+ Color color;
+ if(value<0)
+ {
+ color.b=255;
+ }
+ else if(value>1)
+ {
+ color.r=255;
+ }
+ else if(value<=0.25)
+ {
+ color.g=static_cast<unsigned char>(255*(value/0.25));
+ color.b=255;
+ }
+ else if(value<=0.5)
+ {
+ color.g=255;
+ color.b=static_cast<unsigned char>(255*(1-(value-0.25)/0.25));
+ }
+ else if(value<=0.75)
+ {
+ color.r=static_cast<unsigned char>(255*((value-0.5)/0.25));
+ color.g=255;
+ }
+ else if(value<=1.0)
+ {
+ color.r=255;
+ color.g=static_cast<unsigned char>(255*(1-(value-0.75)/0.25));
+ }
+ return color;
+ }
+ };
+
+ class BoundingBox
+ {
+ public:
+ BoundingBox() : modified_(false)
+ {
+ const double max_double=std::numeric_limits<double>::max();
+ const double min_double=-max_double;
+ low_=PlainPoint(max_double, max_double, max_double);
+ high_=PlainPoint(min_double, min_double, min_double);
+ }
+
+ template<typename PointType>
+ void update(const PointType& p)
+ {
+ low_.x=std::min(low_.x, p.x);
+ low_.y=std::min(low_.y, p.y);
+ low_.z=std::min(low_.z, p.z);
+ high_.x=std::max(high_.x, p.x);
+ high_.y=std::max(high_.y, p.y);
+ high_.z=std::max(high_.z, p.z);
+ modified_=true;
+ }
+
+ std::pair<PlainPoint, double> calc_normal_transformation() const
+ {
+ if(modified_)
+ {
+ const PlainPoint translation(0.0-((low_.x+high_.x)*0.5), 0.0-((low_.y+high_.y)*0.5), 0.0-((low_.z+high_.z)*0.5));
+ const double max_side=std::max(high_.x-low_.x, std::max(high_.y-low_.y, high_.z-low_.z));
+ return std::make_pair(translation, (max_side>0.0 ? 2.0/max_side : 1.0));
+ }
+ else
+ {
+ return std::make_pair(PlainPoint(), 1.0);
+ }
+ }
+
+ private:
+ bool modified_;
+ PlainPoint low_;
+ PlainPoint high_;
+ };
+
+ template<typename PointType>
+ static void write_point_to_stream(const PointType& p, const std::string& start, const std::string& sep, const std::string& end, std::ostream& output)
+ {
+ output << start;
+ output.precision(3);
+ output << std::fixed << p.x << sep << p.y << sep << p.z;
+ output << end;
+ }
+
+ template<typename PointType>
+ static void write_point_to_stream(const PointType& p, std::ostream& output)
+ {
+ write_point_to_stream(p, "", " ", " ", output);
+ }
+
+ static PlainPoint read_point_from_stream(std::istream& input)
+ {
+ PlainPoint p;
+ input >> p.x >> p.y >> p.z;
+ return p;
+ }
+
+ template<typename PointType>
+ static void write_points_vector_to_stream(const std::vector<PointType>& v, std::ostream& output)
+ {
+ output << v.size() << " ";
+ for(std::size_t i=0;i<v.size();i++)
+ {
+ write_point_to_stream(v[i], output);
+ }
+ }
+
+ static std::vector<PlainPoint> read_points_vector_from_stream(std::istream& input)
+ {
+ std::size_t n=0;
+ input >> n;
+ std::vector<PlainPoint> v(n);
+ for(std::size_t i=0;i<v.size();i++)
+ {
+ v[i]=read_point_from_stream(input);
+ }
+ return v;
+ }
+
+ static void write_color_to_stream(const Color& c, const bool normalized, const std::string& start, const std::string& sep, const std::string& end, std::ostream& output)
+ {
+ output << start;
+ if(normalized)
+ {
+ output.precision(3);
+ output << std::fixed << (static_cast<double>(c.r)/255.0) << sep << (static_cast<double>(c.g)/255.0) << sep << (static_cast<double>(c.b)/255.0);
+ }
+ else
+ {
+ output << c.r << sep << c.g << sep << c.b;
+ }
+ output << end;
+ }
+
+ static void write_color_to_stream(const Color& c, std::ostream& output)
+ {
+ write_color_to_stream(c, false, "", " ", " ", output);
+ }
+
+ static Color read_color_from_stream(std::istream& input)
+ {
+ Color c;
+ input >> c.r >> c.g >> c.b;
+ return c;
+ }
+
+ static bool read_strip_or_fan_from_stream(
+ const bool tstrip,
+ const bool tfan,
+ const bool tfanc,
+ std::istream& input,
+ std::vector<PlainPoint>& vertices,
+ std::vector<PlainPoint>& normals)
+ {
+ vertices.clear();
+ normals.clear();
+ if(tstrip || tfan)
+ {
+ vertices=read_points_vector_from_stream(input);
+ normals=read_points_vector_from_stream(input);
+ }
+ else if(tfanc)
+ {
+ const PlainPoint center=read_point_from_stream(input);
+ const PlainPoint normal=read_point_from_stream(input);
+ const std::vector<PlainPoint> outer_vertices=read_points_vector_from_stream(input);
+ if(!outer_vertices.empty())
+ {
+ vertices.push_back(center);
+ vertices.insert(vertices.end(), outer_vertices.begin(), outer_vertices.end());
+ vertices.push_back(outer_vertices.front());
+ normals.resize(vertices.size(), normal);
+ }
+ }
+ return (vertices.size()>=3 && vertices.size()==normals.size());
+ }
+
+ static void print_jmol_polygon(
+ std::vector<PlainPoint>& vertices,
+ std::vector<PlainTriple>& triples,
+ const Color& color,
+ const double alpha,
+ const std::string& id,
+ std::ostream& output)
+ {
+ static int use_num=0;
+ if(!(vertices.empty() || triples.empty()))
+ {
+ output << "draw " << id << use_num << " ";
+ output << "POLYGON " << vertices.size() << " ";
+ for(std::size_t i=0;i<vertices.size();i++)
+ {
+ write_point_to_stream(vertices[i], "{", " ", "} ", output);
+ }
+ output << triples.size();
+ for(std::size_t i=0;i<triples.size();i++)
+ {
+ const PlainTriple& t=triples[i];
+ output << " [" << t.a << " " << t.b << " " << t.c << " 0]";
+ }
+ output << "\n";
+ output << "color $" << id << use_num;
+ if(alpha>0.0)
+ {
+ output << " TRANSLUCENT " << alpha;
+ }
+ write_color_to_stream(color, false, " [", ",", "]\n", output);
+ use_num++;
+ }
+ vertices.clear();
+ triples.clear();
+ }
+
+ static void print_scenejs_polygon(
+ std::vector<PlainPoint>& vertices,
+ std::vector<PlainPoint>& normals,
+ std::vector<PlainTriple>& triples,
+ const Color& color,
+ const std::string& id,
+ std::ostream& output)
+ {
+ if(!(vertices.empty() || normals.size()!=vertices.size() || triples.empty()))
+ {
+ output << "{type:\"name\",name:\"" << restore_unsafe_characters_in_string(id) << "\",\n";
+ {
+ output << "nodes:[{type:\"material\",\n";
+ output.precision(3);
+ output << "color:{r:" << std::fixed << (static_cast<double>(color.r)/255.0) << ",g:" << (static_cast<double>(color.g)/255.0) << ",b:" << (static_cast<double>(color.b)/255.0) << "},\n";
+ {
+ output << "nodes:[{type:\"geometry\",primitive:\"triangles\",\n";
+ {
+ output << "positions:[\n";
+ for(std::size_t i=0;i<vertices.size();i++)
+ {
+ write_point_to_stream(vertices[i], (i==0 ? "" : ",\n"), ",", "", output);
+ }
+ output << "\n],\n";
+ }
+ {
+ output << "normals:[\n";
+ for(std::size_t i=0;i<normals.size();i++)
+ {
+ write_point_to_stream(normals[i], (i==0 ? "" : ",\n"), ",", "", output);
+ }
+ output << "\n],\n";
+ }
+ {
+ output << "indices:[\n";
+ for(std::size_t i=0;i<triples.size();i++)
+ {
+ const PlainTriple& t=triples[i];
+ output << (i==0 ? "" : ",\n") << t.a << "," << t.b << "," << t.c;
+ }
+ output << "\n],\n";
+ }
+ output << "}]\n";
+ }
+ output << "}]\n";
+ }
+ output << "},\n";
+ }
+ vertices.clear();
+ normals.clear();
+ triples.clear();
+ }
+
+ static void print_scenejs_spheres(
+ std::vector< std::pair<PlainPoint, double> >& spheres,
+ const Color& color,
+ const std::string& id,
+ std::ostream& output)
+ {
+ if(!spheres.empty())
+ {
+ output << "{type:\"name\",name:\"" << restore_unsafe_characters_in_string(id) << "\",\n";
+ {
+ output << "nodes:[{type:\"material\",\n";
+ output.precision(3);
+ output << "color:{r:" << std::fixed << (static_cast<double>(color.r)/255.0) << ",g:" << (static_cast<double>(color.g)/255.0) << ",b:" << (static_cast<double>(color.b)/255.0) << "},\n";
+ {
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ const std::pair<PlainPoint, double>& sphere=spheres[i];
+ output << "nodes:[{type:\"translate\",x:" << std::fixed << sphere.first.x << ",y:" << sphere.first.y << ",z:" << sphere.first.z << ",\n";
+ {
+ output << "nodes:[{type:\"scale\",x:" << std::fixed << sphere.second << ",y:" << sphere.second << ",z:" << sphere.second << ",\n";
+ {
+ output << "nodes:[{type: \"geometry/sphere\"}]\n";
+ }
+ output << "}]\n";
+ }
+ output << "}],\n";
+ }
+ }
+ output << "}]\n";
+ }
+ output << "},\n";
+ }
+ spheres.clear();
+ }
+
+
+ static std::string remove_unsafe_characters_in_string(const std::string& str)
+ {
+ std::ostringstream output;
+ for(std::size_t i=0;i<str.size();i++)
+ {
+ if(str[i]==' ')
+ {
+ output << "__";
+ }
+ else
+ {
+ output << str[i];
+ }
+ }
+ return output.str();
+ }
+
+ static std::string restore_unsafe_characters_in_string(const std::string& str)
+ {
+ std::ostringstream output;
+ std::size_t i=0;
+ while(i<str.size())
+ {
+ if(str[i]=='_' && (i+1)<str.size() && str[i+1]=='_')
+ {
+ output << ' ';
+ i+=2;
+ }
+ else
+ {
+ output << str[i];
+ i++;
+ }
+ }
+ return output.str();
+ }
+
+ ObjectTyper object_typer_;
+ std::ostringstream string_stream_;
+};
+
+}
+
+#endif /* AUXILIARIES_OPENGL_PRINTER_H_ */
diff --git a/src/auxiliaries/pairwise_sequence_alignment.h b/src/auxiliaries/pairwise_sequence_alignment.h
new file mode 100644
index 0000000..8555235
--- /dev/null
+++ b/src/auxiliaries/pairwise_sequence_alignment.h
@@ -0,0 +1,193 @@
+#ifndef AUXILIARIES_PAIRWISE_SEQUENCE_ALIGNMENT_H_
+#define AUXILIARIES_PAIRWISE_SEQUENCE_ALIGNMENT_H_
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <algorithm>
+
+namespace auxiliaries
+{
+
+class PairwiseSequenceAlignment
+{
+public:
+ struct SimpleScorer
+ {
+ int match_score;
+ int mismatch_score;
+ int gap_start_score;
+ int gap_extension_score;
+
+ SimpleScorer(int match_score, int mismatch_score, int gap_start_score, int gap_extension_score) :
+ match_score(match_score),
+ mismatch_score(mismatch_score),
+ gap_start_score(gap_start_score),
+ gap_extension_score(gap_extension_score)
+ {
+ }
+
+ template<typename T>
+ int match(const T& v1, const T& v2) const
+ {
+ return (v1==v2 ? match_score : mismatch_score);
+ }
+
+ int gap_start() const
+ {
+ return gap_start_score;
+ }
+
+ int gap_extension() const
+ {
+ return gap_extension_score;
+ }
+ };
+
+ template<typename T, typename Scorer>
+ static std::vector< std::pair<int, int> > construct_sequence_alignment(const T& seq1, const T& seq2, const Scorer& scorer, const bool local, int* result_score)
+ {
+ std::vector< std::pair<int, int> > alignment;
+ if(!seq1.empty() && !seq2.empty())
+ {
+ std::vector< std::vector<int> > scores_matrix(seq1.size()+1, std::vector<int>(seq2.size()+1, 0));
+ std::vector< std::vector<int> > directions_matrix(seq1.size()+1, std::vector<int>(seq2.size()+1, 0));
+ for(std::size_t i=1;i<=seq1.size();i++)
+ {
+ scores_matrix[i][0]=((i==1) ? scorer.gap_start() : (scores_matrix[i-1][0]+scorer.gap_extension()));
+ directions_matrix[i][0]=1;
+ }
+ for(std::size_t j=1;j<=seq2.size();j++)
+ {
+ scores_matrix[0][j]=((j==1) ? scorer.gap_start() : (scores_matrix[0][j-1]+scorer.gap_extension()));
+ directions_matrix[0][j]=2;
+ }
+ std::pair<std::size_t, std::size_t> result_score_pos(0, 0);
+ for(std::size_t i=1;i<=seq1.size();i++)
+ {
+ for(std::size_t j=1;j<=seq2.size();j++)
+ {
+ const typename T::value_type& v1=seq1[i-1];
+ const typename T::value_type& v2=seq2[j-1];
+ const int match_score=scores_matrix[i-1][j-1]+scorer.match(v1, v2)+(((i==1 && j==1) || (i==seq1.size() && j==seq2.size())) ? -1 : 0);
+ const int deletion_score=scores_matrix[i-1][j]+(directions_matrix[i-1][j]!=1 ? scorer.gap_start() : scorer.gap_extension());
+ const int insertion_score=scores_matrix[i][j-1]+(directions_matrix[i][j-1]!=2 ? scorer.gap_start() : scorer.gap_extension());
+ const int max_score=std::max(match_score, std::max(deletion_score, insertion_score));
+ directions_matrix[i][j]=(max_score==insertion_score ? 2 : (max_score==deletion_score ? 1 : 0));
+ scores_matrix[i][j]=(local ? std::max(0, max_score) : max_score);
+ if(local && scores_matrix[i][j]>scores_matrix[result_score_pos.first][result_score_pos.second])
+ {
+ result_score_pos=std::make_pair(i, j);
+ }
+ }
+ }
+ if(!local)
+ {
+ result_score_pos.first=seq1.size();
+ result_score_pos.second=seq2.size();
+ }
+ if(result_score!=0)
+ {
+ *result_score=scores_matrix[result_score_pos.first][result_score_pos.second];
+ }
+
+ int i=static_cast<int>(seq1.size());
+ int j=static_cast<int>(seq2.size());
+ while(i>static_cast<int>(result_score_pos.first))
+ {
+ i--;
+ alignment.push_back(std::make_pair(i, -1));
+ }
+ while(j>static_cast<int>(result_score_pos.second))
+ {
+ j--;
+ alignment.push_back(std::make_pair(-1, j));
+ }
+ while(i>0 && j>0 && (!local || scores_matrix[i][j]>0))
+ {
+ const int dir=directions_matrix[i][j];
+ if(dir==0)
+ {
+ i--;
+ j--;
+ alignment.push_back(std::make_pair(i, j));
+ }
+ else if(dir==1)
+ {
+ i--;
+ alignment.push_back(std::make_pair(i, -1));
+ }
+ else
+ {
+ j--;
+ alignment.push_back(std::make_pair(-1, j));
+ }
+ }
+ while(i>0)
+ {
+ i--;
+ alignment.push_back(std::make_pair(i, -1));
+ }
+ while(j>0)
+ {
+ j--;
+ alignment.push_back(std::make_pair(-1, j));
+ }
+ std::reverse(alignment.begin(), alignment.end());
+ }
+ return alignment;
+ }
+
+ static bool print_sequence_alignment(const std::string& seq1, const std::string& seq2, const std::vector< std::pair<int, int> >& alignment, std::ostream& output)
+ {
+ for(std::size_t i=0;i<alignment.size();i++)
+ {
+ if(alignment[i].first>=static_cast<int>(seq1.size()) || alignment[i].second>=static_cast<int>(seq2.size()))
+ {
+ return false;
+ }
+ }
+
+ for(std::size_t i=0;i<alignment.size();i++)
+ {
+ const int j=alignment[i].first;
+ output << (j>=0 ? seq1.at(j) : '-');
+ }
+ output << "\n";
+
+ for(std::size_t i=0;i<alignment.size();i++)
+ {
+ const int j=alignment[i].second;
+ output << (j>=0 ? seq2.at(j) : '-');
+ }
+ output << "\n";
+
+ return true;
+ }
+
+ static std::vector< std::pair<int, int> > read_sequence_alignment(const std::string& alignment_seq1, const std::string& alignment_seq2)
+ {
+ const std::size_t alignment_size=std::min(alignment_seq1.size(), alignment_seq2.size());
+ std::vector< std::pair<int, int> > alignment(alignment_size, std::pair<int, int>(-1, -1));
+ int pos1=0;
+ int pos2=0;
+ for(std::size_t i=0;i<alignment_size;i++)
+ {
+ if(alignment_seq1.at(i)!='-')
+ {
+ alignment[i].first=pos1;
+ pos1++;
+ }
+ if(alignment_seq2.at(i)!='-')
+ {
+ alignment[i].second=pos2;
+ pos2++;
+ }
+ }
+ return alignment;
+ }
+};
+
+}
+
+#endif /* AUXILIARIES_PAIRWISE_SEQUENCE_ALIGNMENT_H_ */
diff --git a/src/auxiliaries/program_options_handler.h b/src/auxiliaries/program_options_handler.h
new file mode 100644
index 0000000..da7a4a9
--- /dev/null
+++ b/src/auxiliaries/program_options_handler.h
@@ -0,0 +1,454 @@
+#ifndef AUXILIARIES_PROGRAM_OPTIONS_HANDLER_H_
+#define AUXILIARIES_PROGRAM_OPTIONS_HANDLER_H_
+
+#include <string>
+#include <map>
+#include <vector>
+#include <sstream>
+#include <stdexcept>
+#include <iostream>
+#include <iomanip>
+#include <algorithm>
+
+namespace auxiliaries
+{
+
+class ProgramOptionsHandler
+{
+public:
+ class Exception : public std::runtime_error
+ {
+ public:
+ explicit Exception(const std::string& msg) : std::runtime_error(msg)
+ {
+ }
+ };
+
+ ProgramOptionsHandler(const int argc, const char** argv)
+ {
+ if(argc>0)
+ {
+ original_argv_.resize(argc);
+ for(int i=0;i<argc;i++)
+ {
+ original_argv_[i]=unquote_string(std::string(argv[i]));
+ }
+ for(std::size_t i=0;i<original_argv_.size();i++)
+ {
+ const std::string& str=original_argv_[i];
+ if(i>0 && str.compare(0, option_prefix_str().size(), option_prefix_str())==0)
+ {
+ options_[str]="";
+ }
+ else if(i>1 && original_argv_[i-1].compare(0, option_prefix_str().size(), option_prefix_str())==0)
+ {
+ options_[original_argv_[i-1]]=str;
+ }
+ else
+ {
+ unused_argv_.push_back(str);
+ }
+ }
+ }
+ }
+
+ const std::vector<std::string>& original_argv() const
+ {
+ return original_argv_;
+ }
+
+ std::string original_arg(const std::size_t pos) const
+ {
+ return (pos<original_argv_.size() ? original_argv_[pos] : std::string());
+ }
+
+ const std::vector<std::string>& unused_argv() const
+ {
+ return unused_argv_;
+ }
+
+ const std::map<std::string, std::string>& options() const
+ {
+ return options_;
+ }
+
+ bool empty() const
+ {
+ return options_.empty();
+ }
+
+ void set_option(const std::string& name)
+ {
+ if(name.compare(0, option_prefix_str().size(), option_prefix_str())==0)
+ {
+ options_[name]="";
+ }
+ }
+
+ template<typename T>
+ void set_option_with_argument(const std::string& name, const T value)
+ {
+ if(name.compare(0, option_prefix_str().size(), option_prefix_str())==0)
+ {
+ std::ostringstream output;
+ output << value;
+ options_[name]=output.str();
+ }
+ }
+
+ bool contains_option(const std::string& name) const
+ {
+ return (options_.count(name)>0);
+ }
+
+ bool contains_option_with_argument(const std::string& name) const
+ {
+ return (contains_option(name) && !(options_.find(name)->second.empty()));
+ }
+
+ const std::string& argument_string(const std::string& name) const
+ {
+ if(!contains_option_with_argument(name))
+ {
+ throw Exception(std::string("Missing command line argument for option '")+name+"'.");
+ }
+ return options_.find(name)->second;
+ }
+
+ template<typename T>
+ T argument(const std::string& name) const
+ {
+ std::istringstream input(argument_string(name));
+ T value;
+ input >> value;
+ if(input.fail())
+ {
+ throw Exception(std::string("Invalid command line argument for option '")+name+"'.");
+ }
+ return value;
+ }
+
+ template<typename T>
+ T argument(const std::string& name, const T default_value) const
+ {
+ if(contains_option(name))
+ {
+ return argument<T>(name);
+ }
+ else
+ {
+ return default_value;
+ }
+ }
+
+ std::vector<std::string> argument_strings_vector(const std::string& name, const char delimiter) const
+ {
+ std::vector<std::string> result;
+ if(contains_option(name))
+ {
+ result=split_string(argument_string(name), delimiter);
+ if(result.empty())
+ {
+ throw Exception(std::string("Missing command line vector argument for option '")+name+"'.");
+ }
+ }
+ return result;
+ }
+
+ template<typename T>
+ std::vector<T> argument_vector(const std::string& name, const char delimiter) const
+ {
+ std::vector<T> result;
+ const std::vector<std::string> result_as_strings=argument_strings_vector(name, delimiter);
+ if(!result_as_strings.empty())
+ {
+ result=convert_string_vector_to_typed_vector<T>(result_as_strings);
+ }
+ return result;
+ }
+
+ template<typename T>
+ std::vector<T> argument_vector(const std::string& name, const char delimiter, const std::vector<T>& default_value) const
+ {
+ if(contains_option(name))
+ {
+ return argument_vector<T>(name, delimiter);
+ }
+ else
+ {
+ return default_value;
+ }
+ }
+
+ void remove_option(const std::string& name)
+ {
+ options_.erase(name);
+ }
+
+ template<typename T>
+ static T convert_hex_string_to_integer(const std::string& str)
+ {
+ std::istringstream input(str);
+ T value=0;
+ input >> std::hex >> value;
+ if(input.fail())
+ {
+ throw Exception(std::string("Invalid hex string '")+str+"'.");
+ }
+ return value;
+ }
+
+ template<typename T>
+ static T restrict_value_in_range(const T min_value, const T max_value, const T value)
+ {
+ return std::max(min_value, std::min(max_value, value));
+ }
+
+private:
+ static const std::string& option_prefix_str()
+ {
+ static const std::string str("--");
+ return str;
+ }
+
+ static std::string unquote_string(const std::string& str)
+ {
+ if(str.size()>2 && str[0]==str[str.size()-1] && (str[0]=='\'' || str[0]=='"'))
+ {
+ return str.substr(1, str.size()-2);
+ }
+ return str;
+ }
+
+ static std::vector<std::string> split_string(const std::string& str, const char delimiter)
+ {
+ std::vector<std::string> result;
+ std::istringstream input(str);
+ while(input.good())
+ {
+ std::string token;
+ std::getline(input, token, delimiter);
+ if(token.empty())
+ {
+ throw Exception(std::string("Empty substring encountered when splitting '")+str+"'.");
+ }
+ result.push_back(token);
+ }
+ return result;
+ }
+
+ template<typename T>
+ static std::vector<T> convert_string_vector_to_typed_vector(const std::vector<std::string>& strs)
+ {
+ std::vector<T> result;
+ for(std::size_t i=0;i<strs.size();i++)
+ {
+ std::string token=strs[i];
+ const std::size_t end_pos=token.find_last_not_of(' ');
+ if(end_pos!=std::string::npos && (end_pos+1)<=token.size())
+ {
+ token=token.substr(0, end_pos+1);
+ }
+ std::istringstream token_input(token);
+ T value;
+ token_input >> value;
+ if(token_input.fail())
+ {
+ throw Exception(std::string("Failed to convert token '")+token+"'.");
+ }
+ result.push_back(value);
+ if(!token_input.eof())
+ {
+ throw Exception(std::string("Too many spaces in token '")+token+"'.");
+ }
+ }
+ return result;
+ }
+
+ std::vector<std::string> original_argv_;
+ std::vector<std::string> unused_argv_;
+ std::map<std::string, std::string> options_;
+};
+
+class ProgramOptionsHandlerWrapper
+{
+public:
+ class Exception : public std::runtime_error
+ {
+ public:
+ explicit Exception(const std::string& msg) : std::runtime_error(msg)
+ {
+ }
+ };
+
+ const ProgramOptionsHandler& poh;
+
+ explicit ProgramOptionsHandlerWrapper(const ProgramOptionsHandler& poh) : poh(poh)
+ {
+ }
+
+ std::string describe_option(const std::string& name, const std::string& argument_type, const std::string& description_text, const bool required=false)
+ {
+ list_of_option_descriptions_.push_back(OptionDescription(name, argument_type, description_text, required));
+ return name;
+ }
+
+ void describe_io(const std::string& name, const bool from, const bool to, const std::string& description)
+ {
+ list_of_io_descriptions_.push_back(IODescription(name, from, to, description));
+ }
+
+ bool assert_or_print_help(const bool allow_unrecognized_options) const
+ {
+ if(poh.contains_option("--help"))
+ {
+ {
+ std::vector<OptionDescription> basic_list_of_option_descriptions=list_of_option_descriptions_;
+ basic_list_of_option_descriptions.push_back(OptionDescription("--help", "", "flag to print usage help to stdout and exit", false));
+ print_list_of_option_descriptions(basic_list_of_option_descriptions, std::cout);
+ }
+ print_list_of_io_descriptions(list_of_io_descriptions_, std::cout);
+ return false;
+ }
+ else
+ {
+ assert_list_of_option_descriptions(allow_unrecognized_options);
+ return true;
+ }
+ }
+
+private:
+ struct OptionDescription
+ {
+ std::string name;
+ std::string argument_type;
+ std::string description_text;
+ bool required;
+
+ OptionDescription(const std::string& name, const std::string& argument_type, const std::string& description_text, const bool required) :
+ name(name), argument_type(argument_type), description_text(description_text), required(required)
+ {
+ }
+
+ bool operator==(const std::string& check_name) const
+ {
+ return (check_name==name);
+ }
+
+ void print(const std::size_t max_option_name_length, const std::size_t max_argument_type_length, std::ostream& output) const
+ {
+ output << name << std::string(std::max(max_option_name_length, name.size())+2-name.size(), ' ');
+ output << argument_type << std::string(std::max(max_argument_type_length, argument_type.size())+2-argument_type.size(), ' ');
+ output << (required ? "*" : " ") << " ";
+ output << description_text << "\n";
+ }
+ };
+
+ struct IODescription
+ {
+ std::string name;
+ bool from;
+ bool to;
+ std::string description;
+
+ IODescription(const std::string& name, const bool from, const bool to, const std::string& description) :
+ name(name), from(from), to(to), description(description)
+ {
+ }
+
+ void print(std::ostream& output) const
+ {
+ const std::size_t max_name_length=std::max(static_cast<std::size_t>(7), name.size());
+ output << name << std::string(max_name_length+1-name.size(), ' ');
+ if(from && to)
+ {
+ output << "<->";
+ }
+ else if(from)
+ {
+ output << "<- ";
+ }
+ else if(to)
+ {
+ output << "-> ";
+ }
+ std::istringstream strstream(description);
+ int linescount=0;
+ while(strstream.good())
+ {
+ std::string line;
+ std::getline(strstream, line);
+ if(!line.empty())
+ {
+ if(linescount>0)
+ {
+ output << std::string(max_name_length+6, ' ');
+ }
+ output << " " << line << "\n";
+ linescount++;
+ }
+ }
+ }
+ };
+
+ static void print_list_of_option_descriptions(const std::vector<OptionDescription>& list_of_option_descriptions, std::ostream& output)
+ {
+ std::size_t max_option_name_length=30;
+ std::size_t max_argument_type_length=7;
+ for(std::vector<OptionDescription>::const_iterator it=list_of_option_descriptions.begin();it!=list_of_option_descriptions.end();++it)
+ {
+ max_option_name_length=std::max(max_option_name_length, it->name.size());
+ max_argument_type_length=std::max(max_argument_type_length, it->argument_type.size());
+ }
+ for(std::vector<OptionDescription>::const_iterator it=list_of_option_descriptions.begin();it!=list_of_option_descriptions.end();++it)
+ {
+ it->print(max_option_name_length, max_argument_type_length, output);
+ }
+ }
+
+ static void print_list_of_io_descriptions(const std::vector<IODescription>& list_of_io_descriptions, std::ostream& output)
+ {
+ for(std::vector<IODescription>::const_iterator it=list_of_io_descriptions.begin();it!=list_of_io_descriptions.end();++it)
+ {
+ it->print(output);
+ }
+ }
+
+ void assert_list_of_option_descriptions(const bool allow_unrecognized) const
+ {
+ for(std::vector<OptionDescription>::const_iterator it=list_of_option_descriptions_.begin();it!=list_of_option_descriptions_.end();++it)
+ {
+ if(it->required && poh.options().count(it->name)==0)
+ {
+ throw Exception(std::string("Missing required option '")+(it->name)+"'.");
+ }
+ }
+ for(std::map<std::string, std::string>::const_iterator it=poh.options().begin();it!=poh.options().end();++it)
+ {
+ const std::string& option=it->first;
+ std::vector<OptionDescription>::const_iterator jt=std::find(list_of_option_descriptions_.begin(), list_of_option_descriptions_.end(), option);
+ if(jt==list_of_option_descriptions_.end())
+ {
+ if(!allow_unrecognized)
+ {
+ throw Exception(std::string("Unrecognized command line option '")+option+"'.");
+ }
+ }
+ else if(it->second.empty() && !jt->argument_type.empty())
+ {
+ throw Exception(std::string("Command line option '")+option+"' should have arguments.");
+ }
+ else if(!it->second.empty() && jt->argument_type.empty())
+ {
+ throw Exception(std::string("Command line option '")+option+"' cannot have arguments.");
+ }
+ }
+ }
+
+ std::vector<OptionDescription> list_of_option_descriptions_;
+ std::vector<IODescription> list_of_io_descriptions_;
+};
+
+}
+
+#endif /* AUXILIARIES_PROGRAM_OPTIONS_HANDLER_H_ */
diff --git a/src/auxiliaries/residue_atoms_reference.h b/src/auxiliaries/residue_atoms_reference.h
new file mode 100644
index 0000000..86bf715
--- /dev/null
+++ b/src/auxiliaries/residue_atoms_reference.h
@@ -0,0 +1,53 @@
+#ifndef AUXILIARIES_RESIDUE_ATOMS_REFERENCE_H_
+#define AUXILIARIES_RESIDUE_ATOMS_REFERENCE_H_
+
+#include <string>
+#include <map>
+
+namespace auxiliaries
+{
+
+class ResidueAtomsReference
+{
+public:
+ inline static int get_residue_atoms_count(const std::string& code)
+ {
+ static const std::map<std::string, int> m=create_map_of_residue_atoms_counts();
+ const std::map<std::string, int>::const_iterator it=m.find(code);
+ return (it==m.end() ? 1 : it->second);
+ }
+
+private:
+ static std::map<std::string, int> create_map_of_residue_atoms_counts()
+ {
+ std::map<std::string, int> m;
+ m["ALA"]=5;
+ m["ARG"]=11;
+ m["ASN"]=8;
+ m["ASP"]=8;
+ m["ASX"]=8;
+ m["CYS"]=6;
+ m["GLU"]=9;
+ m["GLN"]=9;
+ m["GLX"]=9;
+ m["GLY"]=4;
+ m["HIS"]=10;
+ m["ILE"]=8;
+ m["LEU"]=8;
+ m["XLE"]=8;
+ m["LYS"]=9;
+ m["MET"]=8;
+ m["PHE"]=11;
+ m["PRO"]=7;
+ m["SER"]=6;
+ m["THR"]=7;
+ m["TRP"]=14;
+ m["TYR"]=12;
+ m["VAL"]=7;
+ return m;
+ }
+};
+
+}
+
+#endif /* AUXILIARIES_RESIDUE_ATOMS_REFERENCE_H_ */
diff --git a/src/auxiliaries/residue_letters_coding.h b/src/auxiliaries/residue_letters_coding.h
new file mode 100644
index 0000000..9bcf963
--- /dev/null
+++ b/src/auxiliaries/residue_letters_coding.h
@@ -0,0 +1,76 @@
+#ifndef AUXILIARIES_RESIDUE_LETTERS_CODING_H_
+#define AUXILIARIES_RESIDUE_LETTERS_CODING_H_
+
+#include <string>
+#include <map>
+
+namespace auxiliaries
+{
+
+class ResidueLettersCoding
+{
+public:
+ inline static std::string convert_residue_code_big_to_small(const std::string& big_code)
+ {
+ static const std::map<std::string, std::string> m=create_map_of_residue_codes_big_to_small();
+ const std::map<std::string, std::string>::const_iterator it=m.find(big_code);
+ return (it==m.end() ? std::string("X") : it->second);
+ }
+
+ inline static std::string convert_residue_code_small_to_big(const std::string& small_code)
+ {
+ static const std::map<std::string, std::string> m=create_map_of_residue_codes_small_to_big();
+ const std::map<std::string, std::string>::const_iterator it=m.find(small_code);
+ return (it==m.end() ? std::string("XAA") : it->second);
+ }
+private:
+ static std::map<std::string, std::string> create_map_of_residue_codes_big_to_small()
+ {
+ std::map<std::string, std::string> m;
+ m["LEU"]="L";
+ m["VAL"]="V";
+ m["ILE"]="I";
+ m["ALA"]="A";
+ m["PHE"]="F";
+ m["TRP"]="W";
+ m["MET"]="M";
+ m["PRO"]="P";
+ m["ASP"]="D";
+ m["GLU"]="E";
+ m["LYS"]="K";
+ m["ARG"]="R";
+ m["HIS"]="H";
+ m["CYS"]="C";
+ m["SER"]="S";
+ m["THR"]="T";
+ m["TYR"]="Y";
+ m["ASN"]="N";
+ m["GLN"]="Q";
+ m["GLY"]="G";
+ m["ASX"]="B";
+ m["GLX"]="Z";
+ m["XLE"]="J";
+ m["A"]="a";
+ m["C"]="c";
+ m["G"]="g";
+ m["T"]="t";
+ m["U"]="u";
+ m["XAA"]="X";
+ return m;
+ }
+
+ static std::map<std::string, std::string> create_map_of_residue_codes_small_to_big()
+ {
+ const std::map<std::string, std::string> m_big_to_small=create_map_of_residue_codes_big_to_small();
+ std::map<std::string, std::string> m;
+ for(std::map<std::string, std::string>::const_iterator it=m_big_to_small.begin();it!=m_big_to_small.end();++it)
+ {
+ m[it->second]=it->first;
+ }
+ return m;
+ }
+};
+
+}
+
+#endif /* AUXILIARIES_RESIDUE_LETTERS_CODING_H_ */
diff --git a/src/auxiliaries/xml_writer.h b/src/auxiliaries/xml_writer.h
new file mode 100644
index 0000000..766cc22
--- /dev/null
+++ b/src/auxiliaries/xml_writer.h
@@ -0,0 +1,75 @@
+#ifndef AUXILIARIES_XML_WRITER_H_
+#define AUXILIARIES_XML_WRITER_H_
+
+#include <sstream>
+#include <string>
+#include <vector>
+#include <map>
+
+namespace auxiliaries
+{
+
+class XMLWriter
+{
+public:
+ explicit XMLWriter(const std::string& type) : type_(type)
+ {
+ }
+
+ template<typename T>
+ XMLWriter& set(const std::string& name, const T& value, const std::string& units="")
+ {
+ std::ostringstream output;
+ output << value << units;
+ parameters_[name]=output.str();
+ return (*this);
+ }
+
+ XMLWriter& set(const std::string& contents)
+ {
+ contents_=contents;
+ return (*this);
+ }
+
+ XMLWriter& add_child(const XMLWriter& child)
+ {
+ children_.push_back(child);
+ return (*this);
+ }
+
+ void write(std::ostream& output, const std::size_t tabs=0) const
+ {
+ output << std::string(tabs, ' ') << "<" << type_;
+ for(std::map<std::string, std::string>::const_iterator it=parameters_.begin();it!=parameters_.end();++it)
+ {
+ output << " " << it->first << "=\"" << it->second << "\"";
+ }
+ if(contents_.empty() && children_.empty())
+ {
+ output << "/>\n";
+ }
+ else
+ {
+ output << ">\n";
+ if(!contents_.empty())
+ {
+ output << std::string(tabs+2, ' ') << contents_ << "\n";
+ }
+ for(std::size_t i=0;i<children_.size();i++)
+ {
+ children_[i].write(output, tabs+2);
+ }
+ output << "</" << type_ << ">\n";
+ }
+ }
+
+private:
+ std::string type_;
+ std::map<std::string, std::string> parameters_;
+ std::string contents_;
+ std::vector<XMLWriter> children_;
+};
+
+}
+
+#endif /* AUXILIARIES_XML_WRITER_H_ */
diff --git a/src/compatability_macros.h b/src/compatability_macros.h
new file mode 100644
index 0000000..24bb248
--- /dev/null
+++ b/src/compatability_macros.h
@@ -0,0 +1,16 @@
+#ifndef COMPATABILITY_MACROS_H_
+#define COMPATABILITY_MACROS_H_
+
+#ifndef USE_TR1
+#if __cplusplus >= 201103L
+#define USE_TR1 0
+#elif defined(__clang__)
+#define USE_TR1 0
+#elif defined(__GNUC__)
+#define USE_TR1 1
+#else
+#define USE_TR1 0
+#endif
+#endif
+
+#endif /* COMPATABILITY_MACROS_H_ */
diff --git a/src/main.cpp b/src/main.cpp
new file mode 100644
index 0000000..abba14f
--- /dev/null
+++ b/src/main.cpp
@@ -0,0 +1,212 @@
+#include <iostream>
+#include <functional>
+#include <exception>
+#include <limits>
+#include <vector>
+#include <algorithm>
+
+#include "auxiliaries/program_options_handler.h"
+
+void get_balls_from_atoms_file(const auxiliaries::ProgramOptionsHandler&);
+void calculate_vertices(const auxiliaries::ProgramOptionsHandler&);
+void calculate_vertices_in_parallel(const auxiliaries::ProgramOptionsHandler&);
+void calculate_contacts(const auxiliaries::ProgramOptionsHandler&);
+void query_balls(const auxiliaries::ProgramOptionsHandler&);
+void query_contacts(const auxiliaries::ProgramOptionsHandler&);
+void draw_contacts(const auxiliaries::ProgramOptionsHandler&);
+void score_contacts_energy(const auxiliaries::ProgramOptionsHandler&);
+void score_contacts_quality(const auxiliaries::ProgramOptionsHandler&);
+void score_contacts_potential(const auxiliaries::ProgramOptionsHandler&);
+void compare_contacts(const auxiliaries::ProgramOptionsHandler&);
+void write_balls_to_atoms_file(const auxiliaries::ProgramOptionsHandler&);
+void query_balls_clashes(const auxiliaries::ProgramOptionsHandler&);
+void expand_descriptors(const auxiliaries::ProgramOptionsHandler&);
+
+void query_balls_sequences_pairings_stats(const auxiliaries::ProgramOptionsHandler&);
+void draw_balls(const auxiliaries::ProgramOptionsHandler&);
+void query_contacts_depth_values(const auxiliaries::ProgramOptionsHandler&);
+void plot_contacts(const auxiliaries::ProgramOptionsHandler&);
+void score_contacts_potentials_stats(const auxiliaries::ProgramOptionsHandler&);
+void score_contacts_energy_stats(const auxiliaries::ProgramOptionsHandler&);
+void vectorize_contacts(const auxiliaries::ProgramOptionsHandler&);
+void vectorize_points(const auxiliaries::ProgramOptionsHandler&);
+void calculate_mock_solvent(const auxiliaries::ProgramOptionsHandler&);
+void query_contacts_simulating_unfolding(const auxiliaries::ProgramOptionsHandler&);
+void vectorize_contact_environments(const auxiliaries::ProgramOptionsHandler&);
+void wrapped_get_balls_from_atoms_file_and_calculate_vertices(const auxiliaries::ProgramOptionsHandler&);
+void write_qa_scores_in_casp_format(const auxiliaries::ProgramOptionsHandler&);
+void score_contacts_global_energy_by_cuts(const auxiliaries::ProgramOptionsHandler&);
+void simulate_potential_for_membrane_proteins(const auxiliaries::ProgramOptionsHandler&);
+void query_contacts_solvation_values(const auxiliaries::ProgramOptionsHandler&);
+void score_scores(const auxiliaries::ProgramOptionsHandler&);
+void demo_ses(const auxiliaries::ProgramOptionsHandler&);
+void rotational_optimization_demo(const auxiliaries::ProgramOptionsHandler&);
+void place_membrane(const auxiliaries::ProgramOptionsHandler&);
+void demo_polygon_triangulation(const auxiliaries::ProgramOptionsHandler& poh);
+void demo_hypercut(const auxiliaries::ProgramOptionsHandler&);
+
+struct ModeDescriptor
+{
+ typedef std::pointer_to_unary_function<const auxiliaries::ProgramOptionsHandler&, void> FunctionPtr;
+
+ std::string name;
+ FunctionPtr func_ptr;
+
+ ModeDescriptor(const std::string& name, const FunctionPtr& func_ptr) : name(name), func_ptr(func_ptr)
+ {
+ }
+
+ bool operator==(const std::string& check_name) const
+ {
+ return (check_name==name);
+ }
+};
+
+std::vector<ModeDescriptor> get_list_of_modes()
+{
+ std::vector<ModeDescriptor> list_of_modes;
+ list_of_modes.push_back(ModeDescriptor("get-balls-from-atoms-file", ModeDescriptor::FunctionPtr(get_balls_from_atoms_file)));
+ list_of_modes.push_back(ModeDescriptor("calculate-vertices", ModeDescriptor::FunctionPtr(calculate_vertices)));
+ list_of_modes.push_back(ModeDescriptor("calculate-vertices-in-parallel", ModeDescriptor::FunctionPtr(calculate_vertices_in_parallel)));
+ list_of_modes.push_back(ModeDescriptor("calculate-contacts", ModeDescriptor::FunctionPtr(calculate_contacts)));
+ list_of_modes.push_back(ModeDescriptor("query-balls", ModeDescriptor::FunctionPtr(query_balls)));
+ list_of_modes.push_back(ModeDescriptor("query-contacts", ModeDescriptor::FunctionPtr(query_contacts)));
+ list_of_modes.push_back(ModeDescriptor("draw-contacts", ModeDescriptor::FunctionPtr(draw_contacts)));
+ list_of_modes.push_back(ModeDescriptor("score-contacts-energy", ModeDescriptor::FunctionPtr(score_contacts_energy)));
+ list_of_modes.push_back(ModeDescriptor("score-contacts-quality", ModeDescriptor::FunctionPtr(score_contacts_quality)));
+ list_of_modes.push_back(ModeDescriptor("score-contacts-potential", ModeDescriptor::FunctionPtr(score_contacts_potential)));
+ list_of_modes.push_back(ModeDescriptor("compare-contacts", ModeDescriptor::FunctionPtr(compare_contacts)));
+ list_of_modes.push_back(ModeDescriptor("write-balls-to-atoms-file", ModeDescriptor::FunctionPtr(write_balls_to_atoms_file)));
+ list_of_modes.push_back(ModeDescriptor("query-balls-clashes", ModeDescriptor::FunctionPtr(query_balls_clashes)));
+ list_of_modes.push_back(ModeDescriptor("expand-descriptors", ModeDescriptor::FunctionPtr(expand_descriptors)));
+ return list_of_modes;
+}
+
+std::vector<ModeDescriptor> get_list_of_xmodes()
+{
+ std::vector<ModeDescriptor> list_of_modes;
+ list_of_modes.push_back(ModeDescriptor("x-query-balls-sequences-pairings-stats", ModeDescriptor::FunctionPtr(query_balls_sequences_pairings_stats)));
+ list_of_modes.push_back(ModeDescriptor("x-draw-balls", ModeDescriptor::FunctionPtr(draw_balls)));
+ list_of_modes.push_back(ModeDescriptor("x-query-contacts-depth-values", ModeDescriptor::FunctionPtr(query_contacts_depth_values)));
+ list_of_modes.push_back(ModeDescriptor("x-plot-contacts", ModeDescriptor::FunctionPtr(plot_contacts)));
+ list_of_modes.push_back(ModeDescriptor("x-score-contacts-potentials-stats", ModeDescriptor::FunctionPtr(score_contacts_potentials_stats)));
+ list_of_modes.push_back(ModeDescriptor("x-score-contacts-energy-stats", ModeDescriptor::FunctionPtr(score_contacts_energy_stats)));
+ list_of_modes.push_back(ModeDescriptor("x-vectorize-contacts", ModeDescriptor::FunctionPtr(vectorize_contacts)));
+ list_of_modes.push_back(ModeDescriptor("x-vectorize-points", ModeDescriptor::FunctionPtr(vectorize_points)));
+ list_of_modes.push_back(ModeDescriptor("x-calculate-mock-solvent", ModeDescriptor::FunctionPtr(calculate_mock_solvent)));
+ list_of_modes.push_back(ModeDescriptor("x-query-contacts-simulating-unfolding", ModeDescriptor::FunctionPtr(query_contacts_simulating_unfolding)));
+ list_of_modes.push_back(ModeDescriptor("x-vectorize-contact-environments", ModeDescriptor::FunctionPtr(vectorize_contact_environments)));
+ list_of_modes.push_back(ModeDescriptor("x-wrapped-get-balls-from-atoms-file-and-calculate-vertices", ModeDescriptor::FunctionPtr(wrapped_get_balls_from_atoms_file_and_calculate_vertices)));
+ list_of_modes.push_back(ModeDescriptor("x-write-qa-scores-in-casp-format", ModeDescriptor::FunctionPtr(write_qa_scores_in_casp_format)));
+ list_of_modes.push_back(ModeDescriptor("x-score-contacts-global-energy-by-cuts", ModeDescriptor::FunctionPtr(score_contacts_global_energy_by_cuts)));
+ list_of_modes.push_back(ModeDescriptor("x-simulate-potential-for-membrane-proteins", ModeDescriptor::FunctionPtr(simulate_potential_for_membrane_proteins)));
+ list_of_modes.push_back(ModeDescriptor("x-query-contacts-solvation-values", ModeDescriptor::FunctionPtr(query_contacts_solvation_values)));
+ list_of_modes.push_back(ModeDescriptor("x-score-scores", ModeDescriptor::FunctionPtr(score_scores)));
+ list_of_modes.push_back(ModeDescriptor("x-demo-ses", ModeDescriptor::FunctionPtr(demo_ses)));
+ list_of_modes.push_back(ModeDescriptor("x-rotational-optimization-demo", ModeDescriptor::FunctionPtr(rotational_optimization_demo)));
+ list_of_modes.push_back(ModeDescriptor("x-place-membrane", ModeDescriptor::FunctionPtr(place_membrane)));
+ list_of_modes.push_back(ModeDescriptor("x-demo-polygon-triangulation", ModeDescriptor::FunctionPtr(demo_polygon_triangulation)));
+ list_of_modes.push_back(ModeDescriptor("x-demo-hypercut", ModeDescriptor::FunctionPtr(demo_hypercut)));
+ return list_of_modes;
+}
+
+std::string version()
+{
+ static const std::string str="Voronota version 1.18";
+ return str;
+}
+
+void print_error_message(const std::string& mode, const std::string& message)
+{
+ std::cerr << version();
+ if(!mode.empty())
+ {
+ std::cerr << " command '" << mode << "'";
+ }
+ std::cerr << " exit error: " << message;
+ std::cerr << std::endl;
+}
+
+int main(const int argc, const char** argv)
+{
+ const std::string mode=(argc>1 ? std::string(argv[1]) : std::string());
+
+ const std::string xmode_prefix="x-";
+ const bool xmode=(mode.compare(0, xmode_prefix.size(), xmode_prefix)==0);
+
+ std::cin.exceptions(std::istream::badbit);
+ std::cout.exceptions(std::ostream::badbit);
+ std::ios_base::sync_with_stdio(false);
+
+ try
+ {
+ auxiliaries::ProgramOptionsHandler poh(argc, argv);
+
+ const bool help=poh.contains_option("--help");
+
+ {
+ const std::string output_precision_option_name="--stdout-precision";
+ if(poh.contains_option_with_argument(output_precision_option_name))
+ {
+ std::cout << std::fixed;
+ std::cout.precision(poh.argument<int>(output_precision_option_name));
+ poh.remove_option(output_precision_option_name);
+ }
+ }
+
+ if(!xmode)
+ {
+ const std::vector<ModeDescriptor> list_of_modes=get_list_of_modes();
+ if(!mode.empty() && std::count(list_of_modes.begin(), list_of_modes.end(), mode)>0)
+ {
+ std::find(list_of_modes.begin(), list_of_modes.end(), mode)->func_ptr(poh);
+ return (help ? 1 : 0);
+ }
+ else
+ {
+ std::ostream& output=std::cout;
+ output << version() << "\n\n";
+ output << "Commands:\n\n";
+ for(std::vector<ModeDescriptor>::const_iterator it=list_of_modes.begin();it!=list_of_modes.end();++it)
+ {
+ output << it->name << "\n";
+ }
+ output << "\n";
+ if(help)
+ {
+ for(std::vector<ModeDescriptor>::const_iterator it=list_of_modes.begin();it!=list_of_modes.end();++it)
+ {
+ output << "Command '" << it->name << "' options:\n";
+ it->func_ptr(poh);
+ output << "\n";
+ }
+ }
+ }
+ }
+ else
+ {
+ const std::vector<ModeDescriptor> list_of_modes=get_list_of_xmodes();
+ if(!mode.empty() && std::count(list_of_modes.begin(), list_of_modes.end(), mode)>0)
+ {
+ std::find(list_of_modes.begin(), list_of_modes.end(), mode)->func_ptr(poh);
+ return (help ? 1 : 0);
+ }
+ else
+ {
+ throw std::runtime_error("Invalid xmode.");
+ }
+ }
+
+ return 1;
+ }
+ catch(const std::exception& e)
+ {
+ print_error_message(mode, e.what());
+ }
+ catch(...)
+ {
+ print_error_message(mode, "Unknown exception caught.");
+ }
+
+ return 2;
+}
diff --git a/src/mode_calculate_contacts.cpp b/src/mode_calculate_contacts.cpp
new file mode 100644
index 0000000..8af6371
--- /dev/null
+++ b/src/mode_calculate_contacts.cpp
@@ -0,0 +1,291 @@
+#include <iostream>
+#include <stdexcept>
+
+#include "apollota/constrained_contacts_construction.h"
+#include "apollota/constrained_contacts_utilities.h"
+#include "apollota/spheres_boundary_construction.h"
+#include "apollota/spherical_contacts_construction.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+#include "auxiliaries/opengl_printer.h"
+
+#include "modescommon/ball_value.h"
+#include "modescommon/contact_value.h"
+#include "modescommon/mock_solvent_utilities.h"
+
+void calculate_contacts(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false,
+ "list of balls\n(default mode line format: 'x y z r')\n(annotated mode line format: 'annotation x y z r tags adjuncts')");
+ pohw.describe_io("stdout", false, true,
+ "list of contacts\n(default mode line format: 'b1 b2 area')\n(annotated mode line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')");
+
+ const bool annotated=poh.contains_option(pohw.describe_option("--annotated", "", "flag to enable annotated mode"));
+ const double probe=poh.restrict_value_in_range(0.01, 14.0, poh.argument<double>(pohw.describe_option("--probe", "number", "probe radius"), 1.4));
+ const bool exclude_hidden_balls=poh.contains_option(pohw.describe_option("--exclude-hidden-balls", "", "flag to exclude hidden input balls"));
+ const double step=poh.restrict_value_in_range(0.05, 0.5, poh.argument<double>(pohw.describe_option("--step", "number", "curve step length"), 0.2));
+ const int projections=poh.restrict_value_in_range(1, 10, poh.argument<int>(pohw.describe_option("--projections", "number", "curve optimization depth"), 5));
+ const int sih_depth=poh.restrict_value_in_range(1, 5, poh.argument<int>(pohw.describe_option("--sih-depth", "number", "spherical surface optimization depth"), 3));
+ const bool add_mirrored=poh.contains_option(pohw.describe_option("--add-mirrored", "", "flag to add mirrored contacts to non-annnotated output"));
+ const bool draw=poh.contains_option(pohw.describe_option("--draw", "", "flag to output graphics for annotated contacts"));
+ const bool tag_centrality=poh.contains_option(pohw.describe_option("--tag-centrality", "", "flag to tag contacts centrality"));
+ const bool tag_peripherial=poh.contains_option(pohw.describe_option("--tag-peripherial", "", "flag to tag peripherial contacts"));
+ const std::string old_contacts_output=poh.argument<std::string>(pohw.describe_option("--old-contacts-output", "string", "file path to output spherical contacts"), "");
+ const std::string volumes_output=poh.argument<std::string>(pohw.describe_option("--volumes-output", "string", "file path to output constrained cells volumes"), "");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::vector<apollota::SimpleSphere> spheres;
+ std::vector< std::pair<auxiliaries::ChainResidueAtomDescriptor, BallValue> > input_ball_records;
+ std::set<std::size_t> mock_solvent_ids;
+ if(annotated)
+ {
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, input_ball_records);
+ spheres.reserve(input_ball_records.size());
+ for(std::size_t i=0;i<input_ball_records.size();i++)
+ {
+ spheres.push_back(apollota::SimpleSphere(input_ball_records[i].second));
+ if(identify_mock_solvent(input_ball_records[i].first))
+ {
+ mock_solvent_ids.insert(i);
+ }
+ }
+ }
+ else
+ {
+ auxiliaries::IOUtilities().read_lines_to_set(std::cin, spheres);
+ }
+ if(spheres.size()<4)
+ {
+ throw std::runtime_error("Less than 4 balls provided to stdin.");
+ }
+
+ const std::size_t input_spheres_count=spheres.size();
+ const std::vector<apollota::SimpleSphere> artificial_boundary=apollota::construct_artificial_boundary(spheres, probe*2.0);
+ spheres.insert(spheres.end(), artificial_boundary.begin(), artificial_boundary.end());
+
+ const apollota::Triangulation::Result triangulation_result=apollota::Triangulation::construct_result(spheres, 3.5, exclude_hidden_balls, false);
+ const apollota::Triangulation::VerticesVector vertices_vector=apollota::Triangulation::collect_vertices_vector_from_quadruples_map(triangulation_result.quadruples_map);
+
+ std::map<apollota::Pair, double> interactions_map;
+ std::pair< bool, std::map<std::size_t, double> > volumes_map_bundle(!volumes_output.empty(), std::map<std::size_t, double>());
+
+ {
+ const std::map<apollota::Pair, double> constrained_contacts=apollota::ConstrainedContactsConstruction::construct_contacts(spheres, vertices_vector, probe, step, projections, mock_solvent_ids, volumes_map_bundle);
+ for(std::map<apollota::Pair, double>::const_iterator it=constrained_contacts.begin();it!=constrained_contacts.end();++it)
+ {
+ if(it->first.get(0)<input_spheres_count && it->first.get(1)<input_spheres_count)
+ {
+ interactions_map[it->first]=it->second;
+ }
+ }
+ }
+
+ if(mock_solvent_ids.empty())
+ {
+ const std::map<std::size_t, double> constrained_contact_remainders=apollota::ConstrainedContactsConstruction::construct_contact_remainders(spheres, vertices_vector, probe, sih_depth, volumes_map_bundle);
+ for(std::map<std::size_t, double>::const_iterator it=constrained_contact_remainders.begin();it!=constrained_contact_remainders.end();++it)
+ {
+ if(it->first<input_spheres_count)
+ {
+ interactions_map[apollota::Pair(it->first, it->first)]=it->second;
+ }
+ }
+ }
+
+ if(!input_ball_records.empty())
+ {
+ const apollota::TriangulationQueries::PairsMap pairs_vertices=((draw || tag_peripherial) ? apollota::TriangulationQueries::collect_pairs_vertices_map_from_vertices_vector(vertices_vector) : apollota::TriangulationQueries::PairsMap());
+ const apollota::TriangulationQueries::IDsMap ids_vertices=(draw ? apollota::TriangulationQueries::collect_vertices_map_from_vertices_vector(vertices_vector) : apollota::TriangulationQueries::IDsMap());
+ const apollota::SubdividedIcosahedron sih(draw ? sih_depth : 0);
+ const apollota::TriangulationQueries::PairsMap pairs_neighbors=(tag_centrality ? apollota::TriangulationQueries::collect_pairs_neighbors_map_from_quadruples_map(triangulation_result.quadruples_map) : apollota::TriangulationQueries::PairsMap());
+
+ std::map< auxiliaries::ChainResidueAtomDescriptorsPair, ContactValue > output_map_of_contacts;
+ for(std::map<apollota::Pair, double>::const_iterator it=interactions_map.begin();it!=interactions_map.end();++it)
+ {
+ const double area=it->second;
+ if(area>0.0)
+ {
+ const std::size_t a_id=it->first.get(0);
+ const std::size_t b_id=it->first.get(1);
+ auxiliaries::ChainResidueAtomDescriptor crad_a=input_ball_records[a_id].first;
+ auxiliaries::ChainResidueAtomDescriptor crad_b=input_ball_records[b_id].first;
+ if(identify_mock_solvent(crad_a))
+ {
+ crad_a=auxiliaries::ChainResidueAtomDescriptor::solvent();
+ }
+ if(a_id==b_id || identify_mock_solvent(crad_b))
+ {
+ crad_b=auxiliaries::ChainResidueAtomDescriptor::solvent();
+ }
+ if(crad_a!=auxiliaries::ChainResidueAtomDescriptor::solvent() || crad_b!=auxiliaries::ChainResidueAtomDescriptor::solvent())
+ {
+ ContactValue value;
+ value.area=area;
+ if(a_id!=b_id)
+ {
+ value.dist=apollota::distance_from_point_to_point(spheres[a_id], spheres[b_id]);
+ }
+ else
+ {
+ value.dist=(spheres[a_id].r+(probe*3.0));
+ }
+ if(draw)
+ {
+ value.graphics=(a_id==b_id ?
+ apollota::draw_solvent_contact<auxiliaries::OpenGLPrinter>(spheres, vertices_vector, ids_vertices, a_id, probe, sih) :
+ apollota::draw_inter_atom_contact<auxiliaries::OpenGLPrinter>(spheres, vertices_vector, pairs_vertices, a_id, b_id, probe, step, projections));
+ }
+ if(tag_centrality && crad_a!=auxiliaries::ChainResidueAtomDescriptor::solvent() && crad_b!=auxiliaries::ChainResidueAtomDescriptor::solvent() && check_inter_atom_contact_centrality(spheres, pairs_neighbors, a_id, b_id))
+ {
+ value.props.tags.insert("central");
+ }
+ if(tag_peripherial && crad_a!=auxiliaries::ChainResidueAtomDescriptor::solvent() && crad_b!=auxiliaries::ChainResidueAtomDescriptor::solvent() && check_inter_atom_contact_peripherial(spheres, vertices_vector, pairs_vertices, a_id, b_id, probe))
+ {
+ value.props.tags.insert("peripherial");
+ }
+ output_map_of_contacts[auxiliaries::ChainResidueAtomDescriptorsPair(crad_a, crad_b)].add(value);
+ }
+ }
+ }
+ auxiliaries::IOUtilities().write_map(output_map_of_contacts, std::cout);
+ }
+ else
+ {
+ if(add_mirrored)
+ {
+ std::map< std::pair<std::size_t, std::size_t>, double > mirrored_interactions_map;
+ for(std::map<apollota::Pair, double>::const_iterator it=interactions_map.begin();it!=interactions_map.end();++it)
+ {
+ mirrored_interactions_map[std::make_pair(it->first.get(0), it->first.get(1))]=it->second;
+ if(it->first.get(0)!=it->first.get(1))
+ {
+ mirrored_interactions_map[std::make_pair(it->first.get(1), it->first.get(0))]=it->second;
+ }
+ }
+ for(std::map< std::pair<std::size_t, std::size_t>, double >::const_iterator it=mirrored_interactions_map.begin();it!=mirrored_interactions_map.end();++it)
+ {
+ std::cout << it->first.first << " " << it->first.second << " " << it->second << "\n";
+ }
+ }
+ else
+ {
+ for(std::map<apollota::Pair, double>::const_iterator it=interactions_map.begin();it!=interactions_map.end();++it)
+ {
+ std::cout << it->first.get(0) << " " << it->first.get(1) << " " << it->second << "\n";
+ }
+ }
+ }
+
+ if(volumes_map_bundle.first && !volumes_map_bundle.second.empty() && !volumes_output.empty())
+ {
+ const std::map<std::size_t, double>& volumes_map=volumes_map_bundle.second;
+ if(!input_ball_records.empty())
+ {
+ std::map<auxiliaries::ChainResidueAtomDescriptor, double> output_volumes_map;
+ for(std::map<std::size_t, double>::const_iterator it=volumes_map.begin();it!=volumes_map.end();++it)
+ {
+ const double volume=it->second;
+ if(volume>0.0)
+ {
+ const std::size_t a_id=it->first;
+ if(a_id<input_ball_records.size())
+ {
+ const auxiliaries::ChainResidueAtomDescriptor& crad_a=input_ball_records[a_id].first;
+ output_volumes_map[crad_a]=volume;
+ }
+ }
+ }
+ auxiliaries::IOUtilities().write_map_to_file(output_volumes_map, volumes_output);
+ }
+ else
+ {
+ std::map<std::size_t, double> output_volumes_map;
+ for(std::map<std::size_t, double>::const_iterator it=volumes_map.begin();it!=volumes_map.end();++it)
+ {
+ const double volume=it->second;
+ if(volume>0.0)
+ {
+ const std::size_t a_id=it->first;
+ if(a_id<input_spheres_count)
+ {
+ output_volumes_map[a_id]=volume;
+ }
+ }
+ }
+ auxiliaries::IOUtilities().write_map_to_file(output_volumes_map, volumes_output);
+ }
+ }
+
+ if(!old_contacts_output.empty() && mock_solvent_ids.empty())
+ {
+ std::ofstream foutput(old_contacts_output.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ const std::vector< std::vector<std::size_t> > graph=apollota::TriangulationQueries::collect_ids_graph_from_ids_map(apollota::TriangulationQueries::collect_neighbors_map_from_quadruples_map(vertices_vector), input_spheres_count);
+ std::map<std::pair<std::size_t, std::size_t>, double> old_interactions_map;
+ apollota::SphericalContactsConstruction sc_construction(sih_depth);
+ for(std::size_t i=0;i<graph.size();i++)
+ {
+ const apollota::SphericalContactsConstruction::Result sc_result=sc_construction.construct_contacts(probe, spheres, i, graph[i]);
+ for(std::map<std::size_t, double>::const_iterator it=sc_result.areas.begin();it!=sc_result.areas.end();++it)
+ {
+ old_interactions_map[std::pair<std::size_t, std::size_t>(i, it->first)]=it->second;
+ }
+ }
+ if(!input_ball_records.empty())
+ {
+ std::map< std::pair<auxiliaries::ChainResidueAtomDescriptor, auxiliaries::ChainResidueAtomDescriptor>, ContactValue > output_map_of_contacts;
+ for(std::map<std::pair<std::size_t, std::size_t>, double>::const_iterator it=old_interactions_map.begin();it!=old_interactions_map.end();++it)
+ {
+ const double area=it->second;
+ if(area>0.0)
+ {
+ const std::size_t a_id=it->first.first;
+ const std::size_t b_id=it->first.second;
+ auxiliaries::ChainResidueAtomDescriptor crad_a=input_ball_records[a_id].first;
+ auxiliaries::ChainResidueAtomDescriptor crad_b=input_ball_records[b_id].first;
+ if(crad_a!=auxiliaries::ChainResidueAtomDescriptor::solvent())
+ {
+ if(a_id==b_id)
+ {
+ crad_b=auxiliaries::ChainResidueAtomDescriptor::solvent();
+ }
+ ContactValue value;
+ value.area=area;
+ if(a_id!=b_id)
+ {
+ value.dist=apollota::distance_from_point_to_point(spheres[a_id], spheres[b_id]);
+ }
+ else
+ {
+ value.dist=(spheres[a_id].r+(probe*3.0));
+ }
+ if(crad_b!=auxiliaries::ChainResidueAtomDescriptor::solvent())
+ {
+ crad_b.altLoc="m";
+ }
+ output_map_of_contacts[std::make_pair(crad_a, crad_b)].add(value);
+ }
+ }
+ }
+ for(std::map< std::pair<auxiliaries::ChainResidueAtomDescriptor, auxiliaries::ChainResidueAtomDescriptor>, ContactValue >::const_iterator it=output_map_of_contacts.begin();it!=output_map_of_contacts.end();++it)
+ {
+ foutput << it->first.first << " " << it->first.second << " " << it->second << "\n";
+ }
+ }
+ else
+ {
+ for(std::map<std::pair<std::size_t, std::size_t>, double>::const_iterator it=old_interactions_map.begin();it!=old_interactions_map.end();++it)
+ {
+ foutput << it->first.first << " " << it->first.second << " " << it->second << "\n";
+ }
+ }
+ }
+ }
+}
diff --git a/src/mode_calculate_mock_solvent.cpp b/src/mode_calculate_mock_solvent.cpp
new file mode 100644
index 0000000..08fdcfc
--- /dev/null
+++ b/src/mode_calculate_mock_solvent.cpp
@@ -0,0 +1,176 @@
+#include <iostream>
+#include <stdexcept>
+
+#include "apollota/triangulation_queries.h"
+#include "apollota/subdivided_icosahedron.h"
+#include "apollota/spheres_boundary_construction.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+#include "modescommon/ball_value.h"
+#include "modescommon/mock_solvent_utilities.h"
+
+void calculate_mock_solvent(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+ pohw.describe_io("stdout", false, true, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+
+ const double solvent_radius=poh.restrict_value_in_range(1.0, 2.0, poh.argument<double>(pohw.describe_option("--solvent-radius", "number", "solvent atom radius"), 1.4));
+ const double solvent_distance=poh.restrict_value_in_range(0.0, 10.0, poh.argument<double>(pohw.describe_option("--solvent-distance", "number", "min distance from non-solvent atoms to solvent atoms"), 1.0));
+ const int sih_depth=poh.restrict_value_in_range(0, 3, poh.argument<int>(pohw.describe_option("--sih-depth", "number", "spherical surface optimization depth"), 1));
+ const bool sparse_mode=poh.contains_option(pohw.describe_option("--sparse-mode", "", "flag to use sparse mode"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const double probe=(solvent_radius+solvent_distance);
+
+ std::vector<apollota::SimpleSphere> input_spheres;
+ std::vector< std::pair<auxiliaries::ChainResidueAtomDescriptor, BallValue> > ball_records;
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, ball_records);
+ input_spheres.reserve(ball_records.size());
+ for(std::size_t i=0;i<ball_records.size();i++)
+ {
+ input_spheres.push_back(apollota::SimpleSphere(ball_records[i].second));
+ }
+ if(input_spheres.size()<4)
+ {
+ throw std::runtime_error("Less than 4 balls provided to stdin.");
+ }
+
+ std::vector<apollota::SimpleSphere> mock_solvent_spheres;
+
+ if(sparse_mode)
+ {
+ int stage=0;
+ while(stage<1)
+ {
+ std::vector<apollota::SimpleSphere> spheres=input_spheres;
+ if(!mock_solvent_spheres.empty())
+ {
+ spheres.insert(spheres.end(), mock_solvent_spheres.begin(), mock_solvent_spheres.end());
+ }
+ const std::size_t real_spheres_count=spheres.size();
+
+ const std::vector<apollota::SimpleSphere> artificial_boundary=apollota::construct_artificial_boundary(spheres, probe*2.0);
+ spheres.insert(spheres.end(), artificial_boundary.begin(), artificial_boundary.end());
+
+ const apollota::Triangulation::Result triangulation_result=apollota::Triangulation::construct_result(spheres, 3.5, false, false);
+ const apollota::Triangulation::VerticesVector vertices=apollota::Triangulation::collect_vertices_vector_from_quadruples_map(triangulation_result.quadruples_map);
+ const apollota::TriangulationQueries::IDsGraph ids_graph=apollota::TriangulationQueries::collect_ids_graph_from_ids_map(apollota::TriangulationQueries::collect_neighbors_map_from_quadruples_map(triangulation_result.quadruples_map), real_spheres_count);
+
+ apollota::TriangulationQueries::TriplesMap triples_exposed;
+ for(std::size_t i=0;i<vertices.size();i++)
+ {
+ if(vertices[i].second.r>probe)
+ {
+ const apollota::Quadruple& q=vertices[i].first;
+ for(unsigned int j=0;j<4;j++)
+ {
+ const apollota::Triple& t=q.exclude(j);
+ const std::size_t n=q.get(j);
+ if((stage==0 && t.get_min_max().second<real_spheres_count && t.get_min_max().first<input_spheres.size()) || stage>0)
+ {
+ triples_exposed[t].insert(n);
+ }
+ }
+ }
+ }
+
+ std::vector<apollota::SimpleSphere> new_mock_solvent_spheres;
+ new_mock_solvent_spheres.reserve(triples_exposed.size()*2);
+ for(apollota::TriangulationQueries::TriplesMap::const_iterator it=triples_exposed.begin();it!=triples_exposed.end();++it)
+ {
+ const apollota::Triple& t=it->first;
+ const std::vector<apollota::SimpleSphere> tangents=apollota::TangentSphereOfThreeSpheres::calculate(spheres[t.get(0)], spheres[t.get(1)], spheres[t.get(2)], probe);
+ if(!tangents.empty())
+ {
+ std::set<std::size_t> ns;
+ ns.insert(ids_graph[t.get(0)].begin(), ids_graph[t.get(0)].end());
+ ns.insert(ids_graph[t.get(1)].begin(), ids_graph[t.get(1)].end());
+ ns.insert(ids_graph[t.get(2)].begin(), ids_graph[t.get(2)].end());
+ for(std::size_t i=0;i<tangents.size();i++)
+ {
+ bool candidate_good=true;
+ for(std::set<std::size_t>::const_iterator jt=ns.begin();jt!=ns.end() && candidate_good;++jt)
+ {
+ if(apollota::sphere_intersects_sphere(tangents[i], spheres[*jt]))
+ {
+ candidate_good=false;
+ }
+ }
+ if(candidate_good)
+ {
+ new_mock_solvent_spheres.push_back(apollota::SimpleSphere(tangents[i], solvent_radius));
+ }
+ }
+ }
+ }
+
+ if(!new_mock_solvent_spheres.empty())
+ {
+ mock_solvent_spheres.insert(mock_solvent_spheres.end(), new_mock_solvent_spheres.begin(), new_mock_solvent_spheres.end());
+ }
+
+ if((stage==0 && new_mock_solvent_spheres.empty()) || stage>0)
+ {
+ stage++;
+ }
+ }
+ }
+ else
+ {
+ std::vector<apollota::SimpleSphere> spheres=input_spheres;
+ const std::vector<apollota::SimpleSphere> artificial_boundary=apollota::construct_artificial_boundary(spheres, probe*2.0);
+ spheres.insert(spheres.end(), artificial_boundary.begin(), artificial_boundary.end());
+
+ const apollota::Triangulation::Result triangulation_result=apollota::Triangulation::construct_result(spheres, 3.5, false, false);
+ const apollota::TriangulationQueries::IDsMap ids_map=apollota::TriangulationQueries::collect_neighbors_map_from_quadruples_map(triangulation_result.quadruples_map);
+ const apollota::TriangulationQueries::IDsGraph ids_graph=apollota::TriangulationQueries::collect_ids_graph_from_ids_map(ids_map, input_spheres.size());
+
+ const apollota::SubdividedIcosahedron initial_sih(sih_depth);
+
+ mock_solvent_spheres.reserve(ids_graph.size()*2);
+ for(std::size_t i=0;i<ids_graph.size();i++)
+ {
+ apollota::SubdividedIcosahedron sih=initial_sih;
+ sih.fit_into_sphere(spheres[i], spheres[i].r+probe);
+ for(std::size_t l=0;l<sih.vertices().size();l++)
+ {
+ apollota::SimpleSphere sphere_l(sih.vertices()[l], solvent_radius);
+ const double dist_i=apollota::minimal_distance_from_point_to_sphere(sphere_l, spheres[i]);
+ bool good=true;
+ for(std::size_t j=0;j<ids_graph[i].size() && good;j++)
+ {
+ const double dist_j=apollota::minimal_distance_from_point_to_sphere(sphere_l, spheres[ids_graph[i][j]]);
+ good=(dist_i<dist_j);
+ }
+ if(good)
+ {
+ mock_solvent_spheres.push_back(sphere_l);
+ }
+ }
+ }
+ }
+
+ ball_records.reserve(ball_records.size()+mock_solvent_spheres.size());
+ for(std::size_t i=0;i<mock_solvent_spheres.size();i++)
+ {
+ const apollota::SimpleSphere& sphere=mock_solvent_spheres[i];
+ const BallValue value=apollota::custom_sphere<BallValue>(sphere.x, sphere.y, sphere.z, sphere.r);
+ auxiliaries::ChainResidueAtomDescriptor crad(mock_solvent_name());
+ crad.resSeq=(i+1);
+ crad.resName=mock_solvent_name();
+ crad.name=mock_solvent_name();
+ ball_records.push_back(std::make_pair(crad, value));
+ }
+
+ for(std::size_t i=0;i<ball_records.size();i++)
+ {
+ std::cout << ball_records[i].first << " " << ball_records[i].second << "\n";
+ }
+}
diff --git a/src/mode_calculate_vertices.cpp b/src/mode_calculate_vertices.cpp
new file mode 100644
index 0000000..9ca3c73
--- /dev/null
+++ b/src/mode_calculate_vertices.cpp
@@ -0,0 +1,59 @@
+#include <iostream>
+
+#include "apollota/triangulation.h"
+#include "apollota/triangulation_output.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+void calculate_vertices(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'x y z r')");
+ pohw.describe_io("stdout", false, true, "list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')");
+
+ const bool print_log=poh.contains_option(pohw.describe_option("--print-log", "", "flag to print log of calculations"));
+ const bool exclude_hidden_balls=poh.contains_option(pohw.describe_option("--exclude-hidden-balls", "", "flag to exclude hidden input balls"));
+ const bool include_surplus_quadruples=poh.contains_option(pohw.describe_option("--include-surplus-quadruples", "", "flag to include surplus quadruples"));
+ const bool link=poh.contains_option(pohw.describe_option("--link", "", "flag to output links between vertices"));
+ const double init_radius_for_BSH=poh.argument<double>(pohw.describe_option("--init-radius-for-BSH", "number", "initial radius for bounding sphere hierarchy"), 3.5);
+ const bool check=poh.contains_option(pohw.describe_option("--check", "", "flag to slowly check the resulting vertices (used only for testing)"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ if(init_radius_for_BSH<=1.0)
+ {
+ throw std::runtime_error("Bounding spheres hierarchy initial radius should be greater than 1.");
+ }
+
+ const std::vector<apollota::SimpleSphere> spheres=auxiliaries::IOUtilities().read_lines_to_set< std::vector<apollota::SimpleSphere> >(std::cin);
+ if(spheres.size()<4)
+ {
+ throw std::runtime_error("Less than 4 balls provided to stdin.");
+ }
+
+ const apollota::Triangulation::Result triangulation_result=apollota::Triangulation::construct_result(spheres, init_radius_for_BSH, exclude_hidden_balls, include_surplus_quadruples);
+
+ if(link)
+ {
+ apollota::TriangulationOutput::print_vertices_vector_with_vertices_graph(apollota::Triangulation::collect_vertices_vector_from_quadruples_map(triangulation_result.quadruples_map), apollota::Triangulation::construct_vertices_graph(spheres, triangulation_result.quadruples_map), std::cout);
+ }
+ else
+ {
+ apollota::TriangulationOutput::print_vertices_vector(apollota::Triangulation::collect_vertices_vector_from_quadruples_map(triangulation_result.quadruples_map), std::cout);
+ }
+
+ if(print_log)
+ {
+ std::clog << "balls " << spheres.size() << "\n";
+ apollota::TriangulationOutput::print_status(triangulation_result, std::clog);
+ }
+
+ if(check)
+ {
+ std::clog << "check " << (apollota::Triangulation::check_quadruples_map(spheres, triangulation_result.quadruples_map)) << "\n";
+ }
+}
diff --git a/src/mode_calculate_vertices_in_parallel.cpp b/src/mode_calculate_vertices_in_parallel.cpp
new file mode 100644
index 0000000..4a58802
--- /dev/null
+++ b/src/mode_calculate_vertices_in_parallel.cpp
@@ -0,0 +1,450 @@
+#include <iostream>
+#include <fstream>
+
+#ifdef ENABLE_MPI
+#include <mpi.h>
+#include <cstring>
+#endif
+
+#include "apollota/triangulation.h"
+#include "apollota/triangulation_output.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+namespace
+{
+
+struct ParallelComputationResult
+{
+ ParallelComputationResult() : number_of_initialized_parts(0), number_of_produced_quadruples(0)
+ {
+ }
+
+ std::vector<apollota::SimpleSphere> input_spheres;
+ std::size_t number_of_initialized_parts;
+ std::size_t number_of_produced_quadruples;
+ apollota::Triangulation::QuadruplesMap merged_quadruples_map;
+};
+
+class ParallelComputationProcessingSimulated
+{
+public:
+ static void process(
+ const std::size_t parts,
+ const double init_radius_for_BSH,
+ const bool include_surplus_quadruples,
+ ParallelComputationResult& result)
+ {
+ result.input_spheres.clear();
+ std::vector<apollota::SimpleSphere>& spheres=result.input_spheres;
+ auxiliaries::IOUtilities().read_lines_to_set(std::cin, spheres);
+
+ const std::vector< std::vector<std::size_t> > distributed_ids=apollota::SplittingOfSpheres::split_for_number_of_parts(spheres, parts);
+ result.number_of_initialized_parts=distributed_ids.size();
+
+ const apollota::BoundingSpheresHierarchy bsh(spheres, init_radius_for_BSH, 1);
+
+ for(std::size_t i=0;i<distributed_ids.size();i++)
+ {
+ const apollota::Triangulation::QuadruplesMap partial_quadruples_map=apollota::Triangulation::construct_result_for_admittance_set(bsh, distributed_ids[i], include_surplus_quadruples).quadruples_map;
+ result.number_of_produced_quadruples+=partial_quadruples_map.size();
+ apollota::Triangulation::merge_quadruples_maps(partial_quadruples_map, result.merged_quadruples_map);
+ }
+ }
+};
+
+#ifdef _OPENMP
+class ParallelComputationProcessingWithOpenMP
+{
+public:
+ static void process(
+ const std::size_t parts,
+ const double init_radius_for_BSH,
+ const bool include_surplus_quadruples,
+ ParallelComputationResult& result)
+ {
+ result.input_spheres.clear();
+ std::vector<apollota::SimpleSphere>& spheres=result.input_spheres;
+ auxiliaries::IOUtilities().read_lines_to_set(std::cin, spheres);
+
+ const std::vector< std::vector<std::size_t> > distributed_ids=apollota::SplittingOfSpheres::split_for_number_of_parts(spheres, parts);
+ result.number_of_initialized_parts=distributed_ids.size();
+
+ const apollota::BoundingSpheresHierarchy bsh(spheres, init_radius_for_BSH, 1);
+
+ std::vector<apollota::Triangulation::QuadruplesMap> distributed_quadruples_maps(distributed_ids.size());
+ std::vector<int> distributed_errors(distributed_ids.size(), 0);
+
+ const int distributed_ids_size=static_cast<int>(distributed_ids.size());
+ {
+ #pragma omp parallel for
+ for(int i=0;i<distributed_ids_size;i++)
+ {
+ try
+ {
+ distributed_quadruples_maps[i]=apollota::Triangulation::construct_result_for_admittance_set(bsh, distributed_ids[i], include_surplus_quadruples).quadruples_map;
+ }
+ catch(...)
+ {
+ distributed_errors[i]=1;
+ }
+ }
+ }
+
+ {
+ std::ostringstream errors_summary_stream;
+ for(std::size_t i=0;i<distributed_errors.size();i++)
+ {
+ if(distributed_errors[i]!=0)
+ {
+ errors_summary_stream << " " << i;
+ }
+ }
+ const std::string errors_summary=errors_summary_stream.str();
+ if(!errors_summary.empty())
+ {
+ throw std::runtime_error("Parallel processing failed because of exceptions in parts:"+errors_summary+".");
+ }
+ }
+
+ for(std::size_t i=0;i<distributed_quadruples_maps.size();i++)
+ {
+ result.number_of_produced_quadruples+=distributed_quadruples_maps[i].size();
+ apollota::Triangulation::merge_quadruples_maps(distributed_quadruples_maps[i], result.merged_quadruples_map);
+ }
+ }
+};
+#endif
+
+#ifdef ENABLE_MPI
+class ParallelComputationProcessingWithMPI
+{
+public:
+ static bool process(
+ const std::vector<std::string>& argv,
+ const std::size_t parts,
+ const double init_radius_for_BSH,
+ const bool include_surplus_quadruples,
+ ParallelComputationResult& result)
+ {
+ MPIHandle mpi_handle(argv);
+
+ if(mpi_handle.size()<=2)
+ {
+ ParallelComputationProcessingSimulated::process(parts, init_radius_for_BSH, include_surplus_quadruples, result);
+ }
+ else
+ {
+ result.input_spheres.clear();
+ std::vector<apollota::SimpleSphere>& spheres=result.input_spheres;
+ {
+ std::vector<double> spheres_plain_vector;
+ int spheres_plain_vector_length=0;
+ if(mpi_handle.rank()==0)
+ {
+ auxiliaries::IOUtilities().read_lines_to_set(std::cin, spheres);
+ fill_plain_vector_from_spheres(spheres, spheres_plain_vector);
+ spheres_plain_vector_length=static_cast<int>(spheres_plain_vector.size());
+ }
+ MPI_Bcast(&spheres_plain_vector_length, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
+ if(mpi_handle.rank()!=0)
+ {
+ spheres_plain_vector.resize(static_cast<std::size_t>(spheres_plain_vector_length));
+ }
+ MPI_Bcast(spheres_plain_vector.data(), spheres_plain_vector_length, MPI_DOUBLE, 0, MPI_COMM_WORLD);
+ if(mpi_handle.rank()!=0)
+ {
+ fill_spheres_from_plain_vector(spheres_plain_vector, spheres);
+ }
+ }
+
+ const std::vector< std::vector<std::size_t> > distributed_ids=apollota::SplittingOfSpheres::split_for_number_of_parts(spheres, parts);
+ result.number_of_initialized_parts=distributed_ids.size();
+
+ {
+ const int QUADRUPLES_MAP_DATA_TAG=1;
+ std::vector<double> plain_vector;
+ if(mpi_handle.rank()==0)
+ {
+ for(std::size_t i=0;i<distributed_ids.size();i++)
+ {
+ MPI_Status status;
+ MPI_Probe(MPI_ANY_SOURCE, QUADRUPLES_MAP_DATA_TAG, MPI_COMM_WORLD, &status);
+ int plain_vector_size=0;
+ MPI_Get_count(&status, MPI_DOUBLE, &plain_vector_size);
+ if(plain_vector_size>0)
+ {
+ plain_vector.resize(static_cast<std::size_t>(plain_vector_size));
+ MPI_Recv(plain_vector.data(), plain_vector_size, MPI_DOUBLE, status.MPI_SOURCE, QUADRUPLES_MAP_DATA_TAG, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+ apollota::Triangulation::QuadruplesMap partial_quadruples_map;
+ fill_quadruples_map_from_plain_vector(plain_vector, partial_quadruples_map);
+ result.number_of_produced_quadruples+=partial_quadruples_map.size();
+ apollota::Triangulation::merge_quadruples_maps(partial_quadruples_map, result.merged_quadruples_map);
+ }
+ }
+ }
+ else
+ {
+ const apollota::BoundingSpheresHierarchy bsh(spheres, init_radius_for_BSH, 1);
+ for(std::size_t i=0;i<distributed_ids.size();i++)
+ {
+ if(mpi_handle.rank()==(static_cast<int>(i)%(mpi_handle.size()-1)+1))
+ {
+ fill_plain_vector_from_quadruples_map(apollota::Triangulation::construct_result_for_admittance_set(bsh, distributed_ids[i], include_surplus_quadruples).quadruples_map, plain_vector);
+ MPI_Send(plain_vector.data(), static_cast<int>(plain_vector.size()), MPI_DOUBLE, 0, QUADRUPLES_MAP_DATA_TAG, MPI_COMM_WORLD);
+ }
+ }
+ }
+ }
+ }
+
+ mpi_handle.set_abort_on_destruction(false);
+ return (mpi_handle.rank()==0);
+ }
+
+private:
+ class MPIHandle
+ {
+ public:
+ explicit MPIHandle(const std::vector<std::string>& argv) :
+ abort_on_destruction_(true),
+ argc_(static_cast<int>(argv.size())),
+ argv_(0),
+ size_(0),
+ rank_(0),
+ start_time_(0.0)
+ {
+ argv_=new char*[argc_];
+ for(int i=0;i<argc_;i++)
+ {
+ argv_[i]=new char[argv[i].size()+1];
+ strcpy(argv_[i], argv[i].c_str());
+ }
+ MPI_Init(&argc_, &argv_);
+ MPI_Comm_size(MPI_COMM_WORLD, &size_);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank_);
+
+ start_time_=MPI_Wtime();
+ }
+
+ ~MPIHandle()
+ {
+ if(abort_on_destruction_)
+ {
+ MPI_Abort(MPI_COMM_WORLD, 1);
+ }
+ else
+ {
+ const double elapsed_time=MPI_Wtime()-start_time_;
+ std::cerr << "MPI process " << rank_ << " of " << size_ << " took " << elapsed_time << " seconds" << std::endl;
+ MPI_Finalize();
+ }
+
+ for(int i=0;i<argc_;i++)
+ {
+ delete[] argv_[i];
+ }
+ delete argv_;
+ }
+
+ void set_abort_on_destruction(const bool abort_on_destruction)
+ {
+ abort_on_destruction_=abort_on_destruction;
+ }
+
+ const int size() const
+ {
+ return size_;
+ }
+
+ const int rank() const
+ {
+ return rank_;
+ }
+
+ private:
+ MPIHandle(const MPIHandle&);
+ MPIHandle& operator=(const MPIHandle&);
+
+ bool abort_on_destruction_;
+ int argc_;
+ char** argv_;
+ int size_;
+ int rank_;
+ double start_time_;
+ };
+
+ static void fill_plain_vector_from_spheres(const std::vector<apollota::SimpleSphere>& spheres, std::vector<double>& plain_vector)
+ {
+ plain_vector.resize(spheres.size()*4);
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ plain_vector[i*4+0]=spheres[i].x;
+ plain_vector[i*4+1]=spheres[i].y;
+ plain_vector[i*4+2]=spheres[i].z;
+ plain_vector[i*4+3]=spheres[i].r;
+ }
+ }
+
+ static void fill_spheres_from_plain_vector(const std::vector<double>& plain_vector, std::vector<apollota::SimpleSphere>& spheres)
+ {
+ spheres.resize(plain_vector.size()/4);
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ spheres[i].x=plain_vector[i*4+0];
+ spheres[i].y=plain_vector[i*4+1];
+ spheres[i].z=plain_vector[i*4+2];
+ spheres[i].r=plain_vector[i*4+3];
+ }
+ }
+
+ static void fill_plain_vector_from_quadruples_map(const apollota::Triangulation::QuadruplesMap& quadruples_map, std::vector<double>& plain_vector)
+ {
+ plain_vector.resize(apollota::Triangulation::count_tangent_spheres_in_quadruples_map(quadruples_map)*8);
+ std::size_t i=0;
+ for(apollota::Triangulation::QuadruplesMap::const_iterator it=quadruples_map.begin();it!=quadruples_map.end();++it)
+ {
+ const apollota::Quadruple& q=it->first;
+ const std::vector<apollota::SimpleSphere>& ts=it->second;
+ for(std::size_t j=0;j<ts.size();j++)
+ {
+ plain_vector[i*8+0]=q.get(0);
+ plain_vector[i*8+1]=q.get(1);
+ plain_vector[i*8+2]=q.get(2);
+ plain_vector[i*8+3]=q.get(3);
+ plain_vector[i*8+4]=ts[j].x;
+ plain_vector[i*8+5]=ts[j].y;
+ plain_vector[i*8+6]=ts[j].z;
+ plain_vector[i*8+7]=ts[j].r;
+ i++;
+ }
+ }
+ }
+
+ static void fill_quadruples_map_from_plain_vector(const std::vector<double>& plain_vector, apollota::Triangulation::QuadruplesMap& quadruples_map)
+ {
+ quadruples_map.clear();
+ const std::size_t n=(plain_vector.size()/8);
+ for(std::size_t i=0;i<n;i++)
+ {
+ quadruples_map[apollota::Quadruple(
+ static_cast<std::size_t>(plain_vector[i*8+0]+0.5),
+ static_cast<std::size_t>(plain_vector[i*8+1]+0.5),
+ static_cast<std::size_t>(plain_vector[i*8+2]+0.5),
+ static_cast<std::size_t>(plain_vector[i*8+3]+0.5))].push_back(apollota::SimpleSphere(
+ plain_vector[i*8+4],
+ plain_vector[i*8+5],
+ plain_vector[i*8+6],
+ plain_vector[i*8+7]));
+ }
+ }
+};
+#endif
+
+inline bool number_is_power_of_two(const unsigned long x)
+{
+ return ( (x>0) && ((x & (x-1))==0) );
+}
+
+}
+
+void calculate_vertices_in_parallel(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ std::set<std::string> available_processing_method_names;
+ {
+ available_processing_method_names.insert("simulated");
+#ifdef _OPENMP
+ available_processing_method_names.insert("openmp");
+#endif
+#ifdef ENABLE_MPI
+ available_processing_method_names.insert("mpi");
+#endif
+ }
+
+ std::string available_processing_method_names_string;
+ {
+ std::ostringstream output;
+ for(std::set<std::string>::const_iterator it=available_processing_method_names.begin();it!=available_processing_method_names.end();++it)
+ {
+ output << " '" << (*it) << "'";
+ }
+ available_processing_method_names_string=output.str();
+ }
+
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'x y z r')");
+ pohw.describe_io("stdout", false, true, "list of Voronoi vertices, i.e. quadruples with tangent spheres (line format: 'q1 q2 q3 q4 x y z r')");
+
+ const std::string method=poh.argument<std::string>(pohw.describe_option("--method", "string", "parallelization method name, variants are:"+available_processing_method_names_string, true), "");
+ const std::size_t parts=poh.argument<std::size_t>(pohw.describe_option("--parts", "number", "number of parts for splitting, must be power of 2", true), 0);
+ const bool print_log=poh.contains_option(pohw.describe_option("--print-log", "", "flag to print log of calculations"));
+ const bool include_surplus_quadruples=poh.contains_option(pohw.describe_option("--include-surplus-quadruples", "", "flag to include surplus quadruples"));
+ const bool link=poh.contains_option(pohw.describe_option("--link", "", "flag to output links between vertices"));
+ const double init_radius_for_BSH=poh.argument<double>(pohw.describe_option("--init-radius-for-BSH", "number", "initial radius for bounding sphere hierarchy"), 3.5);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ if(available_processing_method_names.count(method)==0)
+ {
+ throw std::runtime_error("Invalid processing method name, acceptable values are:"+available_processing_method_names_string+".");
+ }
+
+ if(!number_is_power_of_two(parts))
+ {
+ throw std::runtime_error("Number of parts must be power of 2.");
+ }
+
+ if(init_radius_for_BSH<=1.0)
+ {
+ throw std::runtime_error("Bounding spheres hierarchy initial radius should be greater than 1.");
+ }
+
+ ParallelComputationResult result;
+ bool master_finished=true;
+
+ if(method=="simulated")
+ {
+ ParallelComputationProcessingSimulated::process(parts, init_radius_for_BSH, include_surplus_quadruples, result);
+ }
+#ifdef _OPENMP
+ else if(method=="openmp")
+ {
+ ParallelComputationProcessingWithOpenMP::process(parts, init_radius_for_BSH, include_surplus_quadruples, result);
+ }
+#endif
+#ifdef ENABLE_MPI
+ else if(method=="mpi")
+ {
+ master_finished=ParallelComputationProcessingWithMPI::process(poh.unused_argv(), parts, init_radius_for_BSH, include_surplus_quadruples, result);
+ }
+#endif
+ else
+ {
+ throw std::runtime_error("Processing method '"+method+"' is not available.");
+ }
+
+ if(master_finished)
+ {
+ if(link)
+ {
+ apollota::TriangulationOutput::print_vertices_vector_with_vertices_graph(apollota::Triangulation::collect_vertices_vector_from_quadruples_map(result.merged_quadruples_map), apollota::Triangulation::construct_vertices_graph(result.input_spheres, result.merged_quadruples_map), std::cout);
+ }
+ else
+ {
+ apollota::TriangulationOutput::print_vertices_vector(apollota::Triangulation::collect_vertices_vector_from_quadruples_map(result.merged_quadruples_map), std::cout);
+ }
+
+ if(print_log)
+ {
+ std::clog << "balls " << result.input_spheres.size() << "\n";
+ std::clog << "parts " << result.number_of_initialized_parts << "\n";
+ std::clog << "produced_quadruples " << result.number_of_produced_quadruples << "\n";
+ std::clog << "merged_quadruples " << result.merged_quadruples_map.size() << "\n";
+ std::clog << "tangent_spheres " << apollota::Triangulation::count_tangent_spheres_in_quadruples_map(result.merged_quadruples_map) << "\n";
+ }
+ }
+}
diff --git a/src/mode_compare_contacts.cpp b/src/mode_compare_contacts.cpp
new file mode 100644
index 0000000..caef98b
--- /dev/null
+++ b/src/mode_compare_contacts.cpp
@@ -0,0 +1,425 @@
+#include <iostream>
+#include <stdexcept>
+#include <fstream>
+#include <cmath>
+#include <algorithm>
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+struct CADDescriptor
+{
+ double target_area_sum;
+ double model_area_sum;
+ double raw_differences_sum;
+ double constrained_differences_sum;
+ double model_target_area_sum;
+
+ CADDescriptor() : target_area_sum(0), model_area_sum(0), raw_differences_sum(), constrained_differences_sum(0), model_target_area_sum(0)
+ {
+ }
+
+ void add(const double target_area, const double model_area)
+ {
+ target_area_sum+=target_area;
+ model_area_sum+=model_area;
+ raw_differences_sum+=fabs(target_area-model_area);
+ constrained_differences_sum+=std::min(fabs(target_area-model_area), target_area);
+ model_target_area_sum+=(target_area>0.0 ? model_area : 0.0);
+ }
+
+ void add(const CADDescriptor& cadd)
+ {
+ target_area_sum+=cadd.target_area_sum;
+ model_area_sum+=cadd.model_area_sum;
+ raw_differences_sum+=cadd.raw_differences_sum;
+ constrained_differences_sum+=cadd.constrained_differences_sum;
+ model_target_area_sum+=cadd.model_target_area_sum;
+ }
+
+ double score() const
+ {
+ return ((target_area_sum>0.0) ? (1.0-(constrained_differences_sum/target_area_sum)) : -1.0);
+ }
+};
+
+inline bool& detailed_output_of_CADDescriptor()
+{
+ static bool detailed_output=false;
+ return detailed_output;
+}
+
+inline std::ostream& operator<<(std::ostream& output, const CADDescriptor& cadd)
+{
+ output << cadd.score();
+ if(detailed_output_of_CADDescriptor())
+ {
+ output << " " << cadd.target_area_sum
+ << " " << cadd.model_area_sum
+ << " " << cadd.raw_differences_sum
+ << " " << cadd.constrained_differences_sum
+ << " " << cadd.model_target_area_sum;
+ }
+ return output;
+}
+
+std::map< CRADsPair, double > summarize_pair_mapping_of_values(const std::map< CRADsPair, double >& map, const bool ignore_residue_names)
+{
+ std::map< CRADsPair, double > result;
+ for(std::map< CRADsPair, double >::const_iterator it=map.begin();it!=map.end();++it)
+ {
+ const CRADsPair& crads=it->first;
+ result[CRADsPair(crads.a.without_some_info(true, true, false, ignore_residue_names), crads.b.without_some_info(true, true, false, ignore_residue_names))]+=it->second;
+ }
+ return result;
+}
+
+std::map< CRADsPair, std::pair<double, double> > combine_two_pair_mappings_of_values(const std::map< CRADsPair, double >& map1, const std::map< CRADsPair, double >& map2)
+{
+ std::map< CRADsPair, std::pair<double, double> > result;
+ for(std::map< CRADsPair, double >::const_iterator it=map1.begin();it!=map1.end();++it)
+ {
+ result[it->first].first=it->second;
+ }
+ for(std::map< CRADsPair, double >::const_iterator it=map2.begin();it!=map2.end();++it)
+ {
+ result[it->first].second=it->second;
+ }
+ return result;
+}
+
+std::map< CRADsPair, CADDescriptor > construct_map_of_cad_descriptors(const std::map< CRADsPair, std::pair<double, double> >& map_of_value_pairs)
+{
+ std::map< CRADsPair, CADDescriptor > result;
+ for(std::map< CRADsPair, std::pair<double, double> >::const_iterator it=map_of_value_pairs.begin();it!=map_of_value_pairs.end();++it)
+ {
+ result[it->first].add(it->second.first, it->second.second);
+ }
+ return result;
+}
+
+CADDescriptor construct_global_cad_descriptor(const std::map< CRADsPair, CADDescriptor >& map_of_descriptors)
+{
+ CADDescriptor result;
+ for(std::map< CRADsPair, CADDescriptor >::const_iterator it=map_of_descriptors.begin();it!=map_of_descriptors.end();++it)
+ {
+ result.add(it->second);
+ }
+ return result;
+}
+
+CADDescriptor construct_global_cad_descriptor(const std::map<CRADsPair, double>& map_of_target_contacts, const std::map<CRADsPair, double>& map_of_contacts, const bool ignore_residue_names)
+{
+ return construct_global_cad_descriptor(
+ construct_map_of_cad_descriptors(
+ combine_two_pair_mappings_of_values(
+ summarize_pair_mapping_of_values(map_of_target_contacts, ignore_residue_names),
+ summarize_pair_mapping_of_values(map_of_contacts, ignore_residue_names))));
+}
+
+std::map<CRAD, CADDescriptor> filter_map_of_cad_descriptors_by_target_presence(const std::map<CRAD, CADDescriptor>& input_map)
+{
+ std::map<CRAD, CADDescriptor> result;
+ for(std::map<CRAD, CADDescriptor>::const_iterator it=input_map.begin();it!=input_map.end();++it)
+ {
+ if(it->second.target_area_sum>0.0 && it->first.altLoc!="m" && it->first!=CRAD::any())
+ {
+ result[it->first]=it->second;
+ }
+ }
+ return result;
+}
+
+double calculate_average_score_from_map_of_cad_descriptors(const std::map<CRAD, CADDescriptor>& input_map)
+{
+ double sum=0.0;
+ for(std::map<CRAD, CADDescriptor>::const_iterator it=input_map.begin();it!=input_map.end();++it)
+ {
+ sum+=it->second.score();
+ }
+ return (sum/static_cast<double>(input_map.size()));
+}
+
+std::map<CRAD, double> collect_scores_from_map_of_cad_descriptors(const std::map<CRAD, CADDescriptor>& input_map)
+{
+ std::map<CRAD, double> result;
+ for(std::map<CRAD, CADDescriptor>::const_iterator it=input_map.begin();it!=input_map.end();++it)
+ {
+ result[it->first]=it->second.score();
+ }
+ return result;
+}
+
+std::string rename_by_map(const std::map<std::string, std::string>& map_of_renamings, const std::string& name)
+{
+ std::map<std::string, std::string>::const_iterator it=map_of_renamings.find(name);
+ if(it!=map_of_renamings.end())
+ {
+ return it->second;
+ }
+ else
+ {
+ return name;
+ }
+}
+
+std::map<CRADsPair, double> rename_chains_in_map_of_contacts(const std::map<CRADsPair, double>& map_of_contacts, const std::map<std::string, std::string>& map_of_renamings)
+{
+ if(map_of_renamings.empty())
+ {
+ return map_of_contacts;
+ }
+ std::map<CRADsPair, double> result;
+ for(std::map<CRADsPair, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ CRAD a=it->first.a;
+ CRAD b=it->first.b;
+ a.chainID=rename_by_map(map_of_renamings, a.chainID);
+ b.chainID=rename_by_map(map_of_renamings, b.chainID);
+ result[CRADsPair(a, b)]+=it->second;
+ }
+ return result;
+}
+
+std::map<CRADsPair, double> select_contacts_with_defined_chain_names(const std::map<CRADsPair, double>& map_of_contacts)
+{
+ std::map<CRADsPair, double> result;
+ for(std::map<CRADsPair, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ if(!it->first.a.chainID.empty() || !it->first.b.chainID.empty())
+ {
+ result[it->first]=it->second;
+ }
+ }
+ return result;
+}
+
+std::vector<std::string> get_sorted_chain_names_from_map_of_contacts(const std::map<CRADsPair, double>& map_of_contacts)
+{
+ std::set<std::string> set_of_names;
+ for(std::map<CRADsPair, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ if(it->first.a!=CRAD::solvent() && it->first.a!=CRAD::any())
+ {
+ set_of_names.insert(it->first.a.chainID);
+ }
+ if(it->first.b!=CRAD::solvent() && it->first.b!=CRAD::any())
+ {
+ set_of_names.insert(it->first.b.chainID);
+ }
+ }
+ return std::vector<std::string>(set_of_names.begin(), set_of_names.end());
+}
+
+std::map<std::string, std::string> generate_map_of_renamings_from_two_lists(const std::vector<std::string>& left, const std::vector<std::string>& right)
+{
+ std::map<std::string, std::string> result;
+ if(left.size()==right.size())
+ {
+ for(std::size_t i=0;i<left.size();i++)
+ {
+ result[left[i]]=right[i];
+ }
+ }
+ return result;
+}
+
+void remap_chains_optimally(
+ const std::map<CRADsPair, double>& map_of_target_contacts,
+ const bool ignore_residue_names,
+ const std::string& remapped_chains_file,
+ const bool print_log,
+ std::map<CRADsPair, double>& map_of_contacts)
+{
+ const std::vector<std::string> chain_names=get_sorted_chain_names_from_map_of_contacts(map_of_contacts);
+ if(chain_names.size()<2)
+ {
+ return;
+ }
+ if(chain_names.size()<=5)
+ {
+ std::pair<std::map<std::string, std::string>, double> best_renaming(generate_map_of_renamings_from_two_lists(chain_names, chain_names), 0.0);
+ std::vector<std::string> permutated_chain_names=chain_names;
+ do
+ {
+ const std::map<std::string, std::string> map_of_renamings=generate_map_of_renamings_from_two_lists(chain_names, permutated_chain_names);
+ const double score=construct_global_cad_descriptor(map_of_target_contacts, rename_chains_in_map_of_contacts(map_of_contacts, map_of_renamings), ignore_residue_names).score();
+ if(score>best_renaming.second)
+ {
+ best_renaming.first=map_of_renamings;
+ best_renaming.second=score;
+ }
+ if(print_log)
+ {
+ for(std::size_t i=0;i<permutated_chain_names.size();i++)
+ {
+ std::cerr << permutated_chain_names[i] << " ";
+ }
+ std::cerr << " " << score << "\n";
+ }
+ }
+ while(std::next_permutation(permutated_chain_names.begin(), permutated_chain_names.end()));
+ map_of_contacts=rename_chains_in_map_of_contacts(map_of_contacts, best_renaming.first);
+ if(print_log)
+ {
+ std::cerr << "remapping:\n";
+ auxiliaries::IOUtilities().write_map(best_renaming.first, std::cerr);
+ }
+ auxiliaries::IOUtilities().write_map_to_file(best_renaming.first, remapped_chains_file);
+ }
+ else
+ {
+ std::map<std::string, std::string> map_of_renamings;
+ std::map<std::string, std::string> map_of_renamings_in_target;
+ for(std::size_t i=0;i<chain_names.size();i++)
+ {
+ map_of_renamings[chain_names[i]]=std::string();
+ map_of_renamings_in_target[chain_names[i]]=std::string();
+ }
+ std::set<std::string> set_of_free_chains_left(chain_names.begin(), chain_names.end());
+ std::set<std::string> set_of_free_chains_right(chain_names.begin(), chain_names.end());
+ while(!set_of_free_chains_left.empty())
+ {
+ std::pair<std::string, std::string> best_pair(*set_of_free_chains_left.begin(), *set_of_free_chains_right.begin());
+ double best_score=0.0;
+ for(std::set<std::string>::const_iterator it_left=set_of_free_chains_left.begin();it_left!=set_of_free_chains_left.end();++it_left)
+ {
+ for(std::set<std::string>::const_iterator it_right=set_of_free_chains_right.begin();it_right!=set_of_free_chains_right.end();++it_right)
+ {
+ std::map<std::string, std::string> new_map_of_renamings=map_of_renamings;
+ std::map<std::string, std::string> new_map_of_renamings_in_target=map_of_renamings_in_target;
+ new_map_of_renamings[*it_left]=(*it_right);
+ new_map_of_renamings_in_target[*it_right]=(*it_right);
+ const CADDescriptor cad_descriptor=construct_global_cad_descriptor(
+ select_contacts_with_defined_chain_names(rename_chains_in_map_of_contacts(map_of_target_contacts, new_map_of_renamings_in_target)),
+ select_contacts_with_defined_chain_names(rename_chains_in_map_of_contacts(map_of_contacts, new_map_of_renamings)),
+ ignore_residue_names);
+ const double score=cad_descriptor.score()*cad_descriptor.target_area_sum;
+ if(score>best_score)
+ {
+ best_pair=std::make_pair(*it_left, *it_right);
+ best_score=score;
+ }
+ if(print_log)
+ {
+ std::cerr << (*it_left) << " " << (*it_right) << " " << score << "\n";
+ }
+ }
+ }
+ if(print_log)
+ {
+ std::cerr << best_pair.first << " " << best_pair.second << " " << best_score << " fixed\n";
+ }
+ map_of_renamings[best_pair.first]=best_pair.second;
+ map_of_renamings_in_target[best_pair.second]=best_pair.second;
+ set_of_free_chains_left.erase(best_pair.first);
+ set_of_free_chains_right.erase(best_pair.second);
+ }
+ map_of_contacts=rename_chains_in_map_of_contacts(map_of_contacts, map_of_renamings);
+ if(print_log)
+ {
+ std::cerr << "remapping:\n";
+ auxiliaries::IOUtilities().write_map(map_of_renamings, std::cerr);
+ }
+ auxiliaries::IOUtilities().write_map_to_file(map_of_renamings, remapped_chains_file);
+ }
+}
+
+}
+
+void compare_contacts(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of model contacts (line format: 'annotation1 annotation2 area')");
+ pohw.describe_io("stdout", false, true, "global scores (atom-level and residue-level)");
+
+ const std::string target_contacts_file=poh.argument<std::string>(pohw.describe_option("--target-contacts-file", "string", "file path to input target contacts", true), "");
+ const std::string inter_atom_scores_file=poh.argument<std::string>(pohw.describe_option("--inter-atom-scores-file", "string", "file path to output inter-atom scores"), "");
+ const std::string inter_residue_scores_file=poh.argument<std::string>(pohw.describe_option("--inter-residue-scores-file", "string", "file path to output inter-residue scores"), "");
+ const std::string atom_scores_file=poh.argument<std::string>(pohw.describe_option("--atom-scores-file", "string", "file path to output atom scores"), "");
+ const std::string residue_scores_file=poh.argument<std::string>(pohw.describe_option("--residue-scores-file", "string", "file path to output residue scores"), "");
+ const int depth=poh.argument<int>(pohw.describe_option("--depth", "number", "local neighborhood depth"), 0);
+ const unsigned int smoothing_window=poh.argument<unsigned int>(pohw.describe_option("--smoothing-window", "number", "window to smooth residue scores along sequence"), 0);
+ const std::string smoothed_scores_file=poh.argument<std::string>(pohw.describe_option("--smoothed-scores-file", "string", "file path to output smoothed residue scores"), "");
+ const bool ignore_residue_names=poh.contains_option(pohw.describe_option("--ignore-residue-names", "", "flag to consider just residue numbers and ignore residue names"));
+ const bool residue_level_only=poh.contains_option(pohw.describe_option("--residue-level-only", "", "flag to output only residue-level results"));
+ detailed_output_of_CADDescriptor()=poh.contains_option(pohw.describe_option("--detailed-output", "", "flag to enable detailed output"));
+ const std::string chains_renaming_file=poh.argument<std::string>(pohw.describe_option("--chains-renaming-file", "string", "file path to input chains renaming"), "");
+ const bool remap_chains=poh.contains_option(pohw.describe_option("--remap-chains", "", "flag to calculate optimal chains remapping"));
+ const bool remap_chains_log=poh.contains_option(pohw.describe_option("--remap-chains-log", "", "flag output remapping progress to stderr"));
+ const std::string remapped_chains_file=poh.argument<std::string>(pohw.describe_option("--remapped-chains-file", "string", "file path to output calculated chains remapping"), "");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::map<CRADsPair, double> map_of_contacts=auxiliaries::IOUtilities().read_lines_to_map< std::map<CRADsPair, double> >(std::cin);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No contacts input.");
+ }
+
+ const std::map<CRADsPair, double> map_of_target_contacts=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRADsPair, double> >(target_contacts_file);
+ if(map_of_target_contacts.empty())
+ {
+ throw std::runtime_error("No target contacts input.");
+ }
+
+ if(!chains_renaming_file.empty())
+ {
+ const std::map<std::string, std::string> map_of_renamings=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<std::string, std::string> >(chains_renaming_file);
+ if(!map_of_renamings.empty())
+ {
+ map_of_contacts=rename_chains_in_map_of_contacts(map_of_contacts, map_of_renamings);
+ }
+ }
+
+ if(remap_chains)
+ {
+ remap_chains_optimally(map_of_target_contacts, ignore_residue_names, remapped_chains_file, remap_chains_log, map_of_contacts);
+ }
+
+ if(!residue_level_only)
+ {
+ const std::map< CRADsPair, CADDescriptor > map_of_inter_atom_cad_descriptors=construct_map_of_cad_descriptors(
+ combine_two_pair_mappings_of_values(map_of_target_contacts, map_of_contacts));
+ auxiliaries::IOUtilities().write_map_to_file(map_of_inter_atom_cad_descriptors, inter_atom_scores_file);
+
+ const std::map<CRAD, CADDescriptor> map_of_atom_cad_descriptors=filter_map_of_cad_descriptors_by_target_presence(
+ auxiliaries::ChainResidueAtomDescriptorsGraphOperations::accumulate_mapped_values_by_graph_neighbors(map_of_inter_atom_cad_descriptors, depth));
+ auxiliaries::IOUtilities().write_map_to_file(map_of_atom_cad_descriptors, atom_scores_file);
+
+ std::cout << "atom_level_global " << construct_global_cad_descriptor(map_of_inter_atom_cad_descriptors) << "\n";
+ std::cout << "atom_average_local " << calculate_average_score_from_map_of_cad_descriptors(map_of_atom_cad_descriptors) << "\n";
+ std::cout << "atom_count " << map_of_atom_cad_descriptors.size() << "\n";
+ }
+
+ {
+ const std::map< CRADsPair, CADDescriptor > map_of_inter_residue_cad_descriptors=construct_map_of_cad_descriptors(
+ combine_two_pair_mappings_of_values(summarize_pair_mapping_of_values(map_of_target_contacts, ignore_residue_names), summarize_pair_mapping_of_values(map_of_contacts, ignore_residue_names)));
+ auxiliaries::IOUtilities().write_map_to_file(map_of_inter_residue_cad_descriptors, inter_residue_scores_file);
+
+ const std::map<CRAD, CADDescriptor> map_of_residue_cad_descriptors=filter_map_of_cad_descriptors_by_target_presence(
+ auxiliaries::ChainResidueAtomDescriptorsGraphOperations::accumulate_mapped_values_by_graph_neighbors(map_of_inter_residue_cad_descriptors, depth));
+ auxiliaries::IOUtilities().write_map_to_file(map_of_residue_cad_descriptors, residue_scores_file);
+
+ if(!smoothed_scores_file.empty())
+ {
+ auxiliaries::IOUtilities().write_map_to_file(
+ auxiliaries::ChainResidueAtomDescriptorsSequenceOperations::smooth_residue_scores_along_sequence(
+ collect_scores_from_map_of_cad_descriptors(map_of_residue_cad_descriptors), smoothing_window), smoothed_scores_file);
+ }
+
+ std::cout << "residue_level_global " << construct_global_cad_descriptor(map_of_inter_residue_cad_descriptors) << "\n";
+ std::cout << "residue_average_local " << calculate_average_score_from_map_of_cad_descriptors(map_of_residue_cad_descriptors) << "\n";
+ std::cout << "residue_count " << map_of_residue_cad_descriptors.size() << "\n";
+ }
+}
diff --git a/src/mode_demo_hypercut.cpp b/src/mode_demo_hypercut.cpp
new file mode 100644
index 0000000..8876b34
--- /dev/null
+++ b/src/mode_demo_hypercut.cpp
@@ -0,0 +1,616 @@
+#include "apollota/basic_operations_on_spheres.h"
+#include "apollota/subdivided_icosahedron.h"
+#include "apollota/hyperboloid_between_two_spheres.h"
+
+#include "auxiliaries/io_utilities.h"
+#include "auxiliaries/opengl_printer.h"
+#include "auxiliaries/program_options_handler.h"
+
+namespace
+{
+
+struct Triangle
+{
+ std::vector<apollota::SimplePoint> p;
+
+ Triangle() : p(3)
+ {
+ }
+
+ Triangle(const apollota::SimplePoint& a, const apollota::SimplePoint& b, const apollota::SimplePoint& c) : p(3)
+ {
+ p[0]=a;
+ p[1]=b;
+ p[2]=c;
+ }
+};
+
+typedef std::vector<Triangle> TriangleList;
+
+typedef std::pair<TriangleList, TriangleList> TriangleListSplit;
+
+inline TriangleList subdivide_triangle_in_four(const Triangle& t)
+{
+ TriangleList result(4);
+ result[0]=Triangle((t.p[0]+t.p[1])*0.5, (t.p[0]+t.p[2])*0.5, (t.p[1]+t.p[2])*0.5);
+ result[1]=Triangle(t.p[0], result[0].p[0], result[0].p[1]);
+ result[1]=Triangle(t.p[1], result[0].p[0], result[0].p[2]);
+ result[1]=Triangle(t.p[2], result[0].p[1], result[0].p[2]);
+ return result;
+}
+
+inline TriangleList subdivide_triangle_in_three(const Triangle& t)
+{
+ const apollota::SimplePoint c=(t.p[0]+t.p[1]+t.p[2])*(1.0/3.0);
+ TriangleList result(3);
+ result[0]=Triangle(t.p[0], t.p[1], c);
+ result[1]=Triangle(t.p[0], t.p[2], c);
+ result[2]=Triangle(t.p[1], t.p[2], c);
+ return result;
+}
+
+inline TriangleList subdivide_triangle(const Triangle& t, const bool in_three)
+{
+ return (in_three ? subdivide_triangle_in_three(t) : subdivide_triangle_in_four(t));
+}
+
+inline TriangleList multiple_subdivide_triangle(const TriangleList& tl, const bool in_three)
+{
+ TriangleList result;
+ for(std::size_t i=0;i<tl.size();i++)
+ {
+ const TriangleList subresult=subdivide_triangle(tl[i], in_three);
+ result.insert(result.end(), subresult.begin(), subresult.end());
+ }
+ return result;
+}
+
+inline Triangle project_triangle_on_hyperboloid(const Triangle& t, const apollota::SimpleSphere& a, const apollota::SimpleSphere& b)
+{
+ return Triangle(
+ apollota::HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(t.p[0], a, b),
+ apollota::HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(t.p[1], a, b),
+ apollota::HyperboloidBetweenTwoSpheres::project_point_on_hyperboloid(t.p[2], a, b));
+}
+
+inline TriangleList multiple_project_triangle_on_hyperboloid(const TriangleList& tl, const apollota::SimpleSphere& a, const apollota::SimpleSphere& b)
+{
+ TriangleList result;
+ result.reserve(tl.size());
+ for(std::size_t i=0;i<tl.size();i++)
+ {
+ result.push_back(project_triangle_on_hyperboloid(tl[i], a, b));
+ }
+ return result;
+}
+
+inline TriangleListSplit cut_triangle_with_hyperboloid(const Triangle& t, const apollota::SimpleSphere& a, const apollota::SimpleSphere& b)
+{
+ bool mask[3];
+ for(int i=0;i<3;i++)
+ {
+ mask[i]=(apollota::minimal_distance_from_point_to_sphere(t.p[i], a)<apollota::minimal_distance_from_point_to_sphere(t.p[i], b));
+ }
+
+ if(mask[0] && mask[1] && mask[2])
+ {
+ return TriangleListSplit(TriangleList(1, t), TriangleList());
+ }
+ else if(!mask[0] && !mask[1] && !mask[2])
+ {
+ return TriangleListSplit(TriangleList(), TriangleList(1, t));
+ }
+
+ int ids[3]={0, 1, 2};
+ if(mask[0]!=mask[1] && mask[1]==mask[2])
+ {
+ ids[0]=0;
+ ids[1]=1;
+ ids[2]=2;
+ }
+ else if(mask[1]!=mask[0] && mask[0]==mask[2])
+ {
+ ids[0]=1;
+ ids[1]=0;
+ ids[2]=2;
+ }
+ else if(mask[2]!=mask[0] && mask[0]==mask[1])
+ {
+ ids[0]=2;
+ ids[1]=0;
+ ids[2]=1;
+ }
+
+ TriangleListSplit result;
+ {
+ const apollota::SimplePoint m01=t.p[ids[0]]+((t.p[ids[1]]-t.p[ids[0]]).unit()*apollota::HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(t.p[ids[0]], t.p[ids[1]], a, b));
+ const apollota::SimplePoint m02=t.p[ids[0]]+((t.p[ids[2]]-t.p[ids[0]]).unit()*apollota::HyperboloidBetweenTwoSpheres::intersect_vector_with_hyperboloid(t.p[ids[0]], t.p[ids[2]], a, b));
+ result.first.push_back(Triangle(t.p[ids[0]], m01, m02));
+ result.second.push_back(Triangle(m01, t.p[ids[1]], t.p[ids[2]]));
+ result.second.push_back(Triangle(m01, m02, t.p[ids[2]]));
+ if(!mask[ids[0]])
+ {
+ std::swap(result.first, result.second);
+ }
+ }
+ return result;
+}
+
+inline TriangleListSplit multiple_cut_triangle_with_hyperboloid(const TriangleList& tl, const apollota::SimpleSphere& a, const apollota::SimpleSphere& b)
+{
+ TriangleListSplit result;
+ for(std::size_t i=0;i<tl.size();i++)
+ {
+ const TriangleListSplit subresult=cut_triangle_with_hyperboloid(tl[i], a, b);
+ result.first.insert(result.first.end(), subresult.first.begin(), subresult.first.end());
+ result.second.insert(result.second.end(), subresult.second.begin(), subresult.second.end());
+ }
+ return result;
+}
+
+inline TriangleList init_sphere_triangles(const apollota::SimpleSphere& s, const int depth)
+{
+ apollota::SubdividedIcosahedron sih(depth);
+ sih.fit_into_sphere(s, s.r);
+ TriangleList result;
+ result.reserve(sih.triples().size());
+ for(std::size_t i=0;i<sih.triples().size();i++)
+ {
+ const apollota::Triple& t=sih.triples()[i];
+ result.push_back(Triangle(sih.vertices()[t.get(0)], sih.vertices()[t.get(1)], sih.vertices()[t.get(2)]));
+ }
+ return result;
+}
+
+inline TriangleList init_spheres_intersection_hyperboloid_triangles(const apollota::SimpleSphere& a, const apollota::SimpleSphere& b, const int depth)
+{
+ if(a.r<b.r)
+ {
+ return init_spheres_intersection_hyperboloid_triangles(b, a, depth);
+ }
+ if(apollota::sphere_intersects_sphere(a, b))
+ {
+ const TriangleListSplit tls=multiple_cut_triangle_with_hyperboloid(init_sphere_triangles(a, depth), a, b);
+ return multiple_project_triangle_on_hyperboloid((tls.first.size()<tls.second.size() ? tls.first : tls.second), a, b);
+ }
+ else
+ {
+ return TriangleList();
+ }
+}
+
+inline void draw_triangle(auxiliaries::OpenGLPrinter& opengl_printer, const Triangle& t, const Triangle& n)
+{
+ opengl_printer.add_triangle_strip(t.p, n.p);
+}
+
+inline void draw_triangle(auxiliaries::OpenGLPrinter& opengl_printer, const Triangle& t, const apollota::SimplePoint& n)
+{
+ draw_triangle(opengl_printer, t, Triangle(n, n, n));
+}
+
+inline void draw_triangle(auxiliaries::OpenGLPrinter& opengl_printer, const Triangle& t, const apollota::SimpleSphere& a)
+{
+ draw_triangle(opengl_printer, t, Triangle((t.p[0]-apollota::SimplePoint(a)).unit(), (t.p[1]-apollota::SimplePoint(a)).unit(), (t.p[2]-apollota::SimplePoint(a)).unit()));
+}
+
+inline void draw_triangle(auxiliaries::OpenGLPrinter& opengl_printer, const Triangle& t, const std::pair<apollota::SimpleSphere, apollota::SimpleSphere>& ab)
+{
+ Triangle n;
+ for(int i=0;i<3;i++)
+ {
+ const apollota::SimplePoint oa=(apollota::SimplePoint(ab.first)-t.p[i]).unit();
+ const apollota::SimplePoint ob=(apollota::SimplePoint(ab.second)-t.p[i]).unit();
+ const apollota::SimplePoint x=(oa&ob);
+ if(apollota::equal(x.module(), 0.0))
+ {
+ n.p[i]=(apollota::SimplePoint(ab.second)-apollota::SimplePoint(ab.first)).unit();
+ }
+ else
+ {
+ n.p[i]=(x.unit()&((oa+ob)*0.5).unit()).unit();
+ }
+ }
+ draw_triangle(opengl_printer, t, n);
+}
+
+inline void draw_triangle(auxiliaries::OpenGLPrinter& opengl_printer, const Triangle& t, const bool n)
+{
+ draw_triangle(opengl_printer, t, ((t.p[1]-t.p[0])&(t.p[2]-t.p[0])).unit()*(n ? 1.0 : -1.0));
+}
+
+template <typename NormalDescriptor>
+inline void multiple_draw_triangle(auxiliaries::OpenGLPrinter& opengl_printer, const TriangleList& tl, const NormalDescriptor& nd)
+{
+ for(std::size_t i=0;i<tl.size();i++)
+ {
+ draw_triangle(opengl_printer, tl[i], nd);
+ }
+}
+
+inline void draw_triangle_lines(auxiliaries::OpenGLPrinter& opengl_printer, const Triangle& t)
+{
+ opengl_printer.add_line_loop(t.p);
+}
+
+inline void multiple_draw_triangle_lines(auxiliaries::OpenGLPrinter& opengl_printer, const TriangleList& tl)
+{
+ for(std::size_t i=0;i<tl.size();i++)
+ {
+ draw_triangle_lines(opengl_printer, tl[i]);
+ }
+}
+
+}
+
+void demo_hypercut(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "nothing");
+ pohw.describe_io("stdout", false, true, "nothing");
+
+ const double probe=poh.restrict_value_in_range(0.01, 100.0, poh.argument<double>(pohw.describe_option("--probe", "number", "probe radius"), 1.5));
+ const double big_probe=poh.restrict_value_in_range(probe+0.01, 100.0, poh.argument<double>(pohw.describe_option("--big-probe", "number", "big probe radius"), 3.0));
+ const int depth=poh.restrict_value_in_range(0, 6, poh.argument<int>(pohw.describe_option("--depth", "number", "probe radius"), 3));
+ const int balls_count=poh.restrict_value_in_range(3, 4, poh.argument<int>(pohw.describe_option("--balls-count", "number", "number of balls (3 or 4)"), 4));
+ const std::string name_prefix=poh.argument<std::string>(pohw.describe_option("--name-prefix", "string", "name prefix"), "");
+ const std::string output_prefix=poh.argument<std::string>(pohw.describe_option("--output-prefix", "string", "output prefix"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::vector<apollota::SimpleSphere> spheres;
+ spheres.push_back(apollota::SimpleSphere(0, 0, 0, 1));
+ spheres.push_back(apollota::SimpleSphere(2, 0, 0, 0.5));
+ spheres.push_back(apollota::SimpleSphere(1.5, -2, 0, 0.4));
+ spheres.push_back(apollota::SimpleSphere(0.5, 0, 2, 0.75));
+
+ int colors_of_singles[4]={0xFF0000, 0x00FF00, 0x0000FF, 0x888888};
+
+ int colors_of_pairs[4][4];
+ colors_of_pairs[0][1]=0xFFFF00;
+ colors_of_pairs[0][2]=0xFF00FF;
+ colors_of_pairs[0][3]=0xFF8888;
+ colors_of_pairs[1][2]=0x00FFFF;
+ colors_of_pairs[1][3]=0x88FF88;
+ colors_of_pairs[2][3]=0x8888FF;
+ for(int i=0;i<4;i++)
+ {
+ for(int j=i+1;j<4;j++)
+ {
+ colors_of_pairs[j][i]=colors_of_pairs[i][j];
+ }
+ colors_of_pairs[i][i]=colors_of_singles[i];
+ }
+
+ for(int i=0;i<balls_count;i++)
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_singles[i]);
+ opengl_printer.add_sphere(spheres[i]);
+
+ std::ostringstream name;
+ name << name_prefix << "ball_" << i;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ for(int i=0;i<balls_count;i++)
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_singles[i]);
+ opengl_printer.add_sphere(apollota::SimpleSphere(spheres[i], spheres[i].r+probe-0.01));
+
+ std::ostringstream name;
+ name << name_prefix << "sball_" << i;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ for(int i=0;i<balls_count;i++)
+ {
+ for(int j=i+1;j<balls_count;j++)
+ {
+ const TriangleList big_full_face=init_spheres_intersection_hyperboloid_triangles(
+ apollota::SimpleSphere(spheres[i], spheres[i].r+big_probe),
+ apollota::SimpleSphere(spheres[j], spheres[j].r+big_probe),
+ depth);
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_pairs[i][j]);
+ multiple_draw_triangle(opengl_printer, big_full_face, std::make_pair(spheres[i], spheres[j]));
+
+ std::ostringstream name;
+ name << name_prefix << "big_face_" << i << "_" << j;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ if(i==0 && j==1)
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, big_full_face);
+
+ std::ostringstream name;
+ name << name_prefix << "zbig_face_" << i << "_" << j;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ const TriangleList full_face=init_spheres_intersection_hyperboloid_triangles(
+ apollota::SimpleSphere(spheres[i], spheres[i].r+probe),
+ apollota::SimpleSphere(spheres[j], spheres[j].r+probe),
+ depth);
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_pairs[i][j]);
+ multiple_draw_triangle(opengl_printer, full_face, std::make_pair(spheres[i], spheres[j]));
+
+ std::ostringstream name;
+ name << name_prefix << "face_" << i << "_" << j;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ if(i==0 && j==1)
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, full_face);
+
+ std::ostringstream name;
+ name << name_prefix << "zface_" << i << "_" << j;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ for(int m=0;m<balls_count;m++)
+ {
+ if(m!=i && m!=j)
+ {
+ const TriangleList cut_face_m=multiple_cut_triangle_with_hyperboloid(full_face, spheres[i], spheres[m]).first;
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_pairs[i][j]);
+ multiple_draw_triangle(opengl_printer, cut_face_m, std::make_pair(spheres[i], spheres[j]));
+
+ std::ostringstream name;
+ name << name_prefix << "cut_a_" << i << "_" << j << "_" << m;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ if(i==0 && j==1)
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, cut_face_m);
+
+ std::ostringstream name;
+ name << name_prefix << "zcut_a_" << i << "_" << j << "_" << m;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ for(int n=0;n<balls_count;n++)
+ {
+ if(n!=i && n!=j && n>m)
+ {
+ const TriangleList cut_face_m_n=multiple_cut_triangle_with_hyperboloid(cut_face_m, spheres[i], spheres[n]).first;
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_pairs[i][j]);
+ multiple_draw_triangle(opengl_printer, cut_face_m_n, std::make_pair(spheres[i], spheres[j]));
+
+ std::ostringstream name;
+ name << name_prefix << "cut_b_" << i << "_" << j << "_" << m << "_" << n;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, cut_face_m_n);
+
+ std::ostringstream name;
+ name << name_prefix << "zcut_b_" << i << "_" << j << "_" << m << "_" << n;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ for(int i=0;i<balls_count;i++)
+ {
+ TriangleList sface=init_sphere_triangles(apollota::SimpleSphere(spheres[i], spheres[i].r+probe), depth);
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x777777);
+ multiple_draw_triangle_lines(opengl_printer, sface);
+
+ std::ostringstream name;
+ name << name_prefix << "wball_" << i;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ for(int j=0;j<balls_count;j++)
+ {
+ if(j!=i)
+ {
+ sface=multiple_cut_triangle_with_hyperboloid(sface, spheres[i], spheres[j]).first;
+ }
+ }
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_singles[i]);
+ multiple_draw_triangle(opengl_printer, sface, spheres[i]);
+
+ std::ostringstream name;
+ name << name_prefix << "sas_" << i;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, sface);
+
+ std::ostringstream name;
+ name << name_prefix << "zsas_" << i;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+ }
+
+ for(int i=0;i<balls_count;i++)
+ {
+ for(int j=0;j<balls_count;j++)
+ {
+ if(i!=j)
+ {
+ const TriangleList full_face=multiple_cut_triangle_with_hyperboloid(init_sphere_triangles(apollota::SimpleSphere(spheres[i], spheres[i].r+probe), depth), spheres[i], spheres[j]).second;
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_singles[j]);
+ multiple_draw_triangle(opengl_printer, full_face, spheres[i]);
+
+ std::ostringstream name;
+ name << name_prefix << "sf_" << i << "_" << j;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ if(i==0 && j==1)
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, full_face);
+
+ std::ostringstream name;
+ name << name_prefix << "zsf_" << i << "_" << j;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ for(int m=0;m<balls_count;m++)
+ {
+ if(m!=i && m!=j)
+ {
+ const TriangleList cut_face_m=multiple_cut_triangle_with_hyperboloid(full_face, spheres[j], spheres[m]).first;
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_singles[j]);
+ multiple_draw_triangle(opengl_printer, cut_face_m, spheres[i]);
+
+ std::ostringstream name;
+ name << name_prefix << "sc_a_" << i << "_" << j << "_" << m;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ if(i==0 && j==1)
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, cut_face_m);
+
+ std::ostringstream name;
+ name << name_prefix << "zsc_a_" << i << "_" << j << "_" << m;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ for(int n=0;n<balls_count;n++)
+ {
+ if(n!=i && n!=j && n>m)
+ {
+ const TriangleList cut_face_m_n=multiple_cut_triangle_with_hyperboloid(cut_face_m, spheres[j], spheres[n]).first;
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(colors_of_singles[j]);
+ multiple_draw_triangle(opengl_printer, cut_face_m_n, spheres[i]);
+
+ std::ostringstream name;
+ name << name_prefix << "sc_b_" << i << "_" << j << "_" << m << "_" << n;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ if(i==0 && j==1)
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, cut_face_m_n);
+
+ std::ostringstream name;
+ name << name_prefix << "zsc_b_" << i << "_" << j << "_" << m << "_" << n;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ for(int i=0;i<=4;i++)
+ {
+ TriangleList sface=init_sphere_triangles(apollota::SimpleSphere(0, 0, 0, 1), i);
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0xAAAAAA);
+ multiple_draw_triangle(opengl_printer, sface, true);
+
+ std::ostringstream name;
+ name << name_prefix << "ico_" << i;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, sface);
+
+ std::ostringstream name;
+ name << name_prefix << "ico_w_" << i;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0xAAAAAA);
+ multiple_draw_triangle(opengl_printer, sface, true);
+ opengl_printer.add_color(0x111111);
+ multiple_draw_triangle_lines(opengl_printer, sface);
+
+ std::ostringstream name;
+ name << name_prefix << "ico_f_" << i;
+ std::ofstream foutput((output_prefix+name.str()+".py").c_str(), std::ios::out);
+ opengl_printer.print_pymol_script(name.str(), true, foutput);
+ }
+ }
+}
diff --git a/src/mode_demo_polygon_triangulation.cpp b/src/mode_demo_polygon_triangulation.cpp
new file mode 100644
index 0000000..74f139a
--- /dev/null
+++ b/src/mode_demo_polygon_triangulation.cpp
@@ -0,0 +1,100 @@
+#include "apollota/simple_polygon_utilities.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/svg_writer.h"
+
+namespace
+{
+
+std::pair<double, double> fit_points_to_positive_canvas(const double margin, std::vector<apollota::SimplePoint>& points)
+{
+ if(!points.empty())
+ {
+ apollota::SimplePoint p_min=points[0];
+ apollota::SimplePoint p_max=points[0];
+ for(std::size_t i=1;i<points.size();i++)
+ {
+ const apollota::SimplePoint& p=points[i];
+ if(p.x<p_min.x)
+ {
+ p_min.x=p.x;
+ }
+ if(p.y<p_min.y)
+ {
+ p_min.y=p.y;
+ }
+ if(p.x>p_max.x)
+ {
+ p_max.x=p.x;
+ }
+ if(p.y>p_max.y)
+ {
+ p_max.y=p.y;
+ }
+ }
+ p_min=p_min-apollota::SimplePoint(margin, margin, 0);
+ p_max=p_max+apollota::SimplePoint(margin, margin, 0);
+ for(std::size_t i=0;i<points.size();i++)
+ {
+ apollota::SimplePoint& p=points[i];
+ p=(p-p_min);
+ }
+ return std::pair<double, double>(p_max.x-p_min.x, p_max.y-p_min.y);
+ }
+ return std::pair<double, double>(0, 0);
+}
+
+}
+
+void demo_polygon_triangulation(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "polygon points");
+ pohw.describe_io("stdout", false, true, "picture in SVG format");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::vector<apollota::SimplePoint> points;
+ auxiliaries::IOUtilities().read_lines_to_set(std::cin, points);
+ if(points.size()<3)
+ {
+ throw std::runtime_error("Less than 3 points provided to stdin.");
+ }
+
+ const std::pair<double, double> dimensions=fit_points_to_positive_canvas(100.0, points);
+
+ apollota::SimplePolygonUtilities::TriangulationInfo result=apollota::SimplePolygonUtilities::triangulate_simple_polygon(points, apollota::SimplePoint(0, 0, 1));
+ if(result.triangulation.empty())
+ {
+ throw std::runtime_error("Failed to produce triangulation.");
+ }
+
+ SVGWriter svg(dimensions.first, dimensions.second);
+ for(std::size_t i=0;i<points.size();i++)
+ {
+ const apollota::SimplePoint& p=points[i];
+ svg.add_circle(p.x, p.y, 10, (result.convexity_info.convexity[i]<0.0 ? "fill:rgb(255,0,0)" : "fill:rgb(0,0,255)"));
+ }
+ for(std::size_t i=0;i<points.size();i++)
+ {
+ const apollota::SimplePoint& a=points[i];
+ const apollota::SimplePoint& b=points[i+1<points.size() ? i+1 : 0];
+ svg.add_line(a.x, a.y, b.x, b.y, "stroke:rgb(255,255,0);stroke-width:5");
+ }
+ for(std::size_t i=0;i<result.triangulation.size();i++)
+ {
+ const apollota::Triple& t=result.triangulation[i];
+ const apollota::SimplePoint& a=points[t.get(0)];
+ const apollota::SimplePoint& b=points[t.get(1)];
+ const apollota::SimplePoint& c=points[t.get(2)];
+ svg.add_line(a.x, a.y, b.x, b.y, "stroke:rgb(0,0,0);stroke-width:1");
+ svg.add_line(a.x, a.y, c.x, c.y, "stroke:rgb(0,0,0);stroke-width:1");
+ svg.add_line(b.x, b.y, c.x, c.y, "stroke:rgb(0,0,0);stroke-width:1");
+ }
+ svg.write(std::cout);
+}
diff --git a/src/mode_demo_ses.cpp b/src/mode_demo_ses.cpp
new file mode 100644
index 0000000..da450ba
--- /dev/null
+++ b/src/mode_demo_ses.cpp
@@ -0,0 +1,544 @@
+#include "apollota/spheres_boundary_construction.h"
+#include "apollota/triangulation_queries.h"
+#include "apollota/rolling_topology.h"
+
+#include "auxiliaries/io_utilities.h"
+#include "auxiliaries/opengl_printer.h"
+#include "auxiliaries/program_options_handler.h"
+
+namespace
+{
+
+class SubdividedSphericalTriangulation
+{
+public:
+ SubdividedSphericalTriangulation(const int steps) : center_sphere_(0, 0, 0, 1)
+ {
+ const double t=(1+sqrt(5.0))/2.0;
+
+ std::vector<apollota::SimplePoint> vertices;
+ vertices.reserve(12);
+ vertices.push_back(apollota::SimplePoint( t, 1, 0).unit());
+ vertices.push_back(apollota::SimplePoint(-t, 1, 0).unit());
+ vertices.push_back(apollota::SimplePoint( t,-1, 0).unit());
+ vertices.push_back(apollota::SimplePoint(-t,-1, 0).unit());
+ vertices.push_back(apollota::SimplePoint( 1, 0, t).unit());
+ vertices.push_back(apollota::SimplePoint( 1, 0,-t).unit());
+ vertices.push_back(apollota::SimplePoint(-1, 0, t).unit());
+ vertices.push_back(apollota::SimplePoint(-1, 0,-t).unit());
+ vertices.push_back(apollota::SimplePoint( 0, t, 1).unit());
+ vertices.push_back(apollota::SimplePoint( 0,-t, 1).unit());
+ vertices.push_back(apollota::SimplePoint( 0, t,-1).unit());
+ vertices.push_back(apollota::SimplePoint( 0,-t,-1).unit());
+
+ triangles_.push_back(Triangle(vertices[0], vertices[8], vertices[4]));
+ triangles_.push_back(Triangle(vertices[1], vertices[10], vertices[7]));
+ triangles_.push_back(Triangle(vertices[2], vertices[9], vertices[11]));
+ triangles_.push_back(Triangle(vertices[7], vertices[3], vertices[1]));
+ triangles_.push_back(Triangle(vertices[0], vertices[5], vertices[10]));
+ triangles_.push_back(Triangle(vertices[3], vertices[9], vertices[6]));
+ triangles_.push_back(Triangle(vertices[3], vertices[11], vertices[9]));
+ triangles_.push_back(Triangle(vertices[8], vertices[6], vertices[4]));
+ triangles_.push_back(Triangle(vertices[2], vertices[4], vertices[9]));
+ triangles_.push_back(Triangle(vertices[3], vertices[7], vertices[11]));
+ triangles_.push_back(Triangle(vertices[4], vertices[2], vertices[0]));
+ triangles_.push_back(Triangle(vertices[9], vertices[4], vertices[6]));
+ triangles_.push_back(Triangle(vertices[2], vertices[11], vertices[5]));
+ triangles_.push_back(Triangle(vertices[0], vertices[10], vertices[8]));
+ triangles_.push_back(Triangle(vertices[5], vertices[0], vertices[2]));
+ triangles_.push_back(Triangle(vertices[10], vertices[5], vertices[7]));
+ triangles_.push_back(Triangle(vertices[1], vertices[6], vertices[8]));
+ triangles_.push_back(Triangle(vertices[1], vertices[8], vertices[10]));
+ triangles_.push_back(Triangle(vertices[6], vertices[1], vertices[3]));
+ triangles_.push_back(Triangle(vertices[11], vertices[7], vertices[5]));
+
+ subdivide(steps);
+ }
+
+ SubdividedSphericalTriangulation(
+ const apollota::SimpleSphere& tangent,
+ const apollota::SimpleSphere& a,
+ const apollota::SimpleSphere& b,
+ const apollota::SimpleSphere& c,
+ const std::vector<apollota::SimplePoint>& breaks,
+ const int steps) : center_sphere_(tangent)
+ {
+ const apollota::SimplePoint center_point(center_sphere_);
+
+ Triangle t;
+ t.p[0]=(center_point+((apollota::SimplePoint(a)-center_point).unit()*tangent.r));
+ t.p[1]=(center_point+((apollota::SimplePoint(b)-center_point).unit()*tangent.r));
+ t.p[2]=(center_point+((apollota::SimplePoint(c)-center_point).unit()*tangent.r));
+
+ apollota::SimplePoint t_mp=(t.p[0]+t.p[1]+t.p[2])*(1/3.0);
+ t_mp=apollota::SimplePoint(tangent)+((t_mp-center_point).unit()*tangent.r);
+
+ const apollota::SimplePoint t_side_mp=apollota::RollingTopology::construct_circular_arc_approximation_from_start_and_end(center_point, t.p[0]-center_point, t.p[1]-center_point, 2)[1];
+
+ if(breaks.size()==2)
+ {
+ triangles_.push_back(Triangle(t.p[0], breaks[0], t_mp));
+ triangles_.push_back(Triangle(breaks[0], t_side_mp, t_mp));
+ triangles_.push_back(Triangle(t_side_mp, breaks[1], t_mp));
+ triangles_.push_back(Triangle(breaks[1], t.p[1], t_mp));
+ }
+ else
+ {
+ triangles_.push_back(Triangle(t.p[0], t_side_mp, t_mp));
+ triangles_.push_back(Triangle(t_side_mp, t.p[1], t_mp));
+ }
+
+ subdivide(steps-1);
+ }
+
+ const apollota::SimpleSphere& center_sphere() const
+ {
+ return center_sphere_;
+ }
+
+ template<typename InputPointType>
+ void transform(const InputPointType& new_center_point, const double scale)
+ {
+ const apollota::SimplePoint old_center_point(center_sphere_);
+ center_sphere_=apollota::SimpleSphere(new_center_point, center_sphere_.r*scale);
+ for(std::list<Triangle>::iterator triangle_it=triangles_.begin();triangle_it!=triangles_.end();++triangle_it)
+ {
+ Triangle& t=(*triangle_it);
+ for(int i=0;i<3;i++)
+ {
+ t.p[i]=apollota::sum_of_points<apollota::SimplePoint>(new_center_point, ((t.p[i]-old_center_point)*scale));
+ }
+ }
+ }
+
+ template<typename ContainerOfSpheres>
+ void cut(const ContainerOfSpheres& cutting_spheres)
+ {
+ if(!cutting_spheres.empty())
+ {
+ for(typename ContainerOfSpheres::const_iterator cutting_sphere_it=cutting_spheres.begin();cutting_sphere_it!=cutting_spheres.end();++cutting_sphere_it)
+ {
+ const apollota::SimpleSphere& cutting_sphere=(*cutting_sphere_it);
+ if(!(center_sphere_==cutting_sphere) && used_cutting_spheres_.count(cutting_sphere)==0 && apollota::sphere_intersects_sphere(center_sphere_, cutting_sphere))
+ {
+ used_cutting_spheres_.insert(cutting_sphere);
+ const apollota::SimpleSphere intersection_circle=apollota::intersection_circle_of_two_spheres<apollota::SimpleSphere>(center_sphere_, cutting_sphere);
+ const apollota::SimplePoint plane_normal=apollota::sub_of_points<apollota::SimplePoint>(center_sphere_, cutting_sphere).unit();
+ std::list<Triangle>::iterator triangle_it=triangles_.begin();
+ while(triangle_it!=triangles_.end())
+ {
+ const Triangle t=(*triangle_it);
+ int h[3]={0,0,0};
+ for(int i=0;i<3;i++)
+ {
+ h[i]=apollota::halfspace_of_point(intersection_circle, plane_normal, t.p[i]);
+ }
+ if(h[0]>=0 && h[1]>=0 && h[2]>=0)
+ {
+ ++triangle_it;
+ }
+ else
+ {
+ {
+ std::list<Triangle>::iterator deletion_triangle_it=triangle_it;
+ ++triangle_it;
+ triangles_.erase(deletion_triangle_it);
+ }
+ if(h[0]>0 || h[1]>0 || h[2]>0)
+ {
+ std::vector<apollota::SimplePoint> points_in;
+ std::vector<apollota::SimplePoint> points_on;
+ for(int i=0;i<3;i++)
+ {
+ if(h[i]>0)
+ {
+ points_in.push_back(t.p[i]);
+ }
+ else if(h[i]==0)
+ {
+ points_on.push_back(t.p[i]);
+ }
+ }
+ for(int i=0;i<3;i++)
+ {
+ for(int j=0;j<3;j++)
+ {
+ if(i!=j && h[i]>0 && h[j]<0)
+ {
+ points_on.push_back(apollota::intersection_of_plane_and_segment<apollota::SimplePoint>(intersection_circle, plane_normal, t.p[i], t.p[j]));
+ }
+ }
+ }
+ if((points_in.size()==1 || points_in.size()==2) && points_on.size()==2)
+ {
+ for(std::size_t i=0;i<points_on.size();i++)
+ {
+ points_on[i]=apollota::sum_of_points<apollota::SimplePoint>(intersection_circle, apollota::sub_of_points<apollota::SimplePoint>(points_on[i], intersection_circle).unit()*intersection_circle.r);
+ }
+ if(points_in.size()==1)
+ {
+ triangles_.insert(triangle_it, Triangle(points_in[0], points_on[0], points_on[1]));
+ }
+ else if(points_in.size()==2)
+ {
+ triangles_.insert(triangle_it, Triangle(points_in[0], points_on[0], points_on[1]));
+ triangles_.insert(triangle_it, Triangle(points_in[0], points_in[1], points_on[1]));
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ void draw(auxiliaries::OpenGLPrinter& opengl_printer, const bool concave, const bool mesh)
+ {
+ std::vector<apollota::SimplePoint> vertices(3);
+ std::vector<apollota::SimplePoint> normals(3);
+ for(std::list<Triangle>::const_iterator triangle_it=triangles_.begin();triangle_it!=triangles_.end();++triangle_it)
+ {
+ const Triangle& t=(*triangle_it);
+ vertices[0]=t.p[0];
+ vertices[1]=t.p[1];
+ vertices[2]=t.p[2];
+ for(int i=0;i<3;i++)
+ {
+ normals[i]=apollota::sub_of_points<apollota::SimplePoint>(vertices[i], center_sphere_).unit();
+ if(concave)
+ {
+ normals[i]=normals[i].inverted();
+ }
+ }
+ if(mesh)
+ {
+ opengl_printer.add_line_loop(vertices);
+ }
+ else
+ {
+ opengl_printer.add_triangle_strip(vertices, normals);
+ }
+ }
+ }
+
+private:
+ struct Triangle
+ {
+ apollota::SimplePoint p[3];
+
+ Triangle()
+ {
+ }
+
+ Triangle(const apollota::SimplePoint& a, const apollota::SimplePoint& b, const apollota::SimplePoint& c)
+ {
+ p[0]=a;
+ p[1]=b;
+ p[2]=c;
+ }
+ };
+
+ void subdivide(const int steps)
+ {
+ const apollota::SimplePoint center_point(center_sphere_);
+ for(int step=0;step<steps;step++)
+ {
+ std::list<Triangle> new_triangles;
+ for(std::list<Triangle>::const_iterator triangle_it=triangles_.begin();triangle_it!=triangles_.end();++triangle_it)
+ {
+ const Triangle& t=(*triangle_it);
+ Triangle m;
+ m.p[0]=apollota::RollingTopology::construct_circular_arc_approximation_from_start_and_end(center_point, t.p[0]-center_point, t.p[1]-center_point, 2)[1];
+ m.p[1]=apollota::RollingTopology::construct_circular_arc_approximation_from_start_and_end(center_point, t.p[0]-center_point, t.p[2]-center_point, 2)[1];
+ m.p[2]=apollota::RollingTopology::construct_circular_arc_approximation_from_start_and_end(center_point, t.p[1]-center_point, t.p[2]-center_point, 2)[1];
+ new_triangles.push_back(m);
+ {
+ Triangle s=m;
+ s.p[2]=t.p[0];
+ new_triangles.push_back(s);
+ }
+ {
+ Triangle s=m;
+ s.p[1]=t.p[1];
+ new_triangles.push_back(s);
+ }
+ {
+ Triangle s=m;
+ s.p[0]=t.p[2];
+ new_triangles.push_back(s);
+ }
+ }
+ triangles_=new_triangles;
+ }
+ }
+
+ apollota::SimpleSphere center_sphere_;
+ std::list<Triangle> triangles_;
+ std::set<apollota::SimpleSphere> used_cutting_spheres_;
+};
+
+class SubdividedToricQuadrangulation
+{
+public:
+ SubdividedToricQuadrangulation(
+ const apollota::SimpleSphere& tangent1,
+ const apollota::SimpleSphere& tangent2,
+ const apollota::SimpleSphere& a,
+ const apollota::SimpleSphere& b,
+ const int steps) : centers_(apollota::SimplePoint(tangent1), apollota::SimplePoint(tangent2))
+ {
+ points_.first=apollota::RollingTopology::construct_circular_arc_approximation_from_start_and_end(
+ centers_.first,
+ (apollota::SimplePoint(a)-centers_.first).unit()*tangent1.r,
+ (apollota::SimplePoint(b)-centers_.first).unit()*tangent1.r,
+ steps);
+ points_.second=apollota::RollingTopology::construct_circular_arc_approximation_from_start_and_end(
+ centers_.second,
+ (apollota::SimplePoint(a)-centers_.second).unit()*tangent2.r,
+ (apollota::SimplePoint(b)-centers_.second).unit()*tangent2.r,
+ steps);
+ }
+
+ void draw(auxiliaries::OpenGLPrinter& opengl_printer, const bool mesh)
+ {
+ std::vector<apollota::SimplePoint> vertices;
+ vertices.reserve(points_.first.size()*2);
+ std::vector<apollota::SimplePoint> normals;
+ normals.reserve(vertices.size());
+ for(std::size_t i=0;i<std::min(points_.first.size(), points_.second.size());i++)
+ {
+ vertices.push_back(points_.first[i]);
+ vertices.push_back(points_.second[i]);
+ normals.push_back((centers_.first-points_.first[i]).unit());
+ normals.push_back((centers_.second-points_.second[i]).unit());
+ }
+ if(mesh)
+ {
+ std::vector<apollota::SimplePoint> q(4);
+ for(std::size_t i=0;i+3<vertices.size();i+=2)
+ {
+ q[0]=vertices[i];
+ q[1]=vertices[i+1];
+ q[2]=vertices[i+3];
+ q[3]=vertices[i+2];
+ opengl_printer.add_line_loop(q);
+ }
+ }
+ else
+ {
+ opengl_printer.add_triangle_strip(vertices, normals);
+ }
+ }
+
+private:
+ std::pair< apollota::SimplePoint, apollota::SimplePoint > centers_;
+ std::pair< std::vector<apollota::SimplePoint>, std::vector<apollota::SimplePoint> > points_;
+};
+
+}
+
+void demo_ses(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'x y z r')");
+ pohw.describe_io("stdout", false, true, "nothing");
+
+ const double probe=poh.restrict_value_in_range(0.01, 14.0, poh.argument<double>(pohw.describe_option("--probe", "number", "probe radius"), 1.4));
+ const double angle_step=poh.restrict_value_in_range(0.01, 1.0, poh.argument<double>(pohw.describe_option("--angle-step", "number", "angle step in radians for circle approximation"), 0.2));
+ const int depth=poh.restrict_value_in_range(1, 4, poh.argument<int>(pohw.describe_option("--depth", "number", "triangular patches subdivision depth"), 2));
+ const int sih_depth=poh.restrict_value_in_range(0, 4, poh.argument<int>(pohw.describe_option("--sih-depth", "number", "spherical surface optimization depth"), 2));
+ const double alpha=poh.argument<double>(pohw.describe_option("--alpha", "number", "alpha opacity value for drawing output"), 1.0);
+ const std::string drawing_for_pymol=poh.argument<std::string>(pohw.describe_option("--drawing-for-pymol", "string", "file path to output drawing as pymol script"), "");
+ const std::string drawing_for_scenejs=poh.argument<std::string>(pohw.describe_option("--drawing-for-scenejs", "string", "file path to output drawing as scenejs script"), "");
+ const std::string drawing_name=poh.argument<std::string>(pohw.describe_option("--drawing-name", "string", "graphics object name for drawing output"), "ses");
+ const bool mesh=poh.contains_option(pohw.describe_option("--mesh", "", "flag to draw mesh"));
+ const bool trajectory=poh.contains_option(pohw.describe_option("--trajectory", "", "flag to draw rolling probe center trajectory"));
+ const unsigned int solid_color=poh.convert_hex_string_to_integer<unsigned int>(poh.argument<std::string>(pohw.describe_option("--solid-color", "string", "default color for drawing output, in hex format, white is 0xFFFFFF"), "0x0"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const int parts_from_depth=(1 << depth);
+
+ std::vector<apollota::SimpleSphere> spheres;
+ auxiliaries::IOUtilities().read_lines_to_set(std::cin, spheres);
+ if(spheres.size()<4)
+ {
+ throw std::runtime_error("Less than 4 balls provided to stdin.");
+ }
+
+ const std::vector<apollota::SimpleSphere> artificial_boundary=apollota::construct_artificial_boundary(spheres, probe*2.0);
+ spheres.insert(spheres.end(), artificial_boundary.begin(), artificial_boundary.end());
+
+ const apollota::Triangulation::Result triangulation_result=apollota::Triangulation::construct_result(spheres, 3.5, false, false);
+
+ apollota::TriangulationQueries::IDsMap singles_map=apollota::TriangulationQueries::collect_neighbors_map_from_quadruples_map(triangulation_result.quadruples_map);
+ const apollota::TriangulationQueries::PairsMap pairs_map=apollota::TriangulationQueries::collect_pairs_neighbors_map_from_quadruples_map(triangulation_result.quadruples_map);
+
+ std::vector<apollota::RollingTopology::RollingDescriptor> rolling_descriptors;
+ for(apollota::TriangulationQueries::PairsMap::const_iterator pairs_map_it=pairs_map.begin();pairs_map_it!=pairs_map.end();++pairs_map_it)
+ {
+ const apollota::Pair& pair=pairs_map_it->first;
+ const std::set<std::size_t>& neighbor_ids=pairs_map_it->second;
+ const apollota::RollingTopology::RollingDescriptor rolling_descriptor=
+ apollota::RollingTopology::calculate_rolling_descriptor(spheres, pair.get(0), pair.get(1), neighbor_ids, singles_map[pair.get(0)], singles_map[pair.get(1)], probe);
+ if(rolling_descriptor.possible && (!rolling_descriptor.strips.empty() || rolling_descriptor.detached))
+ {
+ rolling_descriptors.push_back(rolling_descriptor);
+ }
+ }
+
+ std::set<std::size_t> set_of_all_generators;
+ for(std::vector<apollota::RollingTopology::RollingDescriptor>::const_iterator rolling_descriptor_it=rolling_descriptors.begin();rolling_descriptor_it!=rolling_descriptors.end();++rolling_descriptor_it)
+ {
+ set_of_all_generators.insert(rolling_descriptor_it->a_id);
+ set_of_all_generators.insert(rolling_descriptor_it->b_id);
+ }
+
+ std::vector< std::set<apollota::SimpleSphere> > map_of_generators_cutting_spheres(spheres.size());
+ for(std::vector<apollota::RollingTopology::RollingDescriptor>::const_iterator rolling_descriptor_it=rolling_descriptors.begin();rolling_descriptor_it!=rolling_descriptors.end();++rolling_descriptor_it)
+ {
+ const apollota::RollingTopology::RollingDescriptor& rolling_descriptor=(*rolling_descriptor_it);
+ if(!rolling_descriptor.strips.empty())
+ {
+ for(std::list<apollota::RollingTopology::RollingStrip>::const_iterator strip_it=rolling_descriptor.strips.begin();strip_it!=rolling_descriptor.strips.end();++strip_it)
+ {
+ map_of_generators_cutting_spheres[rolling_descriptor.a_id].insert(strip_it->start.tangent);
+ map_of_generators_cutting_spheres[rolling_descriptor.b_id].insert(strip_it->start.tangent);
+ map_of_generators_cutting_spheres[strip_it->start.generator].insert(strip_it->start.tangent);
+ map_of_generators_cutting_spheres[strip_it->end.generator].insert(strip_it->start.tangent);
+ map_of_generators_cutting_spheres[rolling_descriptor.a_id].insert(strip_it->end.tangent);
+ map_of_generators_cutting_spheres[rolling_descriptor.b_id].insert(strip_it->end.tangent);
+ map_of_generators_cutting_spheres[strip_it->start.generator].insert(strip_it->end.tangent);
+ map_of_generators_cutting_spheres[strip_it->end.generator].insert(strip_it->end.tangent);
+ }
+ }
+ }
+
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_alpha(alpha);
+
+ if(!trajectory)
+ {
+ const SubdividedSphericalTriangulation start_sst(sih_depth);
+ for(apollota::TriangulationQueries::IDsMap::const_iterator singles_map_it=singles_map.begin();singles_map_it!=singles_map.end();++singles_map_it)
+ {
+ const std::set<std::size_t>& neighbors=singles_map_it->second;
+ if(!neighbors.empty() && set_of_all_generators.count(singles_map_it->first)>0)
+ {
+ SubdividedSphericalTriangulation sst=start_sst;
+ sst.transform(spheres[singles_map_it->first], spheres[singles_map_it->first].r+probe);
+ std::set<apollota::SimpleSphere> cutting_spheres;
+ for(std::set<std::size_t>::const_iterator neighbor_it=neighbors.begin();neighbor_it!=neighbors.end();++neighbor_it)
+ {
+ cutting_spheres.insert(apollota::SimpleSphere(spheres[*neighbor_it], spheres[*neighbor_it].r+probe));
+ }
+ sst.cut(cutting_spheres);
+ sst.transform(sst.center_sphere(), (sst.center_sphere().r-probe)/sst.center_sphere().r);
+ opengl_printer.add_color(solid_color>0 ? solid_color : 0xFF33FF);
+ sst.draw(opengl_printer, false, mesh);
+ }
+ }
+ }
+
+ for(std::vector<apollota::RollingTopology::RollingDescriptor>::const_iterator rolling_descriptor_it=rolling_descriptors.begin();rolling_descriptor_it!=rolling_descriptors.end();++rolling_descriptor_it)
+ {
+ const apollota::RollingTopology::RollingDescriptor& rolling_descriptor=(*rolling_descriptor_it);
+ if(!rolling_descriptor.strips.empty())
+ {
+ for(std::list<apollota::RollingTopology::RollingStrip>::const_iterator strip_it=rolling_descriptor.strips.begin();strip_it!=rolling_descriptor.strips.end();++strip_it)
+ {
+ const std::vector<apollota::SimplePoint> points=apollota::RollingTopology::construct_rolling_strip_approximation(rolling_descriptor, (*strip_it), angle_step);
+ if(trajectory)
+ {
+ opengl_printer.add_color(solid_color>0 ? solid_color : 0xFF7700);
+ opengl_printer.add_line_strip(points);
+ }
+ else
+ {
+ opengl_printer.add_color(solid_color>0 ? solid_color : (rolling_descriptor.breaks.empty() ? 0xFFFF00 : 0x77FF00));
+ for(std::size_t i=0;i+1<points.size();i++)
+ {
+ if(rolling_descriptor.breaks.size()==2)
+ {
+ SubdividedToricQuadrangulation stq1(apollota::SimpleSphere(points[i], probe), apollota::SimpleSphere(points[i+1], probe), spheres[rolling_descriptor.a_id], apollota::SimpleSphere(rolling_descriptor.breaks[0], 0.0), parts_from_depth/2);
+ SubdividedToricQuadrangulation stq2(apollota::SimpleSphere(points[i], probe), apollota::SimpleSphere(points[i+1], probe), apollota::SimpleSphere(rolling_descriptor.breaks[1], 0.0), spheres[rolling_descriptor.b_id], parts_from_depth/2);
+ stq1.draw(opengl_printer, mesh);
+ stq2.draw(opengl_printer, mesh);
+ }
+ else
+ {
+ SubdividedToricQuadrangulation stq(apollota::SimpleSphere(points[i], probe), apollota::SimpleSphere(points[i+1], probe), spheres[rolling_descriptor.a_id], spheres[rolling_descriptor.b_id], parts_from_depth);
+ stq.draw(opengl_printer, mesh);
+ }
+ }
+
+ opengl_printer.add_color(solid_color>0 ? solid_color : 0x00FFFF);
+ {
+ SubdividedSphericalTriangulation sst(strip_it->start.tangent, spheres[rolling_descriptor.a_id], spheres[rolling_descriptor.b_id], spheres[strip_it->start.generator], rolling_descriptor.breaks, depth);
+ sst.cut(map_of_generators_cutting_spheres[strip_it->start.generator]);
+ sst.cut(map_of_generators_cutting_spheres[rolling_descriptor.a_id]);
+ sst.cut(map_of_generators_cutting_spheres[rolling_descriptor.b_id]);
+ sst.draw(opengl_printer, true, mesh);
+ }
+ {
+ SubdividedSphericalTriangulation sst(strip_it->end.tangent, spheres[rolling_descriptor.a_id], spheres[rolling_descriptor.b_id], spheres[strip_it->end.generator], rolling_descriptor.breaks, depth);
+ sst.cut(map_of_generators_cutting_spheres[strip_it->end.generator]);
+ sst.cut(map_of_generators_cutting_spheres[rolling_descriptor.a_id]);
+ sst.cut(map_of_generators_cutting_spheres[rolling_descriptor.b_id]);
+ sst.draw(opengl_printer, true, mesh);
+ }
+ }
+ }
+ }
+ else if(rolling_descriptor.detached)
+ {
+ const std::vector<apollota::SimplePoint> points=apollota::RollingTopology::construct_rolling_circle_approximation(rolling_descriptor, angle_step);
+ if(trajectory)
+ {
+ opengl_printer.add_color(solid_color>0 ? solid_color : 0xFF7700);
+ opengl_printer.add_line_strip(points);
+ }
+ else
+ {
+ opengl_printer.add_color(solid_color>0 ? solid_color : (rolling_descriptor.breaks.empty() ? 0x00FF00 : 0x00FF77));
+ for(std::size_t i=0;i+1<points.size();i++)
+ {
+ if(rolling_descriptor.breaks.size()==2)
+ {
+ SubdividedToricQuadrangulation stq1(apollota::SimpleSphere(points[i], probe), apollota::SimpleSphere(points[i+1], probe), spheres[rolling_descriptor.a_id], apollota::SimpleSphere(rolling_descriptor.breaks[0], 0.0), parts_from_depth/2);
+ SubdividedToricQuadrangulation stq2(apollota::SimpleSphere(points[i], probe), apollota::SimpleSphere(points[i+1], probe), apollota::SimpleSphere(rolling_descriptor.breaks[1], 0.0), spheres[rolling_descriptor.b_id], parts_from_depth/2);
+ stq1.draw(opengl_printer, mesh);
+ stq2.draw(opengl_printer, mesh);
+ }
+ else
+ {
+ SubdividedToricQuadrangulation stq(apollota::SimpleSphere(points[i], probe), apollota::SimpleSphere(points[i+1], probe), spheres[rolling_descriptor.a_id], spheres[rolling_descriptor.b_id], parts_from_depth);
+ stq.draw(opengl_printer, mesh);
+ }
+ }
+ }
+ }
+ }
+
+ if(!drawing_for_pymol.empty())
+ {
+ std::ofstream foutput(drawing_for_pymol.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ opengl_printer.print_pymol_script(drawing_name, false, foutput);
+ }
+ }
+
+ if(!drawing_for_scenejs.empty())
+ {
+ std::ofstream foutput(drawing_for_scenejs.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ opengl_printer.print_scenejs_script(drawing_name, true, foutput);
+ }
+ }
+}
diff --git a/src/mode_draw_balls.cpp b/src/mode_draw_balls.cpp
new file mode 100644
index 0000000..977db74
--- /dev/null
+++ b/src/mode_draw_balls.cpp
@@ -0,0 +1,90 @@
+#include "auxiliaries/program_options_handler.h"
+
+#include "modescommon/drawing_links.h"
+#include "modescommon/drawing_protein_cartoons.h"
+#include "modescommon/drawing_nucleic_acid_cartoons.h"
+
+void draw_balls(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+ pohw.describe_io("stdout", false, true, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+
+ const std::string representation=poh.argument<std::string>(pohw.describe_option("--representation", "string", "representation name: 'vdw', 'sticks', 'trace' or 'cartoon'"), "vdw");
+ const std::string drawing_for_pymol=poh.argument<std::string>(pohw.describe_option("--drawing-for-pymol", "string", "file path to output drawing as pymol script"), "");
+ const std::string drawing_for_scenejs=poh.argument<std::string>(pohw.describe_option("--drawing-for-scenejs", "string", "file path to output drawing as scenejs script"), "");
+ const std::string drawing_name=poh.argument<std::string>(pohw.describe_option("--drawing-name", "string", "graphics object name for drawing output"), "balls");
+ DrawingParametersWrapper drawing_parameters_wrapper;
+ drawing_parameters_wrapper.default_color=poh.convert_hex_string_to_integer<unsigned int>(poh.argument<std::string>(pohw.describe_option("--default-color", "string", "default color for drawing output, in hex format, white is 0xFFFFFF"), "0xFFFFFF"));
+ drawing_parameters_wrapper.adjunct_gradient=poh.argument<std::string>(pohw.describe_option("--adjunct-gradient", "string", "adjunct name to use for gradient-based coloring"), "");
+ drawing_parameters_wrapper.adjunct_gradient_blue=poh.argument<double>(pohw.describe_option("--adjunct-gradient-blue", "number", "blue adjunct gradient value"), 0.0);
+ drawing_parameters_wrapper.adjunct_gradient_red=poh.argument<double>(pohw.describe_option("--adjunct-gradient-red", "number", "red adjunct gradient value"), 1.0);
+ drawing_parameters_wrapper.rainbow_gradient=poh.contains_option(pohw.describe_option("--rainbow-gradient", "", "flag to use rainbow color gradient"));
+ drawing_parameters_wrapper.adjuncts_rgb=poh.contains_option(pohw.describe_option("--adjuncts-rgb", "", "flag to use RGB color values from adjuncts"));
+ drawing_parameters_wrapper.random_colors=poh.contains_option(pohw.describe_option("--random-colors", "", "flag to use random color for each drawn ball"));
+ drawing_parameters_wrapper.random_colors_by_chain=poh.contains_option(pohw.describe_option("--random-colors-by-chain", "", "flag to use random color for each drawn chain"));
+ drawing_parameters_wrapper.use_labels=poh.contains_option(pohw.describe_option("--use-labels", "", "flag to use labels in drawing if possible"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ typedef std::vector< std::pair<CRAD, BallValue> > ListOfBalls;
+ const ListOfBalls list_of_balls=auxiliaries::IOUtilities().read_lines_to_map<ListOfBalls>(std::cin);
+ if(list_of_balls.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(drawing_parameters_wrapper.default_color);
+ if(representation=="vdw")
+ {
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ const BallValue& value=list_of_balls[i].second;
+ drawing_parameters_wrapper.process(crad, value.props.adjuncts, opengl_printer);
+ opengl_printer.add_sphere(value);
+ }
+ }
+ else if(representation=="sticks")
+ {
+ draw_links(list_of_balls, 0.8, 4.0, 0.2, 0.2, 9, false, drawing_parameters_wrapper, opengl_printer);
+ }
+ else if(representation=="trace")
+ {
+ draw_trace(list_of_balls, "CA", 4.0, 0.3, drawing_parameters_wrapper, opengl_printer);
+ draw_trace(list_of_balls, "C3'", 8.0, 0.3, drawing_parameters_wrapper, opengl_printer);
+ }
+ else if(representation=="cartoon")
+ {
+ DrawingProteinCartoons().draw_cartoon(list_of_balls, drawing_parameters_wrapper, opengl_printer);
+ DrawingNucleicAcidCartoons().draw_cartoon(list_of_balls, drawing_parameters_wrapper, opengl_printer);
+ }
+ else
+ {
+ throw std::runtime_error("Invalid representation name.");
+ }
+
+ if(!drawing_for_pymol.empty())
+ {
+ std::ofstream foutput(drawing_for_pymol.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ opengl_printer.print_pymol_script(drawing_name, true, foutput);
+ }
+ }
+
+ if(!drawing_for_scenejs.empty())
+ {
+ std::ofstream foutput(drawing_for_scenejs.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ opengl_printer.print_scenejs_script(drawing_name, true, foutput);
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map(list_of_balls, std::cout);
+}
diff --git a/src/mode_draw_contacts.cpp b/src/mode_draw_contacts.cpp
new file mode 100644
index 0000000..9f83f90
--- /dev/null
+++ b/src/mode_draw_contacts.cpp
@@ -0,0 +1,89 @@
+#include "auxiliaries/program_options_handler.h"
+
+#include "modescommon/contact_value.h"
+#include "modescommon/drawing_utilities.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+}
+
+void draw_contacts(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')");
+ pohw.describe_io("stdout", false, true, "list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts graphics')");
+
+ const std::string drawing_for_pymol=poh.argument<std::string>(pohw.describe_option("--drawing-for-pymol", "string", "file path to output drawing as pymol script"), "");
+ const std::string drawing_for_jmol=poh.argument<std::string>(pohw.describe_option("--drawing-for-jmol", "string", "file path to output drawing as jmol script"), "");
+ const std::string drawing_for_scenejs=poh.argument<std::string>(pohw.describe_option("--drawing-for-scenejs", "string", "file path to output drawing as scenejs script"), "");
+ const std::string drawing_name=poh.argument<std::string>(pohw.describe_option("--drawing-name", "string", "graphics object name for drawing output"), "contacts");
+ DrawingParametersWrapper drawing_parameters_wrapper;
+ drawing_parameters_wrapper.default_color=poh.convert_hex_string_to_integer<unsigned int>(poh.argument<std::string>(pohw.describe_option("--default-color", "string", "default color for drawing output, in hex format, white is 0xFFFFFF"), "0xFFFFFF"));
+ drawing_parameters_wrapper.adjunct_gradient=poh.argument<std::string>(pohw.describe_option("--adjunct-gradient", "string", "adjunct name to use for gradient-based coloring"), "");
+ drawing_parameters_wrapper.adjunct_gradient_blue=poh.argument<double>(pohw.describe_option("--adjunct-gradient-blue", "number", "blue adjunct gradient value"), 0.0);
+ drawing_parameters_wrapper.adjunct_gradient_red=poh.argument<double>(pohw.describe_option("--adjunct-gradient-red", "number", "red adjunct gradient value"), 1.0);
+ drawing_parameters_wrapper.adjuncts_rgb=poh.contains_option(pohw.describe_option("--adjuncts-rgb", "", "flag to use RGB color values from adjuncts"));
+ drawing_parameters_wrapper.random_colors=poh.contains_option(pohw.describe_option("--random-colors", "", "flag to use random color for each drawn contact"));
+ drawing_parameters_wrapper.alpha_opacity=poh.argument<double>(pohw.describe_option("--alpha", "number", "alpha opacity value for drawing output"), 1.0);
+ drawing_parameters_wrapper.use_labels=poh.contains_option(pohw.describe_option("--use-labels", "", "flag to use labels in drawing if possible"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ enabled_output_of_ContactValue_graphics()=true;
+
+ std::map<CRADsPair, ContactValue> map_of_contacts;
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, map_of_contacts);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(drawing_parameters_wrapper.default_color);
+ opengl_printer.add_alpha(drawing_parameters_wrapper.alpha_opacity);
+ for(std::map< CRADsPair, ContactValue >::iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first;
+ const ContactValue& value=it->second;
+ if(!value.graphics.empty())
+ {
+ drawing_parameters_wrapper.process(std::make_pair(crads.a, crads.b), value.props.adjuncts, opengl_printer);
+ opengl_printer.add(value.graphics);
+ }
+ }
+
+ if(!drawing_for_pymol.empty())
+ {
+ std::ofstream foutput(drawing_for_pymol.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ opengl_printer.print_pymol_script(drawing_name, true, foutput);
+ }
+ }
+
+ if(!drawing_for_jmol.empty())
+ {
+ std::ofstream foutput(drawing_for_jmol.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ opengl_printer.print_jmol_script(drawing_name, foutput);
+ }
+ }
+
+ if(!drawing_for_scenejs.empty())
+ {
+ std::ofstream foutput(drawing_for_scenejs.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ opengl_printer.print_scenejs_script(drawing_name, true, foutput);
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map(map_of_contacts, std::cout);
+}
diff --git a/src/mode_expand_descriptors.cpp b/src/mode_expand_descriptors.cpp
new file mode 100644
index 0000000..6a9ea3a
--- /dev/null
+++ b/src/mode_expand_descriptors.cpp
@@ -0,0 +1,78 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+
+inline std::string crad_to_expanded_str(const CRAD& crad)
+{
+ std::ostringstream output;
+ output << (crad.chainID.empty() ? std::string(".") : crad.chainID) << " ";
+ if(crad.resSeq==CRAD::null_num()) { output << "." << " "; } else { output << crad.resSeq << " "; }
+ output << (crad.iCode.empty() ? std::string(".") : crad.iCode) << " ";
+ if(crad.serial==CRAD::null_num()) { output << "." << " "; } else { output << crad.serial << " "; }
+ output << (crad.altLoc.empty() ? std::string(".") : crad.altLoc) << " ";
+ output << (crad.resName.empty() ? std::string(".") : crad.resName) << " ";
+ output << (crad.name.empty() ? std::string(".") : crad.name);
+ return output.str();
+}
+
+}
+
+void expand_descriptors(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "any text containing atom descriptors");
+ pohw.describe_io("stdout", false, true, "text with each atom descriptor expanded to 'chainID resSeq iCode serial altLoc resName name'");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ while(std::cin.good())
+ {
+ std::string line;
+ std::getline(std::cin, line);
+ if(!std::cin.fail())
+ {
+ if(!line.empty())
+ {
+ std::size_t i=0;
+ while(i<line.size())
+ {
+ i=line.find_first_of("crialAR", i);
+ if(i!=std::string::npos)
+ {
+ std::size_t j=line.find_first_of(" \n\t", i+1);
+ if(j==std::string::npos && line[line.size()-1]=='>')
+ {
+ j=line.size();
+ }
+ if((j-1)<line.size() && line[j-1]=='>')
+ {
+ CRAD crad;
+ if(CRAD::from_str(line.substr(i, j-i), crad).empty())
+ {
+ const std::string expanded_str=crad_to_expanded_str(crad);
+ line.replace(i, j-i, expanded_str);
+ i=i+expanded_str.size();
+ }
+ else
+ {
+ i=j;
+ }
+ }
+ else
+ {
+ i=std::string::npos;
+ }
+ }
+ }
+ }
+ std::cout << line << "\n";
+ }
+ }
+}
diff --git a/src/mode_get_balls_from_atoms_file.cpp b/src/mode_get_balls_from_atoms_file.cpp
new file mode 100644
index 0000000..678e344
--- /dev/null
+++ b/src/mode_get_balls_from_atoms_file.cpp
@@ -0,0 +1,141 @@
+#include <iostream>
+#include <fstream>
+
+#include "apollota/spheres_boundary_construction.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/atoms_io.h"
+#include "auxiliaries/atom_radius_assigner.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+#include "modescommon/ball_value.h"
+
+namespace
+{
+
+std::string refine_empty_string(const std::string& x)
+{
+ return (x.empty() ? std::string(".") : x);
+}
+
+}
+
+void get_balls_from_atoms_file(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false,
+ "file in PDB or mmCIF format");
+ pohw.describe_io("stdout", false, true,
+ "list of balls\n(default mode line format: 'x y z r # atomSerial chainID resSeq resName atomName altLoc iCode')\n(annotated mode line format: 'annotation x y z r tags adjuncts')");
+
+ const bool annotated=poh.contains_option(pohw.describe_option("--annotated", "", "flag to enable annotated mode"));
+ const bool include_heteroatoms=poh.contains_option(pohw.describe_option("--include-heteroatoms", "", "flag to include heteroatoms"));
+ const bool include_hydrogens=poh.contains_option(pohw.describe_option("--include-hydrogens", "", "flag to include hydrogen atoms"));
+ const bool multimodel_chains=poh.contains_option(pohw.describe_option("--multimodel-chains", "", "flag to read multiple models in PDB format and rename chains accordingly"));
+ const bool mmcif=poh.contains_option(pohw.describe_option("--mmcif", "", "flag to input in mmCIF format"));
+ const std::string radii_file=poh.argument<std::string>(pohw.describe_option("--radii-file", "string", "path to radii configuration file"), "");
+ const double default_radius=poh.argument<double>(pohw.describe_option("--default-radius", "number", "default atomic radius"), 1.70);
+ const bool only_default_radius=poh.contains_option(pohw.describe_option("--only-default-radius", "", "flag to make all radii equal to the default radius"));
+ const double hull_offset=poh.argument<double>(pohw.describe_option("--hull-offset", "number", "positive offset distance enables adding artificial hull balls"), -1.0);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const std::vector<auxiliaries::AtomsIO::AtomRecord> atoms=(mmcif ?
+ auxiliaries::AtomsIO::MMCIFReader::read_data_from_file_stream(std::cin, include_heteroatoms, include_hydrogens).atom_records :
+ auxiliaries::AtomsIO::PDBReader::read_data_from_file_stream(std::cin, include_heteroatoms, include_hydrogens, multimodel_chains, false).atom_records);
+ if(atoms.empty())
+ {
+ throw std::runtime_error("No atoms provided to stdin.");
+ }
+
+ auxiliaries::AtomRadiusAssigner atom_radius_assigner(default_radius);
+ if(!only_default_radius)
+ {
+ if(radii_file.empty())
+ {
+ atom_radius_assigner.add_radius_by_descriptor("*", "C*", 1.70);
+ atom_radius_assigner.add_radius_by_descriptor("*", "N*", 1.55);
+ atom_radius_assigner.add_radius_by_descriptor("*", "O*", 1.52);
+ atom_radius_assigner.add_radius_by_descriptor("*", "S*", 1.80);
+ atom_radius_assigner.add_radius_by_descriptor("*", "P*", 1.80);
+ atom_radius_assigner.add_radius_by_descriptor("*", "H*", 1.20);
+ }
+ else
+ {
+ std::ifstream radii_file_stream(radii_file.c_str(), std::ios::in);
+ auxiliaries::IOUtilities().read_lines_to_container(radii_file_stream, auxiliaries::AtomRadiusAssigner::add_descriptor_and_radius_from_stream_to_atom_radius_assigner, atom_radius_assigner);
+ }
+ }
+
+ std::vector<apollota::SimpleSphere> all_spheres;
+ all_spheres.reserve(atoms.size());
+
+ for(std::size_t i=0;i<atoms.size();i++)
+ {
+ const auxiliaries::AtomsIO::AtomRecord& atom=atoms[i];
+ const double radius=atom_radius_assigner.get_atom_radius(atom.resName, atom.name);
+ if(annotated)
+ {
+ const auxiliaries::ChainResidueAtomDescriptor crad(atom.serial, atom.chainID, atom.resSeq, atom.resName, atom.name, atom.altLoc, atom.iCode);
+ if(crad.valid())
+ {
+ BallValue value;
+ value.x=atom.x;
+ value.y=atom.y;
+ value.z=atom.z;
+ value.r=radius;
+ if(atom.record_name=="HETATM")
+ {
+ value.props.tags.insert("het");
+ }
+ if(!atom.element.empty())
+ {
+ value.props.tags.insert(std::string("el=")+atom.element);
+ }
+ if(atom.occupancy_valid)
+ {
+ value.props.adjuncts["oc"]=atom.occupancy;
+ }
+ if(atom.tempFactor_valid)
+ {
+ value.props.adjuncts["tf"]=atom.tempFactor;
+ }
+ std::cout << crad << " " << value << "\n";
+ all_spheres.push_back(apollota::SimpleSphere(value));
+ }
+ }
+ else
+ {
+ std::cout << apollota::SimpleSphere(atom, radius);
+ std::cout << " # " << atom.serial << " " << refine_empty_string(atom.chainID) << " " << atom.resSeq << " " << refine_empty_string(atom.resName) << " " << refine_empty_string(atom.name) << " " << refine_empty_string(atom.altLoc) << " " << refine_empty_string(atom.iCode) << "\n";
+ all_spheres.push_back(apollota::SimpleSphere(atom, radius));
+ }
+ }
+
+ if(hull_offset>0.0 && !all_spheres.empty())
+ {
+ const std::vector<apollota::SimpleSphere> artificial_boundary=apollota::construct_artificial_boundary(all_spheres, hull_offset);
+ for(std::size_t i=0;i<artificial_boundary.size();i++)
+ {
+ const apollota::SimpleSphere& s=artificial_boundary[i];
+ if(annotated)
+ {
+ auxiliaries::ChainResidueAtomDescriptor crad;
+ crad.chainID="hull";
+ BallValue value;
+ value.x=s.x;
+ value.y=s.y;
+ value.z=s.z;
+ value.r=s.r;
+ std::cout << crad << " " << value << "\n";
+ }
+ else
+ {
+ std::cout << s << " # artificial hull ball\n";
+ }
+ }
+ }
+}
diff --git a/src/mode_place_membrane.cpp b/src/mode_place_membrane.cpp
new file mode 100644
index 0000000..e32c8f3
--- /dev/null
+++ b/src/mode_place_membrane.cpp
@@ -0,0 +1,318 @@
+#include "apollota/subdivided_icosahedron.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+#include "modescommon/ball_value.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+
+struct PointAndScore
+{
+ apollota::SimplePoint point;
+ double score;
+
+ PointAndScore(const apollota::SimplePoint& point, const double score) : point(point), score(score)
+ {
+ }
+};
+
+struct MembranePlacement
+{
+ double width;
+ double width_extension;
+ double score;
+ apollota::SimplePoint position;
+ apollota::SimplePoint normal;
+
+ MembranePlacement(
+ const double width,
+ const double width_extension,
+ const double score,
+ const apollota::SimplePoint& position,
+ const apollota::SimplePoint& normal) :
+ width(width),
+ width_extension(width_extension),
+ score(score),
+ position(position),
+ normal(normal)
+ {
+ }
+};
+
+struct ScoredShift
+{
+ double score;
+ double shift;
+
+ ScoredShift() : score(0), shift(0)
+ {
+ }
+};
+
+ScoredShift estimate_best_scored_shift(
+ const std::vector<PointAndScore>& points_and_scores,
+ const apollota::SimplePoint& direction,
+ const double width,
+ const double width_extension,
+ std::vector< std::pair<double, double> >& buffer_for_projections)
+{
+ const double length_step=0.5;
+ static std::vector< std::pair<int, double> > bins(1000);
+
+ for(std::size_t i=0;i<points_and_scores.size();i++)
+ {
+ buffer_for_projections[i].first=points_and_scores[i].point*direction;
+ buffer_for_projections[i].second=points_and_scores[i].score;
+ }
+ std::sort(buffer_for_projections.begin(), buffer_for_projections.end());
+
+ const double full_length=(buffer_for_projections.back().first-buffer_for_projections.front().first);
+ bins.resize(static_cast<std::size_t>(ceil(full_length/length_step)));
+ const int bins_n=static_cast<int>(bins.size());
+ const int width_half_bins_n=static_cast<int>(floor(width*0.5/length_step+0.5));
+ const int extended_width_half_bins_n=static_cast<int>(floor((width+width_extension)*0.5/length_step+0.5));
+
+ for(std::size_t i=0;i<bins.size();i++)
+ {
+ bins[i].first=0;
+ bins[i].second=0.0;
+ }
+
+ for(std::size_t i=0;i<buffer_for_projections.size();i++)
+ {
+ int bin_pos=static_cast<int>(floor((buffer_for_projections[i].first-buffer_for_projections.front().first)/length_step));
+ bin_pos=std::min(std::max(bin_pos, 0), bins_n-1);
+ bins[bin_pos].first++;
+ bins[bin_pos].second+=buffer_for_projections[i].second;
+ }
+
+ int count_of_all_bin_values=0;
+ double sum_of_all_bin_values=0.0;
+ for(std::size_t i=0;i<bins.size();i++)
+ {
+ if(bins[i].first>0)
+ {
+ count_of_all_bin_values+=bins[i].first;
+ sum_of_all_bin_values+=bins[i].second;
+ }
+ }
+
+ double best_score=0.0;
+ int best_score_i=0;
+ bool best_initialized=false;
+ for(int i=0;i<bins_n;i++)
+ {
+ int count_in=0;
+ double sum_in=0.0;
+ for(int j=(0-width_half_bins_n);j<=width_half_bins_n;j++)
+ {
+ const int p=(i+j);
+ if(p>=0 && p<bins_n)
+ {
+ count_in+=bins[p].first;
+ sum_in+=bins[p].second;
+ }
+ }
+
+ int count_in_extension=0;
+ double sum_in_extension=0.0;
+ for(int j=(0-extended_width_half_bins_n);j<(0-width_half_bins_n);j++)
+ {
+ const int p=(i+j);
+ if(p>=0 && p<bins_n)
+ {
+ count_in_extension+=bins[p].first;
+ sum_in_extension+=bins[p].second;
+ }
+ }
+ for(int j=(width_half_bins_n+1);j<=extended_width_half_bins_n;j++)
+ {
+ const int p=(i+j);
+ if(p>=0 && p<bins_n)
+ {
+ count_in_extension+=bins[p].first;
+ sum_in_extension+=bins[p].second;
+ }
+ }
+
+ const double score=
+ static_cast<double>(count_of_all_bin_values-count_in-count_in_extension)
+ -(sum_of_all_bin_values-sum_in-sum_in_extension)
+ +sum_in
+ +(static_cast<double>(count_in_extension)*0.5);
+ if(!best_initialized || best_score<score)
+ {
+ best_score=score;
+ best_score_i=i;
+ best_initialized=true;
+ }
+ }
+
+ ScoredShift result;
+ result.score=best_score;
+ result.shift=buffer_for_projections.front().first+(static_cast<double>(best_score_i)*(full_length/static_cast<double>(bins_n)));
+ return result;
+}
+
+MembranePlacement estimate_translated_membrane_placement(const std::vector<PointAndScore>& points_and_scores, const double width, const double width_extension)
+{
+ std::vector< std::pair<double, double> > buffer_for_projections(points_and_scores.size());
+ apollota::SubdividedIcosahedron sih(3);
+ sih.fit_into_sphere(apollota::SimplePoint(0, 0, 0), 1);
+ std::size_t best_id=0;
+ ScoredShift best_scored_shift;
+ double last_cycle_best_score=0.0;
+ int number_of_cycles=0;
+ int number_of_checks=0;
+ while(number_of_cycles<2 || (best_scored_shift.score-last_cycle_best_score)>0.0001 || number_of_cycles>10000)
+ {
+ std::size_t start_id=0;
+ if(number_of_cycles>0)
+ {
+ start_id=sih.vertices().size();
+ sih.grow(best_id, true);
+ last_cycle_best_score=best_scored_shift.score;
+ }
+ for(std::size_t i=start_id;i<sih.vertices().size();i++)
+ {
+ const ScoredShift scored_shift=estimate_best_scored_shift(points_and_scores, sih.vertices()[i].unit(), width, width_extension, buffer_for_projections);
+ if(number_of_checks==0 || scored_shift.score>best_scored_shift.score)
+ {
+ best_id=i;
+ best_scored_shift=scored_shift;
+ }
+ number_of_checks++;
+ }
+ number_of_cycles++;
+ }
+ const apollota::SimplePoint best_direction=sih.vertices()[best_id].unit();
+ return MembranePlacement(width, width_extension, best_scored_shift.score/static_cast<double>(points_and_scores.size()), best_direction*best_scored_shift.shift, best_direction);
+}
+
+MembranePlacement estimate_membrane_placement(const std::vector<PointAndScore>& points_and_scores, const double width, const double width_extension, const bool optimize_width, const bool optimize_width_extension)
+{
+ apollota::SimplePoint original_center(0, 0, 0);
+ for(std::size_t i=0;i<points_and_scores.size();i++)
+ {
+ original_center=(original_center+points_and_scores[i].point);
+ }
+ original_center=original_center*(1.0/static_cast<double>(points_and_scores.size()));
+
+ std::vector<PointAndScore> translated_points_and_scores=points_and_scores;
+ for(std::size_t i=0;i<points_and_scores.size();i++)
+ {
+ translated_points_and_scores[i].point=(points_and_scores[i].point-original_center);
+ }
+
+ std::vector<MembranePlacement> best_result;
+ {
+ const double width_step=5.0;
+ const double width_extension_step=5.0;
+ const double width_start=(optimize_width ? 10.0 : width);
+ const double width_extension_start=(optimize_width_extension ? 0.0 : width_extension);
+ for(double current_width=width_start;current_width<=width;current_width+=width_step)
+ {
+ for(double current_width_extension=width_extension_start;current_width_extension<=width_extension;current_width_extension+=width_extension_step)
+ {
+ const MembranePlacement translated_membrane_placement=estimate_translated_membrane_placement(translated_points_and_scores, current_width, current_width_extension);
+ if(best_result.empty())
+ {
+ best_result.push_back(translated_membrane_placement);
+ }
+ else if(best_result[0].score<translated_membrane_placement.score)
+ {
+ best_result[0]=translated_membrane_placement;
+ }
+ }
+ }
+ }
+ const MembranePlacement translated_membrane_placement=(best_result.empty() ? estimate_translated_membrane_placement(translated_points_and_scores, width, width_extension) : best_result[0]);
+ return MembranePlacement(translated_membrane_placement.width, translated_membrane_placement.width_extension, translated_membrane_placement.score, original_center+translated_membrane_placement.position, translated_membrane_placement.normal);
+}
+
+}
+
+void place_membrane(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+ pohw.describe_io("stdout", false, true, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+
+ const std::string scores_file=poh.argument<std::string>(pohw.describe_option("--scores-file", "string", "file path to input atom scores", true), "");
+ const double membrane_width=poh.argument<double>(pohw.describe_option("--membrane-width", "number", "membrane width", true));
+ const double membrane_width_extension=poh.argument<double>(pohw.describe_option("--membrane-width-extension", "number", "membrane width extension"), 0.0);
+ const bool optimize_width=poh.contains_option(pohw.describe_option("--optimize-width", "", "flag to optimize width"));
+ const bool optimize_width_extension=poh.contains_option(pohw.describe_option("--optimize-width-extension", "", "flag to optimize width extension"));
+ const std::string placement_output=poh.argument<std::string>(pohw.describe_option("--placement-output", "string", "file path to output placement results"), "");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ if(membrane_width<=1.0)
+ {
+ throw std::runtime_error("Invalid membrane width.");
+ }
+
+ std::vector< std::pair<CRAD, BallValue> > list_of_balls;
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, list_of_balls);
+ if(list_of_balls.empty())
+ {
+ throw std::runtime_error("No input balls.");
+ }
+
+ const std::map<CRAD, double> map_of_scores=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRAD, double> >(scores_file);
+ if(map_of_scores.empty())
+ {
+ throw std::runtime_error("No input scores.");
+ }
+
+ std::vector<PointAndScore> points_and_scores;
+ points_and_scores.reserve(map_of_scores.size());
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ std::map<CRAD, double>::const_iterator it=map_of_scores.find(list_of_balls[i].first);
+ if(it!=map_of_scores.end())
+ {
+ points_and_scores.push_back(PointAndScore(apollota::SimplePoint(list_of_balls[i].second), it->second));
+ }
+ }
+
+ std::ostringstream logstream;
+
+ const MembranePlacement membrane_placement=estimate_membrane_placement(points_and_scores, membrane_width, membrane_width_extension, optimize_width, optimize_width_extension);
+
+ logstream << "width " << membrane_placement.width << "\n";
+ logstream << "width_extension " << membrane_placement.width_extension << "\n";
+ logstream << "score " << membrane_placement.score << "\n";
+ logstream << "position " << membrane_placement.position.x << " " << membrane_placement.position.y << " " << membrane_placement.position.z << "\n";
+ logstream << "direction " << membrane_placement.normal.x << " " << membrane_placement.normal.y << " " << membrane_placement.normal.z << "\n";
+
+ if(!placement_output.empty())
+ {
+ std::ofstream foutput(placement_output.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ foutput << logstream.str();
+ }
+ }
+
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ if(fabs((apollota::SimplePoint(list_of_balls[i].second)-membrane_placement.position)*membrane_placement.normal.unit())<(membrane_placement.width*0.5))
+ {
+ list_of_balls[i].second.props.update_adjuncts("membrane=1");
+ }
+ else
+ {
+ list_of_balls[i].second.props.update_adjuncts("membrane=0");
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map(list_of_balls, std::cout);
+}
diff --git a/src/mode_plot_contacts.cpp b/src/mode_plot_contacts.cpp
new file mode 100644
index 0000000..ac2d330
--- /dev/null
+++ b/src/mode_plot_contacts.cpp
@@ -0,0 +1,278 @@
+#include <iostream>
+#include <stdexcept>
+#include <bitset>
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/contact_value.h"
+#include "modescommon/svg_writer.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+std::map< int, std::pair<int, int> > construct_map_of_chains_intervals(const std::map<CRAD, std::size_t>& axis)
+{
+ std::map< std::string, std::pair<int, int> > map_of_chains_intervals;
+ for(std::map<CRAD, std::size_t>::const_iterator axis_it=axis.begin();axis_it!=axis.end();++axis_it)
+ {
+ const std::string& chain=axis_it->first.chainID;
+ const int x=static_cast<int>(axis_it->second);
+ std::map< std::string, std::pair<int, int> >::iterator map_of_chains_intervals_it=map_of_chains_intervals.find(chain);
+ if(map_of_chains_intervals_it==map_of_chains_intervals.end())
+ {
+ map_of_chains_intervals[chain]=std::make_pair(x, x);
+ }
+ else
+ {
+ std::pair<int, int>& interval=map_of_chains_intervals_it->second;
+ if(x<interval.first)
+ {
+ interval.first=x;
+ }
+ if(x>interval.second)
+ {
+ interval.second=x;
+ }
+ }
+ }
+ std::map< int, std::pair<int, int> > map_of_chain_numbers_intervals;
+ {
+ int i=0;
+ for(std::map< std::string, std::pair<int, int> >::const_iterator it=map_of_chains_intervals.begin();it!=map_of_chains_intervals.end();++it)
+ {
+ map_of_chain_numbers_intervals[i++]=it->second;
+ }
+ }
+ return map_of_chain_numbers_intervals;
+}
+
+int get_chain_number_from_coordinate(const std::map< int, std::pair<int, int> >& map_of_chains_intervals, const int x)
+{
+ for(std::map< int, std::pair<int, int> >::const_iterator it=map_of_chains_intervals.begin();it!=map_of_chains_intervals.end();++it)
+ {
+ const std::pair<int, int>& interval=it->second;
+ if(x>=interval.first && x<=interval.second)
+ {
+ return (it->first);
+ }
+ }
+ return 0;
+}
+
+std::set< std::pair<int, int> > collect_points(const std::map<CRAD, std::size_t>& axis, const std::map<CRADsPair, ContactValue>& map_of_contacts)
+{
+ std::set< std::pair<int, int> > points;
+ for(std::map<CRADsPair, ContactValue>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ std::map<CRAD, std::size_t>::const_iterator x_it=axis.find(it->first.a);
+ std::map<CRAD, std::size_t>::const_iterator y_it=axis.find(it->first.b);
+ if(x_it!=axis.end() && y_it!=axis.end())
+ {
+ int x=static_cast<int>(x_it->second);
+ int y=static_cast<int>(y_it->second);
+ if(x>y)
+ {
+ std::swap(x, y);
+ }
+ points.insert(std::make_pair(x, y));
+ }
+ }
+ return points;
+}
+
+std::bitset<49> get_pattern_from_coordinates(
+ const std::map< int, std::pair<int, int> >& map_of_chains_intervals,
+ const std::set< std::pair<int, int> >& points,
+ const int ox,
+ const int oy)
+{
+ const int ox_chain=get_chain_number_from_coordinate(map_of_chains_intervals, ox);
+ const int oy_chain=get_chain_number_from_coordinate(map_of_chains_intervals, oy);
+ std::bitset<49> pattern;
+ int index=0;
+ for(int dx=-3;dx<=3;dx++)
+ {
+ for(int dy=-3;dy<=3;dy++)
+ {
+ const int x=ox+dx;
+ const int y=oy+dy;
+ if(x>=0 && y>=0
+ && points.count(std::make_pair(x, y))
+ && get_chain_number_from_coordinate(map_of_chains_intervals, x)==ox_chain
+ && get_chain_number_from_coordinate(map_of_chains_intervals, y)==oy_chain)
+ {
+ pattern.set(index, true);
+ }
+ index++;
+ }
+ }
+ return pattern;
+}
+
+std::map<int, CRAD> construct_reversed_axis_map(const std::map<CRAD, std::size_t>& axis)
+{
+ std::map<int, CRAD> reversed_axis_map;
+ for(std::map<CRAD, std::size_t>::const_iterator axis_it=axis.begin();axis_it!=axis.end();++axis_it)
+ {
+ reversed_axis_map[static_cast<int>(axis_it->second)]=axis_it->first;
+ }
+ return reversed_axis_map;
+}
+
+}
+
+void plot_contacts(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts')");
+ pohw.describe_io("stdout", false, true, "list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts')");
+
+ const std::string background_color=poh.argument<std::string>(pohw.describe_option("--background-color", "string", "color string in SVG-acceptable format"), "#000000");
+ const std::string default_color=poh.argument<std::string>(pohw.describe_option("--default-color", "string", "color string in SVG-acceptable format"), "#FFFFFF");
+ const std::string adjunct_gradient=poh.argument<std::string>(pohw.describe_option("--adjunct-gradient", "string", "adjunct name to use for gradient-based coloring"), "");
+ const double adjunct_gradient_blue=poh.argument<double>(pohw.describe_option("--adjunct-gradient-blue", "number", "blue adjunct gradient value"), 0.0);
+ const double adjunct_gradient_red=poh.argument<double>(pohw.describe_option("--adjunct-gradient-red", "number", "red adjunct gradient value"), 1.0);
+ const bool adjuncts_rgb=poh.contains_option(pohw.describe_option("--adjuncts-rgb", "", "flag to use RGB color values from adjuncts"));
+ const bool no_contraction=poh.contains_option(pohw.describe_option("--no-contraction", "", "flag to not contract gaps"));
+ const std::string svg_output=poh.argument<std::string>(pohw.describe_option("--svg-output", "string", "file path to output plot of contacts in SVG format"), "");
+ const std::string axis_output=poh.argument<std::string>(pohw.describe_option("--axis-output", "string", "file path to output axis"), "");
+ const std::string points_output=poh.argument<std::string>(pohw.describe_option("--points-output", "string", "file path to output points"), "");
+ const std::string patterns_output=poh.argument<std::string>(pohw.describe_option("--patterns-output", "string", "file path to output 7x7 patterns encoded as numbers"), "");
+ const bool binarize_patterns=poh.contains_option(pohw.describe_option("--binarize-patterns", "", "flag to output patterns in binary format"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::map<CRADsPair, ContactValue> map_of_contacts;
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, map_of_contacts);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ std::map<CRAD, std::size_t> axis;
+ {
+ for(std::map<CRADsPair, ContactValue>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ axis[it->first.a]=0;
+ axis[it->first.b]=0;
+ }
+ std::size_t i=0;
+ for(std::map<CRAD, std::size_t>::iterator it=axis.begin();it!=axis.end();++it)
+ {
+ it->second=i++;
+ }
+ }
+
+ if(no_contraction)
+ {
+ std::size_t i=0;
+ std::map<CRAD, std::size_t>::iterator it=axis.begin();
+ it->second=i++;
+ ++it;
+ while(it!=axis.end())
+ {
+ std::map<CRAD, std::size_t>::iterator prev_it=it;
+ --prev_it;
+ const CRAD& a=prev_it->first;
+ const CRAD& b=it->first;
+ if(a.chainID==b.chainID)
+ {
+ for(int j=1;j<(b.resSeq-a.resSeq);j++)
+ {
+ i++;
+ }
+ }
+ it->second=i++;
+ ++it;
+ }
+ }
+
+ if(!svg_output.empty())
+ {
+ std::ofstream output(svg_output.c_str(), std::ios::out);
+ if(output.good())
+ {
+ const std::size_t max_coordinate=(axis.rbegin()->second+1);
+ SVGWriter svg(max_coordinate, max_coordinate);
+ svg.add_rect(0, 0, max_coordinate, max_coordinate, std::string("fill:")+background_color);
+ for(std::map<CRADsPair, ContactValue>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const std::size_t x=axis[it->first.a];
+ const std::size_t y=axis[it->first.b];
+ std::string color=default_color;
+ const std::map<std::string, double>& adjuncts=it->second.props.adjuncts;
+ if(!adjunct_gradient.empty() && adjunct_gradient_blue!=adjunct_gradient_red)
+ {
+ if(adjuncts.count(adjunct_gradient)==1)
+ {
+ color=SVGWriter::color_from_blue_white_red_gradient(adjuncts.find(adjunct_gradient)->second, adjunct_gradient_blue, adjunct_gradient_red);
+ }
+ }
+ else if(adjuncts_rgb && (adjuncts.count("r")>0 || adjuncts.count("g")>0 || adjuncts.count("b")>0))
+ {
+ const double r=(adjuncts.count("r")>0 ? adjuncts.find("r")->second : 0.0);
+ const double g=(adjuncts.count("g")>0 ? adjuncts.find("g")->second : 0.0);
+ const double b=(adjuncts.count("b")>0 ? adjuncts.find("b")->second : 0.0);
+ color=SVGWriter::color_from_red_green_blue_components(r, g, b, 255);
+ }
+ svg.add_rect(x, y, 1, 1, std::string("fill:")+color);
+ svg.add_rect(y, x, 1, 1, std::string("fill:")+color);
+ }
+ svg.write(output);
+ }
+ }
+
+ if(!axis_output.empty())
+ {
+ auxiliaries::IOUtilities().write_map_to_file(axis, axis_output);
+ }
+
+ if(!points_output.empty())
+ {
+ std::ofstream output(points_output.c_str(), std::ios::out);
+ if(output.good())
+ {
+ for(std::map<CRADsPair, ContactValue>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ output << axis[it->first.a] << " " << axis[it->first.b] << "\n";
+ }
+ }
+ }
+
+ if(!patterns_output.empty())
+ {
+ std::ofstream output(patterns_output.c_str(), std::ios::out);
+ if(output.good())
+ {
+ const std::map< int, std::pair<int, int> > map_of_chains_intervals=construct_map_of_chains_intervals(axis);
+ const std::set< std::pair<int, int> > points=collect_points(axis, map_of_contacts);
+ std::map<int, CRAD> reversed_axis_map=construct_reversed_axis_map(axis);
+ for(std::set< std::pair<int, int> >::const_iterator points_it=points.begin();points_it!=points.end();++points_it)
+ {
+ const std::bitset<49> pattern=get_pattern_from_coordinates(map_of_chains_intervals, points, points_it->first, points_it->second);
+ if(pattern.count()>4)
+ {
+ if(binarize_patterns)
+ {
+ output << pattern;
+ }
+ else
+ {
+ output << reversed_axis_map[points_it->first] << " " << reversed_axis_map[points_it->second] << " " << pattern.to_ulong();
+ }
+ output << "\n";
+ }
+ }
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map(map_of_contacts, std::cout);
+}
diff --git a/src/mode_query_balls.cpp b/src/mode_query_balls.cpp
new file mode 100644
index 0000000..b3002db
--- /dev/null
+++ b/src/mode_query_balls.cpp
@@ -0,0 +1,374 @@
+#include <iostream>
+#include <stdexcept>
+#include <fstream>
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/atoms_io.h"
+
+#include "modescommon/ball_value.h"
+#include "modescommon/sequence_utilities.h"
+#include "modescommon/matching_utilities.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::AtomsIO::DSSPReader::DSSPRecord DSSPRecord;
+
+std::map<CRAD, DSSPRecord> init_map_of_dssp_records(const std::string& dssp_file_name)
+{
+ std::map<CRAD, DSSPRecord> map_of_dssp_records;
+ if(!dssp_file_name.empty())
+ {
+ std::ifstream input_file(dssp_file_name.c_str(), std::ios::in);
+ const auxiliaries::AtomsIO::DSSPReader::Data dssp_file_data=auxiliaries::AtomsIO::DSSPReader::read_data_from_file_stream(input_file);
+ for(std::size_t i=0;i<dssp_file_data.dssp_records.size();i++)
+ {
+ const DSSPRecord& record=dssp_file_data.dssp_records[i];
+ CRAD crad;
+ crad.chainID=record.chainID;
+ crad.resSeq=record.resSeq;
+ crad.iCode=record.iCode;
+ map_of_dssp_records.insert(std::make_pair(crad, record));
+ }
+ }
+ return map_of_dssp_records;
+}
+
+}
+
+void query_balls(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+ pohw.describe_io("stdout", false, true, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+
+ const std::string match=poh.argument<std::string>(pohw.describe_option("--match", "string", "selection"), "");
+ const std::string match_not=poh.argument<std::string>(pohw.describe_option("--match-not", "string", "negative selection"), "");
+ const std::string match_tags=poh.argument<std::string>(pohw.describe_option("--match-tags", "string", "tags to match"), "");
+ const std::string match_tags_not=poh.argument<std::string>(pohw.describe_option("--match-tags-not", "string", "tags to not match"), "");
+ const std::string match_adjuncts=poh.argument<std::string>(pohw.describe_option("--match-adjuncts", "string", "adjuncts intervals to match"), "");
+ const std::string match_adjuncts_not=poh.argument<std::string>(pohw.describe_option("--match-adjuncts-not", "string", "adjuncts intervals to not match"), "");
+ const std::string match_external_annotations=poh.argument<std::string>(pohw.describe_option("--match-external-annotations", "string", "file path to input matchable annotations"), "");
+ const bool invert=poh.contains_option(pohw.describe_option("--invert", "", "flag to invert selection"));
+ const bool whole_residues=poh.contains_option(pohw.describe_option("--whole-residues", "", "flag to select whole residues"));
+ const bool drop_atom_serial=poh.contains_option(pohw.describe_option("--drop-atom-serials", "", "flag to drop atom serial numbers from input"));
+ const bool drop_altloc_indicators=poh.contains_option(pohw.describe_option("--drop-altloc-indicators", "", "flag to drop alternate location indicators from input"));
+ const bool drop_tags=poh.contains_option(pohw.describe_option("--drop-tags", "", "flag to drop all tags from input"));
+ const bool drop_adjuncts=poh.contains_option(pohw.describe_option("--drop-adjuncts", "", "flag to drop all adjuncts from input"));
+ const std::string set_tags=poh.argument<std::string>(pohw.describe_option("--set-tags", "string", "set tags instead of filtering"), "");
+ const std::string set_dssp_info=poh.argument<std::string>(pohw.describe_option("--set-dssp-info", "string", "file path to input DSSP file"), "");
+ const std::string set_adjuncts=poh.argument<std::string>(pohw.describe_option("--set-adjuncts", "string", "set adjuncts instead of filtering"), "");
+ const std::string set_external_adjuncts=poh.argument<std::string>(pohw.describe_option("--set-external-adjuncts", "string", "file path to input external adjuncts"), "");
+ const std::string set_external_adjuncts_name=poh.argument<std::string>(pohw.describe_option("--set-external-adjuncts-name", "string", "name for external adjuncts"), "ex");
+ const bool rename_chains=poh.contains_option(pohw.describe_option("--rename-chains", "", "flag to rename input chains to be in interval from 'A' to 'Z'"));
+ const std::string renumber_from_adjunct=poh.argument<std::string>(pohw.describe_option("--renumber-from-adjunct", "string", "adjunct name to use for input residue renumbering"), "");
+ const bool renumber_positively=poh.contains_option(pohw.describe_option("--renumber-positively", "", "flag to increment residue numbers to make them positive"));
+ const bool reset_serials=poh.contains_option(pohw.describe_option("--reset-serials", "", "flag to reset atom serial numbers"));
+ const bool set_seq_pos_adjunct=poh.contains_option(pohw.describe_option("--set-seq-pos-adjunct", "", "flag to set normalized sequence position adjunct"));
+ const std::string set_ref_seq_num_adjunct=poh.argument<std::string>(pohw.describe_option("--set-ref-seq-num-adjunct", "string", "file path to input reference sequence"), "");
+ const std::string ref_seq_alignment=poh.argument<std::string>(pohw.describe_option("--ref-seq-alignment", "string", "file path to output alignment with reference"), "");
+ const std::string seq_output=poh.argument<std::string>(pohw.describe_option("--seq-output", "string", "file path to output query result sequence string"), "");
+ const std::string chains_summary_output=poh.argument<std::string>(pohw.describe_option("--chains-summary-output", "string", "file path to output chains summary"), "");
+ const double chains_seq_identity=poh.argument<double>(pohw.describe_option("--chains-seq-identity", "number", "sequence identity threshold for chains summary, default is 0.9"), 0.9);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::vector< std::pair<CRAD, BallValue> > list_of_balls;
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, list_of_balls);
+ if(list_of_balls.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ if(rename_chains)
+ {
+ std::set<std::string> current_chain_names_set;
+ std::vector<std::string> current_chain_names;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const std::string& chainID=list_of_balls[i].first.chainID;
+ if(current_chain_names_set.count(chainID)==0)
+ {
+ current_chain_names_set.insert(chainID);
+ current_chain_names.push_back(chainID);
+ }
+ }
+ if(!current_chain_names.empty() && current_chain_names.size()>(static_cast<std::size_t>('Z'-'A')+1))
+ {
+ throw std::runtime_error("Too many chains to rename to be in interval from 'A' to 'Z'.");
+ }
+ else
+ {
+ std::map<std::string, std::string> renaming_map;
+ for(std::vector<std::string>::const_iterator it=current_chain_names.begin();it!=current_chain_names.end();++it)
+ {
+ char index_symbol='A'+static_cast<char>(renaming_map.size());
+ renaming_map[*it]=std::string(1, index_symbol);
+ }
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ list_of_balls[i].first.chainID=renaming_map[list_of_balls[i].first.chainID];
+ }
+ }
+ }
+
+ if(!renumber_from_adjunct.empty())
+ {
+ std::vector< std::pair<CRAD, BallValue> > refined_list_of_balls;
+ refined_list_of_balls.reserve(list_of_balls.size());
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const BallValue& value=list_of_balls[i].second;
+ if(value.props.adjuncts.count(renumber_from_adjunct)>0)
+ {
+ refined_list_of_balls.push_back(list_of_balls[i]);
+ refined_list_of_balls.back().first.resSeq=static_cast<int>(value.props.adjuncts.find(renumber_from_adjunct)->second);
+ refined_list_of_balls.back().second.props.adjuncts.erase(renumber_from_adjunct);
+ }
+ }
+ list_of_balls=refined_list_of_balls;
+ }
+
+ if(renumber_positively)
+ {
+ std::map<std::string, int> min_resSeq;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ if(crad.resSeq!=CRAD::null_num() && (min_resSeq.count(crad.chainID)==0 || crad.resSeq<min_resSeq[crad.chainID]))
+ {
+ min_resSeq[crad.chainID]=crad.resSeq;
+ }
+ }
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ CRAD& crad=list_of_balls[i].first;
+ if(crad.resSeq!=CRAD::null_num() && min_resSeq.count(crad.chainID)>0 && min_resSeq[crad.chainID]<=0)
+ {
+ crad.resSeq=(crad.resSeq-min_resSeq[crad.chainID]+1);
+ }
+ }
+ }
+
+ if(reset_serials)
+ {
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ list_of_balls[i].first.serial=static_cast<int>(i+1);
+ }
+ }
+
+ if(set_seq_pos_adjunct)
+ {
+ typedef std::map<std::string, std::pair<double, double> > MapOfRanges;
+ MapOfRanges chain_seq_num_ranges;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ MapOfRanges::iterator chain_seq_num_ranges_it=chain_seq_num_ranges.find(crad.chainID);
+ if(chain_seq_num_ranges_it==chain_seq_num_ranges.end())
+ {
+ std::pair<double, double>& range=chain_seq_num_ranges[crad.chainID];
+ range.first=crad.resSeq;
+ range.second=crad.resSeq;
+ }
+ else
+ {
+ std::pair<double, double>& range=chain_seq_num_ranges_it->second;
+ range.first=std::min(range.first, static_cast<double>(crad.resSeq));
+ range.second=std::max(range.second, static_cast<double>(crad.resSeq));
+ }
+ }
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ const std::pair<double, double>& range=chain_seq_num_ranges[crad.chainID];
+ list_of_balls[i].second.props.adjuncts["seqpos"]=((range.first<range.second) ? ((crad.resSeq-range.first)/(range.second-range.first)) : 0.0);
+ }
+ }
+
+ std::set<std::size_t> selected_set_of_ball_ids;
+ {
+ const std::set<CRAD> matchable_external_set_of_crads=auxiliaries::IOUtilities().read_file_lines_to_set< std::set<CRAD> >(match_external_annotations);
+
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ const BallValue& value=list_of_balls[i].second;
+ const bool passed=(MatchingUtilities::match_crad(crad, match, match_not) &&
+ MatchingUtilities::match_set_of_tags(value.props.tags, match_tags, match_tags_not) &&
+ MatchingUtilities::match_map_of_adjuncts(value.props.adjuncts, match_adjuncts, match_adjuncts_not) &&
+ (match_external_annotations.empty() || MatchingUtilities::match_crad_with_set_of_crads(crad, matchable_external_set_of_crads)));
+ if((passed && !invert) || (!passed && invert))
+ {
+ selected_set_of_ball_ids.insert(selected_set_of_ball_ids.end(), i);
+ }
+ }
+
+ if(whole_residues)
+ {
+ std::set<CRAD> residues_crads;
+ for(std::set<std::size_t>::const_iterator it=selected_set_of_ball_ids.begin();it!=selected_set_of_ball_ids.end();++it)
+ {
+ residues_crads.insert(list_of_balls[*it].first.without_atom());
+ }
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ if(MatchingUtilities::match_crad_with_set_of_crads(list_of_balls[i].first, residues_crads))
+ {
+ selected_set_of_ball_ids.insert(i);
+ }
+ }
+ }
+ }
+
+ std::vector<CRAD> residue_sequence_vector;
+ {
+ std::set<CRAD> residues_crads;
+ for(std::set<std::size_t>::const_iterator it=selected_set_of_ball_ids.begin();it!=selected_set_of_ball_ids.end();++it)
+ {
+ const CRAD residue_crad=list_of_balls[*it].first.without_atom();
+ if(residues_crads.count(residue_crad)==0)
+ {
+ residue_sequence_vector.push_back(residue_crad);
+ residues_crads.insert(residue_crad);
+ }
+ }
+ }
+
+ const bool update_mode=(drop_atom_serial || drop_altloc_indicators || drop_tags || drop_adjuncts || !set_tags.empty() || !set_adjuncts.empty() || !set_external_adjuncts.empty() || !set_dssp_info.empty() || !set_ref_seq_num_adjunct.empty());
+ if(update_mode && !selected_set_of_ball_ids.empty())
+ {
+ const std::map<CRAD, double> map_of_external_adjunct_values=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRAD, double> >(set_external_adjuncts);
+ const std::map<CRAD, DSSPRecord> map_of_dssp_records=init_map_of_dssp_records(set_dssp_info);
+ const std::string reference_sequence=SequenceUtilities::read_sequence_from_file(set_ref_seq_num_adjunct);
+ const std::map<CRAD, int> sequence_mapping=SequenceUtilities::construct_sequence_mapping(residue_sequence_vector, reference_sequence, ref_seq_alignment);
+
+ for(std::set<std::size_t>::const_iterator it=selected_set_of_ball_ids.begin();it!=selected_set_of_ball_ids.end();++it)
+ {
+ CRAD& crad=list_of_balls[*it].first;
+ BallValue& value=list_of_balls[*it].second;
+ if(drop_atom_serial)
+ {
+ crad.serial=CRAD::null_num();
+ }
+ if(drop_altloc_indicators)
+ {
+ crad.altLoc.clear();
+ }
+ if(drop_tags)
+ {
+ value.props.tags.clear();
+ }
+ if(drop_adjuncts)
+ {
+ value.props.adjuncts.clear();
+ }
+ if(!set_tags.empty())
+ {
+ value.props.update_tags(set_tags);
+ }
+ if(!set_adjuncts.empty())
+ {
+ value.props.update_adjuncts(set_adjuncts);
+ }
+ if(!map_of_external_adjunct_values.empty())
+ {
+ const std::pair<bool, double> adjunct_value=MatchingUtilities::match_crad_with_map_of_crads(crad, map_of_external_adjunct_values);
+ if(adjunct_value.first)
+ {
+ value.props.adjuncts[set_external_adjuncts_name]=adjunct_value.second;
+ }
+ }
+ if(!map_of_dssp_records.empty())
+ {
+ CRAD simplified_crad;
+ simplified_crad.chainID=crad.chainID;
+ simplified_crad.resSeq=crad.resSeq;
+ simplified_crad.iCode=crad.iCode;
+ const std::map<CRAD, DSSPRecord>::const_iterator map_of_dssp_records_it=map_of_dssp_records.find(simplified_crad);
+ if(map_of_dssp_records_it!=map_of_dssp_records.end())
+ {
+ const DSSPRecord& dssp_record=map_of_dssp_records_it->second;
+ if(!dssp_record.resSSE.empty())
+ {
+ value.props.tags.insert(std::string("dssp=")+dssp_record.resSSE);
+ }
+ value.props.adjuncts["phi"]=dssp_record.anglePhi;
+ value.props.adjuncts["psi"]=dssp_record.anglePsi;
+ }
+ }
+ if(!sequence_mapping.empty())
+ {
+ const std::map<CRAD, int>::const_iterator sm_it=sequence_mapping.find(crad.without_atom());
+ if(sm_it!=sequence_mapping.end())
+ {
+ value.props.adjuncts["refseq"]=static_cast<double>(sm_it->second);
+ }
+ }
+ }
+ }
+
+ if(update_mode)
+ {
+ auxiliaries::IOUtilities().write_map(list_of_balls, std::cout);
+ }
+ else
+ {
+ for(std::set<std::size_t>::const_iterator it=selected_set_of_ball_ids.begin();it!=selected_set_of_ball_ids.end();++it)
+ {
+ std::cout << list_of_balls[*it].first << " " << list_of_balls[*it].second << "\n";
+ }
+ }
+
+ if(!residue_sequence_vector.empty() && !seq_output.empty())
+ {
+ std::ofstream foutput(seq_output.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ foutput << SequenceUtilities::convert_residue_sequence_container_to_string(residue_sequence_vector) << "\n";
+ }
+ }
+
+ if(!residue_sequence_vector.empty() && !chains_summary_output.empty())
+ {
+ std::ofstream foutput(chains_summary_output.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ std::map< std::string, std::vector<CRAD> > map_of_chains;
+ for(std::size_t i=0;i<residue_sequence_vector.size();i++)
+ {
+ map_of_chains[residue_sequence_vector[i].chainID].push_back(residue_sequence_vector[i]);
+ }
+ std::map<std::string, std::string> map_of_chains_sequences;
+ for(std::map< std::string, std::vector<CRAD> >::const_iterator it=map_of_chains.begin();it!=map_of_chains.end();++it)
+ {
+ map_of_chains_sequences[it->first]=SequenceUtilities::convert_residue_sequence_container_to_string(it->second);
+ }
+ std::set<std::string> representative_chains;
+ std::set<std::string> repeated_chains;
+ for(std::map<std::string, std::string>::const_iterator it1=map_of_chains_sequences.begin();it1!=map_of_chains_sequences.end();++it1)
+ {
+ if(repeated_chains.count(it1->first)==0)
+ {
+ representative_chains.insert(it1->first);
+ std::map<std::string, std::string>::const_iterator it2=it1;
+ ++it2;
+ for(;it2!=map_of_chains_sequences.end();++it2)
+ {
+ if(SequenceUtilities::calculate_sequence_identity(it1->second, it2->second)>=chains_seq_identity)
+ {
+ repeated_chains.insert(it2->first);
+ }
+ }
+ }
+ }
+ foutput << map_of_chains_sequences.size() << " " << representative_chains.size() << "\n";
+ auxiliaries::IOUtilities().write_set(representative_chains, foutput);
+ }
+ }
+}
diff --git a/src/mode_query_balls_clashes.cpp b/src/mode_query_balls_clashes.cpp
new file mode 100644
index 0000000..4a09204
--- /dev/null
+++ b/src/mode_query_balls_clashes.cpp
@@ -0,0 +1,78 @@
+#include "apollota/search_for_spherical_collisions.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+}
+
+void query_balls_clashes(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'annotation x y z r')");
+ pohw.describe_io("stdout", false, true, "list of clashes (line format: 'annotation1 annotation2 distance min-distance-between-balls')");
+
+ const double clash_distance=poh.argument<double>(pohw.describe_option("--clash-distance", "number", "clash distance threshold in angstroms, default is 3.0"), 3.0);
+ const int min_sequence_separation=poh.argument<int>(pohw.describe_option("--min-seq-sep", "number", "minimum residue sequence separation, default is 2"), 2);
+ const double init_radius_for_BSH=poh.argument<double>(pohw.describe_option("--init-radius-for-BSH", "number", "initial radius for bounding sphere hierarchy"), 3.5);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ if(clash_distance<0.001)
+ {
+ throw std::runtime_error("Clash distance threshold is too small.");
+ }
+
+ std::vector< std::pair<CRAD, apollota::SimpleSphere> > list_of_balls;
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, list_of_balls);
+ if(list_of_balls.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ std::vector<apollota::SimpleSphere> spheres(list_of_balls.size());
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ spheres[i]=apollota::SimpleSphere(list_of_balls[i].second, clash_distance*0.5);
+ }
+
+ const apollota::BoundingSpheresHierarchy bsh(spheres, init_radius_for_BSH, 1);
+
+ std::map< CRADsPair, std::pair<double, double> > map_of_clashes;
+
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ const std::vector<std::size_t> collisions=apollota::SearchForSphericalCollisions::find_all_collisions(bsh, spheres[i]);
+ for(std::size_t j=0;j<collisions.size();j++)
+ {
+ if(collisions[j]!=i)
+ {
+ const double distance=apollota::distance_from_point_to_point(spheres[i], spheres[collisions[j]]);
+ const double distance_between_balls=apollota::minimal_distance_from_sphere_to_sphere(list_of_balls[i].second, list_of_balls[collisions[j]].second);
+ if(distance<clash_distance)
+ {
+ const CRAD& crad_a=list_of_balls[i].first;
+ const CRAD& crad_b=list_of_balls[collisions[j]].first;
+ if(CRAD::match_with_sequence_separation_interval(crad_a, crad_b, min_sequence_separation, CRAD::null_num(), true))
+ {
+ map_of_clashes[CRADsPair(crad_a, crad_b)]=std::make_pair(distance, distance_between_balls);
+ }
+ }
+ }
+ }
+ }
+
+ for(std::map< CRADsPair, std::pair<double, double> >::const_iterator it=map_of_clashes.begin();it!=map_of_clashes.end();++it)
+ {
+ std::cout << it->first << " " << it->second.first << " " << it->second.second << "\n";
+ }
+}
diff --git a/src/mode_query_balls_sequences_pairings_stats.cpp b/src/mode_query_balls_sequences_pairings_stats.cpp
new file mode 100644
index 0000000..8eb3568
--- /dev/null
+++ b/src/mode_query_balls_sequences_pairings_stats.cpp
@@ -0,0 +1,76 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+#include "modescommon/ball_value.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+
+}
+
+void query_balls_sequences_pairings_stats(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls files");
+ pohw.describe_io("stdout", false, true, "list of sequences pairings stats");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::map<CRAD, double> map_of_single_stats;
+ double sum_of_single_stats=0.0;
+ std::map<CRADsPair, double> map_of_pairing_stats;
+ double sum_of_pairings_stats=0.0;
+
+ while(std::cin.good())
+ {
+ std::string balls_file;
+ std::cin >> balls_file;
+ std::vector<CRAD> list_of_balls;
+ auxiliaries::IOUtilities().read_file_lines_to_set(balls_file, list_of_balls);
+ std::map< std::string, std::set<CRAD> > chains;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ chains[list_of_balls[i].chainID].insert(list_of_balls[i].without_atom());
+ }
+ for(std::map< std::string, std::set<CRAD> >::const_iterator chains_it=chains.begin();chains_it!=chains.end();++chains_it)
+ {
+ std::vector<CRAD> residues(chains_it->second.begin(), chains_it->second.end());
+ for(std::size_t i=0;i<residues.size();i++)
+ {
+ map_of_single_stats[residues[i].without_numbering()]+=1;
+ sum_of_single_stats+=1;
+ }
+ for(std::size_t i=0;i+1<residues.size();i++)
+ {
+ if(CRAD::match_with_sequence_separation_interval(residues[i], residues[i+1], 1, 1, false))
+ {
+ map_of_pairing_stats[CRADsPair(residues[i].without_numbering(), residues[i+1].without_numbering())]+=1;
+ sum_of_pairings_stats+=1;
+ }
+ }
+ }
+ }
+
+ double sum_of_p_obs=0.0;
+ double sum_of_p_exp=0.0;
+ for(std::map<CRADsPair, double>::const_iterator it=map_of_pairing_stats.begin();it!=map_of_pairing_stats.end();++it)
+ {
+ const CRADsPair& crads=it->first;
+ const double pairing_stat=it->second;
+ const double single1_stat=map_of_single_stats[crads.a];
+ const double single2_stat=map_of_single_stats[crads.b];
+ const double p_obs=(pairing_stat/sum_of_pairings_stats);
+ const double p_exp=((single1_stat/sum_of_single_stats)*(single2_stat/sum_of_single_stats)*(crads.a==crads.b ? 1.0 : 2.0));
+ sum_of_p_obs+=p_obs;
+ sum_of_p_exp+=p_exp;
+ std::cout << crads << " " << p_obs << " " << p_exp << "\n";
+ }
+ std::cout << CRADsPair(CRAD::any(), CRAD::any()) << " " << sum_of_p_obs << " " << sum_of_p_exp << "\n";
+}
diff --git a/src/mode_query_contacts.cpp b/src/mode_query_contacts.cpp
new file mode 100644
index 0000000..c63ea7c
--- /dev/null
+++ b/src/mode_query_contacts.cpp
@@ -0,0 +1,342 @@
+#include <iostream>
+#include <stdexcept>
+#include <fstream>
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/atoms_io.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+#include "auxiliaries/opengl_printer.h"
+
+#include "modescommon/contact_value.h"
+#include "modescommon/matching_utilities.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+std::set<CRADsPair> init_set_of_hbplus_crad_pairs(const std::string& hbplus_file_name, const bool inter_residue_hbplus_tags)
+{
+ std::set<CRADsPair> set_of_hbplus_crad_pairs;
+ if(!hbplus_file_name.empty())
+ {
+ std::ifstream input_file(hbplus_file_name.c_str(), std::ios::in);
+ auxiliaries::AtomsIO::HBPlusReader::Data hbplus_file_data=auxiliaries::AtomsIO::HBPlusReader::read_data_from_file_stream(input_file);
+ if(!hbplus_file_data.hbplus_records.empty())
+ {
+ for(std::vector<auxiliaries::AtomsIO::HBPlusReader::HBPlusRecord>::const_iterator it=hbplus_file_data.hbplus_records.begin();it!=hbplus_file_data.hbplus_records.end();++it)
+ {
+ const auxiliaries::AtomsIO::HBPlusReader::ShortAtomDescriptor& a=it->first;
+ const auxiliaries::AtomsIO::HBPlusReader::ShortAtomDescriptor& b=it->second;
+ const CRADsPair crads_pair(CRAD(CRAD::null_num(), a.chainID, a.resSeq, a.resName, a.name, "", ""), CRAD(CRAD::null_num(), b.chainID, b.resSeq, b.resName, b.name, "", ""));
+ set_of_hbplus_crad_pairs.insert(inter_residue_hbplus_tags ? CRADsPair(crads_pair.a.without_atom(), crads_pair.b.without_atom()) : crads_pair);
+ }
+ }
+ }
+ return set_of_hbplus_crad_pairs;
+}
+
+void apply_renaming_map_on_contacts(const std::string& renaming_map, std::map<CRADsPair, ContactValue>& map_of_contacts)
+{
+ const std::map<CRAD, CRAD> renaming_map_of_crads=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRAD, CRAD> >(renaming_map);
+ if(!renaming_map_of_crads.empty())
+ {
+ std::map< CRADsPair, ContactValue > map_of_renamed_contacts;
+ for(std::map< CRADsPair, ContactValue >::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ CRAD crads[2]={it->first.a, it->first.b};
+ for(int i=0;i<2;i++)
+ {
+ CRAD& crad=crads[i];
+ std::map<CRAD, CRAD>::const_iterator renaming_it=renaming_map_of_crads.find(crad.without_numbering());
+ if(renaming_it!=renaming_map_of_crads.end())
+ {
+ crad.resName=renaming_it->second.resName;
+ crad.name=renaming_it->second.name;
+ }
+ }
+ map_of_renamed_contacts[CRADsPair(crads[0], crads[1])].add(it->second);
+ }
+ map_of_contacts=map_of_renamed_contacts;
+ }
+}
+
+void sum_contacts_into_inter_residue_contacts(const std::string& summing_exceptions, std::map<CRADsPair, ContactValue>& map_of_contacts)
+{
+ const std::set<CRAD> summing_exceptions_set_of_crads=auxiliaries::IOUtilities().read_file_lines_to_set< std::set<CRAD> >(summing_exceptions);
+ std::map< CRADsPair, ContactValue > map_of_reduced_contacts;
+ for(std::map< CRADsPair, ContactValue >::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& raw_crads=it->first;
+ const bool exclude_a=(!summing_exceptions_set_of_crads.empty() && MatchingUtilities::match_crad_with_set_of_crads(raw_crads.a, summing_exceptions_set_of_crads));
+ const bool exclude_b=(!summing_exceptions_set_of_crads.empty() && MatchingUtilities::match_crad_with_set_of_crads(raw_crads.b, summing_exceptions_set_of_crads));
+ const CRADsPair crads((exclude_a ? raw_crads.a : raw_crads.a.without_atom()), (exclude_b ? raw_crads.b : raw_crads.b.without_atom()), raw_crads.reversed_display);
+ if(!(crads.a==crads.b))
+ {
+ map_of_reduced_contacts[crads].add(it->second);
+ }
+ }
+ map_of_contacts=map_of_reduced_contacts;
+}
+
+}
+
+void query_contacts(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')");
+ pohw.describe_io("stdout", false, true, "list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')");
+
+ const std::string match_first=poh.argument<std::string>(pohw.describe_option("--match-first", "string", "selection for first contacting group"), "");
+ const std::string match_first_not=poh.argument<std::string>(pohw.describe_option("--match-first-not", "string", "negative selection for first contacting group"), "");
+ const std::string match_second=poh.argument<std::string>(pohw.describe_option("--match-second", "string", "selection for second contacting group"), "");
+ const std::string match_second_not=poh.argument<std::string>(pohw.describe_option("--match-second-not", "string", "negative selection for second contacting group"), "");
+ const int match_min_sequence_separation=poh.argument<int>(pohw.describe_option("--match-min-seq-sep", "number", "minimum residue sequence separation"), CRAD::null_num());
+ const int match_max_sequence_separation=poh.argument<int>(pohw.describe_option("--match-max-seq-sep", "number", "maximum residue sequence separation"), CRAD::null_num());
+ const double match_min_area=poh.argument<double>(pohw.describe_option("--match-min-area", "number", "minimum contact area"), std::numeric_limits<double>::min());
+ const double match_max_area=poh.argument<double>(pohw.describe_option("--match-max-area", "number", "maximum contact area"), std::numeric_limits<double>::max());
+ const double match_min_dist=poh.argument<double>(pohw.describe_option("--match-min-dist", "number", "minimum distance"), std::numeric_limits<double>::min());
+ const double match_max_dist=poh.argument<double>(pohw.describe_option("--match-max-dist", "number", "maximum distance"), std::numeric_limits<double>::max());
+ const std::string match_tags=poh.argument<std::string>(pohw.describe_option("--match-tags", "string", "tags to match"), "");
+ const std::string match_tags_not=poh.argument<std::string>(pohw.describe_option("--match-tags-not", "string", "tags to not match"), "");
+ const std::string match_adjuncts=poh.argument<std::string>(pohw.describe_option("--match-adjuncts", "string", "adjuncts intervals to match"), "");
+ const std::string match_adjuncts_not=poh.argument<std::string>(pohw.describe_option("--match-adjuncts-not", "string", "adjuncts intervals to not match"), "");
+ const std::string match_external_first=poh.argument<std::string>(pohw.describe_option("--match-external-first", "string", "file path to input matchable annotations"), "");
+ const std::string match_external_second=poh.argument<std::string>(pohw.describe_option("--match-external-second", "string", "file path to input matchable annotations"), "");
+ const std::string match_external_pairs=poh.argument<std::string>(pohw.describe_option("--match-external-pairs", "string", "file path to input matchable annotation pairs"), "");
+ const bool no_solvent=poh.contains_option(pohw.describe_option("--no-solvent", "", "flag to not include solvent accessible areas"));
+ const bool no_same_chain=poh.contains_option(pohw.describe_option("--no-same-chain", "", "flag to not include same chain contacts"));
+ const bool invert=poh.contains_option(pohw.describe_option("--invert", "", "flag to invert selection"));
+ const bool drop_tags=poh.contains_option(pohw.describe_option("--drop-tags", "", "flag to drop all tags from input"));
+ const bool drop_adjuncts=poh.contains_option(pohw.describe_option("--drop-adjuncts", "", "flag to drop all adjuncts from input"));
+ const std::string set_tags=poh.argument<std::string>(pohw.describe_option("--set-tags", "string", "set tags instead of filtering"), "");
+ const std::string set_hbplus_tags=poh.argument<std::string>(pohw.describe_option("--set-hbplus-tags", "string", "file path to input HBPLUS file"), "");
+ const std::string set_distance_bins_tags=poh.argument<std::string>(pohw.describe_option("--set-distance-bins-tags", "string", "list of distance thresholds"), "");
+ const bool inter_residue_hbplus_tags=poh.contains_option(pohw.describe_option("--inter-residue-hbplus-tags", "", "flag to set inter-residue H-bond tags"));
+ const std::string set_adjuncts=poh.argument<std::string>(pohw.describe_option("--set-adjuncts", "string", "set adjuncts instead of filtering"), "");
+ const std::string set_external_adjuncts=poh.argument<std::string>(pohw.describe_option("--set-external-adjuncts", "string", "file path to input external adjuncts"), "");
+ const std::string set_external_adjuncts_name=poh.argument<std::string>(pohw.describe_option("--set-external-adjuncts-name", "string", "name for external adjuncts"), "ex");
+ const std::string set_external_means=poh.argument<std::string>(pohw.describe_option("--set-external-means", "string", "file path to input external values for averaging"), "");
+ const std::string set_external_means_name=poh.argument<std::string>(pohw.describe_option("--set-external-means-name", "string", "name for external means"), "em");
+ const std::string renaming_map=poh.argument<std::string>(pohw.describe_option("--renaming-map", "string", "file path to input atoms renaming map"), "");
+ const bool inter_residue=poh.contains_option(pohw.describe_option("--inter-residue", "", "flag to convert input to inter-residue contacts"));
+ const bool inter_residue_after=poh.contains_option(pohw.describe_option("--inter-residue-after", "", "flag to convert output to inter-residue contacts"));
+ const std::string summing_exceptions=poh.argument<std::string>(pohw.describe_option("--summing-exceptions", "string", "file path to input inter-residue summing exceptions annotations"), "");
+ const bool summarize=poh.contains_option(pohw.describe_option("--summarize", "", "flag to output only summary of matched contacts"));
+ const bool summarize_by_first=poh.contains_option(pohw.describe_option("--summarize-by-first", "", "flag to output only summary of matched contacts by first identifier"));
+ enabled_output_of_ContactValue_graphics()=poh.contains_option(pohw.describe_option("--preserve-graphics", "", "flag to preserve graphics in output"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::map<CRADsPair, ContactValue> map_of_contacts;
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, map_of_contacts);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ if(!renaming_map.empty())
+ {
+ apply_renaming_map_on_contacts(renaming_map, map_of_contacts);
+ }
+
+ if(inter_residue)
+ {
+ sum_contacts_into_inter_residue_contacts(summing_exceptions, map_of_contacts);
+ }
+
+ std::map<CRADsPair, std::map<CRADsPair, ContactValue>::iterator> selected_contacts;
+
+ const std::set<CRAD> matchable_external_first_set_of_crads=auxiliaries::IOUtilities().read_file_lines_to_set< std::set<CRAD> >(match_external_first);
+ const std::set<CRAD> matchable_external_second_set_of_crads=auxiliaries::IOUtilities().read_file_lines_to_set< std::set<CRAD> >(match_external_second);
+ {
+ const std::set<CRADsPair> matchable_external_set_of_crad_pairs=auxiliaries::IOUtilities().read_file_lines_to_set< std::set<CRADsPair> >(match_external_pairs);
+ for(std::map< CRADsPair, ContactValue >::iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first;
+ const ContactValue& value=it->second;
+ bool passed=false;
+ if(
+ value.area>=match_min_area && value.area<=match_max_area &&
+ value.dist>=match_min_dist && value.dist<=match_max_dist &&
+ (!no_solvent || !(crads.a==CRAD::solvent() || crads.b==CRAD::solvent())) &&
+ (!no_same_chain || crads.a.chainID!=crads.b.chainID) &&
+ CRAD::match_with_sequence_separation_interval(crads.a, crads.b, match_min_sequence_separation, match_max_sequence_separation, true) &&
+ MatchingUtilities::match_set_of_tags(value.props.tags, match_tags, match_tags_not) &&
+ MatchingUtilities::match_map_of_adjuncts(value.props.adjuncts, match_adjuncts, match_adjuncts_not) &&
+ (match_external_pairs.empty() || MatchingUtilities::match_crads_pair_with_set_of_crads_pairs(crads, matchable_external_set_of_crad_pairs))
+ )
+ {
+ const bool matched_first_second=(
+ MatchingUtilities::match_crad(crads.a, match_first, match_first_not) &&
+ MatchingUtilities::match_crad(crads.b, match_second, match_second_not) &&
+ (match_external_first.empty() || MatchingUtilities::match_crad_with_set_of_crads(crads.a, matchable_external_first_set_of_crads)) &&
+ (match_external_second.empty() || MatchingUtilities::match_crad_with_set_of_crads(crads.b, matchable_external_second_set_of_crads)));
+ const bool matched_second_first=matched_first_second || (
+ MatchingUtilities::match_crad(crads.b, match_first, match_first_not) &&
+ MatchingUtilities::match_crad(crads.a, match_second, match_second_not) &&
+ (match_external_first.empty() || MatchingUtilities::match_crad_with_set_of_crads(crads.b, matchable_external_first_set_of_crads)) &&
+ (match_external_second.empty() || MatchingUtilities::match_crad_with_set_of_crads(crads.a, matchable_external_second_set_of_crads)));
+ passed=(matched_first_second || matched_second_first);
+ if(passed && !invert)
+ {
+ selected_contacts.insert(selected_contacts.end(), std::make_pair(CRADsPair(crads.a, crads.b, !matched_first_second), it));
+ }
+ }
+ if(!passed && invert)
+ {
+ selected_contacts.insert(selected_contacts.end(), std::make_pair(crads, it));
+ }
+ }
+ }
+
+ const bool update_mode=(drop_tags || drop_adjuncts || !set_tags.empty() || !set_adjuncts.empty() || !set_external_adjuncts.empty() || !set_external_means.empty() || !set_hbplus_tags.empty() || !set_distance_bins_tags.empty());
+ if(update_mode && !selected_contacts.empty())
+ {
+ const std::map<CRADsPair, double> map_of_external_adjunct_values=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRADsPair, double> >(set_external_adjuncts);
+ const std::map<CRAD, double> map_of_external_values_for_averaging=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRAD, double> >(set_external_means);
+ const std::set<CRADsPair> set_of_hbplus_crad_pairs=init_set_of_hbplus_crad_pairs(set_hbplus_tags, inter_residue_hbplus_tags);
+ const std::set<double> distance_thresholds_for_bins=(set_distance_bins_tags.empty() ? std::set<double>() : auxiliaries::IOUtilities(';').read_string_lines_to_set< std::set<double> >(set_distance_bins_tags));
+
+ for(std::map<CRADsPair, std::map<CRADsPair, ContactValue>::iterator>::iterator selected_map_it=selected_contacts.begin();selected_map_it!=selected_contacts.end();++selected_map_it)
+ {
+ std::map<CRADsPair, ContactValue>::iterator it=selected_map_it->second;
+ if(it!=map_of_contacts.end())
+ {
+ if(drop_tags)
+ {
+ it->second.props.tags.clear();
+ }
+ if(drop_adjuncts)
+ {
+ it->second.props.adjuncts.clear();
+ }
+ if(!set_tags.empty())
+ {
+ it->second.props.update_tags(set_tags);
+ }
+ if(!set_adjuncts.empty())
+ {
+ it->second.props.update_adjuncts(set_adjuncts);
+ }
+ if(!map_of_external_adjunct_values.empty())
+ {
+ const std::pair<bool, double> adjunct_value=MatchingUtilities::match_crad_with_map_of_crads_pairs(it->first, map_of_external_adjunct_values);
+ if(adjunct_value.first)
+ {
+ it->second.props.adjuncts[set_external_adjuncts_name]=adjunct_value.second;
+ }
+ }
+ if(!map_of_external_values_for_averaging.empty())
+ {
+ std::map< CRAD, double >::const_iterator value_a_it=map_of_external_values_for_averaging.find(it->first.a);
+ std::map< CRAD, double >::const_iterator value_b_it=map_of_external_values_for_averaging.find(it->first.b);
+ if(value_a_it!=map_of_external_values_for_averaging.end() || value_b_it!=map_of_external_values_for_averaging.end())
+ {
+ const double value_a=(value_a_it!=map_of_external_values_for_averaging.end() ? value_a_it->second : 0.0);
+ const double value_b=(value_b_it!=map_of_external_values_for_averaging.end() ? value_b_it->second : 0.0);
+ const double mult=((value_a_it!=map_of_external_values_for_averaging.end() && value_b_it!=map_of_external_values_for_averaging.end()) ? 0.5 : 1.0);
+ it->second.props.adjuncts[set_external_means_name]=(value_a+value_b)*mult;
+ }
+ }
+ if(!set_of_hbplus_crad_pairs.empty())
+ {
+ if(MatchingUtilities::match_crads_pair_with_set_of_crads_pairs(it->first, set_of_hbplus_crad_pairs))
+ {
+ it->second.props.tags.insert(inter_residue_hbplus_tags ? "rhb" : "hb");
+ }
+ }
+ if(!distance_thresholds_for_bins.empty())
+ {
+ std::string bin_tag="d0";
+ std::set<double>::const_iterator it_a=distance_thresholds_for_bins.begin();
+ if(it->second.dist>=(*it_a))
+ {
+ bool found=false;
+ int bin=1;
+ while(it_a!=distance_thresholds_for_bins.end() && !found)
+ {
+ std::set<double>::const_iterator it_b=it_a; ++it_b;
+ if(it->second.dist>=(*it_a) && (it_b==distance_thresholds_for_bins.end() || it->second.dist<(*it_b)))
+ {
+ std::ostringstream bin_tag_output;
+ bin_tag_output << "d" << bin;
+ bin_tag=bin_tag_output.str();
+ found=true;
+ }
+ ++it_a;
+ bin++;
+ }
+ }
+ it->second.props.tags.insert(bin_tag);
+ }
+ }
+ }
+ }
+
+ const bool inter_residue_summation_needed=(!inter_residue && inter_residue_after);
+
+ if(summarize)
+ {
+ ContactValue summary;
+ for(std::map<CRADsPair, std::map<CRADsPair, ContactValue>::iterator>::const_iterator it=selected_contacts.begin();it!=selected_contacts.end();++it)
+ {
+ summary.add(it->second->second);
+ summary.graphics.clear();
+ }
+ std::cout << CRADsPair(CRAD::any(), CRAD::any()) << " " << summary << "\n";
+ }
+ else if(summarize_by_first)
+ {
+ std::map< CRADsPair, ContactValue > map_of_summaries;
+ for(std::map<CRADsPair, std::map<CRADsPair, ContactValue>::iterator>::const_iterator it=selected_contacts.begin();it!=selected_contacts.end();++it)
+ {
+ CRAD crads[2]={it->first.a, it->first.b};
+ for(int i=0;i<2;i++)
+ {
+ if(crads[i]!=CRAD::any() && MatchingUtilities::match_crad(crads[i], match_first, match_first_not) && (match_external_first.empty() || MatchingUtilities::match_crad_with_set_of_crads(crads[i], matchable_external_first_set_of_crads)))
+ {
+ ContactValue& cv=map_of_summaries[CRADsPair(crads[i], CRAD::any())];
+ cv.add(it->second->second);
+ cv.graphics.clear();
+ }
+ }
+ }
+ if(inter_residue_summation_needed)
+ {
+ sum_contacts_into_inter_residue_contacts(summing_exceptions, map_of_summaries);
+ }
+ auxiliaries::IOUtilities().write_map(map_of_summaries, std::cout);
+ }
+ else
+ {
+ if(!update_mode && !inter_residue_summation_needed)
+ {
+ for(std::map<CRADsPair, std::map<CRADsPair, ContactValue>::iterator>::const_iterator it=selected_contacts.begin();it!=selected_contacts.end();++it)
+ {
+ std::cout << it->first << " " << it->second->second << "\n";
+ }
+ }
+ else
+ {
+ if(!update_mode)
+ {
+ std::map< CRADsPair, ContactValue > map_of_selected_contacts;
+ for(std::map<CRADsPair, std::map<CRADsPair, ContactValue>::iterator>::const_iterator it=selected_contacts.begin();it!=selected_contacts.end();++it)
+ {
+ map_of_selected_contacts.insert(std::make_pair(it->first, it->second->second));
+ }
+ map_of_contacts=map_of_selected_contacts;
+ }
+ if(inter_residue_summation_needed)
+ {
+ sum_contacts_into_inter_residue_contacts(summing_exceptions, map_of_contacts);
+ }
+ auxiliaries::IOUtilities().write_map(map_of_contacts, std::cout);
+ }
+ }
+}
diff --git a/src/mode_query_contacts_depth_values.cpp b/src/mode_query_contacts_depth_values.cpp
new file mode 100644
index 0000000..cab6465
--- /dev/null
+++ b/src/mode_query_contacts_depth_values.cpp
@@ -0,0 +1,136 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+#include "modescommon/contact_value.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+struct ResidueValuesSummary
+{
+ int count;
+ int min;
+ int max;
+ int sum;
+
+ ResidueValuesSummary() : count(0), min(0), max(0), sum(0)
+ {
+ }
+
+ void record(const int val)
+ {
+ if(count<1)
+ {
+ count=1;
+ min=val;
+ max=val;
+ sum=val;
+ }
+ else
+ {
+ count++;
+ min=std::min(min, val);
+ max=std::max(max, val);
+ sum+=val;
+ }
+ }
+
+ double average() const
+ {
+ return (count>0 ? (static_cast<double>(sum)/static_cast<double>(count)) : 0);
+ }
+};
+
+}
+
+void query_contacts_depth_values(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2')");
+ pohw.describe_io("stdout", false, true, "list of depth values (line format: 'annotation depth')");
+
+ const std::string residue_info=poh.argument<std::string>(pohw.describe_option("--residue-info", "string", "file path to output residue info"), "");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const std::set<CRADsPair> set_of_contacts=auxiliaries::IOUtilities().read_lines_to_set< std::set<CRADsPair> >(std::cin);
+ if(set_of_contacts.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ std::map<CRAD, int> map_crad_to_depth;
+ int level_count=0;
+
+ for(std::set<CRADsPair>::const_iterator it=set_of_contacts.begin();it!=set_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=(*it);
+ if(crads.b==CRAD::solvent())
+ {
+ map_crad_to_depth[crads.a]=1;
+ level_count++;
+ }
+ }
+
+ for(int depth=1;level_count>0;depth++)
+ {
+ level_count=0;
+ for(std::set<CRADsPair>::const_iterator it=set_of_contacts.begin();it!=set_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=(*it);
+ if(!crads.contains(CRAD::solvent()))
+ {
+ const int depth_a=map_crad_to_depth[crads.a];
+ const int depth_b=map_crad_to_depth[crads.b];
+ if(depth_a==depth && depth_b==0)
+ {
+ map_crad_to_depth[crads.b]=(depth+1);
+ level_count++;
+ }
+ else if(depth_b==depth && depth_a==0)
+ {
+ map_crad_to_depth[crads.a]=(depth+1);
+ level_count++;
+ }
+ }
+ }
+ }
+
+ for(std::set<CRADsPair>::const_iterator it=set_of_contacts.begin();it!=set_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=(*it);
+ if(crads.a!=CRAD::solvent() && map_crad_to_depth.find(crads.a)==map_crad_to_depth.end())
+ {
+ map_crad_to_depth[crads.a]=1;
+ }
+ if(crads.b!=CRAD::solvent() && map_crad_to_depth.find(crads.b)==map_crad_to_depth.end())
+ {
+ map_crad_to_depth[crads.b]=1;
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map(map_crad_to_depth, std::cout);
+
+ if(!map_crad_to_depth.empty() && !residue_info.empty())
+ {
+ std::map<CRAD, ResidueValuesSummary> map_crad_to_depth_summary;
+ for(std::map<CRAD, int>::const_iterator it=map_crad_to_depth.begin();it!=map_crad_to_depth.end();++it)
+ {
+ map_crad_to_depth_summary[it->first.without_atom()].record(it->second);
+ }
+ std::ofstream foutput(residue_info.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ for(std::map<CRAD, ResidueValuesSummary>::const_iterator it=map_crad_to_depth_summary.begin();it!=map_crad_to_depth_summary.end();++it)
+ {
+ foutput << it->first << " " << it->second.average() << " " << it->second.min << " " << it->second.max << " " << it->second.count << "\n";
+ }
+ }
+ }
+}
diff --git a/src/mode_query_contacts_simulating_unfolding.cpp b/src/mode_query_contacts_simulating_unfolding.cpp
new file mode 100644
index 0000000..996da5a
--- /dev/null
+++ b/src/mode_query_contacts_simulating_unfolding.cpp
@@ -0,0 +1,61 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+#include "modescommon/contact_value.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+}
+
+void query_contacts_simulating_unfolding(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts [graphics]')");
+ pohw.describe_io("stdout", false, true, "list of contacts (line format: 'annotation1 annotation2 area distance tags adjuncts')");
+
+ const int match_max_sequence_separation=poh.argument<int>(pohw.describe_option("--max-seq-sep", "number", "maximum untouchable residue sequence separation", true), 0);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ enabled_output_of_ContactValue_graphics()=false;
+
+ const std::map<CRADsPair, ContactValue> map_of_contacts=auxiliaries::IOUtilities().read_lines_to_map< std::map<CRADsPair, ContactValue> >(std::cin);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ std::map<CRADsPair, ContactValue> result;
+ for(std::map< CRADsPair, ContactValue >::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first;
+ const ContactValue& value=it->second;
+ if(CRAD::match_with_sequence_separation_interval(crads.a, crads.b, 0, match_max_sequence_separation, true) && !crads.contains(CRAD::solvent()))
+ {
+ result[crads]=value;
+ }
+ else
+ {
+ const CRAD* crads_components[2]={&crads.a, &crads.b};
+ for(int i=0;i<2;i++)
+ {
+ const CRAD& crad=(*(crads_components[i]));
+ if(crad!=CRAD::solvent())
+ {
+ ContactValue& solvent_value=result[CRADsPair(crad, CRAD::solvent())];
+ solvent_value.area+=value.area;
+ solvent_value.dist=std::max(solvent_value.dist, value.dist);
+ }
+ }
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map(result, std::cout);
+}
diff --git a/src/mode_query_contacts_solvation_values.cpp b/src/mode_query_contacts_solvation_values.cpp
new file mode 100644
index 0000000..d438faf
--- /dev/null
+++ b/src/mode_query_contacts_solvation_values.cpp
@@ -0,0 +1,55 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+}
+
+void query_contacts_solvation_values(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of model contacts (line format: 'annotation1 annotation2 area')");
+ pohw.describe_io("stdout", false, true, "list of solvation values (line format: 'annotation sas_area non_sas_area')");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const std::map<CRADsPair, double> map_of_contacts=auxiliaries::IOUtilities().read_lines_to_map< std::map<CRADsPair, double> >(std::cin);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No contacts input.");
+ }
+
+ std::map<CRAD, std::pair<double, double> > map_crad_to_solvation;
+
+ for(std::map<CRADsPair, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first;
+ const double area=it->second;
+ if(crads.a!=CRAD::solvent() && crads.b==CRAD::solvent())
+ {
+ map_crad_to_solvation[crads.a].first+=area;
+ }
+ else if(crads.a==CRAD::solvent() && crads.b!=CRAD::solvent())
+ {
+ map_crad_to_solvation[crads.b].first+=area;
+ }
+ else if(crads.a!=CRAD::solvent() && crads.b!=CRAD::solvent())
+ {
+ map_crad_to_solvation[crads.a].second+=area;
+ map_crad_to_solvation[crads.b].second+=area;
+ }
+ }
+
+ for(std::map<CRAD, std::pair<double, double> >::const_iterator it=map_crad_to_solvation.begin();it!=map_crad_to_solvation.end();++it)
+ {
+ std::cout << it->first << " " << it->second.first << " " << it->second.second << "\n";
+ }
+}
diff --git a/src/mode_rotational_optimization_demo.cpp b/src/mode_rotational_optimization_demo.cpp
new file mode 100644
index 0000000..1620831
--- /dev/null
+++ b/src/mode_rotational_optimization_demo.cpp
@@ -0,0 +1,55 @@
+#include "apollota/subdivided_icosahedron.h"
+
+#include "auxiliaries/program_options_handler.h"
+
+namespace
+{
+
+}
+
+void rotational_optimization_demo(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "x y z");
+ pohw.describe_io("stdout", false, true, "log");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ apollota::SimplePoint goal;
+ std::cin >> goal.x >> goal.y >> goal.z;
+ const double goal_length=goal.module();
+
+ std::cout << "goal " << 0.0 << " " << goal.x << " " << goal.y << " " << goal.z << std::endl;
+
+ apollota::SubdividedIcosahedron sih(2);
+ sih.fit_into_sphere(apollota::SimplePoint(0, 0, 0), 1);
+ std::size_t min_dist_id=0;
+ double min_dist=0.0;
+ int number_of_checks=0;
+ while(number_of_checks==0 || min_dist>0.000001)
+ {
+ std::size_t start_id=0;
+ if(number_of_checks>0)
+ {
+ start_id=sih.vertices().size();
+ sih.grow(min_dist_id, true);
+ }
+ for(std::size_t i=start_id;i<sih.vertices().size();i++)
+ {
+ const double dist=apollota::distance_from_point_to_point(sih.vertices()[i]*goal_length, goal);
+ if(number_of_checks==0 || dist<min_dist)
+ {
+ min_dist_id=i;
+ min_dist=dist;
+ }
+ number_of_checks++;
+ }
+ const apollota::SimplePoint result=sih.vertices()[min_dist_id]*goal_length;
+ std::cout << "result " << min_dist << " " << result.x << " " << result.y << " " << result.z << " edge " << sih.calc_max_edge_length() << std::endl;
+ }
+
+ std::cout << "checks " << number_of_checks << std::endl;
+}
diff --git a/src/mode_score_contacts_energy.cpp b/src/mode_score_contacts_energy.cpp
new file mode 100644
index 0000000..3e969c2
--- /dev/null
+++ b/src/mode_score_contacts_energy.cpp
@@ -0,0 +1,71 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/contacts_scoring_utilities.h"
+
+void score_contacts_energy(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2 conditions area')");
+ pohw.describe_io("stdout", false, true, "global scores");
+
+ const std::string potential_file=poh.argument<std::string>(pohw.describe_option("--potential-file", "string", "file path to input potential values", true), "");
+ const int ignorable_max_seq_sep=poh.argument<int>(pohw.describe_option("--ignorable-max-seq-sep", "number", "maximum residue sequence separation for ignorable contacts"), 1);
+ const std::string inter_atom_scores_file=poh.argument<std::string>(pohw.describe_option("--inter-atom-scores-file", "string", "file path to output inter-atom scores"), "");
+ const std::string atom_scores_file=poh.argument<std::string>(pohw.describe_option("--atom-scores-file", "string", "file path to output atom scores"), "");
+ const int depth=poh.argument<int>(pohw.describe_option("--depth", "number", "neighborhood normalization depth"), 2);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const std::map<InteractionName, double> map_of_contacts=auxiliaries::IOUtilities().read_lines_to_map< std::map<InteractionName, double> >(std::cin);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No contacts input.");
+ }
+
+ const std::map<InteractionName, double> map_of_potential_values=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<InteractionName, double> >(potential_file);
+ if(map_of_potential_values.empty())
+ {
+ throw std::runtime_error("No potential values input.");
+ }
+
+ std::map<CRADsPair, EnergyDescriptor> inter_atom_energy_descriptors;
+ {
+ for(std::map<InteractionName, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first.crads;
+ EnergyDescriptor& ed=inter_atom_energy_descriptors[crads];
+ if(!CRAD::match_with_sequence_separation_interval(crads.a, crads.b, 0, ignorable_max_seq_sep, false) && !check_crads_pair_for_peptide_bond(crads))
+ {
+ ed.total_area=(it->second);
+ ed.contacts_count=1;
+ std::map<InteractionName, double>::const_iterator potential_value_it=
+ map_of_potential_values.find(InteractionName(generalize_crads_pair(crads), it->first.tag));
+ if(potential_value_it!=map_of_potential_values.end())
+ {
+ ed.energy=ed.total_area*(potential_value_it->second);
+ }
+ else
+ {
+ ed.strange_area=ed.total_area;
+ }
+ }
+ }
+ auxiliaries::IOUtilities().write_map_to_file(inter_atom_energy_descriptors, inter_atom_scores_file);
+ }
+
+ const std::map<CRAD, EnergyDescriptor> atom_energy_descriptors=auxiliaries::ChainResidueAtomDescriptorsGraphOperations::accumulate_mapped_values_by_graph_neighbors(inter_atom_energy_descriptors, depth);
+ auxiliaries::IOUtilities().write_map_to_file(atom_energy_descriptors, atom_scores_file);
+
+ {
+ EnergyDescriptor global_ed;
+ for(std::map< CRADsPair, EnergyDescriptor >::const_iterator it=inter_atom_energy_descriptors.begin();it!=inter_atom_energy_descriptors.end();++it)
+ {
+ global_ed.add(it->second);
+ }
+ std::cout << "global " << global_ed << "\n";
+ }
+}
diff --git a/src/mode_score_contacts_energy_stats.cpp b/src/mode_score_contacts_energy_stats.cpp
new file mode 100644
index 0000000..b317c47
--- /dev/null
+++ b/src/mode_score_contacts_energy_stats.cpp
@@ -0,0 +1,49 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/contacts_scoring_utilities.h"
+#include "modescommon/statistics_utilities.h"
+
+namespace
+{
+
+inline bool read_energy_descriptors_and_accumulate_to_map_of_value_stats(std::istream& input, std::map<CRAD, ValueStat>& map_of_value_stats)
+{
+ CRAD crad;
+ EnergyDescriptor ed;
+ input >> crad >> ed;
+ if(!input.fail())
+ {
+ if(ed.total_area>0.0)
+ {
+ map_of_value_stats[generalize_crad(crad)].add(ed.energy/ed.total_area);
+ }
+ return true;
+ }
+ return false;
+}
+
+}
+
+void score_contacts_energy_stats(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of atom energy descriptors");
+ pohw.describe_io("stdout", false, true, "list of normalized energy mean and sd values per atom type");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::map<CRAD, ValueStat> map_of_value_stats;
+ auxiliaries::IOUtilities().read_lines_to_container(std::cin, read_energy_descriptors_and_accumulate_to_map_of_value_stats, map_of_value_stats);
+
+ std::map<CRAD, NormalDistributionParameters> means_and_sds;
+ for(std::map<CRAD, ValueStat>::const_iterator it=map_of_value_stats.begin();it!=map_of_value_stats.end();++it)
+ {
+ means_and_sds[it->first]=NormalDistributionParameters(it->second.mean(), it->second.sd());
+ }
+
+ auxiliaries::IOUtilities().write_map(means_and_sds, std::cout);
+}
diff --git a/src/mode_score_contacts_global_energy_by_cuts.cpp b/src/mode_score_contacts_global_energy_by_cuts.cpp
new file mode 100644
index 0000000..df0183f
--- /dev/null
+++ b/src/mode_score_contacts_global_energy_by_cuts.cpp
@@ -0,0 +1,214 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/contacts_scoring_utilities.h"
+#include "modescommon/sequence_utilities.h"
+
+namespace
+{
+
+std::vector<CRAD> collect_sequence_from_contacts(const std::map<InteractionName, double>& map_of_contacts)
+{
+ std::set<CRAD> set_of_residues;
+ for(std::map<InteractionName, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first.crads;
+ if(crads.a!=CRAD::solvent())
+ {
+ set_of_residues.insert(crads.a.without_atom());
+ }
+ if(crads.b!=CRAD::solvent())
+ {
+ set_of_residues.insert(crads.b.without_atom());
+ }
+ }
+ return std::vector<CRAD>(set_of_residues.begin(), set_of_residues.end());
+}
+
+std::set<CRAD> collect_head_and_tail_of_sequence(const std::vector<CRAD>& sequence, const int cut_from_start, const int cut_from_end)
+{
+ std::set<CRAD> result;
+ if(!sequence.empty())
+ {
+ for(std::size_t i=0;i<sequence.size();i++)
+ {
+ if(sequence[i].resSeq<(sequence.front().resSeq+cut_from_start) || sequence[i].resSeq>(sequence.back().resSeq-cut_from_end))
+ {
+ result.insert(sequence[i]);
+ }
+ }
+ }
+ return result;
+}
+
+std::string get_sequence_string_cut_out(const std::vector<CRAD>& sequence, const int cut_from_start, const int cut_from_end)
+{
+ std::vector<CRAD> inner_sequence;
+ std::set<CRAD> forbidden_residues=collect_head_and_tail_of_sequence(sequence, cut_from_start, cut_from_end);
+ for(std::size_t i=0;i<sequence.size();i++)
+ {
+ if(forbidden_residues.count(sequence[i])==0)
+ {
+ inner_sequence.push_back(sequence[i]);
+ }
+ }
+ return SequenceUtilities::convert_residue_sequence_container_to_string(inner_sequence);
+}
+
+std::map<InteractionName, double> exclude_residues_from_contacts(const std::map<InteractionName, double>& map_of_contacts, const std::set<CRAD>& exclusion_set, const double solvent_expansion)
+{
+ std::map<InteractionName, double> result;
+ for(std::map<InteractionName, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first.crads;
+ const bool exclude_a=(exclusion_set.count(crads.a.without_atom())>0);
+ const bool exclude_b=(exclusion_set.count(crads.b.without_atom())>0);
+ if(!exclude_a && !exclude_b)
+ {
+ result[it->first]=it->second;
+ }
+ else if(!exclude_a && exclude_b && crads.a!=CRAD::solvent())
+ {
+ result[InteractionName(CRADsPair(crads.a, CRAD::solvent()), ".")]+=(it->second*solvent_expansion);
+ }
+ else if(!exclude_b && exclude_a && crads.b!=CRAD::solvent())
+ {
+ result[InteractionName(CRADsPair(crads.b, CRAD::solvent()), ".")]+=(it->second*solvent_expansion);
+ }
+ }
+ return result;
+}
+
+EnergyDescriptor calculate_global_energy(const std::map<InteractionName, double>& map_of_potential_values, const int ignorable_max_seq_sep, const std::map<InteractionName, double>& map_of_contacts)
+{
+ std::map<CRADsPair, EnergyDescriptor> inter_atom_energy_descriptors;
+ for(std::map<InteractionName, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first.crads;
+ EnergyDescriptor& ed=inter_atom_energy_descriptors[crads];
+ if(!CRAD::match_with_sequence_separation_interval(crads.a, crads.b, 0, ignorable_max_seq_sep, false) && !check_crads_pair_for_peptide_bond(crads))
+ {
+ ed.total_area=(it->second);
+ ed.contacts_count=1;
+ std::map<InteractionName, double>::const_iterator potential_value_it=
+ map_of_potential_values.find(InteractionName(generalize_crads_pair(crads), it->first.tag));
+ if(potential_value_it!=map_of_potential_values.end())
+ {
+ ed.energy=ed.total_area*(potential_value_it->second);
+ }
+ else
+ {
+ ed.strange_area=ed.total_area;
+ }
+ }
+ }
+ EnergyDescriptor global_ed;
+ for(std::map< CRADsPair, EnergyDescriptor >::const_iterator it=inter_atom_energy_descriptors.begin();it!=inter_atom_energy_descriptors.end();++it)
+ {
+ global_ed.add(it->second);
+ }
+ return global_ed;
+}
+
+template<typename Set, typename Element>
+void update_limited_set(Set& set, const unsigned long limit, const Element& element)
+{
+ set.insert(element);
+ if(limit>0 && set.size()>limit)
+ {
+ typename Set::iterator it=set.end();
+ --it;
+ set.erase(it);
+ }
+}
+
+}
+
+void score_contacts_global_energy_by_cuts(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2 conditions area')");
+ pohw.describe_io("stdout", false, true, "global scores");
+
+ const std::string potential_file=poh.argument<std::string>(pohw.describe_option("--potential-file", "string", "file path to input potential values", true), "");
+ const int ignorable_max_seq_sep=poh.argument<int>(pohw.describe_option("--ignorable-max-seq-sep", "number", "maximum residue sequence separation for ignorable contacts"), 1);
+ const int cut_step=std::max(1, poh.argument<int>(pohw.describe_option("--cut-step", "number", "big cut length increasing step"), 10));
+ const unsigned long limit_results=poh.argument<unsigned long>(pohw.describe_option("--limit-results", "number", "maximum number of results to print"), 1);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const std::map<InteractionName, double> map_of_contacts=auxiliaries::IOUtilities().read_lines_to_map< std::map<InteractionName, double> >(std::cin);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No contacts input.");
+ }
+
+ const std::map<InteractionName, double> map_of_potential_values=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<InteractionName, double> >(potential_file);
+ if(map_of_potential_values.empty())
+ {
+ throw std::runtime_error("No potential values input.");
+ }
+
+ const std::vector<CRAD> sequence=collect_sequence_from_contacts(map_of_contacts);
+ if(sequence.empty())
+ {
+ throw std::runtime_error("Empty sequence.");
+ }
+
+ const int sequence_length=(sequence.back().resSeq-sequence.front().resSeq+1);
+ const int min_length_after_cuts=std::max(10, sequence_length/5);
+
+ std::set< std::pair<double, std::pair<int, int> > > result_set;
+
+ for(int cut_from_start=0;cut_from_start<sequence_length;cut_from_start+=cut_step)
+ {
+ for(int cut_from_end=0;cut_from_end<sequence_length;cut_from_end+=cut_step)
+ {
+ if((cut_from_start+cut_from_end+min_length_after_cuts)<sequence_length)
+ {
+ const std::map<InteractionName, double> reduced_map_of_contacts=exclude_residues_from_contacts(map_of_contacts, collect_head_and_tail_of_sequence(sequence, cut_from_start, cut_from_end), 3.0);
+ if(!reduced_map_of_contacts.empty())
+ {
+ const EnergyDescriptor global_ed=calculate_global_energy(map_of_potential_values, ignorable_max_seq_sep, reduced_map_of_contacts);
+ if(global_ed.total_area>0)
+ {
+ update_limited_set(result_set, limit_results, std::make_pair((global_ed.energy/global_ed.total_area), std::make_pair(cut_from_start, cut_from_end)));
+ }
+ }
+ }
+ }
+ }
+
+ if(cut_step>1 && !result_set.empty())
+ {
+ int best_so_far_cut_from_start=result_set.begin()->second.first;
+ int best_so_far_cut_from_end=result_set.begin()->second.second;
+ for(int cut_from_start=std::max(0, best_so_far_cut_from_start-cut_step);cut_from_start<std::min(sequence_length, best_so_far_cut_from_start+cut_step);cut_from_start++)
+ {
+ for(int cut_from_end=std::max(0, best_so_far_cut_from_end-cut_step);cut_from_end<std::min(sequence_length, best_so_far_cut_from_end+cut_step);cut_from_end++)
+ {
+ if((cut_from_start+cut_from_end+min_length_after_cuts)<sequence_length)
+ {
+ const std::map<InteractionName, double> reduced_map_of_contacts=exclude_residues_from_contacts(map_of_contacts, collect_head_and_tail_of_sequence(sequence, cut_from_start, cut_from_end), 3.0);
+ if(!reduced_map_of_contacts.empty())
+ {
+ const EnergyDescriptor global_ed=calculate_global_energy(map_of_potential_values, ignorable_max_seq_sep, reduced_map_of_contacts);
+ if(global_ed.total_area>0)
+ {
+ update_limited_set(result_set, limit_results, std::make_pair((global_ed.energy/global_ed.total_area), std::make_pair(cut_from_start, cut_from_end)));
+ }
+ }
+ }
+ }
+ }
+ }
+
+ for(std::set< std::pair<double, std::pair<int, int> > >::const_iterator it=result_set.begin();it!=result_set.end();++it)
+ {
+ std::cout << it->second.first << " " << it->second.second << " " << it->first << " ";
+ std::cout << get_sequence_string_cut_out(sequence, it->second.first, it->second.second) << "\n";
+ }
+}
diff --git a/src/mode_score_contacts_potential.cpp b/src/mode_score_contacts_potential.cpp
new file mode 100644
index 0000000..6c90ad8
--- /dev/null
+++ b/src/mode_score_contacts_potential.cpp
@@ -0,0 +1,322 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/contacts_scoring_utilities.h"
+
+namespace
+{
+
+inline bool read_and_accumulate_to_map_of_interactions_areas(std::istream& input, std::map<InteractionName, double>& map_of_interactions_areas)
+{
+ InteractionName interaction;
+ double area;
+ input >> interaction >> area;
+ if(!input.fail())
+ {
+ map_of_interactions_areas[InteractionName(generalize_crads_pair(interaction.crads), interaction.tag)]+=area;
+ return true;
+ }
+ return false;
+}
+
+inline bool read_to_map_of_crads_pairs_stats(std::istream& input, std::map< CRADsPair, std::pair<double, double> >& map_of_crads_pairs_stats)
+{
+ CRAD a;
+ CRAD b;
+ double p1=0.0;
+ double p2=0.0;
+ input >> a >> b >> p1 >> p2;
+ if(!input.fail())
+ {
+ map_of_crads_pairs_stats[CRADsPair(a, b)]=std::make_pair(p1, p2);
+ return true;
+ }
+ return false;
+}
+
+inline CRAD simplify_crad(const CRAD& input_crad)
+{
+ if(input_crad==CRAD::solvent())
+ {
+ return input_crad;
+ }
+ else
+ {
+ return CRAD::any();
+ }
+}
+
+inline CRADsPair simplify_crads_pair(const CRADsPair& input_crads)
+{
+ return CRADsPair(simplify_crad(input_crads.a), simplify_crad(input_crads.b));
+}
+
+}
+
+void score_contacts_potential(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2 conditions area')");
+ pohw.describe_io("stdout", false, true, "line of contact type area summaries (line format: 'annotation1 annotation2 conditions area')");
+
+ const bool input_file_list=poh.contains_option(pohw.describe_option("--input-file-list", "", "flag to read file list from stdin"));
+ const std::string input_contributions=poh.argument<std::string>(pohw.describe_option("--input-contributions", "string", "file path to input contact types contributions"), "");
+ const std::string input_fixed_types=poh.argument<std::string>(pohw.describe_option("--input-fixed-types", "string", "file path to input fixed types"), "");
+ const std::string input_seq_pairs_stats=poh.argument<std::string>(pohw.describe_option("--input-seq-pairs-stats", "string", "file path to input sequence pairings statistics"), "");
+ const std::string potential_file=poh.argument<std::string>(pohw.describe_option("--potential-file", "string", "file path to output potential values"), "");
+ const std::string probabilities_file=poh.argument<std::string>(pohw.describe_option("--probabilities-file", "string", "file path to output observed and expected probabilities"), "");
+ const std::string single_areas_file=poh.argument<std::string>(pohw.describe_option("--single-areas-file", "string", "file path to output single type total areas"), "");
+ const std::string contributions_file=poh.argument<std::string>(pohw.describe_option("--contributions-file", "string", "file path to output contact types contributions"), "");
+ const double multiply_areas=poh.argument<double>(pohw.describe_option("--multiply-areas", "number", "coefficient to multiply output areas"), -1.0);
+ const std::string toggling_list=poh.argument<std::string>(pohw.describe_option("--toggling-list", "string", "list of toggling subtags"), "");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const std::set<std::string> toggling_subtags=(toggling_list.empty() ? std::set<std::string>() : auxiliaries::IOUtilities(';').read_string_lines_to_set< std::set<std::string> >(toggling_list));
+
+ std::map<InteractionName, double> map_of_interactions_total_areas;
+
+ if(input_file_list)
+ {
+ while(std::cin.good())
+ {
+ std::string file_path;
+ std::cin >> file_path;
+ auxiliaries::IOUtilities().read_file_lines_to_container(file_path, read_and_accumulate_to_map_of_interactions_areas, map_of_interactions_total_areas);
+ }
+ }
+ else
+ {
+ auxiliaries::IOUtilities().read_lines_to_container(std::cin, read_and_accumulate_to_map_of_interactions_areas, map_of_interactions_total_areas);
+ }
+
+ std::map<CRAD, double> map_of_crads_total_areas;
+ std::map< CRADsPair, std::set<std::string> > map_of_crads_possible_subtags;
+ std::map<InteractionName, double> map_of_subtags_total_areas;
+ double sum_of_solvent_areas=0.0;
+ double sum_of_nonsolvent_areas=0.0;
+
+ for(std::map<InteractionName, double>::const_iterator it=map_of_interactions_total_areas.begin();it!=map_of_interactions_total_areas.end();++it)
+ {
+ const InteractionName& interaction=it->first;
+ const double area=it->second;
+ map_of_crads_total_areas[interaction.crads.a]+=area;
+ map_of_crads_total_areas[interaction.crads.b]+=area;
+ if(interaction.crads.b==CRAD::solvent())
+ {
+ sum_of_solvent_areas+=area;
+ }
+ else
+ {
+ sum_of_nonsolvent_areas+=area;
+ const std::set<std::string> subtags=auxiliaries::IOUtilities(';').read_string_lines_to_set< std::set<std::string> >(interaction.tag);
+ map_of_crads_possible_subtags[interaction.crads].insert(subtags.begin(), subtags.end());
+ for(std::set<std::string>::const_iterator subtags_it=subtags.begin();subtags_it!=subtags.end();++subtags_it)
+ {
+ map_of_subtags_total_areas[InteractionName(simplify_crads_pair(interaction.crads), *subtags_it)]+=area;
+ }
+ }
+ }
+
+ const double sum_of_all_areas=(sum_of_solvent_areas+sum_of_nonsolvent_areas*2.0);
+ const double sum_of_contact_areas=(sum_of_solvent_areas+sum_of_nonsolvent_areas);
+
+ std::map<InteractionName, double> map_of_subtags_contributions;
+ if(!input_contributions.empty())
+ {
+ auxiliaries::IOUtilities().read_file_lines_to_map(input_contributions, map_of_subtags_contributions);
+ if(map_of_subtags_contributions.empty())
+ {
+ throw std::runtime_error("No valid contributions input.");
+ }
+ }
+ else
+ {
+ std::map<InteractionName, double> map_of_subtags_possible_areas;
+ for(std::map<InteractionName, double>::const_iterator it=map_of_interactions_total_areas.begin();it!=map_of_interactions_total_areas.end();++it)
+ {
+ const InteractionName& interaction=it->first;
+ const double area=it->second;
+ const std::set<std::string>& subtags=map_of_crads_possible_subtags[interaction.crads];
+ for(std::set<std::string>::const_iterator subtags_it=subtags.begin();subtags_it!=subtags.end();++subtags_it)
+ {
+ map_of_subtags_possible_areas[InteractionName(simplify_crads_pair(interaction.crads), *subtags_it)]+=area;
+ }
+ }
+
+ for(std::map<InteractionName, double>::const_iterator it=map_of_subtags_total_areas.begin();it!=map_of_subtags_total_areas.end();++it)
+ {
+ if(toggling_subtags.count(it->first.tag)>0)
+ {
+ map_of_subtags_contributions[it->first]=(it->second/map_of_subtags_possible_areas[it->first]);
+ }
+ else
+ {
+ map_of_subtags_contributions[it->first]=(it->second/sum_of_nonsolvent_areas);
+ }
+ }
+
+ map_of_subtags_contributions[InteractionName(CRADsPair(CRAD::any(), CRAD::solvent()), "solvent")]=(sum_of_solvent_areas/sum_of_contact_areas);
+ }
+
+ std::map< CRADsPair, std::pair<double, double> > seqsep_modifiers;
+ if(!input_seq_pairs_stats.empty())
+ {
+ std::map< CRADsPair, std::pair<double, double> > seq_pairs_stats;
+ auxiliaries::IOUtilities().read_file_lines_to_container(input_seq_pairs_stats, read_to_map_of_crads_pairs_stats, seq_pairs_stats);
+ if(!seq_pairs_stats.empty())
+ {
+ double sep1_contribution=0.0;
+ for(std::map<InteractionName, double>::const_iterator it=map_of_subtags_contributions.begin();it!=map_of_subtags_contributions.end();++it)
+ {
+ const InteractionName& interaction=it->first;
+ if(interaction.tag.find("sep1")!=std::string::npos)
+ {
+ sep1_contribution+=it->second;
+ }
+ }
+ for(std::map< CRADsPair, std::pair<double, double> >::const_iterator it=seq_pairs_stats.begin();it!=seq_pairs_stats.end();++it)
+ {
+ const double a=(it->second.first/it->second.second);
+ const double b=(1-a*sep1_contribution)/(1-sep1_contribution);
+ seqsep_modifiers[it->first]=std::make_pair(a, b);
+ }
+ }
+ }
+
+ const double solvent_contribution=map_of_subtags_contributions[InteractionName(CRADsPair(CRAD::any(), CRAD::solvent()), "solvent")];
+
+ std::map< InteractionName, std::pair<double, double> > result;
+ std::map< InteractionName, std::pair<double, double> > probabilities;
+ for(std::map<InteractionName, double>::const_iterator it=map_of_interactions_total_areas.begin();it!=map_of_interactions_total_areas.end();++it)
+ {
+ const InteractionName& interaction=it->first;
+ const double abc=it->second;
+ if(abc>0.0)
+ {
+ const double p_obs=(abc/sum_of_contact_areas);
+ double p_exp=0.0;
+ if(interaction.crads.b==CRAD::solvent())
+ {
+ p_exp=(map_of_crads_total_areas[interaction.crads.a]/sum_of_all_areas)*(solvent_contribution);
+ }
+ else
+ {
+ p_exp=(map_of_crads_total_areas[interaction.crads.a]/sum_of_all_areas)*(map_of_crads_total_areas[interaction.crads.b]/sum_of_all_areas)*(1.0-solvent_contribution)*(interaction.crads.a==interaction.crads.b ? 1.0 : 2.0);
+ const std::set<std::string> subtags=auxiliaries::IOUtilities(';').read_string_lines_to_set< std::set<std::string> >(interaction.tag);
+ for(std::set<std::string>::const_iterator subtags_it=subtags.begin();subtags_it!=subtags.end();++subtags_it)
+ {
+ p_exp*=map_of_subtags_contributions[InteractionName(simplify_crads_pair(interaction.crads), *subtags_it)];
+ }
+ for(std::set<std::string>::const_iterator toggling_subtags_it=toggling_subtags.begin();toggling_subtags_it!=toggling_subtags.end();++toggling_subtags_it)
+ {
+ if(map_of_crads_possible_subtags[interaction.crads].count(*toggling_subtags_it)>0 && subtags.count(*toggling_subtags_it)==0)
+ {
+ p_exp*=(1.0-map_of_subtags_contributions[InteractionName(simplify_crads_pair(interaction.crads), *toggling_subtags_it)]);
+ }
+ }
+ if(!seqsep_modifiers.empty() && interaction.tag.find("sep")!=std::string::npos)
+ {
+ std::map< CRADsPair, std::pair<double, double> >::const_iterator seqsep_modifiers_it=seqsep_modifiers.find(CRADsPair(interaction.crads.a.without_atom(), interaction.crads.b.without_atom()));
+ if(seqsep_modifiers_it!=seqsep_modifiers.end())
+ {
+ if(interaction.tag.find("sep1")!=std::string::npos)
+ {
+ p_exp*=seqsep_modifiers_it->second.first;
+ }
+ else
+ {
+ p_exp*=seqsep_modifiers_it->second.second;
+ }
+ }
+ }
+ }
+ if(p_exp>0.0)
+ {
+ result[interaction]=std::make_pair(log(p_exp/p_obs), abc);
+ probabilities[interaction]=std::make_pair(p_obs, p_exp);
+ }
+ }
+ }
+
+ if(!input_fixed_types.empty())
+ {
+ std::set<InteractionName> fixed_types;
+ auxiliaries::IOUtilities().read_file_lines_to_set(input_fixed_types, fixed_types);
+ if(fixed_types.empty())
+ {
+ throw std::runtime_error("No valid fixed types input.");
+ }
+
+ double max_potential_value=0.0;
+ for(std::map< InteractionName, std::pair<double, double> >::const_iterator it=result.begin();it!=result.end();++it)
+ {
+ max_potential_value=std::max(max_potential_value, it->second.first);
+ }
+
+ std::map< InteractionName, std::pair<double, double> > fixed_result;
+ for(std::set<InteractionName>::const_iterator it=fixed_types.begin();it!=fixed_types.end();++it)
+ {
+ const InteractionName& iname=(*it);
+ std::map< InteractionName, std::pair<double, double> >::const_iterator result_it=result.find(iname);
+ fixed_result[iname]=(result_it!=result.end() ? result_it->second : std::make_pair(max_potential_value, 0.0));
+ }
+ result=fixed_result;
+ }
+
+ if(!potential_file.empty())
+ {
+ std::ofstream foutput(potential_file.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ for(std::map< InteractionName, std::pair<double, double> >::const_iterator it=result.begin();it!=result.end();++it)
+ {
+ const InteractionName& interaction=it->first;
+ foutput << interaction << " " << it->second.first << "\n";
+ }
+ }
+ }
+
+ if(!probabilities_file.empty())
+ {
+ std::ofstream foutput(probabilities_file.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ double sum_obs_nonsolvent=0.0;
+ double sum_obs_solvent=0.0;
+ double sum_exp_nonsolvent=0.0;
+ double sum_exp_solvent=0.0;
+ for(std::map< InteractionName, std::pair<double, double> >::const_iterator it=probabilities.begin();it!=probabilities.end();++it)
+ {
+ const InteractionName& interaction=it->first;
+ foutput << interaction << " " << it->second.first << " " << it->second.second << "\n";
+ if(interaction.crads.b==CRAD::solvent())
+ {
+ sum_obs_solvent+=it->second.first;
+ sum_exp_solvent+=it->second.second;
+ }
+ else
+ {
+ sum_obs_nonsolvent+=it->second.first;
+ sum_exp_nonsolvent+=it->second.second;
+ }
+ }
+ foutput << InteractionName(CRADsPair(CRAD("nonsolvent"), CRAD("nonsolvent")), ".") << " " << sum_obs_nonsolvent << " " << sum_exp_nonsolvent << "\n";
+ foutput << InteractionName(CRADsPair(CRAD("nonsolvent"), CRAD::solvent()), ".") << " " << sum_obs_solvent << " " << sum_exp_solvent << "\n";
+ foutput << InteractionName(CRADsPair(CRAD::any(), CRAD::any()), ".") << " " << (sum_obs_nonsolvent+sum_obs_solvent) << " " << (sum_exp_nonsolvent+sum_exp_solvent) << "\n";
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map_to_file(map_of_crads_total_areas, single_areas_file);
+
+ auxiliaries::IOUtilities().write_map_to_file(map_of_subtags_contributions, contributions_file);
+
+ for(std::map< InteractionName, std::pair<double, double> >::const_iterator it=result.begin();it!=result.end();++it)
+ {
+ const InteractionName& interaction=it->first;
+ std::cout << interaction << " " << (multiply_areas>0.0 ? (it->second.second*multiply_areas) : it->second.second) << "\n";
+ }
+}
diff --git a/src/mode_score_contacts_potentials_stats.cpp b/src/mode_score_contacts_potentials_stats.cpp
new file mode 100644
index 0000000..f2b36ff
--- /dev/null
+++ b/src/mode_score_contacts_potentials_stats.cpp
@@ -0,0 +1,37 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/contacts_scoring_utilities.h"
+#include "modescommon/statistics_utilities.h"
+
+void score_contacts_potentials_stats(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of potential files");
+ pohw.describe_io("stdout", false, true, "list of normalized energy mean and sd values per interaction type");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::map<InteractionName, ValueStat> map_of_value_stats;
+ while(std::cin.good())
+ {
+ std::string potential_file;
+ std::cin >> potential_file;
+ const std::map<InteractionName, double> map_of_potential_values=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<InteractionName, double> >(potential_file);
+ for(std::map<InteractionName, double>::const_iterator it=map_of_potential_values.begin();it!=map_of_potential_values.end();++it)
+ {
+ map_of_value_stats[it->first].add(it->second);
+ }
+ }
+
+ std::map<InteractionName, NormalDistributionParameters> means_and_sds;
+ for(std::map<InteractionName, ValueStat>::const_iterator it=map_of_value_stats.begin();it!=map_of_value_stats.end();++it)
+ {
+ means_and_sds[it->first]=NormalDistributionParameters(it->second.mean(), it->second.sd());
+ }
+
+ auxiliaries::IOUtilities().write_map(means_and_sds, std::cout);
+}
diff --git a/src/mode_score_contacts_quality.cpp b/src/mode_score_contacts_quality.cpp
new file mode 100644
index 0000000..bc876bb
--- /dev/null
+++ b/src/mode_score_contacts_quality.cpp
@@ -0,0 +1,129 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/contacts_scoring_utilities.h"
+#include "modescommon/statistics_utilities.h"
+
+namespace
+{
+
+std::map<CRAD, double> average_atom_scores_by_residue(const std::map<CRAD, double>& atom_scores)
+{
+ std::map<CRAD, std::pair<int, double> > summed_scores;
+ for(std::map<CRAD, double>::const_iterator it=atom_scores.begin();it!=atom_scores.end();++it)
+ {
+ std::pair<int, double>& value=summed_scores[it->first.without_atom()];
+ value.first++;
+ value.second+=it->second;
+ }
+ std::map<CRAD, double> average_scores;
+ for(std::map<CRAD, std::pair<int, double> >::const_iterator it=summed_scores.begin();it!=summed_scores.end();++it)
+ {
+ const std::pair<int, double>& value=it->second;
+ average_scores[it->first]=((value.first>0) ? (value.second/static_cast<double>(value.first)) : 0.0);
+ }
+ return average_scores;
+}
+
+}
+
+void score_contacts_quality(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of atom energy descriptors");
+ pohw.describe_io("stdout", false, true, "weighted average local score");
+
+ const double default_mean=poh.argument<double>(pohw.describe_option("--default-mean", "number", "default mean parameter"), 0.4);
+ const double default_sd=poh.argument<double>(pohw.describe_option("--default-sd", "number", "default standard deviation parameter"), 0.3);
+ const std::string mean_and_sds_file=poh.argument<std::string>(pohw.describe_option("--means-and-sds-file", "string", "file path to input atomic mean and sd parameters"), "");
+ const double mean_shift=poh.argument<double>(pohw.describe_option("--mean-shift", "number", "mean shift in standard deviations"), 0.0);
+ const std::string external_weights_file=poh.argument<std::string>(pohw.describe_option("--external-weights-file", "string", "file path to input external weights for global scoring"), "");
+ const std::vector<unsigned int> smoothing_windows=poh.argument_vector<unsigned int>(pohw.describe_option("--smoothing-window", "number", "window to smooth residue quality scores along sequence"), ',', std::vector<unsigned int>(1, 0));
+ const std::string atom_scores_file=poh.argument<std::string>(pohw.describe_option("--atom-scores-file", "string", "file path to output atom scores"), "");
+ const std::string residue_scores_file=poh.argument<std::string>(pohw.describe_option("--residue-scores-file", "string", "file path to output residue scores"), "");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const std::map<CRAD, EnergyDescriptor> atom_energy_descriptors=auxiliaries::IOUtilities().read_lines_to_map< std::map<CRAD, EnergyDescriptor> >(std::cin);
+ if(atom_energy_descriptors.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ const std::map<CRAD, NormalDistributionParameters> means_and_sds=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRAD, NormalDistributionParameters> >(mean_and_sds_file);
+
+ const std::map<CRAD, double> external_weights=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRAD, double> >(external_weights_file);
+
+ std::map<CRAD, double> atom_quality_scores;
+ double sum_of_weighted_scores=0.0;
+ double sum_of_weights=0.0;
+ for(std::map<CRAD, EnergyDescriptor>::const_iterator it=atom_energy_descriptors.begin();it!=atom_energy_descriptors.end();++it)
+ {
+ const CRAD& crad=it->first;
+ const EnergyDescriptor& ed=it->second;
+ if(ed.total_area>0.0)
+ {
+ const double actuality_score=(1.0-(ed.strange_area/ed.total_area));
+ const double normalized_energy=(ed.energy/ed.total_area);
+ std::map<CRAD, NormalDistributionParameters>::const_iterator mean_and_sd_it=means_and_sds.find(generalize_crad(crad));
+ const double mean=(mean_and_sd_it!=means_and_sds.end() ? mean_and_sd_it->second.mean : default_mean);
+ const double sd=(mean_and_sd_it!=means_and_sds.end() ? mean_and_sd_it->second.sd : default_sd);
+ const double adjusted_normalized_energy=((normalized_energy-mean)/sd);
+ const double energy_score=(1.0-(0.5*(1.0+erf((adjusted_normalized_energy-mean_shift)/sqrt(2.0)))));
+ const double unweighted_quality_score=(energy_score*actuality_score);
+ atom_quality_scores[crad]=unweighted_quality_score;
+ {
+ std::map<CRAD, double>::const_iterator external_weights_it=external_weights.find(crad);
+ const double external_weight=(external_weights_it!=external_weights.end() ? external_weights_it->second : 1.0);
+ sum_of_weighted_scores+=(unweighted_quality_score*external_weight);
+ sum_of_weights+=external_weight;
+ }
+ }
+ else
+ {
+ atom_quality_scores[crad]=0.0;
+ sum_of_weights+=1.0;
+ }
+ }
+ auxiliaries::IOUtilities().write_map_to_file(atom_quality_scores, atom_scores_file);
+
+ if(!residue_scores_file.empty())
+ {
+ const std::map<CRAD, double> raw_residue_quality_scores=average_atom_scores_by_residue(atom_quality_scores);
+ if(smoothing_windows.empty() || (smoothing_windows.size()==1 && smoothing_windows.front()==0))
+ {
+ auxiliaries::IOUtilities().write_map_to_file(raw_residue_quality_scores, residue_scores_file);
+ }
+ else if(smoothing_windows.size()==1)
+ {
+ auxiliaries::IOUtilities().write_map_to_file(auxiliaries::ChainResidueAtomDescriptorsSequenceOperations::smooth_residue_scores_along_sequence(raw_residue_quality_scores, smoothing_windows.front()), residue_scores_file);
+ }
+ else
+ {
+ std::ofstream foutput(residue_scores_file.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ std::vector< std::map<CRAD, double> > residue_quality_scores(smoothing_windows.size());
+ for(std::size_t i=0;i<smoothing_windows.size();i++)
+ {
+ residue_quality_scores[i]=auxiliaries::ChainResidueAtomDescriptorsSequenceOperations::smooth_residue_scores_along_sequence(raw_residue_quality_scores, smoothing_windows[i]);
+ }
+ const std::map<CRAD, double>& axis=residue_quality_scores.front();
+ for(std::map<CRAD, double>::const_iterator it=axis.begin();it!=axis.end();++it)
+ {
+ foutput << (it->first);
+ for(std::size_t i=0;i<residue_quality_scores.size();i++)
+ {
+ foutput << " " << residue_quality_scores[i][it->first];
+ }
+ foutput << "\n";
+ }
+ }
+ }
+ }
+
+ std::cout << (sum_of_weights>0.0 ? sum_of_weighted_scores/sum_of_weights : 0.0) << "\n";
+}
diff --git a/src/mode_score_scores.cpp b/src/mode_score_scores.cpp
new file mode 100644
index 0000000..7cf80ec
--- /dev/null
+++ b/src/mode_score_scores.cpp
@@ -0,0 +1,267 @@
+#include <iostream>
+#include <stdexcept>
+#include <set>
+#include <cmath>
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/generic_utilities.h"
+
+namespace
+{
+
+typedef std::set< std::pair<std::string, std::string> > SetOfStringsPairs;
+typedef std::map<std::string, double> MapOfNamedValues;
+typedef std::map<std::string, std::pair<double, double> > MapOfNamedValuesPairs;
+
+struct ClassificationResults
+{
+ unsigned long TP;
+ unsigned long TN;
+ unsigned long FP;
+ unsigned long FN;
+
+ ClassificationResults() : TP(0), TN(0), FP(0), FN(0)
+ {
+ }
+
+ void add(const ClassificationResults& v)
+ {
+ TP+=v.TP;
+ TN+=v.TN;
+ FP+=v.FP;
+ FN+=v.FN;
+ }
+
+ void add(const bool reference_outcome, const bool testable_outcome)
+ {
+ if(reference_outcome)
+ {
+ if(testable_outcome)
+ {
+ TP++;
+ }
+ else
+ {
+ FN++;
+ }
+ }
+ else
+ {
+ if(testable_outcome)
+ {
+ FP++;
+ }
+ else
+ {
+ TN++;
+ }
+ }
+ }
+
+ double TPR() const
+ {
+ return ((TP+FN)>0 ? static_cast<double>(TP)/static_cast<double>(TP+FN) : 0.0);
+ }
+
+ double FPR() const
+ {
+ return ((FP+TN)>0 ? static_cast<double>(FP)/static_cast<double>(FP+TN) : 0.0);
+ }
+
+ double precision() const
+ {
+ return ((TP+FP)>0 ? static_cast<double>(TP)/static_cast<double>(TP+FP) : 1.0);
+ }
+
+ double recall() const
+ {
+ return TPR();
+ }
+
+ double accuracy() const
+ {
+ unsigned long d=(TP+TN+FP+FN);
+ return (d>0 ? static_cast<double>(TP+TN)/static_cast<double>(d) : 0.0);
+ }
+
+ double MCC() const
+ {
+ unsigned long c=((TP*TN)-(FP*FN));
+ unsigned long d1=(TP+FP);
+ unsigned long d2=(TP+FN);
+ unsigned long d3=(TN+FP);
+ unsigned long d4=(TN+FN);
+ if(d1>0 && d2>0 && d3>0 && d4>0)
+ {
+ const double ratio=(c*(1.0/sqrt(d1))*(1.0/sqrt(d2))*(1.0/sqrt(d3))*(1.0/sqrt(d4)));
+ return (fabs(ratio)<=1.0 ? ratio : 0.0);
+ }
+ else
+ {
+ return 0.0;
+ }
+ }
+};
+
+inline std::ostream& operator<<(std::ostream& output, const ClassificationResults& v)
+{
+ output << v.TP << " " << v.TN << " " << v.FP << " " << v.FN;
+ return output;
+}
+
+ClassificationResults calc_classification_results(const MapOfNamedValuesPairs& map_of_pairs, const double reference_threshold, const double testable_threshold)
+{
+ ClassificationResults result;
+ for(MapOfNamedValuesPairs::const_iterator it=map_of_pairs.begin();it!=map_of_pairs.end();++it)
+ {
+ const bool reference_outcome=(it->second.first>reference_threshold);
+ const bool testable_outcome=(it->second.second>testable_threshold);
+ result.add(reference_outcome, testable_outcome);
+ }
+ return result;
+}
+
+void update_classification_results_map(
+ const MapOfNamedValuesPairs& map_of_pairs,
+ const double reference_threshold,
+ const double testable_step,
+ std::map<double, ClassificationResults>& classification_results_map)
+{
+ std::pair<double, double> min_max_testable_value(0.0, 0.0);
+ for(MapOfNamedValuesPairs::const_iterator it=map_of_pairs.begin();it!=map_of_pairs.end();++it)
+ {
+ if(it==map_of_pairs.begin() || it->second.second<min_max_testable_value.first)
+ {
+ min_max_testable_value.first=it->second.second;
+ }
+ if(it==map_of_pairs.begin() || it->second.second>min_max_testable_value.second)
+ {
+ min_max_testable_value.second=it->second.second;
+ }
+ }
+ std::pair<long, long> min_max_integers(static_cast<long>(floor(min_max_testable_value.first/testable_step)), static_cast<long>(ceil(min_max_testable_value.second/testable_step)));
+ for(long i=min_max_integers.first;i<=min_max_integers.second;i++)
+ {
+ const double testable_threshold=static_cast<double>(i)*testable_step;
+ classification_results_map[testable_threshold].add(calc_classification_results(map_of_pairs, reference_threshold, testable_threshold));
+ }
+}
+
+std::set< std::pair<double, double> > calc_ROC_curve_coordinates(const std::map<double, ClassificationResults>& classification_results_map)
+{
+ std::set< std::pair<double, double> > result;
+ for(std::map<double, ClassificationResults>::const_iterator it=classification_results_map.begin();it!=classification_results_map.end();++it)
+ {
+ result.insert(result.end(), std::make_pair(it->second.FPR(), it->second.TPR()));
+ }
+ return result;
+}
+
+std::set< std::pair<double, double> > calc_PR_curve_coordinates(const std::map<double, ClassificationResults>& classification_results_map)
+{
+ std::set< std::pair<double, double> > result;
+ for(std::map<double, ClassificationResults>::const_iterator it=classification_results_map.begin();it!=classification_results_map.end();++it)
+ {
+ result.insert(result.end(), std::make_pair(it->second.recall(), it->second.precision()));
+ }
+ return result;
+}
+
+double calc_AUC(const std::set< std::pair<double, double> >& curve)
+{
+ double result=0.0;
+ std::set< std::pair<double, double> >::const_iterator it=curve.begin();
+ std::set< std::pair<double, double> >::const_iterator next_it=it;
+ ++next_it;
+ while(next_it!=curve.end())
+ {
+ result+=((next_it->first)-(it->first))*((next_it->second)+(it->second))*0.5;
+ ++it;
+ ++next_it;
+ }
+ return result;
+}
+
+std::pair<double, double> calc_best_accuracy(const std::map<double, ClassificationResults>& classification_results_map)
+{
+ std::pair<double, double> result(0.0, 0.0);
+ for(std::map<double, ClassificationResults>::const_iterator it=classification_results_map.begin();it!=classification_results_map.end();++it)
+ {
+ if(it==classification_results_map.begin() || it->second.accuracy()>result.second)
+ {
+ result=std::make_pair(it->first, it->second.accuracy());
+ }
+ }
+ return result;
+}
+
+std::pair<double, double> calc_best_MCC(const std::map<double, ClassificationResults>& classification_results_map)
+{
+ std::pair<double, double> result(0.0, 0.0);
+ for(std::map<double, ClassificationResults>::const_iterator it=classification_results_map.begin();it!=classification_results_map.end();++it)
+ {
+ if(it==classification_results_map.begin() || it->second.MCC()>result.second)
+ {
+ result=std::make_pair(it->first, it->second.MCC());
+ }
+ }
+ return result;
+}
+
+}
+
+void score_scores(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "pairs of reference and testable scores files");
+ pohw.describe_io("stdout", false, true, "global results");
+
+ const double reference_threshold=poh.argument<double>(pohw.describe_option("--reference-threshold", "number", "reference scores classification threshold"), 0.5);
+ const double testable_step=poh.argument<double>(pohw.describe_option("--testable-step", "number", "testable scores threshold step"), 0.02);
+ const std::string outcomes_file=poh.argument<std::string>(pohw.describe_option("--outcomes-file", "string", "file path to output lines of 'threshold TP TN FP FN'"), "");
+ const std::string ROC_curve_file=poh.argument<std::string>(pohw.describe_option("--ROC-curve-file", "string", "file path to output ROC curve"), "");
+ const std::string PR_curve_file=poh.argument<std::string>(pohw.describe_option("--PR-curve-file", "string", "file path to output PR curve"), "");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ const SetOfStringsPairs input_file_pairs=auxiliaries::IOUtilities().read_lines_to_map<SetOfStringsPairs>(std::cin);
+ if(input_file_pairs.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ std::map<double, ClassificationResults> classification_results_map;
+ for(SetOfStringsPairs::const_iterator it=input_file_pairs.begin();it!=input_file_pairs.end();++it)
+ {
+ const MapOfNamedValues reference_scores_map=auxiliaries::IOUtilities().read_file_lines_to_map<MapOfNamedValues>(it->first);
+ const MapOfNamedValues testable_scores_map=auxiliaries::IOUtilities().read_file_lines_to_map<MapOfNamedValues>(it->second);
+ const MapOfNamedValuesPairs merged_scores_map=GenericUtilities::merge_two_maps(reference_scores_map, testable_scores_map);
+ if(!merged_scores_map.empty())
+ {
+ update_classification_results_map(merged_scores_map, reference_threshold, testable_step, classification_results_map);
+ }
+ }
+
+ const std::set< std::pair<double, double> > ROC_curve_coordinates=calc_ROC_curve_coordinates(classification_results_map);
+ const std::set< std::pair<double, double> > PR_curve_coordinates=calc_PR_curve_coordinates(classification_results_map);
+
+ const std::pair<double, double> best_accuracy=calc_best_accuracy(classification_results_map);
+ const std::pair<double, double> best_MCC=calc_best_MCC(classification_results_map);
+
+ auxiliaries::IOUtilities().write_map_to_file(classification_results_map, outcomes_file);
+ auxiliaries::IOUtilities().write_map_to_file(ROC_curve_coordinates, ROC_curve_file);
+ auxiliaries::IOUtilities().write_map_to_file(PR_curve_coordinates, PR_curve_file);
+
+ std::cout << "ROC_AUC " << calc_AUC(ROC_curve_coordinates) << "\n";
+ std::cout << "PR_AUC " << calc_AUC(PR_curve_coordinates) << "\n";
+ std::cout << "best_accuracy_threshold " << best_accuracy.first << "\n";
+ std::cout << "best_accuracy " << best_accuracy.second << "\n";
+ std::cout << "best_MCC_threshold " << best_MCC.first << "\n";
+ std::cout << "best_MCC " << best_MCC.second << "\n";
+ std::cout << "input_file_pairs_count " << input_file_pairs.size() << "\n";
+}
diff --git a/src/mode_simulate_potential_for_membrane_proteins.cpp b/src/mode_simulate_potential_for_membrane_proteins.cpp
new file mode 100644
index 0000000..af29d28
--- /dev/null
+++ b/src/mode_simulate_potential_for_membrane_proteins.cpp
@@ -0,0 +1,81 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/contacts_scoring_utilities.h"
+
+void simulate_potential_for_membrane_proteins(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "normal potential");
+ pohw.describe_io("stdout", false, true, "simulated potential");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::map<InteractionName, double> normal_potential=auxiliaries::IOUtilities().read_lines_to_map< std::map<InteractionName, double> >(std::cin);
+
+ double sum_of_sas_values=0.0;
+ int num_of_sas_values=0;
+ for(std::map<InteractionName, double>::const_iterator it=normal_potential.begin();it!=normal_potential.end();++it)
+ {
+ if(it->first.crads.b==CRAD::solvent())
+ {
+ sum_of_sas_values+=it->second;
+ num_of_sas_values++;
+ }
+ }
+
+ std::set<CRAD> hydrophobic_crads;
+ for(std::map<InteractionName, double>::const_iterator it=normal_potential.begin();it!=normal_potential.end();++it)
+ {
+ const CRAD crads[2]={it->first.crads.a, it->first.crads.b};
+ for(int i=0;i<2;i++)
+ {
+ if((crads[i].resName=="LEU" || crads[i].resName=="ILE") && crads[i].name!="N" && crads[i].name!="C" && crads[i].name!="O" && crads[i].name!="CA")
+ {
+ hydrophobic_crads.insert(crads[i]);
+ }
+ }
+ }
+
+ std::map<InteractionName, double> simulated_potential=normal_potential;
+ for(std::map<InteractionName, double>::iterator it=simulated_potential.begin();it!=simulated_potential.end();++it)
+ {
+ const CRADsPair& crads=it->first.crads;
+ if(crads.b==CRAD::solvent())
+ {
+ double sum=0.0;
+ int counter=0;
+ for(std::set<CRAD>::const_iterator jt=hydrophobic_crads.begin();jt!=hydrophobic_crads.end();++jt)
+ {
+ sum+=normal_potential[InteractionName(CRADsPair(crads.a, (*jt)), "sep2")];
+ counter++;
+ sum+=normal_potential[InteractionName(CRADsPair(crads.a, (*jt)), "central_sep2")];
+ counter++;
+ }
+ it->second=sum/static_cast<double>(counter);
+ }
+ }
+
+ double sum_of_simulated_sas_values=0.0;
+ for(std::map<InteractionName, double>::const_iterator it=simulated_potential.begin();it!=simulated_potential.end();++it)
+ {
+ if(it->first.crads.b==CRAD::solvent())
+ {
+ sum_of_simulated_sas_values+=it->second;
+ }
+ }
+
+ const double shift_for_simulated_sas_values=(sum_of_sas_values-sum_of_simulated_sas_values)/static_cast<double>(num_of_sas_values);
+ for(std::map<InteractionName, double>::iterator it=simulated_potential.begin();it!=simulated_potential.end();++it)
+ {
+ if(it->first.crads.b==CRAD::solvent())
+ {
+ it->second+=shift_for_simulated_sas_values;
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map(simulated_potential, std::cout);
+}
diff --git a/src/mode_vectorize_contact_environments.cpp b/src/mode_vectorize_contact_environments.cpp
new file mode 100644
index 0000000..85b3627
--- /dev/null
+++ b/src/mode_vectorize_contact_environments.cpp
@@ -0,0 +1,180 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+#include "modescommon/contacts_scoring_utilities.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+std::string generate_generalized_crad_file_name(const CRAD& crad, const std::string& prefix)
+{
+ const CRAD generalized_crad=generalize_crad(crad);
+ return (prefix+generalized_crad.resName+"_"+generalized_crad.name);
+}
+
+}
+
+void vectorize_contact_environments(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts (line format: 'annotation1 annotation2 area')");
+ pohw.describe_io("stdout", false, true, "table of environments");
+
+ const std::string names_file=poh.argument<std::string>(pohw.describe_option("--names-file", "string", "file path to environment names list", true), "");
+ const bool inter_residue=poh.contains_option(pohw.describe_option("--inter-residue", "", "flag to use inter-residue contacts"));
+ const bool normalize=poh.contains_option(pohw.describe_option("--normalize", "", "flag to normalize output"));
+ const bool binarize=poh.contains_option(pohw.describe_option("--binarize", "", "flag to binarize output"));
+ const std::string output_files_prefix=poh.argument<std::string>(pohw.describe_option("--output-files-prefix", "string", "file path prefix for per-type output"), "");
+ const bool append=poh.contains_option(pohw.describe_option("--append", "", "flag to append to per-type output files"));
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::map<CRADsPair, double> map_of_contacts=auxiliaries::IOUtilities().read_lines_to_map< std::map<CRADsPair, double> >(std::cin);
+ if(map_of_contacts.empty())
+ {
+ throw std::runtime_error("No contacts input.");
+ }
+ if(inter_residue)
+ {
+ std::map<CRADsPair, double> map_of_reduced_contacts;
+ for(std::map<CRADsPair, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& raw_crads=it->first;
+ const CRADsPair crads(raw_crads.a.without_atom(), raw_crads.b.without_atom());
+ if(!(crads.a==crads.b))
+ {
+ map_of_reduced_contacts[crads]=it->second;
+ }
+ }
+ map_of_contacts=map_of_reduced_contacts;
+ }
+
+ std::set<CRAD> refined_set_of_names;
+ {
+ const std::set<CRAD> set_of_names=auxiliaries::IOUtilities().read_file_lines_to_set< std::set<CRAD> >(names_file);
+ if(set_of_names.empty())
+ {
+ throw std::runtime_error("No environment names input.");
+ }
+ for(std::set<CRAD>::const_iterator it=set_of_names.begin();it!=set_of_names.end();++it)
+ {
+ refined_set_of_names.insert(inter_residue ? generalize_crad(*it).without_atom() : generalize_crad(*it));
+ }
+ }
+
+ std::map<CRAD, std::size_t> map_of_names_ids;
+ {
+ std::size_t id=0;
+ for(std::set<CRAD>::const_iterator it=refined_set_of_names.begin();it!=refined_set_of_names.end();++it)
+ {
+ map_of_names_ids[*it]=(id++);
+ }
+ }
+
+ std::map<CRAD, std::vector<double> > map_of_environments;
+ for(std::map<CRADsPair, double>::const_iterator it=map_of_contacts.begin();it!=map_of_contacts.end();++it)
+ {
+ const CRADsPair& crads=it->first;
+ const double area=it->second;
+ if(area>0.0)
+ {
+ for(int i=0;i<2;i++)
+ {
+ const CRAD& crad1=(i==0 ? crads.a : crads.b);
+ const CRAD& crad2=(i==0 ? crads.b : crads.a);
+ if(crad1!=CRAD::solvent())
+ {
+ std::vector<double>& environment=map_of_environments[crad1];
+ environment.resize(map_of_names_ids.size(), 0.0);
+ std::map<CRAD, std::size_t>::const_iterator map_of_names_ids_it=map_of_names_ids.find(generalize_crad(crad2));
+ if(map_of_names_ids_it!=map_of_names_ids.end())
+ {
+ environment[map_of_names_ids_it->second]+=area;
+ }
+ }
+ }
+ }
+ }
+
+ std::map<std::string, std::ofstream*> map_of_output_file_streams;
+
+ for(std::map<CRAD, std::vector<double> >::const_iterator it=map_of_environments.begin();it!=map_of_environments.end();++it)
+ {
+ const CRAD& crad=it->first;
+ const std::vector<double>& environment=it->second;
+ double sum_of_areas=0.0;
+ for(std::size_t i=0;i<environment.size();i++)
+ {
+ sum_of_areas+=environment[i];
+ }
+ if(sum_of_areas>0.0)
+ {
+ std::cout << crad;
+ for(std::size_t i=0;i<environment.size();i++)
+ {
+ double output_value=environment[i];
+ if(binarize)
+ {
+ output_value=(output_value>0.0 ? 1.0 : 0.0);
+ }
+ else if(normalize)
+ {
+ output_value=(output_value/sum_of_areas);
+ }
+ std::cout << " " << output_value;
+ }
+ std::cout << "\n";
+ if(!output_files_prefix.empty())
+ {
+ const std::string output_file_name=generate_generalized_crad_file_name(crad, output_files_prefix);
+ std::map<std::string, std::ofstream*>::iterator map_of_output_file_streams_it=map_of_output_file_streams.find(output_file_name);
+ if(map_of_output_file_streams_it==map_of_output_file_streams.end())
+ {
+ map_of_output_file_streams_it=map_of_output_file_streams.insert(std::make_pair(output_file_name, new std::ofstream(output_file_name.c_str(), (append ? std::ios::app : std::ios::out)))).first;
+ }
+ std::ofstream& foutput=(*(map_of_output_file_streams_it->second));
+ foutput << std::fixed;
+ for(std::size_t i=0;i<environment.size();i++)
+ {
+ double output_value=environment[i];
+ if(binarize)
+ {
+ output_value=(output_value>0.0 ? 1.0 : 0.0);
+ }
+ else if(normalize)
+ {
+ output_value=(output_value/sum_of_areas);
+ }
+ if(binarize)
+ {
+ foutput.precision(0);
+ }
+ else
+ {
+ if(fabs(output_value)<0.005)
+ {
+ foutput.precision(0);
+ }
+ else
+ {
+ foutput.precision(2);
+ }
+ }
+ foutput << output_value << ((i+1<environment.size()) ? " " : "\n");
+ }
+ }
+ }
+ }
+
+ for(std::map<std::string, std::ofstream*>::iterator it=map_of_output_file_streams.begin();it!=map_of_output_file_streams.end();++it)
+ {
+ delete (it->second);
+ }
+}
diff --git a/src/mode_vectorize_contacts.cpp b/src/mode_vectorize_contacts.cpp
new file mode 100644
index 0000000..3fdf487
--- /dev/null
+++ b/src/mode_vectorize_contacts.cpp
@@ -0,0 +1,122 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+
+#include "modescommon/vectorization_utilities.h"
+
+namespace
+{
+
+class CRADsPair : public auxiliaries::ChainResidueAtomDescriptorsPair
+{
+};
+
+inline std::ostream& operator<<(std::ostream& output, const CRADsPair& crads_pair)
+{
+ if(crads_pair.reversed_display)
+ {
+ output << crads_pair.b << "__" << crads_pair.a;
+ }
+ else
+ {
+ output << crads_pair.a << "__" << crads_pair.b;
+ }
+ return output;
+}
+
+double calc_configurable_cadscore_of_two_vectors(const std::vector<double>& a, const std::vector<double>& b, const bool symmetric)
+{
+ if(a.size()!=b.size())
+ {
+ throw std::runtime_error("Vector sizes are not equal.");
+ }
+ double sum_diffs=0.0;
+ double sum_all=0.0;
+ for(std::size_t i=0;i<a.size();i++)
+ {
+ const double ref=(symmetric ? std::max(a[i], b[i]) : a[i]);
+ sum_diffs+=std::min(fabs(a[i]-b[i]), ref);
+ sum_all+=ref;
+ }
+ return (1.0-(sum_diffs/sum_all));
+}
+
+double calc_cadscore_of_two_vectors(const std::vector<double>& a, const std::vector<double>& b)
+{
+ return calc_configurable_cadscore_of_two_vectors(a, b, true);
+}
+
+double calc_euclidean_distance_of_two_vectors(const std::vector<double>& a, const std::vector<double>& b)
+{
+ if(a.size()!=b.size())
+ {
+ throw std::runtime_error("Vector sizes are not equal.");
+ }
+ double sum=0.0;
+ for(std::size_t i=0;i<a.size();i++)
+ {
+ sum+=((a[i]-b[i])*(a[i]-b[i]));
+ }
+ return sqrt(sum);
+}
+
+}
+
+void vectorize_contacts(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of contacts files");
+ pohw.describe_io("stdout", false, true, "table of contacts vectors");
+
+ const bool transpose=poh.contains_option(pohw.describe_option("--transpose", "", "flag to transpose output table"));
+ const std::string cadscore_matrix_file=poh.argument<std::string>(pohw.describe_option("--CAD-score-matrix", "string", "file path to output CAD-score matrix"), "");
+ const std::string distance_matrix_file=poh.argument<std::string>(pohw.describe_option("--distance-matrix", "string", "file path to output euclidean distance matrix"), "");
+ const std::string consensus_list_file=poh.argument<std::string>(pohw.describe_option("--consensus-list", "string", "file path to output ordered similarities to consensus (average contacts)"), "");
+ const std::string clustering_output_file=poh.argument<std::string>(pohw.describe_option("--clustering-output", "string", "file path to output clusters"), "");
+ const double clustering_threshold=poh.argument<double>(pohw.describe_option("--clustering-threshold", "string", "clustering threshold value"), 0.5);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ typedef VectorizationUtilities<std::string, CRADsPair, double> Vectorizer;
+
+ const Vectorizer::MapOfMaps maps_of_maps=Vectorizer::read_map_of_maps_from_multiple_files(auxiliaries::IOUtilities().read_lines_to_set< std::set<std::string> >(std::cin));
+ if(maps_of_maps.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ const Vectorizer::MapKeysIDs map_keys_ids=Vectorizer::collect_map_keys_ids(maps_of_maps);
+ const Vectorizer::MapOfVectors map_of_vectors=Vectorizer::collect_map_of_vectors(maps_of_maps, map_keys_ids);
+ const Vectorizer::IteratorsOfMapOfVectors iterators_of_map_of_vectors=Vectorizer::collect_iterators_of_map_of_vectors(map_of_vectors);
+
+ Vectorizer::print_similarity_matrix(map_of_vectors, cadscore_matrix_file, calc_cadscore_of_two_vectors);
+ Vectorizer::print_similarity_matrix(map_of_vectors, distance_matrix_file, calc_euclidean_distance_of_two_vectors);
+
+ if(!consensus_list_file.empty())
+ {
+ Vectorizer::print_consensus_similarities(
+ iterators_of_map_of_vectors,
+ Vectorizer::calc_consensus_similarities(iterators_of_map_of_vectors, calc_cadscore_of_two_vectors),
+ consensus_list_file);
+ }
+
+ if(!clustering_output_file.empty())
+ {
+ Vectorizer::print_clusters(
+ iterators_of_map_of_vectors,
+ Vectorizer::calc_clusters(iterators_of_map_of_vectors, calc_cadscore_of_two_vectors, clustering_threshold, true, false),
+ clustering_output_file);
+ }
+
+ if(transpose)
+ {
+ Vectorizer::print_map_of_areas_vectors_transposed(map_keys_ids, map_of_vectors);
+ }
+ else
+ {
+ Vectorizer::print_map_of_areas_vectors(map_keys_ids, map_of_vectors);
+ }
+}
diff --git a/src/mode_vectorize_points.cpp b/src/mode_vectorize_points.cpp
new file mode 100644
index 0000000..6db3413
--- /dev/null
+++ b/src/mode_vectorize_points.cpp
@@ -0,0 +1,78 @@
+#include "apollota/basic_operations_on_points.h"
+
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/io_utilities.h"
+
+#include "modescommon/vectorization_utilities.h"
+
+namespace
+{
+
+typedef apollota::SimplePoint Point;
+
+double calc_rmsd(const std::vector<Point>& a, const std::vector<Point>& b)
+{
+ if(a.size()!=b.size())
+ {
+ throw std::runtime_error("Vector sizes are not equal.");
+ }
+ double sum=0.0;
+ if(!a.empty())
+ {
+ for(std::size_t i=0;i<a.size();i++)
+ {
+ sum+=apollota::squared_distance_from_point_to_point(a[i], b[i]);
+ }
+ sum/=static_cast<double>(a.size());
+ }
+ return sqrt(sum);
+}
+
+}
+
+void vectorize_points(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of points files");
+ pohw.describe_io("stdout", false, true, "nothing");
+
+ const std::string rmsd_matrix_file=poh.argument<std::string>(pohw.describe_option("--RMSD-matrix", "string", "file path to output RMSD matrix"), "");
+ const std::string consensus_list_file=poh.argument<std::string>(pohw.describe_option("--consensus-list", "string", "file path to output ordered similarities to consensus (average points)"), "");
+ const std::string clustering_output_file=poh.argument<std::string>(pohw.describe_option("--clustering-output", "string", "file path to output clusters"), "");
+ const double clustering_threshold=poh.argument<double>(pohw.describe_option("--clustering-threshold", "string", "clustering threshold value"), 0.0);
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ typedef VectorizationUtilities<std::string, std::string, Point> Vectorizer;
+
+ const Vectorizer::MapOfMaps maps_of_maps=Vectorizer::read_map_of_maps_from_multiple_files(auxiliaries::IOUtilities().read_lines_to_set< std::set<std::string> >(std::cin));
+ if(maps_of_maps.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ const Vectorizer::MapKeysIDs map_keys_ids=Vectorizer::collect_map_keys_ids(maps_of_maps);
+ const Vectorizer::MapOfVectors map_of_vectors=Vectorizer::collect_map_of_vectors(maps_of_maps, map_keys_ids);
+ const Vectorizer::IteratorsOfMapOfVectors iterators_of_map_of_vectors=Vectorizer::collect_iterators_of_map_of_vectors(map_of_vectors);
+
+ Vectorizer::print_similarity_matrix(map_of_vectors, rmsd_matrix_file, calc_rmsd);
+
+ if(!consensus_list_file.empty())
+ {
+ Vectorizer::print_consensus_similarities(
+ iterators_of_map_of_vectors,
+ Vectorizer::calc_consensus_similarities(iterators_of_map_of_vectors, calc_rmsd),
+ consensus_list_file);
+ }
+
+ if(!clustering_output_file.empty())
+ {
+ Vectorizer::print_clusters(
+ iterators_of_map_of_vectors,
+ Vectorizer::calc_clusters(iterators_of_map_of_vectors, calc_rmsd, clustering_threshold, true, true),
+ clustering_output_file);
+ }
+}
diff --git a/src/mode_wrapped_get_balls_from_atoms_file_and_calculate_vertices.cpp b/src/mode_wrapped_get_balls_from_atoms_file_and_calculate_vertices.cpp
new file mode 100644
index 0000000..6cce66c
--- /dev/null
+++ b/src/mode_wrapped_get_balls_from_atoms_file_and_calculate_vertices.cpp
@@ -0,0 +1,69 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/opengl_printer.h"
+
+#include "wrapper_get_balls_from_atoms_file_and_calculate_vertices.h"
+
+void wrapped_get_balls_from_atoms_file_and_calculate_vertices(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ typedef WrapperGetBallsFromAtomsFileAndCalculateVertices Wrapper;
+
+ const std::string input_file=poh.argument<std::string>("--input-file");
+ const std::string sketch_file=poh.argument<std::string>("--sketch-file", "");
+
+ const Wrapper::Result result=Wrapper::get_balls_from_atoms_file_and_calculate_vertices(input_file);
+
+ if(result.error.empty())
+ {
+ std::cout << "balls " << result.balls.size() << "\n";
+ for(std::size_t i=0;i<result.balls.size();i++)
+ {
+ const Wrapper::Ball& b=result.balls[i];
+ std::cout << b.x << " " << b.y << " " << b.z << " " << b.r << " " << b.name << "\n";
+ }
+
+ std::cout << "vertices " << result.vertices.size() << "\n";
+ for(std::size_t i=0;i<result.vertices.size();i++)
+ {
+ const Wrapper::Vertex& v=result.vertices[i];
+ for(int j=0;j<4;j++)
+ {
+ std::cout << v.ball_id[j] << " ";
+ }
+ std::cout << v.x << " " << v.y << " " << v.z << " " << v.r;
+ for(int j=0;j<4;j++)
+ {
+ std::cout << " " << ((v.link_vertex_id[j]!=Wrapper::null_id) ? static_cast<long>(v.link_vertex_id[j]) : static_cast<long>(-1));
+ }
+ std::cout << "\n";
+ }
+ }
+ else
+ {
+ throw std::runtime_error(result.error);
+ }
+
+ if(!sketch_file.empty())
+ {
+ auxiliaries::OpenGLPrinter opengl_printer;
+ opengl_printer.add_color(0x00FFFF);
+ for(std::size_t i=0;i<result.balls.size();i++)
+ {
+ opengl_printer.add_sphere(result.balls[i]);
+ }
+ opengl_printer.add_color(0xFFFF00);
+ for(std::size_t i=0;i<result.vertices.size();i++)
+ {
+ const Wrapper::Vertex& v=result.vertices[i];
+ for(int j=0;j<4;j++)
+ {
+ const std::size_t link_vertex_id=v.link_vertex_id[j];
+ if(link_vertex_id<i)
+ {
+ opengl_printer.add_line_strip(v, result.vertices[link_vertex_id]);
+ }
+ }
+ }
+ std::ofstream sketch_file_stream(sketch_file.c_str(), std::ios::out);
+ opengl_printer.print_pymol_script("sketch", false, sketch_file_stream);
+ }
+}
diff --git a/src/mode_write_balls_to_atoms_file.cpp b/src/mode_write_balls_to_atoms_file.cpp
new file mode 100644
index 0000000..8c52b2a
--- /dev/null
+++ b/src/mode_write_balls_to_atoms_file.cpp
@@ -0,0 +1,192 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+#include "auxiliaries/atoms_io.h"
+
+#include "modescommon/ball_value.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+
+inline auxiliaries::AtomsIO::AtomRecord convert_ball_record_to_single_atom_record(const CRAD& crad, const BallValue& value, const std::string& temperature_factor_adjunct_name)
+{
+ auxiliaries::AtomsIO::AtomRecord atom_record=auxiliaries::AtomsIO::AtomRecord();
+ atom_record.record_name=(value.props.tags.count("het")>0 ? std::string("HETATM") : std::string("ATOM"));
+ if(crad.serial!=CRAD::null_num())
+ {
+ atom_record.serial=crad.serial;
+ atom_record.serial_valid=true;
+ }
+ atom_record.name=crad.name;
+ atom_record.altLoc=crad.altLoc;
+ atom_record.resName=crad.resName;
+ atom_record.chainID=crad.chainID;
+ if(crad.resSeq!=CRAD::null_num())
+ {
+ atom_record.resSeq=crad.resSeq;
+ atom_record.resSeq_valid=true;
+ }
+ atom_record.iCode=crad.iCode;
+ atom_record.x=value.x;
+ atom_record.x_valid=true;
+ atom_record.y=value.y;
+ atom_record.y_valid=true;
+ atom_record.z=value.z;
+ atom_record.z_valid=true;
+ {
+ const std::map<std::string, double>::const_iterator oc_it=value.props.adjuncts.find("oc");
+ if(oc_it!=value.props.adjuncts.end())
+ {
+ atom_record.occupancy=oc_it->second;
+ atom_record.occupancy_valid=true;
+ }
+ else
+ {
+ atom_record.occupancy=1.0;
+ atom_record.occupancy_valid=true;
+ }
+ }
+ {
+ const std::map<std::string, double>::const_iterator tf_it=value.props.adjuncts.find(temperature_factor_adjunct_name);
+ if(tf_it!=value.props.adjuncts.end())
+ {
+ atom_record.tempFactor=tf_it->second;
+ atom_record.tempFactor_valid=true;
+ }
+ }
+ {
+ for(std::set<std::string>::const_iterator tags_it=value.props.tags.begin();tags_it!=value.props.tags.end() && atom_record.element.empty();++tags_it)
+ {
+ if(tags_it->find("el=")!=std::string::npos)
+ {
+ atom_record.element=tags_it->substr(3, 2);
+ }
+ }
+ }
+ return atom_record;
+}
+
+inline int decode_model_number_from_chain_id(const std::string& chainID)
+{
+ int model_number=1;
+ if(chainID.size()>1)
+ {
+ std::istringstream input(chainID.substr(1));
+ int value=0;
+ input >> value;
+ if(!input.fail() && value>0)
+ {
+ model_number=value;
+ }
+ }
+ return model_number;
+}
+
+}
+
+void write_balls_to_atoms_file(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ auxiliaries::ProgramOptionsHandlerWrapper pohw(poh);
+ pohw.describe_io("stdin", true, false, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+ pohw.describe_io("stdout", false, true, "list of balls (line format: 'annotation x y z r tags adjuncts')");
+
+ const std::string pdb_output=poh.argument<std::string>(pohw.describe_option("--pdb-output", "string", "file path to output query result in PDB format"), "");
+ const std::string pdb_output_b_factor=poh.argument<std::string>(pohw.describe_option("--pdb-output-b-factor", "string", "name of adjunct to output as B-factor in PDB format"), "tf");
+ const std::string pdb_output_template=poh.argument<std::string>(pohw.describe_option("--pdb-output-template", "string", "file path to input template for B-factor insertions"), "");
+
+ if(!pohw.assert_or_print_help(false))
+ {
+ return;
+ }
+
+ std::vector< std::pair<CRAD, BallValue> > list_of_balls;
+ auxiliaries::IOUtilities().read_lines_to_map(std::cin, list_of_balls);
+ if(list_of_balls.empty())
+ {
+ throw std::runtime_error("No input.");
+ }
+
+ if(!pdb_output.empty())
+ {
+ if(pdb_output_template.empty())
+ {
+ std::ofstream foutput(pdb_output.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ std::map< int, std::vector<std::size_t> > models;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ models[decode_model_number_from_chain_id(list_of_balls[i].first.chainID)].push_back(i);
+ }
+ for(std::map< int, std::vector<std::size_t> >::const_iterator models_it=models.begin();models_it!=models.end();++models_it)
+ {
+ if(models.size()>1)
+ {
+ std::ostringstream line_output;
+ line_output << "MODEL" << std::right << std::setw(9) << models_it->first;
+ foutput << line_output.str() << "\n";
+ }
+ for(std::size_t j=0;j<models_it->second.size();j++)
+ {
+ const std::size_t i=models_it->second[j];
+ foutput << auxiliaries::AtomsIO::PDBWriter::write_atom_record_in_line(convert_ball_record_to_single_atom_record(list_of_balls[i].first, list_of_balls[i].second, pdb_output_b_factor)) << "\n";
+ }
+ if(models.size()>1)
+ {
+ foutput << "ENDMDL\n";
+ }
+ }
+ }
+ }
+ else
+ {
+ auxiliaries::AtomsIO::PDBReader::Data pdb_file_data;
+ {
+ std::ifstream finput(pdb_output_template.c_str(), std::ios::in);
+ pdb_file_data=auxiliaries::AtomsIO::PDBReader::read_data_from_file_stream(finput, true, true, true, true);
+ }
+ if(!pdb_file_data.valid())
+ {
+ throw std::runtime_error("Invalid PDB file output template.");
+ }
+ else
+ {
+ std::ofstream foutput(pdb_output.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ std::map<CRAD, std::size_t> output_map_of_ball_ids;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ output_map_of_ball_ids[list_of_balls[i].first]=i;
+ }
+ int icount=0;
+ for(std::size_t i=0;i<pdb_file_data.atom_records.size();i++)
+ {
+ const auxiliaries::AtomsIO::AtomRecord& atom_record=pdb_file_data.atom_records[i];
+ const std::map<CRAD, std::size_t>::const_iterator ball_id_it=output_map_of_ball_ids.find(CRAD(atom_record.serial, atom_record.chainID, atom_record.resSeq, atom_record.resName, atom_record.name, atom_record.altLoc, atom_record.iCode));
+ if(ball_id_it!=output_map_of_ball_ids.end())
+ {
+ const std::map<std::string, double>& ball_adjuncts=list_of_balls[ball_id_it->second].second.props.adjuncts;
+ const std::map<std::string, double>::const_iterator temperature_factor_it=ball_adjuncts.find(pdb_output_b_factor);
+ std::string& ball_line=pdb_file_data.all_lines[pdb_file_data.map_of_atom_records_to_all_lines.at(i)];
+ ball_line=(temperature_factor_it!=ball_adjuncts.end()) ?
+ auxiliaries::AtomsIO::PDBWriter::write_temperature_factor_to_line(ball_line, true, temperature_factor_it->second) :
+ auxiliaries::AtomsIO::PDBWriter::write_temperature_factor_to_line(ball_line, false, 0);
+ icount++;
+ }
+ }
+ for(std::size_t i=0;i<pdb_file_data.all_lines.size();i++)
+ {
+ if((i+1<pdb_file_data.all_lines.size()) || !pdb_file_data.all_lines[i].empty())
+ {
+ foutput << pdb_file_data.all_lines[i] << "\n";
+ }
+ }
+ }
+ }
+ }
+ }
+
+ auxiliaries::IOUtilities().write_map(list_of_balls, std::cout);
+}
diff --git a/src/mode_write_qa_scores_in_casp_format.cpp b/src/mode_write_qa_scores_in_casp_format.cpp
new file mode 100644
index 0000000..4d8791b
--- /dev/null
+++ b/src/mode_write_qa_scores_in_casp_format.cpp
@@ -0,0 +1,101 @@
+#include "auxiliaries/program_options_handler.h"
+#include "auxiliaries/chain_residue_atom_descriptor.h"
+#include "auxiliaries/io_utilities.h"
+
+namespace
+{
+
+double rescale_global_score(const double score, const double completeness, const double completeness_threshold)
+{
+ return ((completeness<completeness_threshold) ? score*completeness : score);
+}
+
+double rescale_local_score(const double score)
+{
+ const double a_mean=0.310;
+ const double a_sd=0.097;
+ const double b_mean=0.487;
+ const double b_sd=0.203;
+ const double d0=3.0;
+
+ double s=(((score-a_mean)/a_sd)*b_sd+b_mean);
+ s=std::max(s, 0.01);
+ s=std::min(s, 1.0);
+ return (d0*sqrt((1-s)/s));
+}
+
+}
+
+void write_qa_scores_in_casp_format(const auxiliaries::ProgramOptionsHandler& poh)
+{
+ typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+
+ const std::string name=poh.argument<std::string>("--name");
+ const double global_score=poh.argument<double>("--global-score");
+ const int sequence_length=poh.argument<int>("--sequence-length");
+ const std::string local_scores=poh.argument<std::string>("--local-scores");
+ const int wrap_size=poh.argument<int>("--wrap-size", 20);
+ const double completeness_threshold=poh.argument<double>("--completeness-threshold", 0.85);
+ const std::string converted_local_scores=poh.argument<std::string>("--converted-local-scores", "");
+
+ if(name.empty() || global_score<0.0 || global_score>1.0 || sequence_length<3 || wrap_size<1 || completeness_threshold>0.99)
+ {
+ throw std::runtime_error("Invalid parameters.");
+ }
+
+ const std::map<CRAD, double> map_of_crad_scores=auxiliaries::IOUtilities().read_file_lines_to_map< std::map<CRAD, double> >(local_scores);
+
+ if(map_of_crad_scores.empty())
+ {
+ throw std::runtime_error("No local scores.");
+ }
+
+ std::map<int, double> map_of_position_scores;
+ for(std::map<CRAD, double>::const_iterator it=map_of_crad_scores.begin();it!=map_of_crad_scores.end();++it)
+ {
+ const int pos=it->first.resSeq;
+ if(pos>=1 && pos<=sequence_length && map_of_position_scores.count(pos)==0)
+ {
+ map_of_position_scores[pos]=(it->second);
+ }
+ }
+
+ if(map_of_position_scores.empty())
+ {
+ throw std::runtime_error("No local scores in required range.");
+ }
+
+ const double local_scores_completeness=static_cast<double>(map_of_position_scores.size())/static_cast<double>(sequence_length);
+
+ std::cout << name << " ";
+ std::cout.precision(3);
+ std::cout << std::fixed << rescale_global_score(global_score, local_scores_completeness, completeness_threshold);
+
+ for(int i=1;i<=sequence_length;i++)
+ {
+ std::cout << ((i>1 && ((i-1)%wrap_size==0)) ? "\t" : " ");
+ std::map<int, double>::const_iterator it=map_of_position_scores.find(i);
+ if(it!=map_of_position_scores.end())
+ {
+ std::cout.precision(2);
+ std::cout << std::fixed << rescale_local_score(it->second);
+ }
+ else
+ {
+ std::cout << "X";
+ }
+ }
+ std::cout << "\n";
+
+ if(!converted_local_scores.empty())
+ {
+ std::ofstream foutput(converted_local_scores.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ for(std::map<CRAD, double>::const_iterator it=map_of_crad_scores.begin();it!=map_of_crad_scores.end();++it)
+ {
+ foutput << (it->first) << " " << rescale_local_score(it->second) << "\n";
+ }
+ }
+ }
+}
diff --git a/src/modescommon/ball_value.h b/src/modescommon/ball_value.h
new file mode 100644
index 0000000..a2e909c
--- /dev/null
+++ b/src/modescommon/ball_value.h
@@ -0,0 +1,36 @@
+#ifndef BALL_VALUE_H_
+#define BALL_VALUE_H_
+
+#include "properties_value.h"
+
+namespace
+{
+
+struct BallValue
+{
+ double x;
+ double y;
+ double z;
+ double r;
+ PropertiesValue props;
+
+ BallValue() : x(0.0), y(0.0), z(0.0), r(0.0)
+ {
+ }
+};
+
+inline std::ostream& operator<<(std::ostream& output, const BallValue& value)
+{
+ output << value.x << " " << value.y << " " << value.z << " " << value.r << " " << value.props;
+ return output;
+}
+
+inline std::istream& operator>>(std::istream& input, BallValue& value)
+{
+ input >> value.x >> value.y >> value.z >> value.r >> value.props;
+ return input;
+}
+
+}
+
+#endif /* BALL_VALUE_H_ */
diff --git a/src/modescommon/contact_value.h b/src/modescommon/contact_value.h
new file mode 100644
index 0000000..10def21
--- /dev/null
+++ b/src/modescommon/contact_value.h
@@ -0,0 +1,80 @@
+#ifndef CONTACT_VALUE_H_
+#define CONTACT_VALUE_H_
+
+#include "properties_value.h"
+
+namespace
+{
+
+struct ContactValue
+{
+ double area;
+ double dist;
+ bool accumulated;
+ PropertiesValue props;
+ std::string graphics;
+
+ ContactValue() : area(0.0), dist(0.0), accumulated(false)
+ {
+ }
+
+ void add(const ContactValue& v)
+ {
+ area+=v.area;
+ dist=(!accumulated ? v.dist : std::min(dist, v.dist));
+ props.tags.insert(v.props.tags.begin(), v.props.tags.end());
+ for(std::map<std::string, double>::const_iterator it=v.props.adjuncts.begin();it!=v.props.adjuncts.end();++it)
+ {
+ props.adjuncts[it->first]+=it->second;
+ }
+ if(!v.graphics.empty())
+ {
+ if(graphics.empty())
+ {
+ graphics=v.graphics;
+ }
+ else
+ {
+ if(graphics[graphics.size()-1]!=' ' || v.graphics[0]!=' ')
+ {
+ graphics+=" ";
+ }
+ graphics+=v.graphics;
+ }
+ }
+ accumulated=true;
+ }
+};
+
+inline bool& enabled_output_of_ContactValue_graphics()
+{
+ static bool enabled_output=true;
+ return enabled_output;
+}
+
+inline std::ostream& operator<<(std::ostream& output, const ContactValue& value)
+{
+ output << value.area << " " << value.dist << " " << value.props;
+ if(enabled_output_of_ContactValue_graphics() && !value.graphics.empty())
+ {
+ output << " \"";
+ output << value.graphics;
+ output << "\"";
+ }
+ return output;
+}
+
+inline std::istream& operator>>(std::istream& input, ContactValue& value)
+{
+ input >> value.area >> value.dist >> value.props;
+ if(input.good())
+ {
+ std::getline(input, value.graphics, '"');
+ std::getline(input, value.graphics, '"');
+ }
+ return input;
+}
+
+}
+
+#endif /* CONTACT_VALUE_H_ */
diff --git a/src/modescommon/contacts_scoring_utilities.h b/src/modescommon/contacts_scoring_utilities.h
new file mode 100644
index 0000000..d8aeea3
--- /dev/null
+++ b/src/modescommon/contacts_scoring_utilities.h
@@ -0,0 +1,147 @@
+#ifndef CONTACTS_SCORING_UTILITIES_H_
+#define CONTACTS_SCORING_UTILITIES_H_
+
+#include "../auxiliaries/chain_residue_atom_descriptor.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+typedef auxiliaries::ChainResidueAtomDescriptorsPair CRADsPair;
+
+struct InteractionName
+{
+ CRADsPair crads;
+ std::string tag;
+
+ InteractionName()
+ {
+ }
+
+ InteractionName(const CRADsPair& crads, const std::string& tag) : crads(crads), tag(tag)
+ {
+ }
+
+ bool operator==(const InteractionName& v) const
+ {
+ return (crads==v.crads && tag==v.tag);
+ }
+
+ bool operator<(const InteractionName& v) const
+ {
+ return ((crads<v.crads) || (crads==v.crads && tag<v.tag));
+ }
+};
+
+inline std::ostream& operator<<(std::ostream& output, const InteractionName& v)
+{
+ output << v.crads << " " << v.tag;
+ return output;
+}
+
+inline std::istream& operator>>(std::istream& input, InteractionName& v)
+{
+ input >> v.crads >> v.tag;
+ return input;
+}
+
+struct EnergyDescriptor
+{
+ double total_area;
+ double strange_area;
+ double energy;
+ int contacts_count;
+
+ EnergyDescriptor() : total_area(0), strange_area(0), energy(0), contacts_count(0)
+ {
+ }
+
+ void add(const EnergyDescriptor& ed)
+ {
+ total_area+=ed.total_area;
+ strange_area+=ed.strange_area;
+ energy+=ed.energy;
+ contacts_count+=ed.contacts_count;
+ }
+};
+
+inline std::ostream& operator<<(std::ostream& output, const EnergyDescriptor& v)
+{
+ output << v.total_area << " " << v.strange_area << " " << v.energy << " " << v.contacts_count;
+ return output;
+}
+
+inline std::istream& operator>>(std::istream& input, EnergyDescriptor& v)
+{
+ input >> v.total_area >> v.strange_area >> v.energy >> v.contacts_count;
+ return input;
+}
+
+inline CRAD generalize_crad(const CRAD& input_crad)
+{
+ CRAD crad=input_crad.without_numbering();
+ if(crad.resName=="ARG" && (crad.name=="NH1" || crad.name=="NH2"))
+ {
+ crad.name="NH1";
+ }
+ else if(crad.resName=="ASP" && (crad.name=="OD1" || crad.name=="OD2"))
+ {
+ crad.name="OD1";
+ }
+ else if(crad.resName=="GLU" && (crad.name=="OE1" || crad.name=="OE2"))
+ {
+ crad.name="OE1";
+ }
+ else if(crad.resName=="PHE" && (crad.name=="CD1" || crad.name=="CD2"))
+ {
+ crad.name="CD1";
+ }
+ else if(crad.resName=="PHE" && (crad.name=="CE1" || crad.name=="CE2"))
+ {
+ crad.name="CE1";
+ }
+ else if(crad.resName=="TYR" && (crad.name=="CD1" || crad.name=="CD2"))
+ {
+ crad.name="CD1";
+ }
+ else if(crad.resName=="TYR" && (crad.name=="CE1" || crad.name=="CE2"))
+ {
+ crad.name="CE1";
+ }
+ else if(crad.name=="OXT")
+ {
+ crad.name="O";
+ }
+ else if(crad.resName=="MSE")
+ {
+ crad.resName="MET";
+ if(crad.name=="SE")
+ {
+ crad.name="SD";
+ }
+ }
+ else if(crad.resName=="SEC")
+ {
+ crad.resName="CYS";
+ if(crad.name=="SE")
+ {
+ crad.name="SG";
+ }
+ }
+ return crad;
+}
+
+inline CRADsPair generalize_crads_pair(const CRADsPair& input_crads)
+{
+ return CRADsPair(generalize_crad(input_crads.a), generalize_crad(input_crads.b));
+}
+
+inline bool check_crads_pair_for_peptide_bond(const CRADsPair& crads)
+{
+ return (((crads.a.name=="C" && crads.b.name=="N" && crads.a.resSeq<crads.b.resSeq) || (crads.a.name=="N" && crads.b.name=="C" && crads.b.resSeq<crads.a.resSeq))
+ && CRAD::match_with_sequence_separation_interval(crads.a, crads.b, 0, 1, false));
+}
+
+}
+
+#endif /* CONTACTS_SCORING_UTILITIES_H_ */
diff --git a/src/modescommon/drawing_cylinder.h b/src/modescommon/drawing_cylinder.h
new file mode 100644
index 0000000..aac9cfe
--- /dev/null
+++ b/src/modescommon/drawing_cylinder.h
@@ -0,0 +1,49 @@
+#ifndef DRAWING_CYLINDER_H_
+#define DRAWING_CYLINDER_H_
+
+#include "../apollota/basic_operations_on_spheres.h"
+#include "../apollota/rotation.h"
+
+#include "drawing_utilities.h"
+
+namespace
+{
+
+void draw_cylinder(
+ const apollota::SimpleSphere& a,
+ const apollota::SimpleSphere& b,
+ const int sides,
+ auxiliaries::OpenGLPrinter& opengl_printer)
+{
+ apollota::SimplePoint pa(a);
+ apollota::SimplePoint pb(b);
+ const apollota::SimplePoint axis=(pb-pa);
+ apollota::Rotation rotation(axis, 0);
+ const apollota::SimplePoint first_point=apollota::any_normal_of_vector<apollota::SimplePoint>(rotation.axis);
+ const double angle_step=360.0/static_cast<double>(std::min(std::max(sides, 6), 30));
+ std::vector<apollota::SimplePoint> contour;
+ contour.reserve(sides+1);
+ contour.push_back(first_point);
+ for(rotation.angle=angle_step;rotation.angle<360;rotation.angle+=angle_step)
+ {
+ contour.push_back(rotation.rotate<apollota::SimplePoint>(first_point));
+ }
+ contour.push_back(first_point);
+ std::vector<apollota::SimplePoint> vertices;
+ std::vector<apollota::SimplePoint> normals;
+ vertices.reserve(contour.size()*2);
+ normals.reserve(vertices.size());
+ for(std::size_t i=0;i<contour.size();i++)
+ {
+ const apollota::SimplePoint& p=contour[i];
+ vertices.push_back(pa+(p*a.r));
+ vertices.push_back(pb+(p*b.r));
+ normals.push_back(p);
+ normals.push_back(p);
+ }
+ opengl_printer.add_triangle_strip(vertices, normals);
+}
+
+}
+
+#endif /* DRAWING_CYLINDER_H_ */
diff --git a/src/modescommon/drawing_links.h b/src/modescommon/drawing_links.h
new file mode 100644
index 0000000..e578810
--- /dev/null
+++ b/src/modescommon/drawing_links.h
@@ -0,0 +1,75 @@
+#ifndef DRAWING_LINKS_H_
+#define DRAWING_LINKS_H_
+
+#include "../apollota/search_for_spherical_collisions.h"
+
+#include "drawing_cylinder.h"
+#include "ball_value.h"
+
+namespace
+{
+
+void draw_links(
+ const std::vector< std::pair<CRAD, BallValue> >& list_of_balls,
+ const double ball_collision_radius,
+ const double bsh_initial_radius,
+ const double ball_drawing_radius,
+ const double cylinder_drawing_radius,
+ const int cylinder_sides,
+ const bool check_sequence,
+ const DrawingParametersWrapper& drawing_parameters_wrapper,
+ auxiliaries::OpenGLPrinter& opengl_printer)
+{
+ std::vector<apollota::SimpleSphere> spheres(list_of_balls.size());
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ spheres[i]=apollota::SimpleSphere(list_of_balls[i].second, ball_collision_radius);
+ }
+ apollota::BoundingSpheresHierarchy bsh(spheres, bsh_initial_radius, 1);
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const apollota::SimpleSphere& a=spheres[i];
+ const CRAD& a_crad=list_of_balls[i].first;
+ drawing_parameters_wrapper.process(a_crad, list_of_balls[i].second.props.adjuncts, opengl_printer);
+ opengl_printer.add_sphere(apollota::SimpleSphere(a, ball_drawing_radius));
+ std::vector<std::size_t> collisions=apollota::SearchForSphericalCollisions::find_all_collisions(bsh, a);
+ for(std::size_t j=0;j<collisions.size();j++)
+ {
+ const std::size_t collision_id=collisions[j];
+ if(i!=collision_id)
+ {
+ const apollota::SimpleSphere& b=spheres[collision_id];
+ const CRAD& b_crad=list_of_balls[collision_id].first;
+ if(!check_sequence || (a_crad.chainID==b_crad.chainID && abs(a_crad.resSeq-b_crad.resSeq)<=1))
+ draw_cylinder(
+ apollota::SimpleSphere(a, cylinder_drawing_radius),
+ apollota::SimpleSphere(apollota::sum_of_points<apollota::SimplePoint>(a, b)*0.5, cylinder_drawing_radius),
+ cylinder_sides,
+ opengl_printer);
+ }
+ }
+ }
+}
+
+void draw_trace(
+ const std::vector< std::pair<CRAD, BallValue> >& list_of_balls,
+ const std::string& atom_name,
+ const double max_distance,
+ const double drawing_radius,
+ const DrawingParametersWrapper& drawing_parameters_wrapper,
+ auxiliaries::OpenGLPrinter& opengl_printer)
+{
+ std::vector< std::pair<CRAD, BallValue> > list_of_balls_filtered;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ if(list_of_balls[i].first.name==atom_name)
+ {
+ list_of_balls_filtered.push_back(list_of_balls[i]);
+ }
+ }
+ draw_links(list_of_balls_filtered, max_distance*0.5, 10.0, drawing_radius, drawing_radius, 12, true, drawing_parameters_wrapper, opengl_printer);
+}
+
+}
+
+#endif /* DRAWING_LINKS_H_ */
diff --git a/src/modescommon/drawing_nucleic_acid_cartoons.h b/src/modescommon/drawing_nucleic_acid_cartoons.h
new file mode 100644
index 0000000..b176ebe
--- /dev/null
+++ b/src/modescommon/drawing_nucleic_acid_cartoons.h
@@ -0,0 +1,221 @@
+#ifndef DRAWING_NUCLEIC_ACID_CARTOONS_H_
+#define DRAWING_NUCLEIC_ACID_CARTOONS_H_
+
+#include "../apollota/polynomial_curves.h"
+
+#include "drawing_utilities.h"
+#include "drawing_cylinder.h"
+
+namespace
+{
+
+class DrawingNucleicAcidCartoons
+{
+public:
+ double main_radius;
+ double side_radius;
+ double hermite_spline_k;
+ double hermite_spline_steps;
+ int cylinder_quality;
+
+ DrawingNucleicAcidCartoons() :
+ main_radius(0.5),
+ side_radius(0.3),
+ hermite_spline_k(0.5),
+ hermite_spline_steps(4),
+ cylinder_quality(12)
+ {
+ }
+
+ void draw_cartoon(
+ const std::vector< std::pair<CRAD, BallValue> >& list_of_balls,
+ const DrawingParametersWrapper& drawing_parameters_wrapper,
+ auxiliaries::OpenGLPrinter& opengl_printer)
+ {
+ std::map<CRAD, BallValue> map_of_crad_values;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ if(crad.name=="C3'")
+ {
+ map_of_crad_values[crad.without_atom()]=list_of_balls[i].second;
+ }
+ }
+ const std::vector< std::vector<ResidueOrientation> > residue_orientations=collect_residue_orientations(list_of_balls);
+ const std::map< CRAD, std::vector<RibbonVertebra> > spine=construct_ribbon_spine(residue_orientations, hermite_spline_k, hermite_spline_steps);
+ for(std::map< CRAD, std::vector<RibbonVertebra> >::const_iterator it=spine.begin();it!=spine.end();++it)
+ {
+ const CRAD& crad=it->first;
+ const std::vector<RibbonVertebra>& subspine=it->second;
+ drawing_parameters_wrapper.process(crad, map_of_crad_values[crad].props.adjuncts, opengl_printer);
+ for(std::size_t i=0;i+1<subspine.size();i++)
+ {
+ const RibbonVertebra& rv=subspine[i];
+ const RibbonVertebra& next_rv=subspine[i+1];
+ draw_cylinder(apollota::SimpleSphere(rv.center, main_radius), apollota::SimpleSphere(next_rv.center, main_radius), cylinder_quality, opengl_printer);
+ }
+ for(std::size_t i=0;i<subspine.size();i++)
+ {
+ const RibbonVertebra& rv=subspine[i];
+ opengl_printer.add_sphere(apollota::SimpleSphere(rv.center, main_radius));
+ }
+ }
+ for(std::size_t i=0;i<residue_orientations.size();i++)
+ {
+ for(std::size_t j=0;j<residue_orientations[i].size();j++)
+ {
+ const ResidueOrientation& ro=residue_orientations[i][j];
+ const CRAD& crad=ro.crad;
+ const apollota::SimplePoint p=(ro.C3+((ro.C2-ro.C3).unit()*6.0));
+ drawing_parameters_wrapper.process(crad, map_of_crad_values[crad].props.adjuncts, opengl_printer);
+ draw_cylinder(apollota::SimpleSphere(ro.C3, side_radius), apollota::SimpleSphere(p, side_radius), cylinder_quality, opengl_printer);
+ opengl_printer.add_sphere(apollota::SimpleSphere(p, side_radius));
+ }
+ }
+ }
+
+private:
+ class ResidueOrientation
+ {
+ public:
+ CRAD crad;
+ apollota::SimplePoint C3;
+ apollota::SimplePoint C2;
+ bool C3_flag;
+ bool C2_flag;
+
+ ResidueOrientation() : C3_flag(false), C2_flag(false)
+ {
+ }
+
+ bool valid() const
+ {
+ return (C3_flag && C2_flag);
+ }
+ };
+
+ struct RibbonVertebra
+ {
+ apollota::SimplePoint center;
+ };
+
+ static std::vector< std::vector<ResidueOrientation> > collect_residue_orientations(const std::vector< std::pair<CRAD, BallValue> >& list_of_balls)
+ {
+ std::map<CRAD, ResidueOrientation> map_of_residue_orientations;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ const BallValue& ball_value=list_of_balls[i].second;
+ const apollota::SimplePoint ball_center(ball_value);
+ ResidueOrientation& ro=map_of_residue_orientations[crad.without_atom()];
+ ro.crad=crad.without_atom();
+ if(crad.name=="C3'")
+ {
+ ro.C3=ball_center;
+ ro.C3_flag=true;
+ }
+ else if(crad.name=="C2")
+ {
+ ro.C2=ball_center;
+ ro.C2_flag=true;
+ }
+ }
+ std::vector< std::vector<ResidueOrientation> > result;
+ for(std::map<CRAD, ResidueOrientation>::const_iterator it=map_of_residue_orientations.begin();it!=map_of_residue_orientations.end();++it)
+ {
+ const ResidueOrientation& ro=it->second;
+ if(ro.valid())
+ {
+ if(result.empty())
+ {
+ result.push_back(std::vector<ResidueOrientation>(1, ro));
+ }
+ else
+ {
+ const ResidueOrientation& prev_ro=result.back().back();
+ if(prev_ro.crad.chainID==ro.crad.chainID && apollota::distance_from_point_to_point(prev_ro.C3, ro.C3)<8.0)
+ {
+ result.back().push_back(ro);
+ }
+ else
+ {
+ result.push_back(std::vector<ResidueOrientation>(1, ro));
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static std::map< CRAD, std::vector<RibbonVertebra> > construct_ribbon_spine(const std::vector<ResidueOrientation>& ros, const double k, const int steps)
+ {
+ std::map< CRAD, std::vector<RibbonVertebra> > result;
+ std::vector<RibbonVertebra> controls(ros.size());
+ for(std::size_t i=0;i<ros.size();i++)
+ {
+ const ResidueOrientation& ro=ros[i];
+ RibbonVertebra& rv=controls[i];
+ rv.center=ro.C3;
+ }
+ if(controls.size()>=4)
+ {
+ for(std::size_t i=0;i+1<controls.size();i++)
+ {
+ std::vector<apollota::SimplePoint> strip_center;
+ if(i==0)
+ {
+ strip_center=apollota::interpolate_using_cubic_hermite_spline(controls[i].center+(controls[i].center-controls[i+1].center), controls[i].center, controls[i+1].center, controls[i+2].center, k, steps);
+ }
+ else if(i+2==controls.size())
+ {
+ strip_center=apollota::interpolate_using_cubic_hermite_spline(controls[i-1].center, controls[i].center, controls[i+1].center, controls[i+1].center+(controls[i+1].center-controls[i].center), k, steps);
+ }
+ else
+ {
+ strip_center=apollota::interpolate_using_cubic_hermite_spline(controls[i-1].center, controls[i].center, controls[i+1].center, controls[i+2].center, k, steps);
+ }
+ if(!strip_center.empty())
+ {
+ std::vector<RibbonVertebra>& result_a=result[ros[i].crad];
+ std::vector<RibbonVertebra>& result_b=result[ros[i+1].crad];
+ result_a.reserve(strip_center.size()/2+1);
+ result_b.reserve(strip_center.size()/2+1);
+ for(std::size_t j=0;j<strip_center.size();j++)
+ {
+ RibbonVertebra v;
+ v.center=strip_center[j];
+ if(j<strip_center.size()/2)
+ {
+ result_a.push_back(v);
+ }
+ else if(j==strip_center.size()/2)
+ {
+ result_a.push_back(v);
+ result_b.push_back(v);
+ }
+ else
+ {
+ result_b.push_back(v);
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static std::map< CRAD, std::vector<RibbonVertebra> > construct_ribbon_spine(const std::vector< std::vector<ResidueOrientation> >& residue_orientations, const double k, const int steps)
+ {
+ std::map< CRAD, std::vector<RibbonVertebra> > result;
+ for(std::size_t i=0;i<residue_orientations.size();i++)
+ {
+ std::map< CRAD, std::vector<RibbonVertebra> > partial_result=construct_ribbon_spine(residue_orientations[i], k, steps);
+ result.insert(partial_result.begin(), partial_result.end());
+ }
+ return result;
+ }
+};
+
+}
+
+#endif /* DRAWING_NUCLEIC_ACID_CARTOONS_H_ */
diff --git a/src/modescommon/drawing_protein_cartoons.h b/src/modescommon/drawing_protein_cartoons.h
new file mode 100644
index 0000000..91613dd
--- /dev/null
+++ b/src/modescommon/drawing_protein_cartoons.h
@@ -0,0 +1,443 @@
+#ifndef DRAWING_CARTOONS_H_
+#define DRAWING_CARTOONS_H_
+
+#include "../apollota/polynomial_curves.h"
+
+#include "drawing_utilities.h"
+
+namespace
+{
+
+class DrawingProteinCartoons
+{
+public:
+ double loop_width;
+ double loop_height;
+ double nonloop_width;
+ double nonloop_height;
+ double arrow_width;
+ double hermite_spline_k;
+ double hermite_spline_steps;
+ bool enable_arrows;
+
+ DrawingProteinCartoons() :
+ loop_width(0.30),
+ loop_height(0.15),
+ nonloop_width(1.2),
+ nonloop_height(0.15),
+ arrow_width(1.6),
+ hermite_spline_k(0.8),
+ hermite_spline_steps(10),
+ enable_arrows(true)
+ {
+ }
+
+ void draw_cartoon(
+ const std::vector< std::pair<CRAD, BallValue> >& list_of_balls,
+ const DrawingParametersWrapper& drawing_parameters_wrapper,
+ auxiliaries::OpenGLPrinter& opengl_printer)
+ {
+ std::map<CRAD, BallValue> map_of_crad_values;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ if(crad.name=="CA")
+ {
+ map_of_crad_values[crad.without_atom()]=list_of_balls[i].second;
+ }
+ }
+ const std::map< CRAD, std::vector<RibbonVertebra> > spine=construct_ribbon_spine(list_of_balls, hermite_spline_k, hermite_spline_steps);
+ for(std::map< CRAD, std::vector<RibbonVertebra> >::const_iterator it=spine.begin();it!=spine.end();++it)
+ {
+ const CRAD& crad=it->first;
+ const BallValue& ball_value=map_of_crad_values[crad];
+ const std::vector<RibbonVertebra>& subspine=it->second;
+ if(subspine.size()>1)
+ {
+ drawing_parameters_wrapper.process(crad, ball_value.props.adjuncts, opengl_printer);
+
+ const int ss_type=subspine.front().ss_type;
+
+ int prev_ss_type=0;
+ if(it!=spine.begin())
+ {
+ std::map< CRAD, std::vector<RibbonVertebra> >::const_iterator prev_it=it;
+ --prev_it;
+ prev_ss_type=prev_it->second.front().ss_type;
+ }
+
+ int next_ss_type=0;
+ {
+ std::map< CRAD, std::vector<RibbonVertebra> >::const_iterator next_it=it;
+ ++next_it;
+ if(next_it!=spine.end())
+ {
+ next_ss_type=next_it->second.front().ss_type;
+ }
+ }
+
+ const bool loop=(ss_type==0);
+ const double wk=(loop ? loop_width : nonloop_width);
+ const double hk=(loop ? loop_height : nonloop_height);
+
+ const bool arrow=(enable_arrows && (prev_ss_type==2 && ss_type==2 && next_ss_type!=2));
+
+ for(int e=0;e<2;e++)
+ {
+ for(int o=0;o<2;o++)
+ {
+ std::vector<apollota::SimplePoint> vertices;
+ std::vector<apollota::SimplePoint> normals;
+ for(std::size_t i=0;i<subspine.size();i++)
+ {
+ double mwk=wk;
+ if(arrow)
+ {
+ mwk=(1.0-static_cast<double>(i)/static_cast<double>(subspine.size()-1))*arrow_width+loop_width;
+ }
+ const RibbonVertebra& rv=subspine[i];
+ const apollota::SimplePoint c=rv.center;
+ const apollota::SimplePoint u=(o==0 ? ((rv.up-c).unit()*(e==0 ? 1.0 : -1.0)*hk) : ((rv.right-c).unit()*(e==0 ? 1.0 : -1.0)*mwk));
+ const apollota::SimplePoint r=(o==0 ? ((rv.right-c).unit()*mwk) : ((rv.up-c).unit()*hk));
+ const apollota::SimplePoint l=r.inverted();
+ vertices.push_back(c+l+u);
+ vertices.push_back(c+r+u);
+ normals.push_back(u.unit());
+ normals.push_back(u.unit());
+ }
+ opengl_printer.add_triangle_strip(vertices, normals);
+ }
+
+ {
+ double mwk=wk;
+ if(arrow)
+ {
+ mwk=(e==0 ? (arrow_width+loop_width) : loop_width);
+ }
+ const RibbonVertebra& rv=(e==0 ? subspine.front() : subspine.back());
+ const apollota::SimplePoint c=rv.center;
+ const apollota::SimplePoint u=(rv.up-c).unit()*hk;
+ const apollota::SimplePoint d=u.inverted();
+ const apollota::SimplePoint r=(rv.right-c).unit()*mwk;
+ const apollota::SimplePoint l=r.inverted();
+ const apollota::SimplePoint n=((subspine.front().center-subspine.back().center)*(e==0 ? 1.0 : -1.0)).unit();
+ std::vector<apollota::SimplePoint> vertices;
+ std::vector<apollota::SimplePoint> normals;
+ vertices.push_back(c+d+l);
+ vertices.push_back(c+d+r);
+ vertices.push_back(c+u+l);
+ vertices.push_back(c+u+r);
+ normals.push_back(n.unit());
+ normals.push_back(n.unit());
+ normals.push_back(n.unit());
+ normals.push_back(n.unit());
+ opengl_printer.add_triangle_strip(vertices, normals);
+ }
+ }
+ }
+ }
+ }
+
+private:
+ class ResidueOrientation
+ {
+ public:
+ CRAD crad;
+ apollota::SimplePoint CA;
+ apollota::SimplePoint C;
+ apollota::SimplePoint N;
+ apollota::SimplePoint O;
+ apollota::SimplePoint up;
+ apollota::SimplePoint right;
+ bool CA_flag;
+ bool C_flag;
+ bool N_flag;
+ bool O_flag;
+ int ss_type;
+
+ ResidueOrientation() : CA_flag(false), C_flag(false), N_flag(false), O_flag(false), ss_type(0)
+ {
+ }
+
+ static void orient_sequence(std::vector<ResidueOrientation>& seq)
+ {
+ if(seq.size()>1)
+ {
+ for(std::size_t i=0;(i+1)<seq.size();i++)
+ {
+ seq[i].orient(seq[i+1].CA-seq[i].CA);
+ }
+ seq[seq.size()-1].orient(seq[seq.size()-1].CA-seq[seq.size()-2].CA);
+ for(std::size_t i=1;i<seq.size();i++)
+ {
+ seq[i].reorient(seq[i-1]);
+ }
+ }
+ }
+
+ bool orientable() const
+ {
+ return (CA_flag && C_flag && N_flag && O_flag);
+ }
+
+ void orient(const apollota::SimplePoint& forward)
+ {
+ if(orientable())
+ {
+ up=(forward&((O-C).unit()+(N-CA).unit()*0.5)).unit();
+ right=(forward&up).unit();
+ }
+ }
+
+ void reorient(const ResidueOrientation& reference)
+ {
+ const double v_plus=(right*reference.right);
+ const double v_minus=(right.inverted()*reference.right);
+ if(v_minus>v_plus)
+ {
+ up=up.inverted();
+ right=right.inverted();
+ }
+ }
+ };
+
+ struct RibbonVertebra
+ {
+ apollota::SimplePoint center;
+ apollota::SimplePoint up;
+ apollota::SimplePoint right;
+ int ss_type;
+ };
+
+ static int ss_type_from_ball_value(const BallValue& ball_value)
+ {
+ if(ball_value.props.tags.count("dssp=H")>0 || ball_value.props.tags.count("dssp=G")>0 || ball_value.props.tags.count("dssp=I")>0)
+ {
+ return 1;
+ }
+ else if(ball_value.props.tags.count("dssp=B")>0 || ball_value.props.tags.count("dssp=E")>0)
+ {
+ return 2;
+ }
+ return 0;
+ }
+
+ static std::vector< std::vector<ResidueOrientation> > collect_residue_orientations(const std::vector< std::pair<CRAD, BallValue> >& list_of_balls)
+ {
+ std::map<CRAD, ResidueOrientation> map_of_residue_orientations;
+ for(std::size_t i=0;i<list_of_balls.size();i++)
+ {
+ const CRAD& crad=list_of_balls[i].first;
+ const BallValue& ball_value=list_of_balls[i].second;
+ const apollota::SimplePoint ball_center(ball_value);
+ ResidueOrientation& ro=map_of_residue_orientations[crad.without_atom()];
+ ro.crad=crad.without_atom();
+ if(crad.name=="CA")
+ {
+ ro.CA=ball_center;
+ ro.CA_flag=true;
+ }
+ else if(crad.name=="C")
+ {
+ ro.C=ball_center;
+ ro.C_flag=true;
+ }
+ else if(crad.name=="N")
+ {
+ ro.N=ball_center;
+ ro.N_flag=true;
+ }
+ else if(crad.name=="O")
+ {
+ ro.O=ball_center;
+ ro.O_flag=true;
+ }
+ ro.ss_type=ss_type_from_ball_value(ball_value);
+ }
+ std::vector< std::vector<ResidueOrientation> > result;
+ for(std::map<CRAD, ResidueOrientation>::const_iterator it=map_of_residue_orientations.begin();it!=map_of_residue_orientations.end();++it)
+ {
+ const ResidueOrientation& ro=it->second;
+ if(ro.orientable())
+ {
+ if(result.empty())
+ {
+ result.push_back(std::vector<ResidueOrientation>(1, ro));
+ }
+ else
+ {
+ const ResidueOrientation& prev_ro=result.back().back();
+ if(prev_ro.crad.chainID==ro.crad.chainID && apollota::distance_from_point_to_point(prev_ro.C, ro.N)<1.6)
+ {
+ result.back().push_back(ro);
+ }
+ else
+ {
+ result.push_back(std::vector<ResidueOrientation>(1, ro));
+ }
+ }
+ }
+ }
+ for(std::size_t i=0;i<result.size();i++)
+ {
+ ResidueOrientation::orient_sequence(result[i]);
+ }
+ return result;
+ }
+
+ static std::map< CRAD, std::vector<RibbonVertebra> > construct_ribbon_spine(const std::vector<ResidueOrientation>& ros, const double k, const int steps)
+ {
+ std::map< CRAD, std::vector<RibbonVertebra> > result;
+ std::vector<RibbonVertebra> controls(ros.size());
+ std::vector<std::size_t> beta_ids;
+ for(std::size_t i=0;i<ros.size();i++)
+ {
+ const ResidueOrientation& ro=ros[i];
+ RibbonVertebra& rv=controls[i];
+ rv.center=ro.CA;
+ rv.up=ro.CA+(ro.up*0.2);
+ rv.right=ro.CA+(ro.right*0.5);
+ rv.ss_type=ro.ss_type;
+ }
+ for(std::size_t i=1;i+1<controls.size();i++)
+ {
+ RibbonVertebra& rv=controls[i];
+ const ResidueOrientation& prev_ro=ros[i-1];
+ const ResidueOrientation& next_ro=ros[i+1];
+ if(rv.ss_type==2 && prev_ro.ss_type==2 && next_ro.ss_type==1)
+ {
+ rv.ss_type=0;
+ }
+ else if(rv.ss_type==2 && prev_ro.ss_type==1 && next_ro.ss_type==2)
+ {
+ rv.ss_type=0;
+ }
+ else if(rv.ss_type!=0 && prev_ro.ss_type==0 && next_ro.ss_type==0)
+ {
+ rv.ss_type=0;
+ }
+ }
+ for(std::size_t i=0;i<controls.size();i++)
+ {
+ const RibbonVertebra& rv=controls[i];
+ if(rv.ss_type==2)
+ {
+ beta_ids.push_back(i);
+ }
+ if(rv.ss_type!=2 || (i+1)==controls.size())
+ {
+ if(beta_ids.size()>2)
+ {
+ std::vector<apollota::SimplePoint> controls_center(beta_ids.size());
+ std::vector<apollota::SimplePoint> controls_up(beta_ids.size());
+ std::vector<apollota::SimplePoint> controls_right(beta_ids.size());
+ for(std::size_t j=0;j<beta_ids.size();j++)
+ {
+ const RibbonVertebra& rv=controls[beta_ids[j]];
+ controls_center[j]=rv.center;
+ controls_up[j]=rv.up;
+ controls_right[j]=rv.right;
+ }
+ for(std::size_t j=1;(j+1)<beta_ids.size();j++)
+ {
+ const double t=1.0/static_cast<double>(beta_ids.size()-1)*static_cast<double>(j);
+ RibbonVertebra& rv=controls[beta_ids[j]];
+ rv.center=apollota::bezier_curve_point(controls_center, t);
+ rv.up=apollota::bezier_curve_point(controls_up, t);
+ rv.right=apollota::bezier_curve_point(controls_right, t);
+ }
+ }
+ beta_ids.clear();
+ }
+ }
+ if(controls.size()>=4)
+ {
+ for(std::size_t i=0;i+1<controls.size();i++)
+ {
+ int ss_types[4]={(i>0 ? controls[i-1].ss_type : 0), controls[i].ss_type, controls[i+1].ss_type, (i+2<controls.size() ? controls[i+2].ss_type : 0)};
+ std::vector<apollota::SimplePoint> strip_center;
+ std::vector<apollota::SimplePoint> strip_up;
+ std::vector<apollota::SimplePoint> strip_right;
+ if(i==0 || (ss_types[0]!=2 && ss_types[1]==2 && ss_types[2]==2))
+ {
+ strip_center=apollota::interpolate_using_cubic_hermite_spline(controls[i].center+(controls[i].center-controls[i+1].center), controls[i].center, controls[i+1].center, controls[i+2].center, k, steps);
+ strip_up=apollota::interpolate_using_cubic_hermite_spline(controls[i].up+(controls[i].up-controls[i+1].up), controls[i].up, controls[i+1].up, controls[i+2].up, k, steps);
+ strip_right=apollota::interpolate_using_cubic_hermite_spline(controls[i].right+(controls[i].right-controls[i+1].right), controls[i].right, controls[i+1].right, controls[i+2].right, k, steps);
+ }
+ else if(i+2==controls.size() || (ss_types[1]==2 && ss_types[2]==2 && ss_types[3]!=2))
+ {
+ strip_center=apollota::interpolate_using_cubic_hermite_spline(controls[i-1].center, controls[i].center, controls[i+1].center, controls[i+1].center+(controls[i+1].center-controls[i].center), k, steps);
+ strip_up=apollota::interpolate_using_cubic_hermite_spline(controls[i-1].up, controls[i].up, controls[i+1].up, controls[i+1].up+(controls[i+1].up-controls[i].up), k, steps);
+ strip_right=apollota::interpolate_using_cubic_hermite_spline(controls[i-1].right, controls[i].right, controls[i+1].right, controls[i+1].right+(controls[i+1].right-controls[i].right), k, steps);
+ }
+ else
+ {
+ strip_center=apollota::interpolate_using_cubic_hermite_spline(controls[i-1].center, controls[i].center, controls[i+1].center, controls[i+2].center, k, steps);
+ strip_up=apollota::interpolate_using_cubic_hermite_spline(controls[i-1].up, controls[i].up, controls[i+1].up, controls[i+2].up, k, steps);
+ strip_right=apollota::interpolate_using_cubic_hermite_spline(controls[i-1].right, controls[i].right, controls[i+1].right, controls[i+2].right, k, steps);
+ }
+ if(!strip_center.empty() && strip_center.size()==strip_up.size() && strip_center.size()==strip_right.size())
+ {
+ std::vector<RibbonVertebra>& result_a=result[ros[i].crad];
+ std::vector<RibbonVertebra>& result_b=result[ros[i+1].crad];
+ result_a.reserve(strip_center.size()/2+1);
+ result_b.reserve(strip_center.size()/2+1);
+ for(std::size_t j=0;j<strip_center.size();j++)
+ {
+ RibbonVertebra v;
+ v.center=strip_center[j];
+ v.up=strip_up[j];
+ v.right=strip_right[j];
+ if(ss_types[1]==0 && ss_types[2]!=0 && ss_types[3]!=0 && ss_types[2]==ss_types[3])
+ {
+ v.ss_type=controls[i].ss_type;
+ result_a.push_back(v);
+ }
+ else if(ss_types[0]!=0 && ss_types[1]!=0 && ss_types[2]==0 && ss_types[0]==ss_types[1])
+ {
+ v.ss_type=controls[i+1].ss_type;
+ result_b.push_back(v);
+ }
+ else
+ {
+ if(j<strip_center.size()/2)
+ {
+ v.ss_type=controls[i].ss_type;
+ result_a.push_back(v);
+ }
+ else if(j==strip_center.size()/2)
+ {
+ v.ss_type=controls[i].ss_type;
+ result_a.push_back(v);
+ v.ss_type=controls[i+1].ss_type;
+ result_b.push_back(v);
+ }
+ else
+ {
+ v.ss_type=controls[i+1].ss_type;
+ result_b.push_back(v);
+ }
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static std::map< CRAD, std::vector<RibbonVertebra> > construct_ribbon_spine(const std::vector< std::pair<CRAD, BallValue> >& list_of_balls, const double k, const int steps)
+ {
+ std::map< CRAD, std::vector<RibbonVertebra> > result;
+ const std::vector< std::vector<ResidueOrientation> > residue_orientations=collect_residue_orientations(list_of_balls);
+ for(std::size_t i=0;i<residue_orientations.size();i++)
+ {
+ std::map< CRAD, std::vector<RibbonVertebra> > partial_result=construct_ribbon_spine(residue_orientations[i], k, steps);
+ result.insert(partial_result.begin(), partial_result.end());
+ }
+ return result;
+ }
+};
+
+}
+
+#endif /* DRAWING_CARTOONS_H_ */
diff --git a/src/modescommon/drawing_utilities.h b/src/modescommon/drawing_utilities.h
new file mode 100644
index 0000000..b232f1a
--- /dev/null
+++ b/src/modescommon/drawing_utilities.h
@@ -0,0 +1,185 @@
+#ifndef DRAWING_UTILITIES_H_
+#define DRAWING_UTILITIES_H_
+
+#include "../auxiliaries/chain_residue_atom_descriptor.h"
+#include "../auxiliaries/opengl_printer.h"
+
+namespace
+{
+
+typedef auxiliaries::ChainResidueAtomDescriptor CRAD;
+
+class DrawingParametersWrapper
+{
+public:
+ unsigned int default_color;
+ std::string adjunct_gradient;
+ double adjunct_gradient_blue;
+ double adjunct_gradient_red;
+ bool adjuncts_rgb;
+ bool random_colors;
+ bool random_colors_by_chain;
+ double alpha_opacity;
+ bool use_labels;
+ bool rainbow_gradient;
+
+ DrawingParametersWrapper() :
+ default_color(0xFFFFFF),
+ adjunct_gradient(""),
+ adjunct_gradient_blue(0.0),
+ adjunct_gradient_red(1.0),
+ adjuncts_rgb(false),
+ random_colors(false),
+ random_colors_by_chain(false),
+ alpha_opacity(1.0),
+ use_labels(false),
+ rainbow_gradient(false)
+ {
+ }
+
+ template<typename T>
+ void process(const T& descriptor, const std::map<std::string, double>& adjuncts, auxiliaries::OpenGLPrinter& opengl_printer) const
+ {
+ if(use_labels)
+ {
+ opengl_printer.add_label(construct_label(descriptor));
+ }
+
+ if(!adjunct_gradient.empty() && adjunct_gradient_blue!=adjunct_gradient_red)
+ {
+ if(adjuncts.count(adjunct_gradient)<1)
+ {
+ opengl_printer.add_color(default_color);
+ }
+ else
+ {
+ double value=adjuncts.find(adjunct_gradient)->second;
+ if(adjunct_gradient_blue<adjunct_gradient_red)
+ {
+ value=(value-adjunct_gradient_blue)/(adjunct_gradient_red-adjunct_gradient_blue);
+ }
+ else
+ {
+ value=1.0-((value-adjunct_gradient_red)/(adjunct_gradient_blue-adjunct_gradient_red));
+ }
+ if(rainbow_gradient)
+ {
+ opengl_printer.add_color_from_rainbow_gradient(value);
+ }
+ else
+ {
+ opengl_printer.add_color_from_blue_white_red_gradient(value);
+ }
+ }
+ }
+ else if(adjuncts_rgb)
+ {
+ const bool rp=adjuncts.count("r")>0;
+ const bool gp=adjuncts.count("g")>0;
+ const bool bp=adjuncts.count("b")>0;
+ if(!(rp || gp || bp))
+ {
+ opengl_printer.add_color(default_color);
+ }
+ else
+ {
+ opengl_printer.add_color(
+ (rp ? adjuncts.find("r")->second : 0.0),
+ (gp ? adjuncts.find("g")->second : 0.0),
+ (bp ? adjuncts.find("b")->second : 0.0));
+ }
+ }
+ else if(random_colors)
+ {
+ opengl_printer.add_color(calc_color_integer(descriptor));
+ }
+ else if(random_colors_by_chain)
+ {
+ opengl_printer.add_color(calc_color_integer_by_chain(descriptor));
+ }
+ }
+
+private:
+ static unsigned int calc_string_color_integer(const std::string& str)
+ {
+ const long generator=123456789;
+ const long limiter=0xFFFFFF;
+ long hash=generator;
+ for(std::size_t i=0;i<str.size();i++)
+ {
+ hash+=static_cast<long>(str[i]+1)*static_cast<long>(i+1)*generator;
+ }
+ return static_cast<unsigned int>(hash%limiter);
+ }
+
+ static unsigned int calc_lighter_color_integer(const unsigned int color)
+ {
+ return std::min(color+static_cast<unsigned int>(0x444444), static_cast<unsigned int>(0xFFFFFF));
+ }
+
+ static unsigned int calc_color_integer(const CRAD& crad)
+ {
+ return calc_string_color_integer(crad.str());
+ }
+
+ static unsigned int calc_color_integer(const std::pair<CRAD, CRAD>& crads)
+ {
+ return calc_string_color_integer(
+ crads.first<crads.second ?
+ (crads.first.str()+crads.second.str()) :
+ (crads.second.str()+crads.first.str()));
+ }
+
+ static unsigned int calc_color_integer_by_chain(const CRAD& crad)
+ {
+ return calc_lighter_color_integer(calc_string_color_integer(crad.chainID));
+ }
+
+ static unsigned int calc_color_integer_by_chain(const std::pair<CRAD, CRAD>& crads)
+ {
+ return calc_lighter_color_integer(calc_string_color_integer(crads.first.chainID<crads.second.chainID ? (crads.first.chainID+crads.second.chainID) : (crads.second.chainID+crads.first.chainID)));
+ }
+
+ static std::string construct_label(const CRAD& crad)
+ {
+ std::ostringstream output;
+ output << "[ ";
+ if(!crad.chainID.empty())
+ {
+ output << crad.chainID;
+ output << " ";
+ }
+ if(crad.resSeq!=CRAD::null_num())
+ {
+ output << crad.resSeq;
+ if(!crad.iCode.empty())
+ {
+ output << crad.iCode;
+ }
+ output << " ";
+ }
+ if(!crad.resName.empty())
+ {
+ output << crad.resName;
+ output << " ";
+ }
+ if(!crad.name.empty())
+ {
+ output << crad.name;
+ output << " ";
+ }
+ output << "]";
+ return output.str();
+ }
+
+ static std::string construct_label(const std::pair<CRAD, CRAD>& crads)
+ {
+ std::ostringstream output;
+ output << construct_label(crads.first) << " " << construct_label(crads.second);
+ return output.str();
+ }
+};
+
+}
+
+#endif /* DRAWING_UTILITIES_H_ */
diff --git a/src/modescommon/filepath_utilities.h b/src/modescommon/filepath_utilities.h
new file mode 100644
index 0000000..94d783e
--- /dev/null
+++ b/src/modescommon/filepath_utilities.h
@@ -0,0 +1,38 @@
+#ifndef FILEPATH_UTILITIES_H_
+#define FILEPATH_UTILITIES_H_
+
+#include <string>
+#include <set>
+
+namespace
+{
+
+std::size_t calc_common_path_start_length(const std::set<std::string>& filenames)
+{
+ std::size_t common_path_start_length=0;
+ if(filenames.size()>1)
+ {
+ const std::string& first_filename=(*filenames.begin());
+ bool common_start=true;
+ for(std::size_t pos=0;(common_start && pos<first_filename.size());pos++)
+ {
+ for(std::set<std::string>::const_iterator it=filenames.begin();(common_start && it!=filenames.end());++it)
+ {
+ const std::string& filename=(*it);
+ if(!(pos<filename.size() && filename[pos]==first_filename[pos]))
+ {
+ common_start=false;
+ }
+ }
+ if(common_start && (first_filename[pos]=='/' || first_filename[pos]=='\\'))
+ {
+ common_path_start_length=(pos+1);
+ }
+ }
+ }
+ return common_path_start_length;
+}
+
+}
+
+#endif /* FILEPATH_UTILITIES_H_ */
diff --git a/src/modescommon/generic_utilities.h b/src/modescommon/generic_utilities.h
new file mode 100644
index 0000000..2326abd
--- /dev/null
+++ b/src/modescommon/generic_utilities.h
@@ -0,0 +1,42 @@
+#ifndef GENERIC_UTILITIES_H_
+#define GENERIC_UTILITIES_H_
+
+#include <map>
+
+namespace
+{
+
+class GenericUtilities
+{
+public:
+ template<typename T>
+ static std::map<typename T::key_type, std::pair<typename T::mapped_type, typename T::mapped_type> > merge_two_maps(const T& a, const T& b)
+ {
+ std::map<typename T::key_type, std::pair<typename T::mapped_type, typename T::mapped_type> > result;
+ typename T::const_iterator a_it=a.begin();
+ typename T::const_iterator b_it=b.begin();
+ while(a_it!=a.end() && b_it!=b.end())
+ {
+ if(a_it->first==b_it->first)
+ {
+ result.insert(result.end(), std::make_pair(a_it->first, std::make_pair(a_it->second, b_it->second)));
+ ++a_it;
+ ++b_it;
+ }
+ else if(a_it->first<b_it->first)
+ {
+ ++a_it;
+ }
+ else if(b_it->first<a_it->first)
+ {
+ ++b_it;
+ }
+ }
+ return result;
+ }
+};
+
+}
+
+
+#endif /* GENERIC_UTILITIES_H_ */
diff --git a/src/modescommon/matching_utilities.h b/src/modescommon/matching_utilities.h
new file mode 100644
index 0000000..0824db7
--- /dev/null
+++ b/src/modescommon/matching_utilities.h
@@ -0,0 +1,189 @@
+#ifndef MATCHING_UTILITIES_H_
+#define MATCHING_UTILITIES_H_
+
+#include "../auxiliaries/chain_residue_atom_descriptor.h"
+#include "../auxiliaries/io_utilities.h"
+
+namespace
+{
+
+class MatchingUtilities
+{
+public:
+ static bool match_crad(const auxiliaries::ChainResidueAtomDescriptor& crad, const std::string& positive_values, const std::string& negative_values)
+ {
+ return ((positive_values.empty() || match_container_with_multiple_values(crad, functor_match_crad_with_single_value(), positive_values))
+ && (negative_values.empty() || !match_container_with_multiple_values(crad, functor_match_crad_with_single_value(), negative_values)));
+ }
+
+ static bool match_set_of_tags(const std::set<std::string>& tags, const std::string& positive_values, const std::string& negative_values)
+ {
+ return ((positive_values.empty() || match_container_with_multiple_values(tags, functor_match_set_of_tags_with_single_value(), positive_values))
+ && (negative_values.empty() || !match_container_with_multiple_values(tags, functor_match_set_of_tags_with_single_value(), negative_values)));
+ }
+
+ static bool match_map_of_adjuncts(const std::map<std::string, double>& adjuncts, const std::string& positive_values, const std::string& negative_values)
+ {
+ return ((positive_values.empty() || match_container_with_multiple_values(adjuncts, functor_match_map_of_adjuncts_with_single_value(), positive_values))
+ && (negative_values.empty() || !match_container_with_multiple_values(adjuncts, functor_match_map_of_adjuncts_with_single_value(), negative_values)));
+ }
+
+ static bool match_crad_with_set_of_crads(const auxiliaries::ChainResidueAtomDescriptor& crad, const std::set<auxiliaries::ChainResidueAtomDescriptor>& set_of_crads)
+ {
+ if(set_of_crads.count(crad)>0)
+ {
+ return true;
+ }
+ for(std::set<auxiliaries::ChainResidueAtomDescriptor>::const_iterator it=set_of_crads.begin();it!=set_of_crads.end();++it)
+ {
+ if(crad.contains(*it))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ static bool match_crads_pair_with_set_of_crads_pairs(
+ const auxiliaries::ChainResidueAtomDescriptorsPair& crads_pair,
+ const std::set<auxiliaries::ChainResidueAtomDescriptorsPair>& crads_pairs)
+ {
+ if(crads_pairs.count(crads_pair)>0)
+ {
+ return true;
+ }
+ for(std::set<auxiliaries::ChainResidueAtomDescriptorsPair>::const_iterator it=crads_pairs.begin();it!=crads_pairs.end();++it)
+ {
+ if((crads_pair.a.contains(it->a) && crads_pair.b.contains(it->b)) ||
+ (crads_pair.a.contains(it->b) && crads_pair.b.contains(it->a)))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ static std::pair<bool, double> match_crad_with_map_of_crads(const auxiliaries::ChainResidueAtomDescriptor& crad, const std::map<auxiliaries::ChainResidueAtomDescriptor, double>& map_of_crads)
+ {
+ std::map<auxiliaries::ChainResidueAtomDescriptor, double>::const_iterator result_it=map_of_crads.find(crad);
+ if(result_it==map_of_crads.end())
+ {
+ result_it=map_of_crads.find(crad.without_atom());
+ }
+ if(result_it==map_of_crads.end())
+ {
+ for(std::map<auxiliaries::ChainResidueAtomDescriptor, double>::const_iterator it=map_of_crads.begin();result_it==map_of_crads.end() && it!=map_of_crads.end();++it)
+ {
+ if(crad.contains(it->first))
+ {
+ result_it=it;
+ }
+ }
+ }
+ if(result_it!=map_of_crads.end())
+ {
+ return std::pair<bool, double>(true, result_it->second);
+ }
+ return std::pair<bool, double>(false, 0.0);
+ }
+
+ static std::pair<bool, double> match_crad_with_map_of_crads_pairs(const auxiliaries::ChainResidueAtomDescriptorsPair& crads_pair, const std::map<auxiliaries::ChainResidueAtomDescriptorsPair, double>& map_of_crads_pairs)
+ {
+ std::map<auxiliaries::ChainResidueAtomDescriptorsPair, double>::const_iterator result_it=map_of_crads_pairs.find(crads_pair);
+ if(result_it==map_of_crads_pairs.end())
+ {
+ result_it=map_of_crads_pairs.find(auxiliaries::ChainResidueAtomDescriptorsPair(crads_pair.a.without_atom(), crads_pair.b.without_atom()));
+ }
+ if(result_it==map_of_crads_pairs.end())
+ {
+ for(std::map<auxiliaries::ChainResidueAtomDescriptorsPair, double>::const_iterator it=map_of_crads_pairs.begin();result_it==map_of_crads_pairs.end() && it!=map_of_crads_pairs.end();++it)
+ {
+ if((crads_pair.a.contains(it->first.a) && crads_pair.b.contains(it->first.b)) ||
+ (crads_pair.a.contains(it->first.b) && crads_pair.b.contains(it->first.a)))
+ {
+ result_it=it;
+ }
+ }
+ }
+ if(result_it!=map_of_crads_pairs.end())
+ {
+ return std::pair<bool, double>(true, result_it->second);
+ }
+ return std::pair<bool, double>(false, 0.0);
+ }
+
+private:
+ template<typename T, typename F>
+ static bool match_container_with_multiple_values(const T& container, const F& matcher, const std::string& values)
+ {
+ std::set<std::string> or_set;
+ auxiliaries::IOUtilities('|').read_string_lines_to_set(values, or_set);
+ for(std::set<std::string>::const_iterator it=or_set.begin();it!=or_set.end();++it)
+ {
+ std::set<std::string> and_set;
+ auxiliaries::IOUtilities('&').read_string_lines_to_set(*it, and_set);
+ bool and_result=true;
+ for(std::set<std::string>::const_iterator jt=and_set.begin();and_result && jt!=and_set.end();++jt)
+ {
+ and_result=(and_result && matcher(container, *jt));
+ }
+ if(and_result)
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ struct functor_match_crad_with_single_value
+ {
+ inline bool operator()(const auxiliaries::ChainResidueAtomDescriptor& crad, const std::string& value) const
+ {
+ return auxiliaries::ChainResidueAtomDescriptor::match_with_member_selection_string(crad, value);
+ }
+ };
+
+ struct functor_match_set_of_tags_with_single_value
+ {
+ inline bool operator()(const std::set<std::string>& tags, const std::string& value) const
+ {
+ return (tags.count(value)>0);
+ }
+ };
+
+ struct functor_match_map_of_adjuncts_with_single_value
+ {
+ inline bool operator()(const std::map<std::string, double>& adjuncts, const std::string& value) const
+ {
+ const std::size_t eq_pos=value.find('=');
+ if(eq_pos!=std::string::npos)
+ {
+ const std::size_t sep_pos=value.find(':', eq_pos);
+ if(sep_pos!=std::string::npos)
+ {
+ std::string spaced_value=value;
+ spaced_value[eq_pos]=' ';
+ spaced_value[sep_pos]=' ';
+ std::istringstream input(spaced_value);
+ if(input.good())
+ {
+ std::string name;
+ double a=0.0;
+ double b=0.0;
+ input >> name >> a >> b;
+ if(!input.fail() && !name.empty() && a<=b)
+ {
+ std::map<std::string, double>::const_iterator it=adjuncts.find(name);
+ return (it!=adjuncts.end() && it->second>=a && it->second<=b);
+ }
+ }
+ }
+ }
+ return false;
+ }
+ };
+};
+
+}
+
+#endif /* MATCHING_UTILITIES_H_ */
diff --git a/src/modescommon/mock_solvent_utilities.h b/src/modescommon/mock_solvent_utilities.h
new file mode 100644
index 0000000..7f186ec
--- /dev/null
+++ b/src/modescommon/mock_solvent_utilities.h
@@ -0,0 +1,21 @@
+#ifndef MOCK_SOLVENT_UTILITIES_H_
+#define MOCK_SOLVENT_UTILITIES_H_
+
+#include "../auxiliaries/chain_residue_atom_descriptor.h"
+
+namespace
+{
+
+inline std::string mock_solvent_name()
+{
+ return std::string("w");
+}
+
+inline bool identify_mock_solvent(const auxiliaries::ChainResidueAtomDescriptor& crad)
+{
+ return (crad.name==mock_solvent_name() && crad.resName==mock_solvent_name());
+}
+
+}
+
+#endif /* MOCK_SOLVENT_UTILITIES_H_ */
diff --git a/src/modescommon/properties_value.h b/src/modescommon/properties_value.h
new file mode 100644
index 0000000..716cfc8
--- /dev/null
+++ b/src/modescommon/properties_value.h
@@ -0,0 +1,81 @@
+#ifndef PROPERTIES_VALUE_H_
+#define PROPERTIES_VALUE_H_
+
+#include <set>
+#include <map>
+
+#include "../auxiliaries/io_utilities.h"
+
+namespace
+{
+
+struct PropertiesValue
+{
+ std::set<std::string> tags;
+ std::map<std::string, double> adjuncts;
+
+ void update_tags(const std::string& str)
+ {
+ if(!str.empty() && str[0]!='.')
+ {
+ std::set<std::string> input_tags;
+ auxiliaries::IOUtilities(';').read_string_lines_to_set(str, input_tags);
+ if(!input_tags.empty())
+ {
+ tags.insert(input_tags.begin(), input_tags.end());
+ }
+ }
+ }
+
+ void update_adjuncts(const std::string& str)
+ {
+ if(!str.empty() && str[0]!='.')
+ {
+ std::map<std::string, double> input_adjuncts;
+ auxiliaries::IOUtilities(';', '=').read_string_lines_to_map(str, input_adjuncts);
+ for(std::map<std::string, double>::const_iterator it=input_adjuncts.begin();it!=input_adjuncts.end();++it)
+ {
+ adjuncts[it->first]=it->second;
+ }
+ }
+ }
+};
+
+inline std::ostream& operator<<(std::ostream& output, const PropertiesValue& value)
+{
+ if(value.tags.empty())
+ {
+ output << ".";
+ }
+ else
+ {
+ auxiliaries::IOUtilities(';').write_set(value.tags, output);
+ }
+ output << " ";
+ if(value.adjuncts.empty())
+ {
+ output << ".";
+ }
+ else
+ {
+ auxiliaries::IOUtilities(';', '=').write_map(value.adjuncts, output);
+ }
+ return output;
+}
+
+inline std::istream& operator>>(std::istream& input, PropertiesValue& value)
+{
+ std::string tags_str;
+ std::string adjuncts_str;
+ input >> tags_str >> adjuncts_str;
+ if(!input.fail())
+ {
+ value.update_tags(tags_str);
+ value.update_adjuncts(adjuncts_str);
+ }
+ return input;
+}
+
+}
+
+#endif /* PROPERTIES_VALUE_H_ */
diff --git a/src/modescommon/sequence_utilities.h b/src/modescommon/sequence_utilities.h
new file mode 100644
index 0000000..5c8e112
--- /dev/null
+++ b/src/modescommon/sequence_utilities.h
@@ -0,0 +1,127 @@
+#ifndef SEQUENCE_UTILITIES_H_
+#define SEQUENCE_UTILITIES_H_
+
+#include <fstream>
+#include <sstream>
+
+#include "../auxiliaries/chain_residue_atom_descriptor.h"
+#include "../auxiliaries/residue_letters_coding.h"
+#include "../auxiliaries/pairwise_sequence_alignment.h"
+#include "../auxiliaries/residue_atoms_reference.h"
+
+namespace
+{
+
+class SequenceUtilities
+{
+public:
+ static std::string read_sequence_from_stream(std::istream& input)
+ {
+ std::string result;
+ while(input.good())
+ {
+ std::string line;
+ std::getline(input, line);
+ if(!line.empty() && line[0]!='>')
+ {
+ std::istringstream sinput(line);
+ while(sinput.good())
+ {
+ std::string token;
+ sinput >> token;
+ for(std::size_t i=0;i<token.size();i++)
+ {
+ const char c=token[i];
+ if(c>='A' && c<='Z')
+ {
+ result.append(1, c);
+ }
+ else if(c>='a' && c<='z')
+ {
+ result.append(1, c-('a'-'A'));
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static std::string read_sequence_from_file(const std::string& filename)
+ {
+ if(!filename.empty())
+ {
+ std::ifstream finput(filename.c_str(), std::ios::in);
+ return read_sequence_from_stream(finput);
+ }
+ else
+ {
+ return std::string();
+ }
+ }
+
+ template<typename T>
+ static std::string convert_residue_sequence_container_to_string(const T& residue_sequence_container)
+ {
+ std::string seq;
+ for(typename T::const_iterator it=residue_sequence_container.begin();it!=residue_sequence_container.end();++it)
+ {
+ seq+=auxiliaries::ResidueLettersCoding::convert_residue_code_big_to_small(it->resName);
+ }
+ return seq;
+ }
+
+ static std::map<auxiliaries::ChainResidueAtomDescriptor, int> construct_sequence_mapping(const std::vector<auxiliaries::ChainResidueAtomDescriptor>& residue_sequence_vector, const std::string& reference_sequence, const std::string& ref_seq_alignment_output_filename)
+ {
+ std::map<auxiliaries::ChainResidueAtomDescriptor, int> result;
+ if(!residue_sequence_vector.empty() && !reference_sequence.empty())
+ {
+ const std::string seq=convert_residue_sequence_container_to_string(residue_sequence_vector);
+ if(residue_sequence_vector.size()==seq.size())
+ {
+ const std::vector< std::pair<int, int> >& alignment=auxiliaries::PairwiseSequenceAlignment::construct_sequence_alignment(reference_sequence, seq, auxiliaries::PairwiseSequenceAlignment::SimpleScorer(10, -10, -11, -1), false, 0);
+ for(std::size_t i=0;i<alignment.size();i++)
+ {
+ const std::pair<int, int>& p=alignment[i];
+ if(p.first>=0 && p.second>=0)
+ {
+ result[residue_sequence_vector.at(p.second)]=(p.first+1);
+ }
+ }
+ if(!ref_seq_alignment_output_filename.empty())
+ {
+ std::ofstream foutput(ref_seq_alignment_output_filename.c_str(), std::ios::out);
+ if(foutput.good())
+ {
+ auxiliaries::PairwiseSequenceAlignment::print_sequence_alignment(reference_sequence, seq, alignment, foutput);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ static double calculate_sequence_identity(const std::string& seq_a, const std::string& seq_b)
+ {
+ const std::size_t max_seq_size=std::max(seq_a.size(), seq_b.size());
+ if(max_seq_size>0)
+ {
+ int matches=0.0;
+ const std::vector< std::pair<int, int> >& alignment=auxiliaries::PairwiseSequenceAlignment::construct_sequence_alignment(seq_a, seq_b, auxiliaries::PairwiseSequenceAlignment::SimpleScorer(10, -10, -11, -1), false, 0);
+ for(std::size_t i=0;i<alignment.size();i++)
+ {
+ const std::pair<int, int>& p=alignment[i];
+ if(p.first>=0 && p.first<static_cast<int>(seq_a.size()) && p.second>=0 && p.second<static_cast<int>(seq_b.size()) && seq_a[p.first]==seq_b[p.second])
+ {
+ matches++;
+ }
+ }
+ return (static_cast<double>(matches)/static_cast<double>(max_seq_size));
+ }
+ return 0.0;
+ }
+};
+
+}
+
+#endif /* SEQUENCE_UTILITIES_H_ */
diff --git a/src/modescommon/statistics_utilities.h b/src/modescommon/statistics_utilities.h
new file mode 100644
index 0000000..580ec76
--- /dev/null
+++ b/src/modescommon/statistics_utilities.h
@@ -0,0 +1,63 @@
+#ifndef STATISTICS_UTILITIES_H_
+#define STATISTICS_UTILITIES_H_
+
+namespace
+{
+
+struct ValueStat
+{
+ double sum;
+ double sum_of_squares;
+ unsigned long count;
+
+ ValueStat() : sum(0.0), sum_of_squares(0.0), count(0)
+ {
+ }
+
+ void add(const double value)
+ {
+ sum+=value;
+ sum_of_squares+=(value*value);
+ count++;
+ }
+
+ double mean() const
+ {
+ return (sum/static_cast<double>(count));
+ }
+
+ double sd() const
+ {
+ return sqrt((sum_of_squares/static_cast<double>(count))-(mean()*mean()));
+ }
+};
+
+struct NormalDistributionParameters
+{
+ double mean;
+ double sd;
+
+ NormalDistributionParameters() : mean(0.0), sd(1.0)
+ {
+ }
+
+ NormalDistributionParameters(const double mean, const double sd) : mean(mean), sd(sd)
+ {
+ }
+};
+
+inline std::ostream& operator<<(std::ostream& output, const NormalDistributionParameters& v)
+{
+ output << v.mean << " " << v.sd;
+ return output;
+}
+
+inline std::istream& operator>>(std::istream& input, NormalDistributionParameters& v)
+{
+ input >> v.mean >> v.sd;
+ return input;
+}
+
+}
+
+#endif /* STATISTICS_UTILITIES_H_ */
diff --git a/src/modescommon/svg_writer.h b/src/modescommon/svg_writer.h
new file mode 100644
index 0000000..7d56b52
--- /dev/null
+++ b/src/modescommon/svg_writer.h
@@ -0,0 +1,83 @@
+#ifndef SVG_WRITER_H_
+#define SVG_WRITER_H_
+
+#include "../auxiliaries/xml_writer.h"
+
+namespace
+{
+
+class SVGWriter : public auxiliaries::XMLWriter
+{
+public:
+ SVGWriter(const unsigned int width, const unsigned int height) : XMLWriter("svg")
+ {
+ set("width", width);
+ set("height", height);
+ }
+
+ static std::string color_from_red_green_blue_components(const double r, const double g, const double b, const double scale)
+ {
+ std::ostringstream output;
+ output << "rgb(" << static_cast<unsigned int>(r*scale) << "," << static_cast<unsigned int>(g*scale) << "," << static_cast<unsigned int>(b*scale) << ")";
+ return output.str();
+ }
+
+ static std::string color_from_blue_white_red_gradient(const double input_value, const double blue_value, const double red_value)
+ {
+ double value=input_value;
+ if(blue_value<red_value)
+ {
+ value=(value-blue_value)/(red_value-blue_value);
+ }
+ else
+ {
+ value=1.0-((value-red_value)/(blue_value-red_value));
+ }
+ double r=0;
+ double g=0;
+ double b=0;
+ if(value<0.0)
+ {
+ b=1.0;
+ }
+ else if(value>1.0)
+ {
+ r=1.0;
+ }
+ else if(value<=0.5)
+ {
+ b=1.0;
+ r=(value/0.5);
+ g=r;
+ }
+ else if(value>0.5)
+ {
+ r=1.0;
+ b=(1.0-(value-0.5)/0.5);
+ g=b;
+ }
+ return color_from_red_green_blue_components(r, g, b, 255.0);
+ }
+
+ SVGWriter& add_rect(const unsigned int x, const unsigned int y, const unsigned int width, const unsigned int height, const std::string& style)
+ {
+ add_child(XMLWriter("rect").set("x", x).set("y", y).set("width", width).set("height", height).set("style", style));
+ return (*this);
+ }
+
+ SVGWriter& add_circle(const unsigned int cx, const unsigned int cy, const unsigned int r, const std::string& style)
+ {
+ add_child(XMLWriter("circle").set("cx", cx).set("cy", cy).set("r", r).set("style", style));
+ return (*this);
+ }
+
+ SVGWriter& add_line(const unsigned int x1, const unsigned int y1, const unsigned int x2, const unsigned int y2, const std::string& style)
+ {
+ add_child(XMLWriter("line").set("x1", x1).set("y1", y1).set("x2", x2).set("y2", y2).set("style", style));
+ return (*this);
+ }
+};
+
+}
+
+#endif /* SVG_WRITER_H_ */
diff --git a/src/modescommon/vectorization_utilities.h b/src/modescommon/vectorization_utilities.h
new file mode 100644
index 0000000..ab27122
--- /dev/null
+++ b/src/modescommon/vectorization_utilities.h
@@ -0,0 +1,400 @@
+#ifndef VECTORIZATION_UTILITIES_H_
+#define VECTORIZATION_UTILITIES_H_
+
+#include <vector>
+#include <list>
+#include <map>
+
+#include "filepath_utilities.h"
+
+namespace
+{
+
+template<typename VectorNameType, typename ValueNameType, typename ValueType>
+class VectorizationUtilities
+{
+public:
+ typedef std::map<ValueNameType, ValueType> Map;
+ typedef std::map<ValueNameType, std::size_t> MapKeysIDs;
+ typedef std::map<VectorNameType, Map> MapOfMaps;
+ typedef std::vector<ValueType> Vector;
+ typedef std::map<std::string, Vector> MapOfVectors;
+ typedef std::vector<typename MapOfVectors::const_iterator> IteratorsOfMapOfVectors;
+ typedef std::vector< std::pair< std::size_t, std::list<std::size_t> > > Clusters;
+
+ static MapOfMaps read_map_of_maps_from_multiple_files(const std::set<std::string>& input_files)
+ {
+ MapOfMaps map_of_maps;
+ if(!input_files.empty())
+ {
+ const std::size_t common_path_start_length=calc_common_path_start_length(input_files);
+ for(std::set<std::string>::const_iterator it=input_files.begin();it!=input_files.end();++it)
+ {
+ const std::string& filename=(*it);
+ const Map map=auxiliaries::IOUtilities().read_file_lines_to_map<Map>(filename);
+ if(!map.empty())
+ {
+ map_of_maps[filename.substr(common_path_start_length)]=map;
+ }
+ }
+ }
+ return map_of_maps;
+ }
+
+ static const MapKeysIDs collect_map_keys_ids(const MapOfMaps& map_of_maps)
+ {
+ MapKeysIDs map_keys_ids;
+ for(typename MapOfMaps::const_iterator it=map_of_maps.begin();it!=map_of_maps.end();++it)
+ {
+ const Map& map=it->second;
+ for(typename Map::const_iterator jt=map.begin();jt!=map.end();++jt)
+ {
+ map_keys_ids[jt->first]=0;
+ }
+ }
+ {
+ std::size_t i=0;
+ for(typename MapKeysIDs::iterator it=map_keys_ids.begin();it!=map_keys_ids.end();++it)
+ {
+ it->second=i;
+ i++;
+ }
+ }
+ return map_keys_ids;
+ }
+
+ static MapOfVectors collect_map_of_vectors(
+ const MapOfMaps& map_of_maps,
+ const MapKeysIDs& map_keys_ids)
+ {
+ MapOfVectors map_of_vectors;
+ for(typename MapOfMaps::const_iterator it=map_of_maps.begin();it!=map_of_maps.end();++it)
+ {
+ const Map& map=it->second;
+ Vector& vector=map_of_vectors[it->first];
+ vector.resize(map_keys_ids.size());
+ for(typename Map::const_iterator jt=map.begin();jt!=map.end();++jt)
+ {
+ typename MapKeysIDs::const_iterator map_keys_ids_it=map_keys_ids.find(jt->first);
+ if(map_keys_ids_it!=map_keys_ids.end())
+ {
+ vector[map_keys_ids_it->second]=jt->second;
+ }
+ }
+ }
+ return map_of_vectors;
+ }
+
+ static void print_map_of_areas_vectors(
+ const MapKeysIDs& map_keys_ids,
+ const MapOfVectors& map_of_vectors)
+ {
+ std::cout << "title";
+ for(typename MapKeysIDs::const_iterator it=map_keys_ids.begin();it!=map_keys_ids.end();++it)
+ {
+ std::cout << " " << it->first;
+ }
+ std::cout << "\n";
+ for(typename MapOfVectors::const_iterator it=map_of_vectors.begin();it!=map_of_vectors.end();++it)
+ {
+ std::cout << it->first;
+ const Vector& vector=it->second;
+ for(std::size_t i=0;i<vector.size();i++)
+ {
+ std::cout << " " << vector[i];
+ }
+ std::cout << "\n";
+ }
+ }
+
+ static void print_map_of_areas_vectors_transposed(
+ const MapKeysIDs& map_keys_ids,
+ const MapOfVectors& map_of_vectors)
+ {
+ std::cout << "contact";
+ for(typename MapOfVectors::const_iterator it=map_of_vectors.begin();it!=map_of_vectors.end();++it)
+ {
+ std::cout << " " << it->first;
+ }
+ std::cout << "\n";
+ std::size_t i=0;
+ for(typename MapKeysIDs::const_iterator it=map_keys_ids.begin();it!=map_keys_ids.end();++it)
+ {
+ std::cout << it->first;
+ for(typename MapOfVectors::const_iterator jt=map_of_vectors.begin();jt!=map_of_vectors.end();++jt)
+ {
+ const Vector& vector=jt->second;
+ std::cout << " " << (i<vector.size() ? vector[i] : 0.0);
+ }
+ std::cout << "\n";
+ i++;
+ }
+ }
+
+ template<typename Functor>
+ static void print_similarity_matrix(const MapOfVectors& map_of_vectors, const std::string& output_file, Functor functor)
+ {
+ if(map_of_vectors.empty() || output_file.empty())
+ {
+ return;
+ }
+ std::ofstream output(output_file.c_str(), std::ios::out);
+ if(!output.good())
+ {
+ return;
+ }
+ for(typename MapOfVectors::const_iterator it=map_of_vectors.begin();it!=map_of_vectors.end();++it)
+ {
+ output << (it==map_of_vectors.begin() ? "" : " ") << it->first;
+ }
+ output << "\n";
+ for(typename MapOfVectors::const_iterator it=map_of_vectors.begin();it!=map_of_vectors.end();++it)
+ {
+ for(typename MapOfVectors::const_iterator jt=map_of_vectors.begin();jt!=map_of_vectors.end();++jt)
+ {
+ output << (jt==map_of_vectors.begin() ? "" : " ") << functor(it->second, jt->second);
+ }
+ output << "\n";
+ }
+ }
+
+ static IteratorsOfMapOfVectors collect_iterators_of_map_of_vectors(const MapOfVectors& map)
+ {
+ IteratorsOfMapOfVectors iterators;
+ iterators.reserve(map.size());
+ for(typename MapOfVectors::const_iterator it=map.begin();it!=map.end();++it)
+ {
+ iterators.push_back(it);
+ }
+ return iterators;
+ }
+
+ template<typename Functor>
+ static Clusters calc_clusters(
+ const IteratorsOfMapOfVectors& iterators_of_map_of_vectors,
+ Functor functor,
+ const double threshold,
+ const bool eliminate_false_singletons,
+ const bool invert_similarity)
+ {
+ typedef std::list<std::size_t> Neighbors;
+ typedef std::vector< std::pair<std::size_t, Neighbors> > ListOfNeighbors;
+ typedef std::map< std::size_t, Neighbors > MapOfNeighbors;
+
+ const double similarity_modifier=(invert_similarity ? -1.0 : 1.0);
+
+ ListOfNeighbors big_clusters;
+ ListOfNeighbors true_singleton_clusters;
+ ListOfNeighbors false_singleton_clusters;
+
+ MapOfNeighbors map_of_available_neighbors;
+ for(std::size_t i=0;i<iterators_of_map_of_vectors.size();i++)
+ {
+ Neighbors& neighbors=map_of_available_neighbors[i];
+ for(std::size_t j=0;j<iterators_of_map_of_vectors.size();j++)
+ {
+ const double similarity=functor(iterators_of_map_of_vectors[i]->second, iterators_of_map_of_vectors[j]->second)*similarity_modifier;
+ if(similarity>=threshold*similarity_modifier)
+ {
+ neighbors.push_back(j);
+ }
+ }
+ }
+
+ std::vector<int> deletion_flags(iterators_of_map_of_vectors.size(), 0);
+ {
+ MapOfNeighbors::iterator map_it=map_of_available_neighbors.begin();
+ while(map_it!=map_of_available_neighbors.end())
+ {
+ if(map_it->second.size()<2)
+ {
+ true_singleton_clusters.push_back(std::make_pair(map_it->first, map_it->second));
+ deletion_flags[map_it->first]=1;
+ MapOfNeighbors::iterator deletion_it=map_it;
+ ++map_it;
+ map_of_available_neighbors.erase(deletion_it);
+ }
+ else
+ {
+ ++map_it;
+ }
+ }
+ }
+
+ while(!map_of_available_neighbors.empty())
+ {
+ MapOfNeighbors::const_iterator map_it_of_most_neighbors=map_of_available_neighbors.end();
+ for(MapOfNeighbors::iterator map_it=map_of_available_neighbors.begin();map_it!=map_of_available_neighbors.end();++map_it)
+ {
+ Neighbors& neighbors=map_it->second;
+ {
+ Neighbors::iterator neighbors_it=neighbors.begin();
+ while(neighbors_it!=neighbors.end())
+ {
+ if(deletion_flags[*neighbors_it]!=0)
+ {
+ Neighbors::iterator deletion_it=neighbors_it;
+ ++neighbors_it;
+ neighbors.erase(deletion_it);
+ }
+ else
+ {
+ ++neighbors_it;
+ }
+ }
+ }
+ if(map_it_of_most_neighbors==map_of_available_neighbors.end() || neighbors.size()>map_it_of_most_neighbors->second.size())
+ {
+ map_it_of_most_neighbors=map_it;
+ }
+ }
+ if(map_it_of_most_neighbors!=map_of_available_neighbors.end())
+ {
+ const std::size_t center=map_it_of_most_neighbors->first;
+ const Neighbors neighbors=map_it_of_most_neighbors->second;
+ for(Neighbors::const_iterator neighbors_it=neighbors.begin();neighbors_it!=neighbors.end();++neighbors_it)
+ {
+ deletion_flags[*neighbors_it]=1;
+ map_of_available_neighbors.erase(*neighbors_it);
+ }
+ deletion_flags[center]=1;
+ map_of_available_neighbors.erase(center);
+ if(neighbors.size()>1)
+ {
+ big_clusters.push_back(std::make_pair(center, neighbors));
+ }
+ else
+ {
+ false_singleton_clusters.push_back(std::make_pair(center, neighbors));
+ }
+ }
+ else
+ {
+ map_of_available_neighbors.clear();
+ }
+ }
+
+ if(eliminate_false_singletons && !false_singleton_clusters.empty())
+ {
+ for(ListOfNeighbors::iterator singletons_it=false_singleton_clusters.begin();singletons_it!=false_singleton_clusters.end();++singletons_it)
+ {
+ double max_similarity=0.0;
+ ListOfNeighbors::iterator big_clusters_it_of_closest=big_clusters.end();
+ for(ListOfNeighbors::iterator big_clusters_it=big_clusters.begin();big_clusters_it!=big_clusters.end();++big_clusters_it)
+ {
+ const double similarity=functor(
+ iterators_of_map_of_vectors[singletons_it->first]->second,
+ iterators_of_map_of_vectors[big_clusters_it->first]->second)*similarity_modifier;
+ if(big_clusters_it_of_closest==big_clusters.end() || similarity>max_similarity)
+ {
+ max_similarity=similarity;
+ big_clusters_it_of_closest=big_clusters_it;
+ }
+ }
+ if(big_clusters_it_of_closest!=big_clusters.end())
+ {
+ big_clusters_it_of_closest->second.push_back(singletons_it->first);
+ }
+ }
+ false_singleton_clusters.clear();
+ }
+
+ ListOfNeighbors clusters=big_clusters;
+ if(!false_singleton_clusters.empty())
+ {
+ clusters.insert(clusters.end(), false_singleton_clusters.begin(), false_singleton_clusters.end());
+ }
+ if(!true_singleton_clusters.empty())
+ {
+ clusters.insert(clusters.end(), true_singleton_clusters.begin(), true_singleton_clusters.end());
+ }
+
+ return clusters;
+ }
+
+ static void print_clusters(
+ const IteratorsOfMapOfVectors& iterators_of_map_of_areas_vectors,
+ const Clusters& clusters,
+ const std::string& output_file)
+ {
+ std::ofstream output(output_file.c_str(), std::ios::out);
+ if(!output.good())
+ {
+ return;
+ }
+
+ for(std::vector< std::pair< std::size_t, std::list<std::size_t> > >::const_iterator clusters_it=clusters.begin();clusters_it!=clusters.end();++clusters_it)
+ {
+ output << iterators_of_map_of_areas_vectors[clusters_it->first]->first;
+ const std::list<std::size_t>& neighbors=clusters_it->second;
+ for(std::list<std::size_t>::const_iterator neighbors_it=neighbors.begin();neighbors_it!=neighbors.end();++neighbors_it)
+ {
+ if((*neighbors_it)!=clusters_it->first)
+ {
+ output << " " << iterators_of_map_of_areas_vectors[*neighbors_it]->first;
+ }
+ }
+ output << "\n";
+ }
+ }
+
+ static Vector calc_consensus_vector(const IteratorsOfMapOfVectors& iterators_of_map_of_vectors)
+ {
+ Vector result;
+ for(std::size_t i=0;i<iterators_of_map_of_vectors.size();i++)
+ {
+ const Vector& v=iterators_of_map_of_vectors[i]->second;
+ if(result.size()<v.size())
+ {
+ result.resize(v.size());
+ }
+ for(std::size_t j=0;j<result.size();j++)
+ {
+ result[j]=result[j]+v[j];
+ }
+ }
+ for(std::size_t j=0;j<result.size();j++)
+ {
+ result[j]=result[j]*(1.0/static_cast<double>(iterators_of_map_of_vectors.size()));
+ }
+ return result;
+ }
+
+ template<typename Functor>
+ static std::multimap<double, std::size_t> calc_consensus_similarities(
+ const IteratorsOfMapOfVectors& iterators_of_map_of_vectors,
+ Functor functor)
+ {
+ std::multimap<double, std::size_t> similarities;
+ const Vector consensus=calc_consensus_vector(iterators_of_map_of_vectors);
+ for(std::size_t i=0;i<iterators_of_map_of_vectors.size();i++)
+ {
+ similarities.insert(std::make_pair(functor(consensus, iterators_of_map_of_vectors[i]->second), i));
+ }
+ return similarities;
+ }
+
+ static void print_consensus_similarities(
+ const IteratorsOfMapOfVectors& iterators_of_map_of_vectors,
+ const std::multimap<double, std::size_t>& similarities,
+ const std::string& output_file)
+ {
+ std::ofstream output(output_file.c_str(), std::ios::out);
+ if(!output.good())
+ {
+ return;
+ }
+
+ for(std::multimap<double, std::size_t>::const_reverse_iterator it=similarities.rbegin();it!=similarities.rend();++it)
+ {
+ if(it->second<iterators_of_map_of_vectors.size())
+ {
+ output << iterators_of_map_of_vectors[it->second]->first << " " << it->first << "\n";
+ }
+ }
+ }
+};
+
+}
+
+#endif /* VECTORIZATION_UTILITIES_H_ */
diff --git a/src/wrapper_get_balls_from_atoms_file_and_calculate_vertices.h b/src/wrapper_get_balls_from_atoms_file_and_calculate_vertices.h
new file mode 100644
index 0000000..b28cbc1
--- /dev/null
+++ b/src/wrapper_get_balls_from_atoms_file_and_calculate_vertices.h
@@ -0,0 +1,229 @@
+#ifndef WRAPPER_GET_BALLS_FROM_ATOMS_FILE_AND_CALCULATE_VERTICES_H_
+#define WRAPPER_GET_BALLS_FROM_ATOMS_FILE_AND_CALCULATE_VERTICES_H_
+
+#include "apollota/spheres_boundary_construction.h"
+#include "apollota/triangulation.h"
+
+#include "auxiliaries/atoms_io.h"
+#include "auxiliaries/atom_radius_assigner.h"
+#include "auxiliaries/io_utilities.h"
+
+class WrapperGetBallsFromAtomsFileAndCalculateVertices
+{
+public:
+ static const std::size_t null_id=apollota::npos;
+
+ struct Ball
+ {
+ double x;
+ double y;
+ double z;
+ double r;
+ std::string name;
+
+ Ball() : x(0.0), y(0.0), z(0.0), r(0.0), name("")
+ {
+ }
+ };
+
+ struct Vertex
+ {
+ double x;
+ double y;
+ double z;
+ double r;
+ unsigned long ball_id[4];
+ bool link_available[4];
+ unsigned long link_vertex_id[4];
+
+ Vertex() : x(0.0), y(0.0), z(0.0), r(0.0)
+ {
+ for(int i=0;i<4;i++)
+ {
+ ball_id[i]=null_id;
+ link_available[i]=false;
+ link_vertex_id[i]=null_id;
+ }
+ }
+ };
+
+ struct Result
+ {
+ std::vector<Ball> balls;
+ std::vector<Vertex> vertices;
+ std::string error;
+ };
+
+ struct Parameters
+ {
+ bool include_heteroatoms;
+ bool include_hydrogens;
+ bool multimodel_chains;
+ bool mmcif;
+ std::string radii_file;
+ double default_radius;
+ bool only_default_radius;
+ double hull_offset;
+ bool exclude_hidden_balls;
+ bool include_surplus_quadruples;
+ double init_radius_for_BSH;
+
+ Parameters() :
+ include_heteroatoms(false),
+ include_hydrogens(false),
+ multimodel_chains(false),
+ mmcif(false),
+ radii_file(""),
+ default_radius(1.70),
+ only_default_radius(false),
+ hull_offset(2.8),
+ exclude_hidden_balls(false),
+ include_surplus_quadruples(false),
+ init_radius_for_BSH(3.5)
+ {
+ }
+ };
+
+ static Result get_balls_from_atoms_file_and_calculate_vertices(std::ifstream& input_file_stream, const Parameters& parameters)
+ {
+ Result result;
+
+ if(!input_file_stream.good())
+ {
+ result.error="Invalid input file stream.";
+ return result;
+ }
+
+ const std::vector<auxiliaries::AtomsIO::AtomRecord> atoms=(parameters.mmcif ?
+ auxiliaries::AtomsIO::MMCIFReader::read_data_from_file_stream(
+ input_file_stream,
+ parameters.include_heteroatoms,
+ parameters.include_hydrogens).atom_records :
+ auxiliaries::AtomsIO::PDBReader::read_data_from_file_stream(input_file_stream,
+ parameters.include_heteroatoms,
+ parameters.include_hydrogens,
+ parameters.multimodel_chains,
+ false).atom_records);
+
+ if(atoms.empty())
+ {
+ result.error="No atoms found in input stream.";
+ return result;
+ }
+
+ auxiliaries::AtomRadiusAssigner atom_radius_assigner(parameters.default_radius);
+ if(!parameters.only_default_radius)
+ {
+ if(parameters.radii_file.empty())
+ {
+ atom_radius_assigner.add_radius_by_descriptor("*", "C*", 1.70);
+ atom_radius_assigner.add_radius_by_descriptor("*", "N*", 1.55);
+ atom_radius_assigner.add_radius_by_descriptor("*", "O*", 1.52);
+ atom_radius_assigner.add_radius_by_descriptor("*", "S*", 1.80);
+ atom_radius_assigner.add_radius_by_descriptor("*", "P*", 1.80);
+ atom_radius_assigner.add_radius_by_descriptor("*", "H*", 1.20);
+ }
+ else
+ {
+ std::ifstream radii_file_stream(parameters.radii_file.c_str(), std::ios::in);
+ auxiliaries::IOUtilities().read_lines_to_container(radii_file_stream, auxiliaries::AtomRadiusAssigner::add_descriptor_and_radius_from_stream_to_atom_radius_assigner, atom_radius_assigner);
+ }
+ }
+
+ std::vector<apollota::SimpleSphere> spheres;
+ spheres.reserve(atoms.size()+8);
+ std::vector<std::string> names;
+ names.reserve(atoms.size()+8);
+ for(std::size_t i=0;i<atoms.size();i++)
+ {
+ const auxiliaries::AtomsIO::AtomRecord& atom=atoms[i];
+ const double radius=atom_radius_assigner.get_atom_radius(atom.resName, atom.name);
+ spheres.push_back(apollota::SimpleSphere(atom, radius));
+ names.push_back(name_atom_ball(atom));
+ }
+ if(parameters.hull_offset>0.0)
+ {
+ const std::vector<apollota::SimpleSphere> artificial_boundary=apollota::construct_artificial_boundary(spheres, parameters.hull_offset);
+ spheres.insert(spheres.end(), artificial_boundary.begin(), artificial_boundary.end());
+ names.insert(names.end(), artificial_boundary.size(), std::string("artificial_hull_ball"));
+ }
+
+ if(spheres.size()!=names.size())
+ {
+ result.error="Could not assign names to all balls.";
+ return result;
+ }
+
+ const apollota::Triangulation::Result triangulation_result=apollota::Triangulation::construct_result(
+ spheres,
+ parameters.init_radius_for_BSH,
+ parameters.exclude_hidden_balls,
+ parameters.include_surplus_quadruples);
+ apollota::Triangulation::VerticesVector vertices_vector=apollota::Triangulation::collect_vertices_vector_from_quadruples_map(triangulation_result.quadruples_map);
+ apollota::Triangulation::VerticesGraph vertices_graph=apollota::Triangulation::construct_vertices_graph(spheres, triangulation_result.quadruples_map);
+
+ if(vertices_vector.size()!=vertices_graph.size())
+ {
+ result.error="Could not construct valid vertices graph.";
+ return result;
+ }
+
+ result.balls.resize(spheres.size());
+ for(std::size_t i=0;i<spheres.size();i++)
+ {
+ const apollota::SimpleSphere& sphere=spheres[i];
+ const std::string& name=names[i];
+ Ball& ball=result.balls[i];
+ ball.x=sphere.x;
+ ball.y=sphere.y;
+ ball.z=sphere.z;
+ ball.r=sphere.r;
+ ball.name=name;
+ }
+
+ result.vertices.resize(vertices_vector.size());
+ for(std::size_t i=0;i<vertices_vector.size();i++)
+ {
+ const apollota::SimpleSphere& tangent_sphere=vertices_vector[i].second;
+ const apollota::Quadruple& quadruple=vertices_vector[i].first;
+ const std::vector<std::size_t> links=vertices_graph[i];
+ Vertex& vertex=result.vertices[i];
+ vertex.x=tangent_sphere.x;
+ vertex.y=tangent_sphere.y;
+ vertex.z=tangent_sphere.z;
+ vertex.r=tangent_sphere.r;
+ for(unsigned int j=0;j<4;j++)
+ {
+ vertex.ball_id[j]=quadruple.get(j);
+ if(links.size()>j)
+ {
+ vertex.link_vertex_id[j]=links[j];
+ vertex.link_available[j]=(vertex.link_vertex_id[j]!=null_id);
+ }
+ }
+ }
+
+ return result;
+ }
+
+ static Result get_balls_from_atoms_file_and_calculate_vertices(const std::string& input_file_path, const Parameters& parameters)
+ {
+ std::ifstream input_file_stream(input_file_path.c_str(), std::ios::in);
+ return get_balls_from_atoms_file_and_calculate_vertices(input_file_stream, parameters);
+ }
+
+ static Result get_balls_from_atoms_file_and_calculate_vertices(const std::string& input_file_path)
+ {
+ return get_balls_from_atoms_file_and_calculate_vertices(input_file_path, Parameters());
+ }
+
+private:
+ static std::string name_atom_ball(const auxiliaries::AtomsIO::AtomRecord& atom)
+ {
+ std::ostringstream output;
+ output << (atom.chainID) << "," << (atom.resSeq) << "," << (atom.resName) << "," << (atom.name) << "," << (atom.altLoc) << "," << (atom.iCode);
+ return output.str();
+ }
+};
+
+#endif /* WRAPPER_GET_BALLS_FROM_ATOMS_FILE_AND_CALCULATE_VERTICES_H_ */
diff --git a/support/generate-arguments-for-query-balls.html b/support/generate-arguments-for-query-balls.html
new file mode 100644
index 0000000..976c74c
--- /dev/null
+++ b/support/generate-arguments-for-query-balls.html
@@ -0,0 +1,226 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+<title>Generating arguments for the 'voronota query-balls'</title>
+<style>
+.background-light-blue {background-color:#B2D9F1;}
+.background-light-magenta {background-color:#FFE0F1;}
+.background-light-gray {background-color:#DDDDDD;}
+.background-white {background-color:#FFFFFF;}
+}
+</style>
+</head>
+
+<body>
+
+This page allows to easily generate a set of arguments for the 'voronota query-balls' command.
+
+<hr/>
+
+<table border="0">
+<tr>
+<td>
+<table border="0">
+ <tr>
+ <td></td>
+ <td>in:<br></td>
+ <td>out:<br></td>
+ </tr>
+ <tr>
+ <td>Chain:</td>
+ <td><input type="text" size="10" id="match_chain" value="" title="Example: A,B" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_not_chain" value="" title="Example: A,B" class="background-light-blue"><br></td>
+ </tr>
+ <tr>
+ <td>Residue number:</td>
+ <td><input type="text" size="10" id="match_residue_number" value="" title="Example: 1:50,100" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_not_residue_number" value="" title="Example: 1:50,100" class="background-light-blue"><br></td>
+ </tr>
+ <tr>
+ <td>Residue name:</td>
+ <td><input type="text" size="10" id="match_residue_name" value="" title="Example: LEU,VAL,ARG" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_not_residue_name" value="" title="Example: LEU,VAL,ARG" class="background-light-blue"><br></td>
+ </tr>
+ <tr>
+ <td>Atom serial:</td>
+ <td><input type="text" size="10" id="match_atom_serial" value="" title="Example: 1:300,350" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_not_atom_serial" value="" title="Example: 1:300,350" class="background-light-blue"><br></td>
+ </tr>
+ <tr>
+ <td>Atom name:</td>
+ <td><input type="text" size="10" id="match_atom_name" value="" title="Example: N,CA,CB" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_not_atom_name" value="" title="Example: N,CA,CB" class="background-light-blue"><br></td>
+ </tr>
+</table>
+</td>
+<td>
+
+</td>
+</tr>
+</table>
+
+<hr/>
+
+<table border="0">
+ <tr>
+ <td>Tags in:</td>
+ <td><input type="text" size="40" id="match_tags" value="" title="Example: tag1&tag2|tag3" class="background-light-magenta"><br></td>
+ </tr>
+ <tr>
+ <td>Tags out:</td>
+ <td><input type="text" size="40" id="match_tags_not" value="" title="Example: tag1&tag2|tag3" class="background-light-magenta"><br></td>
+ </tr>
+</table>
+
+<hr/>
+
+<table border="0">
+ <tr>
+ <td>Adjunct in:</td>
+ <td><input type="text" size="10" id="match_adjunct1_name" value="" title="Example: name1" class="background-light-gray"> = <input type="text" size="5" id="match_adjunct1_min" value="" title="Example: 0.3" class="background-light-gray"> to <input type="text" size="5" id="match_adjunct1_max" value="" title="Example: 2.5" class="background-light-gray"><br></td>
+ </tr>
+ <tr>
+ <td>Adjunct in:</td>
+ <td><input type="text" size="10" id="match_adjunct2_name" value="" title="Example: name2" class="background-light-gray"> = <input type="text" size="5" id="match_adjunct2_min" value="" title="Example: 0.3" class="background-light-gray"> to <input type="text" size="5" id="match_adjunct2_max" value="" title="Example: 2.5" class="background-light-gray"><br></td>
+ </tr>
+ <tr>
+ <td>Adjunct out:</td>
+ <td><input type="text" size="10" id="match_adjunct_not1_name" value="" title="Example: name3" class="background-light-gray"> = <input type="text" size="5" id="match_adjunct_not1_min" value="" title="Example: 0.3" class="background-light-gray"> to <input type="text" size="5" id="match_adjunct_not1_max" value="" title="Example: 2.5" class="background-light-gray"></td>
+ </tr>
+</table>
+
+<hr/>
+
+<p>
+<button onclick="compose()">Generate query arguments</button>
+</p>
+
+<p>
+<div id="result_title"></div>
+<input type="text" size="150" id="result" value="" class="background-white" style="display:none;">
+</p>
+
+<hr/>
+
+<p>
+Some tips:
+<ul>
+ <li>Hover over any input field to see a tool tip with an example of valid input.</li>
+ <li>Any input field can be left empty.</li>
+ <li>Both single values and lists (separated with commas, spaces or semicolons) are accepted in the 'Chain-Residue-Atom' input fields (first five rows of input fields).</li>
+ <li>Integer intervals, denoted using ':' symbol, are accepted in 'Residue number' and 'Atom serial' input fields. <i>a</i>:<i>b</i> means an inclusive interval [<i>a</i>, <i>b</i>].</li>
+ <li>Multiple tags can be specified in magenta input fields using logical operators '|' and '&'.</li>
+</ul>
+</p>
+
+<script>
+
+function get_input_generic_value(str)
+{
+ return str.split(/[\s,;]+/).join(',').replace(/^,+|,+$/gm,'');
+}
+
+function get_input_logical_value(str)
+{
+ return str.split(/[\s,;]+/).join('&').replace(/&+/gm,'&').replace(/&\|/gm,'|').replace(/\|&/gm,'|').replace(/\|+/gm,'|').replace(/^&+|&+$/gm,'').replace(/^\|+|\|+$/gm,'');
+}
+
+function get_input_named_interval_value(val_name, val_min, val_max)
+{
+ var safe_val_name=val_name.replace(/[\s,;&\|]+/gm, '');
+ var safe_val_min=val_min.replace(/[\s,;&\|]+/gm, '');
+ var safe_val_max=val_max.replace(/[\s,;&\|]+/gm, '');
+ if(safe_val_name && safe_val_min && safe_val_max)
+ {
+ return (safe_val_name+"="+safe_val_min+":"+safe_val_max);
+ }
+ else
+ {
+ return "";
+ }
+}
+
+function append_to_local_output(main, suffix, value)
+{
+ result=main;
+ if(value!=="")
+ {
+ if(result!=="")
+ {
+ result+="&";
+ }
+ result+=suffix+"<"+value+">";
+ }
+ return result;
+}
+
+function append_to_global_output(main, suffix, value)
+{
+ result=main;
+ if(value!=="")
+ {
+ if(result!=="")
+ {
+ result+=" ";
+ }
+ result+=suffix+" '"+value+"'";
+ }
+ return result;
+}
+
+function compose()
+{
+ var output=""
+
+ var output_match_first=""
+ output_match_first=append_to_local_output(output_match_first, "c", get_input_generic_value(document.getElementById("match_chain").value));
+ output_match_first=append_to_local_output(output_match_first, "r", get_input_generic_value(document.getElementById("match_residue_number").value));
+ output_match_first=append_to_local_output(output_match_first, "a", get_input_generic_value(document.getElementById("match_atom_serial").value));
+ output_match_first=append_to_local_output(output_match_first, "R", get_input_generic_value(document.getElementById("match_residue_name").value));
+ output_match_first=append_to_local_output(output_match_first, "A", get_input_generic_value(document.getElementById("match_atom_name").value));
+ output=append_to_global_output(output, "--match", output_match_first);
+
+ var output_match_first_not=""
+ output_match_first_not=append_to_local_output(output_match_first_not, "c", get_input_generic_value(document.getElementById("match_not_chain").value));
+ output_match_first_not=append_to_local_output(output_match_first_not, "r", get_input_generic_value(document.getElementById("match_not_residue_number").value));
+ output_match_first_not=append_to_local_output(output_match_first_not, "a", get_input_generic_value(document.getElementById("match_not_atom_serial").value));
+ output_match_first_not=append_to_local_output(output_match_first_not, "R", get_input_generic_value(document.getElementById("match_not_residue_name").value));
+ output_match_first_not=append_to_local_output(output_match_first_not, "A", get_input_generic_value(document.getElementById("match_not_atom_name").value));
+ output=append_to_global_output(output, "--match-not", output_match_first_not);
+
+ output=append_to_global_output(output, "--match-tags", get_input_logical_value(document.getElementById("match_tags").value));
+ output=append_to_global_output(output, "--match-tags-not", get_input_logical_value(document.getElementById("match_tags_not").value));
+
+ output=append_to_global_output(
+ output, "--match-adjuncts", get_input_logical_value(
+ get_input_named_interval_value(document.getElementById("match_adjunct1_name").value, document.getElementById("match_adjunct1_min").value, document.getElementById("match_adjunct1_max").value)
+ +"&"
+ +get_input_named_interval_value(document.getElementById("match_adjunct2_name").value, document.getElementById("match_adjunct2_min").value, document.getElementById("match_adjunct2_max").value)
+ )
+ );
+
+ output=append_to_global_output(
+ output, "--match-adjuncts-not", get_input_logical_value(
+ get_input_named_interval_value(document.getElementById("match_adjunct_not1_name").value, document.getElementById("match_adjunct_not1_min").value, document.getElementById("match_adjunct_not1_max").value)
+ )
+ );
+
+ if(output)
+ {
+ document.getElementById("result_title").innerHTML="Generated result:<br>";
+ document.getElementById("result").value=output;
+ document.getElementById("result").style.display="block";
+ }
+ else
+ {
+ document.getElementById("result_title").innerHTML="Not enough valid input to generate anything.<br>";
+ document.getElementById("result").value="";
+ document.getElementById("result").style.display="none";
+ }
+}
+
+</script>
+
+</body>
+</html>
diff --git a/support/generate-arguments-for-query-contacts.html b/support/generate-arguments-for-query-contacts.html
new file mode 100644
index 0000000..e3e8db5
--- /dev/null
+++ b/support/generate-arguments-for-query-contacts.html
@@ -0,0 +1,317 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+<title>Generating arguments for the 'voronota query-contacts'</title>
+<style>
+.background-light-red {background-color: #FFCEBD;}
+.background-light-green {background-color:#DDFFB9;}
+.background-light-blue {background-color:#B2D9F1;}
+.background-light-cyan {background-color:#D2FFF1;}
+.background-light-magenta {background-color:#FFE0F1;}
+.background-light-yellow {background-color:#FFFFE0;}
+.background-light-gray {background-color:#DDDDDD;}
+.background-white {background-color:#FFFFFF;}
+}
+</style>
+</head>
+
+<body>
+
+This page allows to easily generate a set of arguments for the 'voronota query-contacts' command.
+
+<hr/>
+
+<table border="0">
+<tr>
+<td>
+<table border="0">
+ <tr>
+ <td></td>
+ <td>left in:<br></td>
+ <td>left out:<br></td>
+ <td>right in:<br></td>
+ <td>right out:<br></td>
+ </tr>
+ <tr>
+ <td>Chain:</td>
+ <td><input type="text" size="10" id="match_first_chain" value="" title="Example: A,B" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_first_not_chain" value="" title="Example: A,B" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_second_chain" value="" title="Example: A,B" class="background-light-green"><br></td>
+ <td><input type="text" size="10" id="match_second_not_chain" value="" title="Example: A,B" class="background-light-green"><br></td>
+ </tr>
+ <tr>
+ <td>Residue number:</td>
+ <td><input type="text" size="10" id="match_first_residue_number" value="" title="Example: 1:50,100" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_first_not_residue_number" value="" title="Example: 1:50,100" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_second_residue_number" value="" title="Example: 1:50,100" class="background-light-green"><br></td>
+ <td><input type="text" size="10" id="match_second_not_residue_number" value="" title="Example: 1:50,100" class="background-light-green"><br></td>
+ </tr>
+ <tr>
+ <td>Residue name:</td>
+ <td><input type="text" size="10" id="match_first_residue_name" value="" title="Example: LEU,VAL,ARG" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_first_not_residue_name" value="" title="Example: LEU,VAL,ARG" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_second_residue_name" value="" title="Example: LEU,VAL,ARG" class="background-light-green"><br></td>
+ <td><input type="text" size="10" id="match_second_not_residue_name" value="" title="Example: LEU,VAL,ARG" class="background-light-green"><br></td>
+ </tr>
+ <tr>
+ <td>Atom serial:</td>
+ <td><input type="text" size="10" id="match_first_atom_serial" value="" title="Example: 1:300,350" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_first_not_atom_serial" value="" title="Example: 1:300,350" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_second_atom_serial" value="" title="Example: 1:300,350" class="background-light-green"><br></td>
+ <td><input type="text" size="10" id="match_second_not_atom_serial" value="" title="Example: 1:300,350" class="background-light-green"><br></td>
+ </tr>
+ <tr>
+ <td>Atom name:</td>
+ <td><input type="text" size="10" id="match_first_atom_name" value="" title="Example: N,CA,CB" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_first_not_atom_name" value="" title="Example: N,CA,CB" class="background-light-blue"><br></td>
+ <td><input type="text" size="10" id="match_second_atom_name" value="" title="Example: N,CA,CB" class="background-light-green"><br></td>
+ <td><input type="text" size="10" id="match_second_not_atom_name" value="" title="Example: N,CA,CB" class="background-light-green"><br></td>
+ </tr>
+</table>
+</td>
+<td>
+
+</td>
+</tr>
+</table>
+
+<hr/>
+
+<table border="0">
+ <tr>
+ <td></td>
+ <td>min:</td>
+ <td>max:</td>
+ </tr>
+ <tr>
+ <td>Contact area:</td>
+ <td><input type="text" size="5" id="match_min_area" value="" title="Example: 1.0" class="background-light-red"><br></td>
+ <td><input type="text" size="5" id="match_max_area" value="" title="Example: 5.0" class="background-light-red"><br></td>
+ </tr>
+ <tr>
+ <td>Minimal distance:</td>
+ <td><input type="text" size="5" id="match_min_dist" value="" title="Example: 2.0" class="background-light-cyan"><br></td>
+ <td><input type="text" size="5" id="match_max_dist" value="" title="Example: 4.0" class="background-light-cyan"><br></td>
+ </tr>
+ <tr>
+ <td>Sequence separation:</td>
+ <td><input type="text" size="5" id="match_min_seq_sep" value="" title="Example: 2" class="background-light-yellow"><br></td>
+ <td><input type="text" size="5" id="match_max_seq_sep" value="" title="Example: 6" class="background-light-yellow"><br></td>
+ </tr>
+</table>
+
+<hr/>
+
+<table border="0">
+ <tr>
+ <td>Tags in:</td>
+ <td><input type="text" size="40" id="match_tags" value="" title="Example: tag1&tag2|tag3" class="background-light-magenta"><br></td>
+ </tr>
+ <tr>
+ <td>Tags out:</td>
+ <td><input type="text" size="40" id="match_tags_not" value="" title="Example: tag1&tag2|tag3" class="background-light-magenta"><br></td>
+ </tr>
+</table>
+
+<hr/>
+
+<table border="0">
+ <tr>
+ <td>Adjunct in:</td>
+ <td><input type="text" size="10" id="match_adjunct1_name" value="" title="Example: name1" class="background-light-gray"> = <input type="text" size="5" id="match_adjunct1_min" value="" title="Example: 0.3" class="background-light-gray"> to <input type="text" size="5" id="match_adjunct1_max" value="" title="Example: 2.5" class="background-light-gray"><br></td>
+ </tr>
+ <tr>
+ <td>Adjunct in:</td>
+ <td><input type="text" size="10" id="match_adjunct2_name" value="" title="Example: name2" class="background-light-gray"> = <input type="text" size="5" id="match_adjunct2_min" value="" title="Example: 0.3" class="background-light-gray"> to <input type="text" size="5" id="match_adjunct2_max" value="" title="Example: 2.5" class="background-light-gray"><br></td>
+ </tr>
+ <tr>
+ <td>Adjunct out:</td>
+ <td><input type="text" size="10" id="match_adjunct_not1_name" value="" title="Example: name3" class="background-light-gray"> = <input type="text" size="5" id="match_adjunct_not1_min" value="" title="Example: 0.3" class="background-light-gray"> to <input type="text" size="5" id="match_adjunct_not1_max" value="" title="Example: 2.5" class="background-light-gray"></td>
+ </tr>
+</table>
+
+<hr/>
+
+<p>
+<button onclick="compose()">Generate query arguments</button>
+</p>
+
+<p>
+<div id="result_title"></div>
+<input type="text" size="150" id="result" value="" class="background-white" style="display:none;">
+</p>
+
+<hr/>
+
+<p>
+Some tips:
+<ul>
+ <li>Hover over any input field to see a tool tip with an example of valid input.</li>
+ <li>Any input field can be left empty.</li>
+ <li>Both single values and lists (separated with commas, spaces or semicolons) are accepted in the 'Chain-Residue-Atom' input fields (first five rows of input fields).</li>
+ <li>Integer intervals, denoted using ':' symbol, are accepted in 'Residue number' and 'Atom serial' input fields. <i>a</i>:<i>b</i> means an inclusive interval [<i>a</i>, <i>b</i>].</li>
+ <li>Artificial chain name 'solvent' can be used to query solvent-accessible areas.</li>
+ <li>Multiple tags can be specified in magenta input fields using logical operators '|' and '&'.</li>
+</ul>
+</p>
+
+<script>
+
+function get_input_generic_value(str)
+{
+ return str.split(/[\s,;]+/).join(',').replace(/^,+|,+$/gm,'');
+}
+
+function get_input_float_value(str)
+{
+ if(isNaN(parseFloat(str)))
+ {
+ return "";
+ }
+ else
+ {
+ return parseFloat(str);
+ }
+}
+
+function get_input_int_value(str)
+{
+ if(isNaN(parseInt(str)))
+ {
+ return "";
+ }
+ else
+ {
+ return parseInt(str);
+ }
+}
+
+function get_input_logical_value(str)
+{
+ return str.split(/[\s,;]+/).join('&').replace(/&+/gm,'&').replace(/&\|/gm,'|').replace(/\|&/gm,'|').replace(/\|+/gm,'|').replace(/^&+|&+$/gm,'').replace(/^\|+|\|+$/gm,'');
+}
+
+function get_input_named_interval_value(val_name, val_min, val_max)
+{
+ var safe_val_name=val_name.replace(/[\s,;&\|]+/gm, '');
+ var safe_val_min=val_min.replace(/[\s,;&\|]+/gm, '');
+ var safe_val_max=val_max.replace(/[\s,;&\|]+/gm, '');
+ if(safe_val_name && safe_val_min && safe_val_max)
+ {
+ return (safe_val_name+"="+safe_val_min+":"+safe_val_max);
+ }
+ else
+ {
+ return "";
+ }
+}
+
+function append_to_local_output(main, suffix, value)
+{
+ result=main;
+ if(value!=="")
+ {
+ if(result!=="")
+ {
+ result+="&";
+ }
+ result+=suffix+"<"+value+">";
+ }
+ return result;
+}
+
+function append_to_global_output(main, suffix, value)
+{
+ result=main;
+ if(value!=="")
+ {
+ if(result!=="")
+ {
+ result+=" ";
+ }
+ result+=suffix+" '"+value+"'";
+ }
+ return result;
+}
+
+function compose()
+{
+ var output=""
+
+ var output_match_first=""
+ output_match_first=append_to_local_output(output_match_first, "c", get_input_generic_value(document.getElementById("match_first_chain").value));
+ output_match_first=append_to_local_output(output_match_first, "r", get_input_generic_value(document.getElementById("match_first_residue_number").value));
+ output_match_first=append_to_local_output(output_match_first, "a", get_input_generic_value(document.getElementById("match_first_atom_serial").value));
+ output_match_first=append_to_local_output(output_match_first, "R", get_input_generic_value(document.getElementById("match_first_residue_name").value));
+ output_match_first=append_to_local_output(output_match_first, "A", get_input_generic_value(document.getElementById("match_first_atom_name").value));
+ output=append_to_global_output(output, "--match-first", output_match_first);
+
+ var output_match_first_not=""
+ output_match_first_not=append_to_local_output(output_match_first_not, "c", get_input_generic_value(document.getElementById("match_first_not_chain").value));
+ output_match_first_not=append_to_local_output(output_match_first_not, "r", get_input_generic_value(document.getElementById("match_first_not_residue_number").value));
+ output_match_first_not=append_to_local_output(output_match_first_not, "a", get_input_generic_value(document.getElementById("match_first_not_atom_serial").value));
+ output_match_first_not=append_to_local_output(output_match_first_not, "R", get_input_generic_value(document.getElementById("match_first_not_residue_name").value));
+ output_match_first_not=append_to_local_output(output_match_first_not, "A", get_input_generic_value(document.getElementById("match_first_not_atom_name").value));
+ output=append_to_global_output(output, "--match-first-not", output_match_first_not);
+
+ var output_match_second=""
+ output_match_second=append_to_local_output(output_match_second, "c", get_input_generic_value(document.getElementById("match_second_chain").value));
+ output_match_second=append_to_local_output(output_match_second, "r", get_input_generic_value(document.getElementById("match_second_residue_number").value));
+ output_match_second=append_to_local_output(output_match_second, "a", get_input_generic_value(document.getElementById("match_second_atom_serial").value));
+ output_match_second=append_to_local_output(output_match_second, "R", get_input_generic_value(document.getElementById("match_second_residue_name").value));
+ output_match_second=append_to_local_output(output_match_second, "A", get_input_generic_value(document.getElementById("match_second_atom_name").value));
+ output=append_to_global_output(output, "--match-second", output_match_second);
+
+ var output_match_second_not=""
+ output_match_second_not=append_to_local_output(output_match_second_not, "c", get_input_generic_value(document.getElementById("match_second_not_chain").value));
+ output_match_second_not=append_to_local_output(output_match_second_not, "r", get_input_generic_value(document.getElementById("match_second_not_residue_number").value));
+ output_match_second_not=append_to_local_output(output_match_second_not, "a", get_input_generic_value(document.getElementById("match_second_not_atom_serial").value));
+ output_match_second_not=append_to_local_output(output_match_second_not, "R", get_input_generic_value(document.getElementById("match_second_not_residue_name").value));
+ output_match_second_not=append_to_local_output(output_match_second_not, "A", get_input_generic_value(document.getElementById("match_second_not_atom_name").value));
+ output=append_to_global_output(output, "--match-second-not", output_match_second_not);
+
+ output=append_to_global_output(output, "--match-min-area", get_input_float_value(document.getElementById("match_min_area").value));
+ output=append_to_global_output(output, "--match-max-area", get_input_float_value(document.getElementById("match_max_area").value));
+
+ output=append_to_global_output(output, "--match-min-dist", get_input_float_value(document.getElementById("match_min_dist").value));
+ output=append_to_global_output(output, "--match-max-dist", get_input_float_value(document.getElementById("match_max_dist").value));
+
+ output=append_to_global_output(output, "--match-min-seq-sep", get_input_int_value(document.getElementById("match_min_seq_sep").value));
+ output=append_to_global_output(output, "--match-max-seq-sep", get_input_int_value(document.getElementById("match_max_seq_sep").value));
+
+ output=append_to_global_output(output, "--match-tags", get_input_logical_value(document.getElementById("match_tags").value));
+ output=append_to_global_output(output, "--match-tags-not", get_input_logical_value(document.getElementById("match_tags_not").value));
+
+ output=append_to_global_output(
+ output, "--match-adjuncts", get_input_logical_value(
+ get_input_named_interval_value(document.getElementById("match_adjunct1_name").value, document.getElementById("match_adjunct1_min").value, document.getElementById("match_adjunct1_max").value)
+ +"&"
+ +get_input_named_interval_value(document.getElementById("match_adjunct2_name").value, document.getElementById("match_adjunct2_min").value, document.getElementById("match_adjunct2_max").value)
+ )
+ );
+
+ output=append_to_global_output(
+ output, "--match-adjuncts-not", get_input_logical_value(
+ get_input_named_interval_value(document.getElementById("match_adjunct_not1_name").value, document.getElementById("match_adjunct_not1_min").value, document.getElementById("match_adjunct_not1_max").value)
+ )
+ );
+
+ if(output)
+ {
+ document.getElementById("result_title").innerHTML="Generated result:<br>";
+ document.getElementById("result").value=output;
+ document.getElementById("result").style.display="block";
+ }
+ else
+ {
+ document.getElementById("result_title").innerHTML="Not enough valid input to generate anything.<br>";
+ document.getElementById("result").value="";
+ document.getElementById("result").style.display="none";
+ }
+}
+
+</script>
+
+</body>
+</html>
diff --git a/voronota b/voronota
new file mode 100755
index 0000000..aafff0c
Binary files /dev/null and b/voronota differ
diff --git a/voronota-cadscore b/voronota-cadscore
new file mode 100755
index 0000000..fee0154
--- /dev/null
+++ b/voronota-cadscore
@@ -0,0 +1,468 @@
+#!/bin/bash
+
+function print_help_and_exit
+{
+cat >&2 << EOF
+
+'voronota-cadscore' script is an implementation of CAD-score method using Voronota.
+
+Basic options:
+ --input-target | -t string * input target structure file in PDB format
+ --input-model | -m string * input model structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --output-residue-scores string output text file with residue scores
+ --output-residue-scores-pdb-t string output target PDB file with residue scores as B-factors
+ --output-residue-scores-pdb-m string output model PDB file with residue scores as B-factors
+ --smoothing-window number residue scores smoothing window size, default is 0
+ --contacts-query string contacts query parameters
+ --contacts-query-inter-chain flag to consider only inter-chain contacts
+ --contacts-query-by-code string contacts query code, possible codes are AA, AS, SS, AM, MM, MS
+ --use-all-query-codes flag to output global scores for all query codes, one line per code
+ --cache-dir string path to cache directory
+ --output-header flag to output header before result line
+ --help | -h flag to display help message and exit
+
+Advanced options:
+ --ignore-residue-names flag to consider just residue numbers and ignore residue names
+ --enable-site-based-scoring falg to enable site-based scoring
+ --multiple-models flag to handle multiple models in PDB file
+ --remap-chains flag to automatically rearrange chain names for higher scores
+ --remap-chains-output string output file with chain names rearrangement
+ --old-regime flag to calculate areas as in pre-Voronota CAD-score
+
+Standard output (one line):
+ {target file path} {model file path} {query code} {number of residues} {global score} {target total area} {corresponding model total area}
+ [ {site-based number of residues} {site-based global score} {site-based target total area} {corresponding site-based model total area} ]
+
+EOF
+exit 1
+}
+
+readonly ZEROARG=$0
+INFILE_TARGET_PDB=""
+INFILE_MODEL_PDB=""
+INPUT_FILTER_QUERY_PARAMETERS=""
+CONTACTS_QUERY_PARAMETERS=""
+CONTACTS_QUERY_BY_CODE=""
+CONTACTS_QUERY_INTER_CHAIN=false
+IGNORE_RESIDUE_NAMES_OPTION=""
+OUTFILE_RESIDUE_SCORES=""
+OUTFILE_RESIDUE_SCORES_PDB_TARGET=""
+OUTFILE_RESIDUE_SCORES_PDB_MODEL=""
+USE_ALL_QUERY_CODES=false
+SMOOTHING_WINDOW="0"
+CONTACTS_CACHE_DIRECTORY=""
+MULTIPLE_MODELS_CHAINS_OPTION=""
+INPUT_MODEL_CHAINS_RENAMING=""
+REMAP_CHAINS=false
+REMAP_CHAINS_LOG_OPTION=""
+REMAP_CHAINS_OUTPUT=""
+ENABLE_SITE_BASED_SCORING=false
+OUTPUT_HEADER=false
+OLD_REGIME=false
+HELP_MODE=false
+
+while [[ $# > 0 ]]
+do
+ OPTION="$1"
+ OPTARG="$2"
+ shift
+ case $OPTION in
+ -t|--input-target)
+ INFILE_TARGET_PDB="$OPTARG"
+ shift
+ ;;
+ -m|--input-model)
+ INFILE_MODEL_PDB="$OPTARG"
+ shift
+ ;;
+ --input-filter-query)
+ INPUT_FILTER_QUERY_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --contacts-query)
+ CONTACTS_QUERY_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --contacts-query-by-code)
+ CONTACTS_QUERY_BY_CODE="$OPTARG"
+ shift
+ ;;
+ --contacts-query-inter-chain)
+ CONTACTS_QUERY_INTER_CHAIN=true
+ ;;
+ --ignore-residue-names)
+ IGNORE_RESIDUE_NAMES_OPTION="--ignore-residue-names"
+ ;;
+ --output-residue-scores)
+ OUTFILE_RESIDUE_SCORES="$OPTARG"
+ shift
+ ;;
+ --output-residue-scores-pdb-t)
+ OUTFILE_RESIDUE_SCORES_PDB_TARGET="$OPTARG"
+ shift
+ ;;
+ --output-residue-scores-pdb-m)
+ OUTFILE_RESIDUE_SCORES_PDB_MODEL="$OPTARG"
+ shift
+ ;;
+ --use-all-query-codes)
+ USE_ALL_QUERY_CODES=true
+ ;;
+ --smoothing-window)
+ SMOOTHING_WINDOW="$OPTARG"
+ shift
+ ;;
+ --cache-dir)
+ CONTACTS_CACHE_DIRECTORY="$OPTARG"
+ shift
+ ;;
+ --multiple-models)
+ MULTIPLE_MODELS_CHAINS_OPTION="--multimodel-chains"
+ ;;
+ --input-model-chains-renaming)
+ INPUT_MODEL_CHAINS_RENAMING="$OPTARG"
+ shift
+ ;;
+ --remap-chains)
+ REMAP_CHAINS=true
+ ;;
+ --remap-chains-log)
+ REMAP_CHAINS_LOG_OPTION="--remap-chains-log"
+ ;;
+ --remap-chains-output)
+ REMAP_CHAINS_OUTPUT="$OPTARG"
+ shift
+ ;;
+ --enable-site-based-scoring)
+ ENABLE_SITE_BASED_SCORING=true
+ ;;
+ --output-header)
+ OUTPUT_HEADER=true
+ ;;
+ --old-regime)
+ OLD_REGIME=true
+ ;;
+ -h|--help)
+ HELP_MODE=true
+ ;;
+ *)
+ echo >&2 "Error: invalid command line option '$OPTION'"
+ exit 1
+ ;;
+ esac
+done
+
+if [ -z "$INFILE_TARGET_PDB" ] || [ -z "$INFILE_MODEL_PDB" ] || $HELP_MODE
+then
+ print_help_and_exit
+fi
+
+if [[ $ZEROARG == *"/"* ]]
+then
+ cd $(dirname $ZEROARG)
+ export PATH=$(pwd):$PATH
+ cd - &> /dev/null
+fi
+
+command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; }
+command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; }
+
+if [ ! -s "$INFILE_TARGET_PDB" ]
+then
+ echo >&2 "Error: input target file does not exist"
+ exit 1
+fi
+
+if [ ! -s "$INFILE_MODEL_PDB" ]
+then
+ echo >&2 "Error: input model file does not exist"
+ exit 1
+fi
+
+if [ -n "$CONTACTS_QUERY_BY_CODE" ] \
+ && [ "$CONTACTS_QUERY_BY_CODE" != "AA" ] \
+ && [ "$CONTACTS_QUERY_BY_CODE" != "AS" ] \
+ && [ "$CONTACTS_QUERY_BY_CODE" != "SS" ] \
+ && [ "$CONTACTS_QUERY_BY_CODE" != "AM" ] \
+ && [ "$CONTACTS_QUERY_BY_CODE" != "MM" ] \
+ && [ "$CONTACTS_QUERY_BY_CODE" != "MS" ]
+then
+ echo >&2 "Error: invalid contacts query code '$CONTACTS_QUERY_BY_CODE'"
+ exit 1
+fi
+
+if [ -n "$INPUT_MODEL_CHAINS_RENAMING" ] && [ ! -s "$INPUT_MODEL_CHAINS_RENAMING" ]
+then
+ echo >&2 "Error: input model chains renaming file does not exist"
+ exit 1
+fi
+
+if $CONTACTS_QUERY_INTER_CHAIN
+then
+ CONTACTS_QUERY_PARAMETERS="$CONTACTS_QUERY_PARAMETERS --no-same-chain"
+fi
+
+readonly TMPLDIR=$(mktemp -d)
+trap "rm -r $TMPLDIR" EXIT
+
+{
+ if [[ "$INFILE_TARGET_PDB" == *".gz" ]]
+ then
+ zcat "$INFILE_TARGET_PDB"
+ else
+ cat "$INFILE_TARGET_PDB"
+ fi
+} > $TMPLDIR/target
+
+{
+ if [[ "$INFILE_MODEL_PDB" == *".gz" ]]
+ then
+ zcat "$INFILE_MODEL_PDB"
+ else
+ cat "$INFILE_MODEL_PDB"
+ fi
+} > $TMPLDIR/model
+
+for WORKFILE in $TMPLDIR/target $TMPLDIR/model
+do
+ cat $WORKFILE \
+ | voronota get-balls-from-atoms-file \
+ --annotated $MULTIPLE_MODELS_CHAINS_OPTION \
+ --radii-file <(voronota-resources radii) \
+ --include-heteroatoms \
+ | voronota query-balls \
+ --drop-altloc-indicators \
+ --drop-atom-serials \
+ | voronota query-balls $INPUT_FILTER_QUERY_PARAMETERS \
+ > $WORKFILE.balls
+
+ if [ ! -s "$WORKFILE.balls" ]
+ then
+ echo >&2 "Error: no atoms for $(basename $WORKFILE)"
+ exit 1
+ fi
+
+ BALLS_MD5=""
+ if [ -n "$CONTACTS_CACHE_DIRECTORY" ]
+ then
+ BALLS_MD5=$(cat $WORKFILE.balls | md5sum | awk '{print $1}')
+ if [ -n "$BALLS_MD5" ]
+ then
+ if $OLD_REGIME
+ then
+ BALLS_MD5="${BALLS_MD5}.voronota.cadscore.old"
+ else
+ BALLS_MD5="${BALLS_MD5}.voronota.cadscore"
+ fi
+ if [ -s "$CONTACTS_CACHE_DIRECTORY/$BALLS_MD5" ]
+ then
+ cp $CONTACTS_CACHE_DIRECTORY/$BALLS_MD5 $WORKFILE.all_contacts
+ fi
+ fi
+ fi
+
+ if [ ! -s "$WORKFILE.all_contacts" ]
+ then
+ MAIN_CHAIN_ATOMS_DESCRIPTOR="A<CA,C,N,O,OXT>|A<OP3,O3P,P,OP1,O1P,OP2,O2P,O5',O5*,C5',C5*,C4',C4*,O4',O4*,C3',C3*,O3',O3*,C2',C2*,O2',O2*,C1',C1*>"
+
+ cat $WORKFILE.balls \
+ | \
+ {
+ if $OLD_REGIME
+ then
+ voronota calculate-contacts \
+ --annotated \
+ --old-contacts-output $WORKFILE.old_contacts \
+ > /dev/null
+ cat $WORKFILE.old_contacts
+ else
+ voronota calculate-contacts \
+ --annotated
+ fi
+ } \
+ | voronota query-contacts \
+ --match-min-seq-sep 1 \
+ --no-solvent \
+ | voronota query-contacts \
+ --match-first 'A<C>' \
+ --match-second 'A<N>' \
+ --match-max-seq-sep 1 \
+ --match-max-dist 1.6 \
+ --invert \
+ | voronota query-contacts \
+ --set-tags 'AA' \
+ | voronota query-contacts \
+ --match-first-not $MAIN_CHAIN_ATOMS_DESCRIPTOR \
+ --match-second-not $MAIN_CHAIN_ATOMS_DESCRIPTOR \
+ --set-tags 'SS' \
+ | voronota query-contacts \
+ --match-first $MAIN_CHAIN_ATOMS_DESCRIPTOR \
+ --match-second $MAIN_CHAIN_ATOMS_DESCRIPTOR \
+ --set-tags 'MM' \
+ | voronota query-contacts \
+ --match-first-not 'l<m>' \
+ --match-second $MAIN_CHAIN_ATOMS_DESCRIPTOR \
+ --set-tags 'AM' \
+ | voronota query-contacts \
+ --match-first-not 'l<m>' \
+ --match-second-not $MAIN_CHAIN_ATOMS_DESCRIPTOR \
+ --set-tags 'AS' \
+ | voronota query-contacts \
+ --match-first $MAIN_CHAIN_ATOMS_DESCRIPTOR \
+ --match-first-not 'l<m>' \
+ --match-second-not $MAIN_CHAIN_ATOMS_DESCRIPTOR \
+ --set-tags 'MS' \
+ > $WORKFILE.all_contacts
+
+ if [ -n "$CONTACTS_CACHE_DIRECTORY" ] && [ -n "$BALLS_MD5" ]
+ then
+ mkdir -p $CONTACTS_CACHE_DIRECTORY
+ cp $WORKFILE.all_contacts $CONTACTS_CACHE_DIRECTORY/$BALLS_MD5
+ fi
+ fi
+
+ cat $WORKFILE.all_contacts \
+ | voronota query-contacts $CONTACTS_QUERY_PARAMETERS \
+ > $WORKFILE.contacts
+
+ if [ ! -s "$WORKFILE.contacts" ]
+ then
+ echo >&2 "Error: no contacts for $(basename $WORKFILE)"
+ exit 1
+ fi
+done
+
+function rename_model_chains_by_dictionary()
+{
+ cat "$1" | awk '{print "c<" $1 "> c_replaced<" $2 ">" }' > $TMPLDIR/chains_renaming_dictionary
+ for MFILE in $TMPLDIR/model.balls $TMPLDIR/model.contacts
+ do
+ awk 'NR==FNR{rep[$1]=$2;next}{for(key in rep){gsub(key,rep[key])};print}' $TMPLDIR/chains_renaming_dictionary $MFILE | sed 's/_replaced//g' > $MFILE.renamed
+ mv $MFILE.renamed $MFILE
+ done
+}
+
+if [ -n "$INPUT_MODEL_CHAINS_RENAMING" ]
+then
+ rename_model_chains_by_dictionary "$INPUT_MODEL_CHAINS_RENAMING"
+fi
+
+STANDARD_OPTIONS_FOR_COMPARE_CONTACTS="--depth 0 --residue-level-only --detailed-output $IGNORE_RESIDUE_NAMES_OPTION"
+
+if $REMAP_CHAINS
+then
+ cat $TMPLDIR/model.contacts \
+ | voronota compare-contacts $STANDARD_OPTIONS_FOR_COMPARE_CONTACTS --remap-chains --remapped-chains-file $TMPLDIR/remapped_chains $REMAP_CHAINS_LOG_OPTION \
+ --target-contacts-file $TMPLDIR/target.contacts \
+ > /dev/null
+
+ rename_model_chains_by_dictionary "$TMPLDIR/remapped_chains"
+
+ if [ -n "$REMAP_CHAINS_OUTPUT" ]
+ then
+ mkdir -p $(dirname "$REMAP_CHAINS_OUTPUT")
+ cp "$TMPLDIR/remapped_chains" "$REMAP_CHAINS_OUTPUT"
+ fi
+fi
+
+if [ -n "$OUTFILE_RESIDUE_SCORES" ] || [ -n "$OUTFILE_RESIDUE_SCORES_PDB_TARGET" ] || [ -n "$OUTFILE_RESIDUE_SCORES_PDB_MODEL" ]
+then
+ CONTACTS_QUERY_PARAMETERS_MORE=""
+ if [ -n "$CONTACTS_QUERY_BY_CODE" ]
+ then
+ CONTACTS_QUERY_PARAMETERS_MORE="--match-tags $CONTACTS_QUERY_BY_CODE"
+ fi
+
+ cat $TMPLDIR/model.contacts | voronota query-contacts $CONTACTS_QUERY_PARAMETERS_MORE \
+ | voronota compare-contacts $STANDARD_OPTIONS_FOR_COMPARE_CONTACTS \
+ --target-contacts-file <(cat $TMPLDIR/target.contacts | voronota query-contacts $CONTACTS_QUERY_PARAMETERS_MORE) \
+ --smoothing-window $SMOOTHING_WINDOW \
+ --smoothed-scores-file $TMPLDIR/smoothed_residue_cad_scores \
+ > /dev/null
+
+ if [ -n "$OUTFILE_RESIDUE_SCORES" ]
+ then
+ mkdir -p $(dirname $OUTFILE_RESIDUE_SCORES)
+ cp $TMPLDIR/smoothed_residue_cad_scores "$OUTFILE_RESIDUE_SCORES"
+ fi
+
+ if [ -n "$OUTFILE_RESIDUE_SCORES_PDB_TARGET" ]
+ then
+ mkdir -p $(dirname "$OUTFILE_RESIDUE_SCORES_PDB_TARGET")
+ cat $TMPLDIR/target.balls \
+ | voronota query-balls \
+ --set-external-adjuncts $TMPLDIR/smoothed_residue_cad_scores \
+ --set-external-adjuncts-name score \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output "$OUTFILE_RESIDUE_SCORES_PDB_TARGET" \
+ --pdb-output-b-factor score \
+ > /dev/null
+ fi
+
+ if [ -n "$OUTFILE_RESIDUE_SCORES_PDB_MODEL" ]
+ then
+ mkdir -p $(dirname "$OUTFILE_RESIDUE_SCORES_PDB_MODEL")
+ cat $TMPLDIR/model.balls \
+ | voronota query-balls \
+ --set-external-adjuncts $TMPLDIR/smoothed_residue_cad_scores \
+ --set-external-adjuncts-name score \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output "$OUTFILE_RESIDUE_SCORES_PDB_MODEL" \
+ --pdb-output-b-factor score \
+ > /dev/null
+ fi
+fi
+
+QCODES=(AA)
+
+if [ -n "$CONTACTS_QUERY_BY_CODE" ]
+then
+ QCODES=($CONTACTS_QUERY_BY_CODE)
+fi
+
+if $USE_ALL_QUERY_CODES
+then
+ QCODES=(AA AS SS AM MM MS)
+fi
+
+if $OUTPUT_HEADER
+then
+ HEADER="target_file model_file query_code residues score target_area model_area"
+ if $ENABLE_SITE_BASED_SCORING
+ then
+ HEADER="$HEADER site_residues site_score site_target_area site_model_area"
+ fi
+ echo "$HEADER"
+fi
+
+for QCODE in "${QCODES[@]}"
+do
+ CONTACTS_QUERY_PARAMETERS_MORE="--match-tags $QCODE"
+
+ cat $TMPLDIR/model.contacts | voronota query-contacts $CONTACTS_QUERY_PARAMETERS_MORE \
+ | voronota compare-contacts $STANDARD_OPTIONS_FOR_COMPARE_CONTACTS \
+ --target-contacts-file <(cat $TMPLDIR/target.contacts | voronota query-contacts $CONTACTS_QUERY_PARAMETERS_MORE) \
+ > $TMPLDIR/global_cad_scores_$QCODE
+
+ if $ENABLE_SITE_BASED_SCORING
+ then
+ cat $TMPLDIR/model.contacts | voronota query-contacts $CONTACTS_QUERY_PARAMETERS_MORE | voronota query-contacts --summarize-by-first $CONTACTS_QUERY_PARAMETERS \
+ | voronota compare-contacts $STANDARD_OPTIONS_FOR_COMPARE_CONTACTS \
+ --target-contacts-file <(cat $TMPLDIR/target.contacts | voronota query-contacts $CONTACTS_QUERY_PARAMETERS_MORE | voronota query-contacts --summarize-by-first $CONTACTS_QUERY_PARAMETERS) \
+ > $TMPLDIR/site_based_global_cad_scores_$QCODE
+ fi
+
+ {
+ echo $INFILE_TARGET_PDB $INFILE_MODEL_PDB $QCODE
+ cat $TMPLDIR/global_cad_scores_$QCODE | egrep '^residue_count ' | awk '{print $2}'
+ cat $TMPLDIR/global_cad_scores_$QCODE | egrep '^residue_level_global ' | awk '{print $2 " " $3 " " $7}'
+ if $ENABLE_SITE_BASED_SCORING
+ then
+ cat $TMPLDIR/site_based_global_cad_scores_$QCODE | egrep '^residue_count ' | awk '{print $2}'
+ cat $TMPLDIR/site_based_global_cad_scores_$QCODE | egrep '^residue_level_global ' | awk '{print $2 " " $3 " " $7}'
+ fi
+ } \
+ | tr '\n' ' ' \
+ | sed 's/\s$/\n/'
+done
diff --git a/voronota-contacts b/voronota-contacts
new file mode 100755
index 0000000..645d479
--- /dev/null
+++ b/voronota-contacts
@@ -0,0 +1,237 @@
+#!/bin/bash
+
+function print_help_and_exit
+{
+cat >&2 << EOF
+
+'voronota-contacts' script provides a way for calculating and querying interatomic contacts
+with just one command (without the need to construct a pipeline from 'voronota' calls).
+
+Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --contacts-query string contacts query parameters
+ --contacts-query-additional string additional contacts query parameters
+ --cache-dir string path to cache directory
+ --sum-at-end flag to print sum of areas as the last line in output
+ --help | -h flag to display help message and exit
+
+Advanced options:
+ --output-drawing string output file with drawing script for PyMol
+ --drawing-parameters string drawing parameters
+ --wireframe-drawing flag to draw wireframe representation of contacts
+ --multiple-models flag to handle multiple models in PDB file
+
+Standard output (multiple lines):
+ {contacting atom} {contacting atom} {contact area} {distance between atoms centers} {tags} {adjunct values}
+
+EOF
+exit 1
+}
+
+readonly ZEROARG=$0
+INFILE=""
+INPUT_FILTER_QUERY_PARAMETERS=""
+CONTACTS_QUERY_FIRST_PARAMETERS=""
+CONTACTS_QUERY_SECOND_PARAMETERS=""
+DRAWING_OUTPUT=""
+DRAWING_PARAMETERS=""
+CONTACTS_CACHE_DIRECTORY=""
+MULTIPLE_MODELS_CHAINS_OPTION=""
+SUM_AT_END=false
+WIREFRAME_DRAWING=false
+HELP_MODE=false
+
+while [[ $# > 0 ]]
+do
+ OPTION="$1"
+ OPTARG="$2"
+ shift
+ case $OPTION in
+ -i|--input)
+ INFILE="$OPTARG"
+ shift
+ ;;
+ --input-filter-query)
+ INPUT_FILTER_QUERY_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --contacts-query-additional)
+ CONTACTS_QUERY_FIRST_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --contacts-query)
+ CONTACTS_QUERY_SECOND_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --output-drawing)
+ DRAWING_OUTPUT="$OPTARG"
+ shift
+ ;;
+ --drawing-parameters)
+ DRAWING_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --cache-dir)
+ CONTACTS_CACHE_DIRECTORY="$OPTARG"
+ shift
+ ;;
+ --multiple-models)
+ MULTIPLE_MODELS_CHAINS_OPTION="--multimodel-chains"
+ ;;
+ --sum-at-end)
+ SUM_AT_END=true
+ ;;
+ --wireframe-drawing)
+ WIREFRAME_DRAWING=true
+ ;;
+ -h)
+ HELP_MODE=true
+ ;;
+ *)
+ echo >&2 "Error: invalid command line option '$OPTION'"
+ exit 1
+ ;;
+ esac
+done
+
+if [ -z "$INFILE" ] || $HELP_MODE
+then
+ print_help_and_exit
+fi
+
+if [[ $ZEROARG == *"/"* ]]
+then
+ cd $(dirname $ZEROARG)
+ export PATH=$(pwd):$PATH
+ cd - &> /dev/null
+fi
+
+command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; }
+command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; }
+
+if [ ! -s "$INFILE" ]
+then
+ echo >&2 "Error: input file does not exist"
+ exit 1
+fi
+
+readonly TMPLDIR=$(mktemp -d)
+trap "rm -r $TMPLDIR" EXIT
+
+{
+ if [[ "$INFILE" == *".gz" ]]
+ then
+ zcat "$INFILE"
+ else
+ cat "$INFILE"
+ fi
+} \
+| voronota get-balls-from-atoms-file \
+ --annotated $MULTIPLE_MODELS_CHAINS_OPTION \
+ --radii-file <(voronota-resources radii) \
+ --include-heteroatoms \
+| voronota query-balls \
+ --drop-altloc-indicators \
+| voronota query-balls $INPUT_FILTER_QUERY_PARAMETERS \
+> $TMPLDIR/balls
+
+if [ ! -s "$TMPLDIR/balls" ]
+then
+ echo >&2 "Error: no atoms in input file"
+ exit 1
+fi
+
+BALLS_MD5=""
+if [ -n "$CONTACTS_CACHE_DIRECTORY" ]
+then
+ BALLS_MD5=$(cat $TMPLDIR/balls | md5sum | awk '{print $1}')
+ if [ -n "$BALLS_MD5" ]
+ then
+ BALLS_MD5="${BALLS_MD5}.voronota.contacts"
+ if [ -s "$CONTACTS_CACHE_DIRECTORY/$BALLS_MD5" ]
+ then
+ cp $CONTACTS_CACHE_DIRECTORY/$BALLS_MD5 $TMPLDIR/all_contacts
+ fi
+ fi
+fi
+
+if [ -n "$DRAWING_OUTPUT" ] && [ -s "$TMPLDIR/all_contacts" ]
+then
+ GRAPHICS_TOKEN=$(cat $TMPLDIR/all_contacts | head -1 | awk '{print $8}')
+ if [ -z "$GRAPHICS_TOKEN" ]
+ then
+ rm $TMPLDIR/all_contacts
+ fi
+fi
+
+if [ ! -s "$TMPLDIR/all_contacts" ]
+then
+ cat $TMPLDIR/balls \
+ | \
+ {
+ if [ -n "$DRAWING_OUTPUT" ]
+ then
+ voronota calculate-contacts \
+ --annotated \
+ --draw \
+ --tag-centrality
+ else
+ voronota calculate-contacts \
+ --annotated \
+ --tag-centrality
+ fi
+ } \
+ | voronota query-contacts \
+ --match-min-seq-sep 1 \
+ --preserve-graphics \
+ > $TMPLDIR/all_contacts
+
+ if [ -n "$CONTACTS_CACHE_DIRECTORY" ] && [ -n "$BALLS_MD5" ]
+ then
+ mkdir -p $CONTACTS_CACHE_DIRECTORY
+ cp $TMPLDIR/all_contacts $CONTACTS_CACHE_DIRECTORY/$BALLS_MD5
+ fi
+fi
+
+{
+if [ -n "$DRAWING_OUTPUT" ]
+then
+ cat $TMPLDIR/all_contacts \
+ | voronota query-contacts $CONTACTS_QUERY_FIRST_PARAMETERS \
+ --preserve-graphics \
+ | voronota query-contacts $CONTACTS_QUERY_SECOND_PARAMETERS \
+ --preserve-graphics \
+ > $TMPLDIR/all_contacts_for_drawing
+
+ if $WIREFRAME_DRAWING
+ then
+ cat $TMPLDIR/all_contacts_for_drawing \
+ | sed 's|_tfanc \S\+ \S\+ \S\+ \S\+ \S\+ \S\+|_lloop|g' \
+ | sed 's|_tstrip \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+ \S\+||g' \
+ > $TMPLDIR/all_contacts_for_drawing_wireframe
+ mv $TMPLDIR/all_contacts_for_drawing_wireframe $TMPLDIR/all_contacts_for_drawing
+ fi
+
+ cat $TMPLDIR/all_contacts_for_drawing \
+ | voronota draw-contacts $DRAWING_PARAMETERS \
+ --drawing-for-pymol $DRAWING_OUTPUT \
+ > /dev/null
+
+ cat $TMPLDIR/all_contacts_for_drawing \
+ | awk '{print $1 " " $2 " " $3 " " $4 " " $5 " " $6}'
+else
+ cat $TMPLDIR/all_contacts \
+ | voronota query-contacts $CONTACTS_QUERY_FIRST_PARAMETERS \
+ | voronota query-contacts $CONTACTS_QUERY_SECOND_PARAMETERS
+fi
+} > $TMPLDIR/result_contacts
+
+{
+cat $TMPLDIR/result_contacts
+if $SUM_AT_END
+then
+ cat $TMPLDIR/result_contacts \
+ | voronota query-contacts --summarize
+fi
+} | column -t
diff --git a/voronota-resources b/voronota-resources
new file mode 100755
index 0000000..fae4393
--- /dev/null
+++ b/voronota-resources
@@ -0,0 +1,51977 @@
+#!/bin/bash
+
+RESOURCE_NAME=$1
+
+if [ -z $RESOURCE_NAME ]
+then
+echo -e 'Need resource name as argument, available options are:\n radii\n energy_potential\n energy_means_and_sds' >&2
+fi
+
+if [ "$RESOURCE_NAME" == "radii" ]
+then
+cat << 'EOF'
+# default radii
+
+* * 1.80
+* C* 1.80
+* CL* 1.80
+* F* 1.80
+* FE* 1.80
+* N* 1.60
+* O* 1.50
+* P* 1.90
+* S* 1.90
+* ZN* 1.70
+* H* 1.30
+
+
+# protein main chain radii
+
+* C 1.75
+* CA 1.90
+* N 1.70
+* O 1.49
+
+
+# protein side chain radii
+
+ALA CB 1.92
+
+ARG CB 1.91
+ARG CD* 1.88
+ARG CG* 1.92
+ARG NE* 1.62
+ARG NH1 1.62
+ARG NH2 1.67
+
+ASN CB 1.91
+ASN CG* 1.81
+ASN ND2 1.62
+ASN OD1 1.52
+
+ASP CB 1.91
+ASP CG* 1.76
+ASP OD1 1.49
+ASP OD2 1.49
+
+CYS CB 1.91
+CYS S* 1.88
+
+GLN CB 1.91
+GLN CD* 1.81
+GLN NE2 1.62
+GLN OE1 1.52
+
+GLU CB 1.91
+GLU CD* 1.76
+GLU CG* 1.88
+GLU OE1 1.49
+GLU OE2 1.49
+
+HIS CB 1.91
+HIS CD* 1.74
+HIS CE* 1.74
+HIS ND2 1.65
+HIS NE1 1.65
+
+ILE CB 2.01
+ILE CD1 1.92
+ILE CG1 1.92
+ILE CG2 1.92
+
+LEU CB 1.91
+LEU CD1 1.92
+LEU CD2 1.92
+LEU CG* 2.01
+
+LYS CB 1.91
+LYS CD* 1.92
+LYS CE* 1.88
+LYS CG* 1.92
+LYS NZ* 1.67
+
+MET CB 1.91
+MET CG* 1.92
+MET S* 1.94
+
+PHE CB 1.91
+PHE CD* 1.82
+PHE CE* 1.82
+PHE CG* 1.74
+PHE CZ* 1.82
+
+PRO CB 1.91
+PRO CD* 1.92
+PRO CG* 1.92
+
+SER CB 1.91
+SER OG* 1.54
+
+THR CB 2.01
+THR CG2 1.92
+THR OG* 1.54
+
+TRP CB 1.91
+TRP CD* 1.82
+TRP CE* 1.82
+TRP CE2 1.74
+TRP CG* 1.74
+TRP CH* 1.82
+TRP CZ* 1.82
+TRP NE1 1.66
+
+TYR CB 1.91
+TYR CD* 1.82
+TYR CE* 1.82
+TYR CG* 1.74
+TYR OH* 1.54
+
+VAL CB 2.01
+VAL CG1 1.92
+VAL CG2 1.92
+EOF
+fi
+
+if [ "$RESOURCE_NAME" == "energy_potential" ]
+then
+cat << 'EOF'
+R<ALA>A<C> R<ALA>A<C> central_sep1 4.17568
+R<ALA>A<C> R<ALA>A<C> central_sep2 2.3065
+R<ALA>A<C> R<ALA>A<C> sep1 -2.60148
+R<ALA>A<C> R<ALA>A<C> sep2 1.62686
+R<ALA>A<C> R<ALA>A<CA> central_sep1 3.20641
+R<ALA>A<C> R<ALA>A<CA> central_sep2 1.40236
+R<ALA>A<C> R<ALA>A<CA> sep1 -2.67699
+R<ALA>A<C> R<ALA>A<CA> sep2 0.098818
+R<ALA>A<C> R<ALA>A<CB> central_sep1 1.56691
+R<ALA>A<C> R<ALA>A<CB> central_sep2 -0.0958367
+R<ALA>A<C> R<ALA>A<CB> sep1 0.317846
+R<ALA>A<C> R<ALA>A<CB> sep2 -0.662816
+R<ALA>A<C> R<ALA>A<N> central_sep1 -0.852815
+R<ALA>A<C> R<ALA>A<N> central_sep2 2.60675
+R<ALA>A<C> R<ALA>A<N> sep1 -1.95665
+R<ALA>A<C> R<ALA>A<N> sep2 1.26184
+R<ALA>A<C> R<ALA>A<O> central_sep1 -0.945511
+R<ALA>A<C> R<ALA>A<O> central_sep2 2.13092
+R<ALA>A<C> R<ALA>A<O> sep1 -1.75688
+R<ALA>A<C> R<ALA>A<O> sep2 1.07477
+R<ALA>A<C> R<ARG>A<C> central_sep1 4.63328
+R<ALA>A<C> R<ARG>A<C> central_sep2 3.71944
+R<ALA>A<C> R<ARG>A<C> sep1 -2.51412
+R<ALA>A<C> R<ARG>A<C> sep2 2.22891
+R<ALA>A<C> R<ARG>A<CA> central_sep1 3.98792
+R<ALA>A<C> R<ARG>A<CA> central_sep2 2.24429
+R<ALA>A<C> R<ARG>A<CA> sep1 -2.64487
+R<ALA>A<C> R<ARG>A<CA> sep2 0.730436
+R<ALA>A<C> R<ARG>A<CB> central_sep1 2.24725
+R<ALA>A<C> R<ARG>A<CB> central_sep2 1.22515
+R<ALA>A<C> R<ARG>A<CB> sep1 0.0674803
+R<ALA>A<C> R<ARG>A<CB> sep2 0.164956
+R<ALA>A<C> R<ARG>A<CD> central_sep1 1.99738
+R<ALA>A<C> R<ARG>A<CD> central_sep2 0.70182
+R<ALA>A<C> R<ARG>A<CD> sep1 0.761328
+R<ALA>A<C> R<ARG>A<CD> sep2 -0.154646
+R<ALA>A<C> R<ARG>A<CG> central_sep1 0.787573
+R<ALA>A<C> R<ARG>A<CG> central_sep2 0.853057
+R<ALA>A<C> R<ARG>A<CG> sep1 -0.565042
+R<ALA>A<C> R<ARG>A<CG> sep2 -0.149714
+R<ALA>A<C> R<ARG>A<CZ> central_sep1 0.151272
+R<ALA>A<C> R<ARG>A<CZ> central_sep2 0.800558
+R<ALA>A<C> R<ARG>A<CZ> sep1 1.63398
+R<ALA>A<C> R<ARG>A<CZ> sep2 -0.102201
+R<ALA>A<C> R<ARG>A<N> central_sep1 -0.739681
+R<ALA>A<C> R<ARG>A<N> central_sep2 3.11352
+R<ALA>A<C> R<ARG>A<N> sep1 -1.92963
+R<ALA>A<C> R<ARG>A<N> sep2 1.857
+R<ALA>A<C> R<ARG>A<NE> central_sep1 1.92858
+R<ALA>A<C> R<ARG>A<NE> central_sep2 1.13008
+R<ALA>A<C> R<ARG>A<NE> sep1 1.41219
+R<ALA>A<C> R<ARG>A<NE> sep2 0.0239833
+R<ALA>A<C> R<ARG>A<NH1> central_sep1 1.1341
+R<ALA>A<C> R<ARG>A<NH1> central_sep2 0.889017
+R<ALA>A<C> R<ARG>A<NH1> sep1 2.13247
+R<ALA>A<C> R<ARG>A<NH1> sep2 -0.081254
+R<ALA>A<C> R<ARG>A<O> central_sep1 -0.884465
+R<ALA>A<C> R<ARG>A<O> central_sep2 2.49436
+R<ALA>A<C> R<ARG>A<O> sep1 -1.51304
+R<ALA>A<C> R<ARG>A<O> sep2 1.33153
+R<ALA>A<C> R<ASN>A<C> central_sep1 3.67901
+R<ALA>A<C> R<ASN>A<C> central_sep2 3.1784
+R<ALA>A<C> R<ASN>A<C> sep1 -2.20367
+R<ALA>A<C> R<ASN>A<C> sep2 2.19552
+R<ALA>A<C> R<ASN>A<CA> central_sep1 3.89136
+R<ALA>A<C> R<ASN>A<CA> central_sep2 2.63503
+R<ALA>A<C> R<ASN>A<CA> sep1 -2.41343
+R<ALA>A<C> R<ASN>A<CA> sep2 0.677796
+R<ALA>A<C> R<ASN>A<CB> central_sep1 2.5484
+R<ALA>A<C> R<ASN>A<CB> central_sep2 1.21132
+R<ALA>A<C> R<ASN>A<CB> sep1 -0.294504
+R<ALA>A<C> R<ASN>A<CB> sep2 0.0313399
+R<ALA>A<C> R<ASN>A<CG> central_sep1 1.15706
+R<ALA>A<C> R<ASN>A<CG> central_sep2 1.111
+R<ALA>A<C> R<ASN>A<CG> sep1 -0.707009
+R<ALA>A<C> R<ASN>A<CG> sep2 0.231235
+R<ALA>A<C> R<ASN>A<N> central_sep1 -0.58708
+R<ALA>A<C> R<ASN>A<N> central_sep2 3.02328
+R<ALA>A<C> R<ASN>A<N> sep1 -1.6411
+R<ALA>A<C> R<ASN>A<N> sep2 1.64794
+R<ALA>A<C> R<ASN>A<ND2> central_sep1 1.65155
+R<ALA>A<C> R<ASN>A<ND2> central_sep2 1.19146
+R<ALA>A<C> R<ASN>A<ND2> sep1 0.354795
+R<ALA>A<C> R<ASN>A<ND2> sep2 0.0614459
+R<ALA>A<C> R<ASN>A<O> central_sep1 -0.844204
+R<ALA>A<C> R<ASN>A<O> central_sep2 2.21054
+R<ALA>A<C> R<ASN>A<O> sep1 -1.36642
+R<ALA>A<C> R<ASN>A<O> sep2 1.19216
+R<ALA>A<C> R<ASN>A<OD1> central_sep1 1.42424
+R<ALA>A<C> R<ASN>A<OD1> central_sep2 1.39693
+R<ALA>A<C> R<ASN>A<OD1> sep1 0.222008
+R<ALA>A<C> R<ASN>A<OD1> sep2 0.536747
+R<ALA>A<C> R<ASP>A<C> central_sep1 4.24844
+R<ALA>A<C> R<ASP>A<C> central_sep2 3.75187
+R<ALA>A<C> R<ASP>A<C> sep1 -2.39265
+R<ALA>A<C> R<ASP>A<C> sep2 2.10949
+R<ALA>A<C> R<ASP>A<CA> central_sep1 4.15723
+R<ALA>A<C> R<ASP>A<CA> central_sep2 2.95218
+R<ALA>A<C> R<ASP>A<CA> sep1 -2.61135
+R<ALA>A<C> R<ASP>A<CA> sep2 1.01629
+R<ALA>A<C> R<ASP>A<CB> central_sep1 2.63396
+R<ALA>A<C> R<ASP>A<CB> central_sep2 1.70417
+R<ALA>A<C> R<ASP>A<CB> sep1 -0.0248942
+R<ALA>A<C> R<ASP>A<CB> sep2 0.448863
+R<ALA>A<C> R<ASP>A<CG> central_sep1 2.42725
+R<ALA>A<C> R<ASP>A<CG> central_sep2 2.09026
+R<ALA>A<C> R<ASP>A<CG> sep1 0.23973
+R<ALA>A<C> R<ASP>A<CG> sep2 0.931245
+R<ALA>A<C> R<ASP>A<N> central_sep1 -0.663485
+R<ALA>A<C> R<ASP>A<N> central_sep2 2.81573
+R<ALA>A<C> R<ASP>A<N> sep1 -1.57145
+R<ALA>A<C> R<ASP>A<N> sep2 2.03726
+R<ALA>A<C> R<ASP>A<O> central_sep1 -0.831919
+R<ALA>A<C> R<ASP>A<O> central_sep2 2.73181
+R<ALA>A<C> R<ASP>A<O> sep1 -1.50477
+R<ALA>A<C> R<ASP>A<O> sep2 1.64824
+R<ALA>A<C> R<ASP>A<OD1> central_sep1 2.0955
+R<ALA>A<C> R<ASP>A<OD1> central_sep2 2.50686
+R<ALA>A<C> R<ASP>A<OD1> sep1 0.411845
+R<ALA>A<C> R<ASP>A<OD1> sep2 1.29485
+R<ALA>A<C> R<CYS>A<C> central_sep1 2.81683
+R<ALA>A<C> R<CYS>A<C> central_sep2 3.19631
+R<ALA>A<C> R<CYS>A<C> sep1 -2.32294
+R<ALA>A<C> R<CYS>A<C> sep2 1.92368
+R<ALA>A<C> R<CYS>A<CA> central_sep1 3.61535
+R<ALA>A<C> R<CYS>A<CA> central_sep2 2.01532
+R<ALA>A<C> R<CYS>A<CA> sep1 -2.46976
+R<ALA>A<C> R<CYS>A<CA> sep2 0.426816
+R<ALA>A<C> R<CYS>A<CB> central_sep1 1.69744
+R<ALA>A<C> R<CYS>A<CB> central_sep2 0.545427
+R<ALA>A<C> R<CYS>A<CB> sep1 -0.16045
+R<ALA>A<C> R<CYS>A<CB> sep2 -0.434824
+R<ALA>A<C> R<CYS>A<N> central_sep1 -0.487439
+R<ALA>A<C> R<CYS>A<N> central_sep2 3.15366
+R<ALA>A<C> R<CYS>A<N> sep1 -1.72732
+R<ALA>A<C> R<CYS>A<N> sep2 1.44356
+R<ALA>A<C> R<CYS>A<O> central_sep1 -0.802291
+R<ALA>A<C> R<CYS>A<O> central_sep2 1.86935
+R<ALA>A<C> R<CYS>A<O> sep1 -1.28479
+R<ALA>A<C> R<CYS>A<O> sep2 1.10211
+R<ALA>A<C> R<CYS>A<SG> central_sep1 0.587122
+R<ALA>A<C> R<CYS>A<SG> central_sep2 -0.249541
+R<ALA>A<C> R<CYS>A<SG> sep1 -0.0851084
+R<ALA>A<C> R<CYS>A<SG> sep2 -0.62062
+R<ALA>A<C> R<GLN>A<C> central_sep1 5.03827
+R<ALA>A<C> R<GLN>A<C> central_sep2 4.18034
+R<ALA>A<C> R<GLN>A<C> sep1 -2.52178
+R<ALA>A<C> R<GLN>A<C> sep2 2.64108
+R<ALA>A<C> R<GLN>A<CA> central_sep1 3.59672
+R<ALA>A<C> R<GLN>A<CA> central_sep2 2.09362
+R<ALA>A<C> R<GLN>A<CA> sep1 -2.63973
+R<ALA>A<C> R<GLN>A<CA> sep2 1.0259
+R<ALA>A<C> R<GLN>A<CB> central_sep1 2.51627
+R<ALA>A<C> R<GLN>A<CB> central_sep2 1.43759
+R<ALA>A<C> R<GLN>A<CB> sep1 0.146758
+R<ALA>A<C> R<GLN>A<CB> sep2 0.362281
+R<ALA>A<C> R<GLN>A<CD> central_sep1 1.43414
+R<ALA>A<C> R<GLN>A<CD> central_sep2 1.0957
+R<ALA>A<C> R<GLN>A<CD> sep1 -0.0185153
+R<ALA>A<C> R<GLN>A<CD> sep2 0.237039
+R<ALA>A<C> R<GLN>A<CG> central_sep1 1.22497
+R<ALA>A<C> R<GLN>A<CG> central_sep2 1.0193
+R<ALA>A<C> R<GLN>A<CG> sep1 -0.351899
+R<ALA>A<C> R<GLN>A<CG> sep2 -0.0230916
+R<ALA>A<C> R<GLN>A<N> central_sep1 -0.775034
+R<ALA>A<C> R<GLN>A<N> central_sep2 3.66683
+R<ALA>A<C> R<GLN>A<N> sep1 -1.8872
+R<ALA>A<C> R<GLN>A<N> sep2 2.23066
+R<ALA>A<C> R<GLN>A<NE2> central_sep1 1.24372
+R<ALA>A<C> R<GLN>A<NE2> central_sep2 1.1757
+R<ALA>A<C> R<GLN>A<NE2> sep1 0.991382
+R<ALA>A<C> R<GLN>A<NE2> sep2 0.16954
+R<ALA>A<C> R<GLN>A<O> central_sep1 -0.970654
+R<ALA>A<C> R<GLN>A<O> central_sep2 2.77865
+R<ALA>A<C> R<GLN>A<O> sep1 -1.58999
+R<ALA>A<C> R<GLN>A<O> sep2 1.51424
+R<ALA>A<C> R<GLN>A<OE1> central_sep1 1.73988
+R<ALA>A<C> R<GLN>A<OE1> central_sep2 1.53806
+R<ALA>A<C> R<GLN>A<OE1> sep1 1.26366
+R<ALA>A<C> R<GLN>A<OE1> sep2 0.500482
+R<ALA>A<C> R<GLU>A<C> central_sep1 4.34937
+R<ALA>A<C> R<GLU>A<C> central_sep2 3.94773
+R<ALA>A<C> R<GLU>A<C> sep1 -2.52061
+R<ALA>A<C> R<GLU>A<C> sep2 2.53345
+R<ALA>A<C> R<GLU>A<CA> central_sep1 3.77627
+R<ALA>A<C> R<GLU>A<CA> central_sep2 2.6635
+R<ALA>A<C> R<GLU>A<CA> sep1 -2.64261
+R<ALA>A<C> R<GLU>A<CA> sep2 1.15674
+R<ALA>A<C> R<GLU>A<CB> central_sep1 2.69342
+R<ALA>A<C> R<GLU>A<CB> central_sep2 1.93088
+R<ALA>A<C> R<GLU>A<CB> sep1 0.285005
+R<ALA>A<C> R<GLU>A<CB> sep2 0.672364
+R<ALA>A<C> R<GLU>A<CD> central_sep1 2.1679
+R<ALA>A<C> R<GLU>A<CD> central_sep2 1.87698
+R<ALA>A<C> R<GLU>A<CD> sep1 0.117291
+R<ALA>A<C> R<GLU>A<CD> sep2 1.09907
+R<ALA>A<C> R<GLU>A<CG> central_sep1 1.55228
+R<ALA>A<C> R<GLU>A<CG> central_sep2 1.2649
+R<ALA>A<C> R<GLU>A<CG> sep1 -0.149305
+R<ALA>A<C> R<GLU>A<CG> sep2 0.411109
+R<ALA>A<C> R<GLU>A<N> central_sep1 -0.72613
+R<ALA>A<C> R<GLU>A<N> central_sep2 3.36742
+R<ALA>A<C> R<GLU>A<N> sep1 -1.78613
+R<ALA>A<C> R<GLU>A<N> sep2 2.23856
+R<ALA>A<C> R<GLU>A<O> central_sep1 -0.88292
+R<ALA>A<C> R<GLU>A<O> central_sep2 2.98172
+R<ALA>A<C> R<GLU>A<O> sep1 -1.54591
+R<ALA>A<C> R<GLU>A<O> sep2 1.74875
+R<ALA>A<C> R<GLU>A<OE1> central_sep1 2.22843
+R<ALA>A<C> R<GLU>A<OE1> central_sep2 2.52864
+R<ALA>A<C> R<GLU>A<OE1> sep1 1.62936
+R<ALA>A<C> R<GLU>A<OE1> sep2 1.44944
+R<ALA>A<C> R<GLY>A<C> central_sep1 3.45146
+R<ALA>A<C> R<GLY>A<C> central_sep2 1.97199
+R<ALA>A<C> R<GLY>A<C> sep1 -1.92202
+R<ALA>A<C> R<GLY>A<C> sep2 0.859819
+R<ALA>A<C> R<GLY>A<CA> central_sep1 2.94283
+R<ALA>A<C> R<GLY>A<CA> central_sep2 0.886299
+R<ALA>A<C> R<GLY>A<CA> sep1 -1.80364
+R<ALA>A<C> R<GLY>A<CA> sep2 -0.170091
+R<ALA>A<C> R<GLY>A<N> central_sep1 -0.240724
+R<ALA>A<C> R<GLY>A<N> central_sep2 2.00847
+R<ALA>A<C> R<GLY>A<N> sep1 -1.716
+R<ALA>A<C> R<GLY>A<N> sep2 0.731702
+R<ALA>A<C> R<GLY>A<O> central_sep1 -0.586018
+R<ALA>A<C> R<GLY>A<O> central_sep2 1.84247
+R<ALA>A<C> R<GLY>A<O> sep1 -1.476
+R<ALA>A<C> R<GLY>A<O> sep2 0.85497
+R<ALA>A<C> R<HIS>A<C> central_sep1 3.33343
+R<ALA>A<C> R<HIS>A<C> central_sep2 3.41733
+R<ALA>A<C> R<HIS>A<C> sep1 -2.29571
+R<ALA>A<C> R<HIS>A<C> sep2 2.43425
+R<ALA>A<C> R<HIS>A<CA> central_sep1 4.15362
+R<ALA>A<C> R<HIS>A<CA> central_sep2 2.56589
+R<ALA>A<C> R<HIS>A<CA> sep1 -2.50974
+R<ALA>A<C> R<HIS>A<CA> sep2 0.71151
+R<ALA>A<C> R<HIS>A<CB> central_sep1 2.32777
+R<ALA>A<C> R<HIS>A<CB> central_sep2 0.921735
+R<ALA>A<C> R<HIS>A<CB> sep1 0.00209615
+R<ALA>A<C> R<HIS>A<CB> sep2 -0.108185
+R<ALA>A<C> R<HIS>A<CD2> central_sep1 0.144872
+R<ALA>A<C> R<HIS>A<CD2> central_sep2 0.678521
+R<ALA>A<C> R<HIS>A<CD2> sep1 -0.118141
+R<ALA>A<C> R<HIS>A<CD2> sep2 -0.282698
+R<ALA>A<C> R<HIS>A<CE1> central_sep1 1.64797
+R<ALA>A<C> R<HIS>A<CE1> central_sep2 0.655122
+R<ALA>A<C> R<HIS>A<CE1> sep1 1.79629
+R<ALA>A<C> R<HIS>A<CE1> sep2 -0.145393
+R<ALA>A<C> R<HIS>A<CG> central_sep1 0.458388
+R<ALA>A<C> R<HIS>A<CG> central_sep2 0.845188
+R<ALA>A<C> R<HIS>A<CG> sep1 -1.35889
+R<ALA>A<C> R<HIS>A<CG> sep2 0.276668
+R<ALA>A<C> R<HIS>A<N> central_sep1 -0.636831
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+R<ARG>A<C> R<TRP>A<CD2> central_sep2 1.01836
+R<ARG>A<C> R<TRP>A<CD2> sep1 -0.62446
+R<ARG>A<C> R<TRP>A<CD2> sep2 0.47979
+R<ARG>A<C> R<TRP>A<CE2> central_sep1 0.09698
+R<ARG>A<C> R<TRP>A<CE2> central_sep2 1.04734
+R<ARG>A<C> R<TRP>A<CE2> sep1 1.10454
+R<ARG>A<C> R<TRP>A<CE2> sep2 0.151111
+R<ARG>A<C> R<TRP>A<CE3> central_sep1 -0.581654
+R<ARG>A<C> R<TRP>A<CE3> central_sep2 -1.19406
+R<ARG>A<C> R<TRP>A<CE3> sep1 0.394449
+R<ARG>A<C> R<TRP>A<CE3> sep2 -0.560879
+R<ARG>A<C> R<TRP>A<CG> central_sep1 1.36218
+R<ARG>A<C> R<TRP>A<CG> central_sep2 0.830331
+R<ARG>A<C> R<TRP>A<CG> sep1 -1.33401
+R<ARG>A<C> R<TRP>A<CG> sep2 -0.0879551
+R<ARG>A<C> R<TRP>A<CH2> central_sep1 2.16063
+R<ARG>A<C> R<TRP>A<CH2> central_sep2 -0.442291
+R<ARG>A<C> R<TRP>A<CH2> sep1 3.25661
+R<ARG>A<C> R<TRP>A<CH2> sep2 -0.782144
+R<ARG>A<C> R<TRP>A<CZ2> central_sep1 1.71043
+R<ARG>A<C> R<TRP>A<CZ2> central_sep2 -0.220953
+R<ARG>A<C> R<TRP>A<CZ2> sep1 2.8528
+R<ARG>A<C> R<TRP>A<CZ2> sep2 -0.656579
+R<ARG>A<C> R<TRP>A<CZ3> central_sep1 0.702011
+R<ARG>A<C> R<TRP>A<CZ3> central_sep2 -0.548862
+R<ARG>A<C> R<TRP>A<CZ3> sep1 1.87868
+R<ARG>A<C> R<TRP>A<CZ3> sep2 -0.988638
+R<ARG>A<C> R<TRP>A<N> central_sep1 -0.671934
+R<ARG>A<C> R<TRP>A<N> central_sep2 1.86869
+R<ARG>A<C> R<TRP>A<N> sep1 -1.81729
+R<ARG>A<C> R<TRP>A<N> sep2 1.62168
+R<ARG>A<C> R<TRP>A<NE1> central_sep1 1.07576
+R<ARG>A<C> R<TRP>A<NE1> central_sep2 0.370473
+R<ARG>A<C> R<TRP>A<NE1> sep1 1.62426
+R<ARG>A<C> R<TRP>A<NE1> sep2 -0.400132
+R<ARG>A<C> R<TRP>A<O> central_sep1 -1.0156
+R<ARG>A<C> R<TRP>A<O> central_sep2 2.28089
+R<ARG>A<C> R<TRP>A<O> sep1 -1.3818
+R<ARG>A<C> R<TRP>A<O> sep2 1.53257
+R<ARG>A<C> R<TYR>A<C> central_sep1 3.51821
+R<ARG>A<C> R<TYR>A<C> central_sep2 3.52625
+R<ARG>A<C> R<TYR>A<C> sep1 -2.54659
+R<ARG>A<C> R<TYR>A<C> sep2 2.13894
+R<ARG>A<C> R<TYR>A<CA> central_sep1 3.63461
+R<ARG>A<C> R<TYR>A<CA> central_sep2 2.37403
+R<ARG>A<C> R<TYR>A<CA> sep1 -2.75412
+R<ARG>A<C> R<TYR>A<CA> sep2 0.570403
+R<ARG>A<C> R<TYR>A<CB> central_sep1 1.92183
+R<ARG>A<C> R<TYR>A<CB> central_sep2 0.749296
+R<ARG>A<C> R<TYR>A<CB> sep1 -0.0905361
+R<ARG>A<C> R<TYR>A<CB> sep2 -0.344656
+R<ARG>A<C> R<TYR>A<CD1> central_sep1 -0.728064
+R<ARG>A<C> R<TYR>A<CD1> central_sep2 -0.310012
+R<ARG>A<C> R<TYR>A<CD1> sep1 -0.587862
+R<ARG>A<C> R<TYR>A<CD1> sep2 -0.618673
+R<ARG>A<C> R<TYR>A<CE1> central_sep1 0.341827
+R<ARG>A<C> R<TYR>A<CE1> central_sep2 0.0987637
+R<ARG>A<C> R<TYR>A<CE1> sep1 1.39544
+R<ARG>A<C> R<TYR>A<CE1> sep2 -0.400817
+R<ARG>A<C> R<TYR>A<CG> central_sep1 0.88199
+R<ARG>A<C> R<TYR>A<CG> central_sep2 0.795837
+R<ARG>A<C> R<TYR>A<CG> sep1 -2.07093
+R<ARG>A<C> R<TYR>A<CG> sep2 0.15355
+R<ARG>A<C> R<TYR>A<CZ> central_sep1 0.875092
+R<ARG>A<C> R<TYR>A<CZ> central_sep2 0.735235
+R<ARG>A<C> R<TYR>A<CZ> sep1 1.55008
+R<ARG>A<C> R<TYR>A<CZ> sep2 0.0364753
+R<ARG>A<C> R<TYR>A<N> central_sep1 -0.476712
+R<ARG>A<C> R<TYR>A<N> central_sep2 3.17682
+R<ARG>A<C> R<TYR>A<N> sep1 -1.65642
+R<ARG>A<C> R<TYR>A<N> sep2 1.74215
+R<ARG>A<C> R<TYR>A<O> central_sep1 -0.95874
+R<ARG>A<C> R<TYR>A<O> central_sep2 2.41173
+R<ARG>A<C> R<TYR>A<O> sep1 -1.29122
+R<ARG>A<C> R<TYR>A<O> sep2 1.30991
+R<ARG>A<C> R<TYR>A<OH> central_sep1 3.13381
+R<ARG>A<C> R<TYR>A<OH> central_sep2 0.659156
+R<ARG>A<C> R<TYR>A<OH> sep1 3.55323
+R<ARG>A<C> R<TYR>A<OH> sep2 -0.017565
+R<ARG>A<C> R<VAL>A<C> central_sep1 4.82415
+R<ARG>A<C> R<VAL>A<C> central_sep2 4.86895
+R<ARG>A<C> R<VAL>A<C> sep1 -2.74848
+R<ARG>A<C> R<VAL>A<C> sep2 2.8605
+R<ARG>A<C> R<VAL>A<CA> central_sep1 4.52229
+R<ARG>A<C> R<VAL>A<CA> central_sep2 2.77308
+R<ARG>A<C> R<VAL>A<CA> sep1 -2.79996
+R<ARG>A<C> R<VAL>A<CA> sep2 0.91621
+R<ARG>A<C> R<VAL>A<CB> central_sep1 1.97326
+R<ARG>A<C> R<VAL>A<CB> central_sep2 0.920649
+R<ARG>A<C> R<VAL>A<CB> sep1 0.158584
+R<ARG>A<C> R<VAL>A<CB> sep2 -0.490146
+R<ARG>A<C> R<VAL>A<CG1> central_sep1 0.215013
+R<ARG>A<C> R<VAL>A<CG1> central_sep2 0.225112
+R<ARG>A<C> R<VAL>A<CG1> sep1 -0.306161
+R<ARG>A<C> R<VAL>A<CG1> sep2 -0.567874
+R<ARG>A<C> R<VAL>A<CG2> central_sep1 0.681137
+R<ARG>A<C> R<VAL>A<CG2> central_sep2 0.256816
+R<ARG>A<C> R<VAL>A<CG2> sep1 -0.862501
+R<ARG>A<C> R<VAL>A<CG2> sep2 -0.292021
+R<ARG>A<C> R<VAL>A<N> central_sep1 -0.0998318
+R<ARG>A<C> R<VAL>A<N> central_sep2 3.28598
+R<ARG>A<C> R<VAL>A<N> sep1 -1.68273
+R<ARG>A<C> R<VAL>A<N> sep2 1.77326
+R<ARG>A<C> R<VAL>A<O> central_sep1 -0.936838
+R<ARG>A<C> R<VAL>A<O> central_sep2 2.70452
+R<ARG>A<C> R<VAL>A<O> sep1 -1.19742
+R<ARG>A<C> R<VAL>A<O> sep2 1.3911
+R<ARG>A<C> c<solvent> . 1.84464
+R<ARG>A<CA> R<ARG>A<CA> central_sep1 2.00191
+R<ARG>A<CA> R<ARG>A<CA> central_sep2 0.420843
+R<ARG>A<CA> R<ARG>A<CA> sep1 2.27677
+R<ARG>A<CA> R<ARG>A<CA> sep2 0.715081
+R<ARG>A<CA> R<ARG>A<CB> central_sep1 -0.953038
+R<ARG>A<CA> R<ARG>A<CB> central_sep2 0.666005
+R<ARG>A<CA> R<ARG>A<CB> sep1 1.15678
+R<ARG>A<CA> R<ARG>A<CB> sep2 0.700265
+R<ARG>A<CA> R<ARG>A<CD> central_sep1 0.234221
+R<ARG>A<CA> R<ARG>A<CD> central_sep2 0.326836
+R<ARG>A<CA> R<ARG>A<CD> sep1 0.803042
+R<ARG>A<CA> R<ARG>A<CD> sep2 0.262887
+R<ARG>A<CA> R<ARG>A<CG> central_sep1 0.636051
+R<ARG>A<CA> R<ARG>A<CG> central_sep2 0.403743
+R<ARG>A<CA> R<ARG>A<CG> sep1 0.687379
+R<ARG>A<CA> R<ARG>A<CG> sep2 0.523309
+R<ARG>A<CA> R<ARG>A<CZ> central_sep1 -0.647236
+R<ARG>A<CA> R<ARG>A<CZ> central_sep2 0.246962
+R<ARG>A<CA> R<ARG>A<CZ> sep1 0.76086
+R<ARG>A<CA> R<ARG>A<CZ> sep2 -0.39424
+R<ARG>A<CA> R<ARG>A<N> central_sep1 3.15245
+R<ARG>A<CA> R<ARG>A<N> central_sep2 2.17013
+R<ARG>A<CA> R<ARG>A<N> sep1 -2.14807
+R<ARG>A<CA> R<ARG>A<N> sep2 1.37782
+R<ARG>A<CA> R<ARG>A<NE> central_sep1 0.382071
+R<ARG>A<CA> R<ARG>A<NE> central_sep2 0.753301
+R<ARG>A<CA> R<ARG>A<NE> sep1 0.7626
+R<ARG>A<CA> R<ARG>A<NE> sep2 0.0330138
+R<ARG>A<CA> R<ARG>A<NH1> central_sep1 0.559885
+R<ARG>A<CA> R<ARG>A<NH1> central_sep2 0.379039
+R<ARG>A<CA> R<ARG>A<NH1> sep1 1.9333
+R<ARG>A<CA> R<ARG>A<NH1> sep2 0.141259
+R<ARG>A<CA> R<ARG>A<O> central_sep1 0.664991
+R<ARG>A<CA> R<ARG>A<O> central_sep2 -0.122199
+R<ARG>A<CA> R<ARG>A<O> sep1 -2.04657
+R<ARG>A<CA> R<ARG>A<O> sep2 0.798841
+R<ARG>A<CA> R<ASN>A<C> central_sep1 3.28618
+R<ARG>A<CA> R<ASN>A<C> central_sep2 2.06285
+R<ARG>A<CA> R<ASN>A<C> sep1 -2.46073
+R<ARG>A<CA> R<ASN>A<C> sep2 1.04377
+R<ARG>A<CA> R<ASN>A<CA> central_sep1 1.87561
+R<ARG>A<CA> R<ASN>A<CA> central_sep2 0.714514
+R<ARG>A<CA> R<ASN>A<CA> sep1 1.85853
+R<ARG>A<CA> R<ASN>A<CA> sep2 0.904501
+R<ARG>A<CA> R<ASN>A<CB> central_sep1 -0.183638
+R<ARG>A<CA> R<ASN>A<CB> central_sep2 0.68705
+R<ARG>A<CA> R<ASN>A<CB> sep1 1.43662
+R<ARG>A<CA> R<ASN>A<CB> sep2 0.527204
+R<ARG>A<CA> R<ASN>A<CG> central_sep1 1.60225
+R<ARG>A<CA> R<ASN>A<CG> central_sep2 0.412801
+R<ARG>A<CA> R<ASN>A<CG> sep1 1.53557
+R<ARG>A<CA> R<ASN>A<CG> sep2 -0.478151
+R<ARG>A<CA> R<ASN>A<N> central_sep1 3.27643
+R<ARG>A<CA> R<ASN>A<N> central_sep2 2.31275
+R<ARG>A<CA> R<ASN>A<N> sep1 -2.023
+R<ARG>A<CA> R<ASN>A<N> sep2 1.38341
+R<ARG>A<CA> R<ASN>A<ND2> central_sep1 0.769384
+R<ARG>A<CA> R<ASN>A<ND2> central_sep2 0.573716
+R<ARG>A<CA> R<ASN>A<ND2> sep1 1.17865
+R<ARG>A<CA> R<ASN>A<ND2> sep2 0.452014
+R<ARG>A<CA> R<ASN>A<O> central_sep1 1.04982
+R<ARG>A<CA> R<ASN>A<O> central_sep2 0.00283057
+R<ARG>A<CA> R<ASN>A<O> sep1 -1.81531
+R<ARG>A<CA> R<ASN>A<O> sep2 0.787382
+R<ARG>A<CA> R<ASN>A<OD1> central_sep1 1.18715
+R<ARG>A<CA> R<ASN>A<OD1> central_sep2 0.084631
+R<ARG>A<CA> R<ASN>A<OD1> sep1 1.3041
+R<ARG>A<CA> R<ASN>A<OD1> sep2 0.390725
+R<ARG>A<CA> R<ASP>A<C> central_sep1 3.13055
+R<ARG>A<CA> R<ASP>A<C> central_sep2 2.38222
+R<ARG>A<CA> R<ASP>A<C> sep1 -2.57048
+R<ARG>A<CA> R<ASP>A<C> sep2 0.809554
+R<ARG>A<CA> R<ASP>A<CA> central_sep1 1.77499
+R<ARG>A<CA> R<ASP>A<CA> central_sep2 0.347081
+R<ARG>A<CA> R<ASP>A<CA> sep1 2.29924
+R<ARG>A<CA> R<ASP>A<CA> sep2 0.521395
+R<ARG>A<CA> R<ASP>A<CB> central_sep1 -0.469475
+R<ARG>A<CA> R<ASP>A<CB> central_sep2 0.686787
+R<ARG>A<CA> R<ASP>A<CB> sep1 1.61321
+R<ARG>A<CA> R<ASP>A<CB> sep2 0.513529
+R<ARG>A<CA> R<ASP>A<CG> central_sep1 0.978146
+R<ARG>A<CA> R<ASP>A<CG> central_sep2 0.528748
+R<ARG>A<CA> R<ASP>A<CG> sep1 1.15848
+R<ARG>A<CA> R<ASP>A<CG> sep2 -0.390905
+R<ARG>A<CA> R<ASP>A<N> central_sep1 3.15063
+R<ARG>A<CA> R<ASP>A<N> central_sep2 2.09591
+R<ARG>A<CA> R<ASP>A<N> sep1 -2.07774
+R<ARG>A<CA> R<ASP>A<N> sep2 1.17694
+R<ARG>A<CA> R<ASP>A<O> central_sep1 1.12893
+R<ARG>A<CA> R<ASP>A<O> central_sep2 -0.0613289
+R<ARG>A<CA> R<ASP>A<O> sep1 -1.87821
+R<ARG>A<CA> R<ASP>A<O> sep2 0.684612
+R<ARG>A<CA> R<ASP>A<OD1> central_sep1 0.495463
+R<ARG>A<CA> R<ASP>A<OD1> central_sep2 0.427715
+R<ARG>A<CA> R<ASP>A<OD1> sep1 1.155
+R<ARG>A<CA> R<ASP>A<OD1> sep2 0.104223
+R<ARG>A<CA> R<CYS>A<C> central_sep1 2.4986
+R<ARG>A<CA> R<CYS>A<C> central_sep2 1.67223
+R<ARG>A<CA> R<CYS>A<C> sep1 -2.71012
+R<ARG>A<CA> R<CYS>A<C> sep2 0.243136
+R<ARG>A<CA> R<CYS>A<CA> central_sep1 1.9369
+R<ARG>A<CA> R<CYS>A<CA> central_sep2 0.517252
+R<ARG>A<CA> R<CYS>A<CA> sep1 3.01072
+R<ARG>A<CA> R<CYS>A<CA> sep2 0.65358
+R<ARG>A<CA> R<CYS>A<CB> central_sep1 -0.42035
+R<ARG>A<CA> R<CYS>A<CB> central_sep2 0.222526
+R<ARG>A<CA> R<CYS>A<CB> sep1 1.55369
+R<ARG>A<CA> R<CYS>A<CB> sep2 -0.0217901
+R<ARG>A<CA> R<CYS>A<N> central_sep1 1.87969
+R<ARG>A<CA> R<CYS>A<N> central_sep2 1.83683
+R<ARG>A<CA> R<CYS>A<N> sep1 -2.19991
+R<ARG>A<CA> R<CYS>A<N> sep2 1.05955
+R<ARG>A<CA> R<CYS>A<O> central_sep1 0.342308
+R<ARG>A<CA> R<CYS>A<O> central_sep2 -0.383815
+R<ARG>A<CA> R<CYS>A<O> sep1 -2.05013
+R<ARG>A<CA> R<CYS>A<O> sep2 0.449737
+R<ARG>A<CA> R<CYS>A<SG> central_sep1 0.323528
+R<ARG>A<CA> R<CYS>A<SG> central_sep2 -0.490327
+R<ARG>A<CA> R<CYS>A<SG> sep1 1.45356
+R<ARG>A<CA> R<CYS>A<SG> sep2 0.198444
+R<ARG>A<CA> R<GLN>A<C> central_sep1 3.34379
+R<ARG>A<CA> R<GLN>A<C> central_sep2 2.58826
+R<ARG>A<CA> R<GLN>A<C> sep1 -2.68611
+R<ARG>A<CA> R<GLN>A<C> sep2 0.874145
+R<ARG>A<CA> R<GLN>A<CA> central_sep1 2.05257
+R<ARG>A<CA> R<GLN>A<CA> central_sep2 0.665085
+R<ARG>A<CA> R<GLN>A<CA> sep1 2.36498
+R<ARG>A<CA> R<GLN>A<CA> sep2 1.03949
+R<ARG>A<CA> R<GLN>A<CB> central_sep1 -0.980504
+R<ARG>A<CA> R<GLN>A<CB> central_sep2 0.729465
+R<ARG>A<CA> R<GLN>A<CB> sep1 1.25915
+R<ARG>A<CA> R<GLN>A<CB> sep2 0.809237
+R<ARG>A<CA> R<GLN>A<CD> central_sep1 -0.18348
+R<ARG>A<CA> R<GLN>A<CD> central_sep2 0.43486
+R<ARG>A<CA> R<GLN>A<CD> sep1 0.617804
+R<ARG>A<CA> R<GLN>A<CD> sep2 -0.463461
+R<ARG>A<CA> R<GLN>A<CG> central_sep1 0.619918
+R<ARG>A<CA> R<GLN>A<CG> central_sep2 0.713416
+R<ARG>A<CA> R<GLN>A<CG> sep1 0.851584
+R<ARG>A<CA> R<GLN>A<CG> sep2 0.578062
+R<ARG>A<CA> R<GLN>A<N> central_sep1 3.0203
+R<ARG>A<CA> R<GLN>A<N> central_sep2 2.4971
+R<ARG>A<CA> R<GLN>A<N> sep1 -2.01753
+R<ARG>A<CA> R<GLN>A<N> sep2 1.64932
+R<ARG>A<CA> R<GLN>A<NE2> central_sep1 0.400074
+R<ARG>A<CA> R<GLN>A<NE2> central_sep2 0.476424
+R<ARG>A<CA> R<GLN>A<NE2> sep1 1.70213
+R<ARG>A<CA> R<GLN>A<NE2> sep2 0.380595
+R<ARG>A<CA> R<GLN>A<O> central_sep1 0.959912
+R<ARG>A<CA> R<GLN>A<O> central_sep2 -0.0478097
+R<ARG>A<CA> R<GLN>A<O> sep1 -1.9683
+R<ARG>A<CA> R<GLN>A<O> sep2 0.909773
+R<ARG>A<CA> R<GLN>A<OE1> central_sep1 -0.518745
+R<ARG>A<CA> R<GLN>A<OE1> central_sep2 0.182421
+R<ARG>A<CA> R<GLN>A<OE1> sep1 1.26111
+R<ARG>A<CA> R<GLN>A<OE1> sep2 0.367047
+R<ARG>A<CA> R<GLU>A<C> central_sep1 3.81934
+R<ARG>A<CA> R<GLU>A<C> central_sep2 2.26633
+R<ARG>A<CA> R<GLU>A<C> sep1 -2.78241
+R<ARG>A<CA> R<GLU>A<C> sep2 0.948569
+R<ARG>A<CA> R<GLU>A<CA> central_sep1 1.72291
+R<ARG>A<CA> R<GLU>A<CA> central_sep2 0.236897
+R<ARG>A<CA> R<GLU>A<CA> sep1 2.5178
+R<ARG>A<CA> R<GLU>A<CA> sep2 0.809418
+R<ARG>A<CA> R<GLU>A<CB> central_sep1 -0.992542
+R<ARG>A<CA> R<GLU>A<CB> central_sep2 0.583118
+R<ARG>A<CA> R<GLU>A<CB> sep1 1.09805
+R<ARG>A<CA> R<GLU>A<CB> sep2 0.690297
+R<ARG>A<CA> R<GLU>A<CD> central_sep1 -0.407245
+R<ARG>A<CA> R<GLU>A<CD> central_sep2 0.415846
+R<ARG>A<CA> R<GLU>A<CD> sep1 0.474668
+R<ARG>A<CA> R<GLU>A<CD> sep2 -0.122673
+R<ARG>A<CA> R<GLU>A<CG> central_sep1 0.428414
+R<ARG>A<CA> R<GLU>A<CG> central_sep2 0.436008
+R<ARG>A<CA> R<GLU>A<CG> sep1 0.626316
+R<ARG>A<CA> R<GLU>A<CG> sep2 0.373408
+R<ARG>A<CA> R<GLU>A<N> central_sep1 3.0167
+R<ARG>A<CA> R<GLU>A<N> central_sep2 2.14876
+R<ARG>A<CA> R<GLU>A<N> sep1 -2.05817
+R<ARG>A<CA> R<GLU>A<N> sep2 1.39239
+R<ARG>A<CA> R<GLU>A<O> central_sep1 1.00442
+R<ARG>A<CA> R<GLU>A<O> central_sep2 -0.085103
+R<ARG>A<CA> R<GLU>A<O> sep1 -2.06203
+R<ARG>A<CA> R<GLU>A<O> sep2 0.844159
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+R<ARG>A<CD> c<solvent> . -0.448835
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+R<ARG>A<CG> R<ARG>A<O> central_sep2 0.105366
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+R<ARG>A<CG> R<ASN>A<C> central_sep2 0.866002
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+R<ARG>A<CG> R<ASN>A<CA> central_sep1 0.564864
+R<ARG>A<CG> R<ASN>A<CA> central_sep2 0.322574
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+R<ARG>A<CG> R<ASN>A<CB> central_sep2 0.0674899
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+R<ARG>A<CG> R<ASN>A<OD1> sep1 0.654188
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+R<ARG>A<CG> R<ASP>A<C> central_sep1 0.454073
+R<ARG>A<CG> R<ASP>A<C> central_sep2 0.717011
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+R<ARG>A<CG> R<ASP>A<CA> sep1 0.787257
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+R<ARG>A<CG> R<ASP>A<CB> central_sep2 -0.387327
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+R<ARG>A<CG> R<ASP>A<OD1> sep1 0.293169
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+R<ARG>A<CG> R<CYS>A<C> central_sep1 0.286542
+R<ARG>A<CG> R<CYS>A<C> central_sep2 0.686036
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+R<ARG>A<CG> R<CYS>A<CA> central_sep1 1.09094
+R<ARG>A<CG> R<CYS>A<CA> central_sep2 0.136452
+R<ARG>A<CG> R<CYS>A<CA> sep1 1.11084
+R<ARG>A<CG> R<CYS>A<CA> sep2 0.322146
+R<ARG>A<CG> R<CYS>A<CB> central_sep1 0.516815
+R<ARG>A<CG> R<CYS>A<CB> central_sep2 -0.41276
+R<ARG>A<CG> R<CYS>A<CB> sep1 1.19453
+R<ARG>A<CG> R<CYS>A<CB> sep2 -0.119675
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+R<ARG>A<CG> R<CYS>A<N> central_sep2 1.28625
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+R<ARG>A<CG> R<CYS>A<O> sep1 0.490082
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+R<ARG>A<CG> R<CYS>A<SG> central_sep1 -0.159334
+R<ARG>A<CG> R<CYS>A<SG> central_sep2 -0.717393
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+R<ARG>A<CZ> R<VAL>A<C> central_sep1 1.9535
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+R<ARG>A<CZ> c<solvent> . -0.293483
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+R<ARG>A<N> R<ASN>A<CA> central_sep1 2.76454
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+R<ARG>A<N> R<ASN>A<CA> sep1 -2.04092
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+R<ARG>A<N> R<ASN>A<CB> central_sep1 1.47468
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+R<ARG>A<N> R<ASN>A<CG> central_sep1 0.448772
+R<ARG>A<N> R<ASN>A<CG> central_sep2 1.75462
+R<ARG>A<N> R<ASN>A<CG> sep1 -0.0242357
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+R<ARG>A<N> R<ASN>A<N> central_sep1 1.30178
+R<ARG>A<N> R<ASN>A<N> central_sep2 2.84258
+R<ARG>A<N> R<ASN>A<N> sep1 -2.24845
+R<ARG>A<N> R<ASN>A<N> sep2 2.01833
+R<ARG>A<N> R<ASN>A<ND2> central_sep1 1.33114
+R<ARG>A<N> R<ASN>A<ND2> central_sep2 1.0268
+R<ARG>A<N> R<ASN>A<ND2> sep1 1.82701
+R<ARG>A<N> R<ASN>A<ND2> sep2 0.838691
+R<ARG>A<N> R<ASN>A<O> central_sep1 -1.63746
+R<ARG>A<N> R<ASN>A<O> central_sep2 -0.260278
+R<ARG>A<N> R<ASN>A<O> sep1 0.037549
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+R<ARG>A<N> R<ASN>A<OD1> central_sep1 -0.698488
+R<ARG>A<N> R<ASN>A<OD1> central_sep2 0.023553
+R<ARG>A<N> R<ASN>A<OD1> sep1 0.696788
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+R<CYS>A<CA> R<GLN>A<N> central_sep2 1.34893
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+R<GLN>A<C> R<PRO>A<O> central_sep1 -0.633564
+R<GLN>A<C> R<PRO>A<O> central_sep2 2.32545
+R<GLN>A<C> R<PRO>A<O> sep1 -1.9283
+R<GLN>A<C> R<PRO>A<O> sep2 1.44507
+R<GLN>A<C> R<SER>A<C> central_sep1 4.22569
+R<GLN>A<C> R<SER>A<C> central_sep2 3.92441
+R<GLN>A<C> R<SER>A<C> sep1 -2.27767
+R<GLN>A<C> R<SER>A<C> sep2 2.00454
+R<GLN>A<C> R<SER>A<CA> central_sep1 3.29978
+R<GLN>A<C> R<SER>A<CA> central_sep2 2.27306
+R<GLN>A<C> R<SER>A<CA> sep1 -2.45678
+R<GLN>A<C> R<SER>A<CA> sep2 0.856519
+R<GLN>A<C> R<SER>A<CB> central_sep1 2.1881
+R<GLN>A<C> R<SER>A<CB> central_sep2 1.07122
+R<GLN>A<C> R<SER>A<CB> sep1 -0.112373
+R<GLN>A<C> R<SER>A<CB> sep2 0.142504
+R<GLN>A<C> R<SER>A<N> central_sep1 -0.415767
+R<GLN>A<C> R<SER>A<N> central_sep2 2.89165
+R<GLN>A<C> R<SER>A<N> sep1 -1.40994
+R<GLN>A<C> R<SER>A<N> sep2 1.63445
+R<GLN>A<C> R<SER>A<O> central_sep1 -0.529829
+R<GLN>A<C> R<SER>A<O> central_sep2 2.48425
+R<GLN>A<C> R<SER>A<O> sep1 -1.49181
+R<GLN>A<C> R<SER>A<O> sep2 1.51938
+R<GLN>A<C> R<SER>A<OG> central_sep1 1.90586
+R<GLN>A<C> R<SER>A<OG> central_sep2 1.51746
+R<GLN>A<C> R<SER>A<OG> sep1 0.36569
+R<GLN>A<C> R<SER>A<OG> sep2 0.420358
+R<GLN>A<C> R<THR>A<C> central_sep1 4.70821
+R<GLN>A<C> R<THR>A<C> central_sep2 3.44171
+R<GLN>A<C> R<THR>A<C> sep1 -2.45548
+R<GLN>A<C> R<THR>A<C> sep2 2.13661
+R<GLN>A<C> R<THR>A<CA> central_sep1 4.38238
+R<GLN>A<C> R<THR>A<CA> central_sep2 2.5131
+R<GLN>A<C> R<THR>A<CA> sep1 -2.62864
+R<GLN>A<C> R<THR>A<CA> sep2 0.779945
+R<GLN>A<C> R<THR>A<CB> central_sep1 2.30627
+R<GLN>A<C> R<THR>A<CB> central_sep2 1.26639
+R<GLN>A<C> R<THR>A<CB> sep1 0.11239
+R<GLN>A<C> R<THR>A<CB> sep2 -0.00335394
+R<GLN>A<C> R<THR>A<CG2> central_sep1 0.726743
+R<GLN>A<C> R<THR>A<CG2> central_sep2 0.5818
+R<GLN>A<C> R<THR>A<CG2> sep1 -0.320973
+R<GLN>A<C> R<THR>A<CG2> sep2 -0.238327
+R<GLN>A<C> R<THR>A<N> central_sep1 -0.292572
+R<GLN>A<C> R<THR>A<N> central_sep2 3.27366
+R<GLN>A<C> R<THR>A<N> sep1 -1.45793
+R<GLN>A<C> R<THR>A<N> sep2 2.18947
+R<GLN>A<C> R<THR>A<O> central_sep1 -0.634264
+R<GLN>A<C> R<THR>A<O> central_sep2 2.5645
+R<GLN>A<C> R<THR>A<O> sep1 -1.35706
+R<GLN>A<C> R<THR>A<O> sep2 1.41868
+R<GLN>A<C> R<THR>A<OG1> central_sep1 1.81991
+R<GLN>A<C> R<THR>A<OG1> central_sep2 1.31438
+R<GLN>A<C> R<THR>A<OG1> sep1 -0.213897
+R<GLN>A<C> R<THR>A<OG1> sep2 0.484411
+R<GLN>A<C> R<TRP>A<C> central_sep1 4.15274
+R<GLN>A<C> R<TRP>A<C> central_sep2 3.83721
+R<GLN>A<C> R<TRP>A<C> sep1 -2.78111
+R<GLN>A<C> R<TRP>A<C> sep2 2.60787
+R<GLN>A<C> R<TRP>A<CA> central_sep1 4.43288
+R<GLN>A<C> R<TRP>A<CA> central_sep2 3.35949
+R<GLN>A<C> R<TRP>A<CA> sep1 -2.83719
+R<GLN>A<C> R<TRP>A<CA> sep2 0.94464
+R<GLN>A<C> R<TRP>A<CB> central_sep1 1.85274
+R<GLN>A<C> R<TRP>A<CB> central_sep2 0.924304
+R<GLN>A<C> R<TRP>A<CB> sep1 -0.0195613
+R<GLN>A<C> R<TRP>A<CB> sep2 -0.0665485
+R<GLN>A<C> R<TRP>A<CD1> central_sep1 -0.928348
+R<GLN>A<C> R<TRP>A<CD1> central_sep2 0.199626
+R<GLN>A<C> R<TRP>A<CD1> sep1 -0.598903
+R<GLN>A<C> R<TRP>A<CD1> sep2 -0.506629
+R<GLN>A<C> R<TRP>A<CD2> central_sep1 -0.63481
+R<GLN>A<C> R<TRP>A<CD2> central_sep2 0.992397
+R<GLN>A<C> R<TRP>A<CD2> sep1 -0.511336
+R<GLN>A<C> R<TRP>A<CD2> sep2 0.385813
+R<GLN>A<C> R<TRP>A<CE2> central_sep1 0.0207385
+R<GLN>A<C> R<TRP>A<CE2> central_sep2 0.723108
+R<GLN>A<C> R<TRP>A<CE2> sep1 1.02469
+R<GLN>A<C> R<TRP>A<CE2> sep2 0.129298
+R<GLN>A<C> R<TRP>A<CE3> central_sep1 -0.741503
+R<GLN>A<C> R<TRP>A<CE3> central_sep2 -0.849209
+R<GLN>A<C> R<TRP>A<CE3> sep1 0.419993
+R<GLN>A<C> R<TRP>A<CE3> sep2 -0.32728
+R<GLN>A<C> R<TRP>A<CG> central_sep1 1.3557
+R<GLN>A<C> R<TRP>A<CG> central_sep2 0.76799
+R<GLN>A<C> R<TRP>A<CG> sep1 -1.23841
+R<GLN>A<C> R<TRP>A<CG> sep2 0.113077
+R<GLN>A<C> R<TRP>A<CH2> central_sep1 1.75126
+R<GLN>A<C> R<TRP>A<CH2> central_sep2 -0.363812
+R<GLN>A<C> R<TRP>A<CH2> sep1 2.94923
+R<GLN>A<C> R<TRP>A<CH2> sep2 -0.725579
+R<GLN>A<C> R<TRP>A<CZ2> central_sep1 1.77354
+R<GLN>A<C> R<TRP>A<CZ2> central_sep2 -0.191815
+R<GLN>A<C> R<TRP>A<CZ2> sep1 2.87959
+R<GLN>A<C> R<TRP>A<CZ2> sep2 -0.534118
+R<GLN>A<C> R<TRP>A<CZ3> central_sep1 0.674317
+R<GLN>A<C> R<TRP>A<CZ3> central_sep2 -0.470732
+R<GLN>A<C> R<TRP>A<CZ3> sep1 1.79909
+R<GLN>A<C> R<TRP>A<CZ3> sep2 -0.925792
+R<GLN>A<C> R<TRP>A<N> central_sep1 -0.706802
+R<GLN>A<C> R<TRP>A<N> central_sep2 4.32686
+R<GLN>A<C> R<TRP>A<N> sep1 -1.85385
+R<GLN>A<C> R<TRP>A<N> sep2 1.76068
+R<GLN>A<C> R<TRP>A<NE1> central_sep1 0.301527
+R<GLN>A<C> R<TRP>A<NE1> central_sep2 0.613361
+R<GLN>A<C> R<TRP>A<NE1> sep1 1.41277
+R<GLN>A<C> R<TRP>A<NE1> sep2 -0.183195
+R<GLN>A<C> R<TRP>A<O> central_sep1 -1.01874
+R<GLN>A<C> R<TRP>A<O> central_sep2 2.77327
+R<GLN>A<C> R<TRP>A<O> sep1 -1.55476
+R<GLN>A<C> R<TRP>A<O> sep2 1.37983
+R<GLN>A<C> R<TYR>A<C> central_sep1 3.21821
+R<GLN>A<C> R<TYR>A<C> central_sep2 3.51526
+R<GLN>A<C> R<TYR>A<C> sep1 -2.52967
+R<GLN>A<C> R<TYR>A<C> sep2 2.42966
+R<GLN>A<C> R<TYR>A<CA> central_sep1 3.60587
+R<GLN>A<C> R<TYR>A<CA> central_sep2 2.67768
+R<GLN>A<C> R<TYR>A<CA> sep1 -2.64825
+R<GLN>A<C> R<TYR>A<CA> sep2 0.796113
+R<GLN>A<C> R<TYR>A<CB> central_sep1 1.72785
+R<GLN>A<C> R<TYR>A<CB> central_sep2 0.84207
+R<GLN>A<C> R<TYR>A<CB> sep1 -0.0244092
+R<GLN>A<C> R<TYR>A<CB> sep2 -0.135364
+R<GLN>A<C> R<TYR>A<CD1> central_sep1 -0.639535
+R<GLN>A<C> R<TYR>A<CD1> central_sep2 -0.173049
+R<GLN>A<C> R<TYR>A<CD1> sep1 -0.477352
+R<GLN>A<C> R<TYR>A<CD1> sep2 -0.416112
+R<GLN>A<C> R<TYR>A<CE1> central_sep1 0.45528
+R<GLN>A<C> R<TYR>A<CE1> central_sep2 0.145121
+R<GLN>A<C> R<TYR>A<CE1> sep1 1.46169
+R<GLN>A<C> R<TYR>A<CE1> sep2 -0.319301
+R<GLN>A<C> R<TYR>A<CG> central_sep1 1.207
+R<GLN>A<C> R<TYR>A<CG> central_sep2 1.0551
+R<GLN>A<C> R<TYR>A<CG> sep1 -1.85826
+R<GLN>A<C> R<TYR>A<CG> sep2 0.0477889
+R<GLN>A<C> R<TYR>A<CZ> central_sep1 0.870735
+R<GLN>A<C> R<TYR>A<CZ> central_sep2 0.821444
+R<GLN>A<C> R<TYR>A<CZ> sep1 1.60628
+R<GLN>A<C> R<TYR>A<CZ> sep2 0.0504638
+R<GLN>A<C> R<TYR>A<N> central_sep1 -0.572552
+R<GLN>A<C> R<TYR>A<N> central_sep2 3.57646
+R<GLN>A<C> R<TYR>A<N> sep1 -1.72285
+R<GLN>A<C> R<TYR>A<N> sep2 2.02433
+R<GLN>A<C> R<TYR>A<O> central_sep1 -0.994779
+R<GLN>A<C> R<TYR>A<O> central_sep2 2.49964
+R<GLN>A<C> R<TYR>A<O> sep1 -1.36092
+R<GLN>A<C> R<TYR>A<O> sep2 1.59132
+R<GLN>A<C> R<TYR>A<OH> central_sep1 3.08649
+R<GLN>A<C> R<TYR>A<OH> central_sep2 0.560406
+R<GLN>A<C> R<TYR>A<OH> sep1 3.40557
+R<GLN>A<C> R<TYR>A<OH> sep2 -0.00667341
+R<GLN>A<C> R<VAL>A<C> central_sep1 4.21374
+R<GLN>A<C> R<VAL>A<C> central_sep2 3.73296
+R<GLN>A<C> R<VAL>A<C> sep1 -2.73283
+R<GLN>A<C> R<VAL>A<C> sep2 3.07415
+R<GLN>A<C> R<VAL>A<CA> central_sep1 4.3733
+R<GLN>A<C> R<VAL>A<CA> central_sep2 3.01366
+R<GLN>A<C> R<VAL>A<CA> sep1 -2.75115
+R<GLN>A<C> R<VAL>A<CA> sep2 1.23187
+R<GLN>A<C> R<VAL>A<CB> central_sep1 2.00195
+R<GLN>A<C> R<VAL>A<CB> central_sep2 1.20567
+R<GLN>A<C> R<VAL>A<CB> sep1 0.147818
+R<GLN>A<C> R<VAL>A<CB> sep2 -0.267616
+R<GLN>A<C> R<VAL>A<CG1> central_sep1 0.318474
+R<GLN>A<C> R<VAL>A<CG1> central_sep2 0.388281
+R<GLN>A<C> R<VAL>A<CG1> sep1 -0.225084
+R<GLN>A<C> R<VAL>A<CG1> sep2 -0.321774
+R<GLN>A<C> R<VAL>A<CG2> central_sep1 0.68583
+R<GLN>A<C> R<VAL>A<CG2> central_sep2 0.340409
+R<GLN>A<C> R<VAL>A<CG2> sep1 -0.709441
+R<GLN>A<C> R<VAL>A<CG2> sep2 -0.22407
+R<GLN>A<C> R<VAL>A<N> central_sep1 -0.177603
+R<GLN>A<C> R<VAL>A<N> central_sep2 3.6233
+R<GLN>A<C> R<VAL>A<N> sep1 -1.68737
+R<GLN>A<C> R<VAL>A<N> sep2 2.29788
+R<GLN>A<C> R<VAL>A<O> central_sep1 -0.770642
+R<GLN>A<C> R<VAL>A<O> central_sep2 2.73703
+R<GLN>A<C> R<VAL>A<O> sep1 -1.19918
+R<GLN>A<C> R<VAL>A<O> sep2 1.3868
+R<GLN>A<C> c<solvent> . 1.77783
+R<GLN>A<CA> R<GLN>A<CA> central_sep1 1.7153
+R<GLN>A<CA> R<GLN>A<CA> central_sep2 0.489646
+R<GLN>A<CA> R<GLN>A<CA> sep1 2.06918
+R<GLN>A<CA> R<GLN>A<CA> sep2 0.855527
+R<GLN>A<CA> R<GLN>A<CB> central_sep1 -1.31353
+R<GLN>A<CA> R<GLN>A<CB> central_sep2 0.747386
+R<GLN>A<CA> R<GLN>A<CB> sep1 0.978345
+R<GLN>A<CA> R<GLN>A<CB> sep2 0.940901
+R<GLN>A<CA> R<GLN>A<CD> central_sep1 -0.377694
+R<GLN>A<CA> R<GLN>A<CD> central_sep2 0.363854
+R<GLN>A<CA> R<GLN>A<CD> sep1 0.400556
+R<GLN>A<CA> R<GLN>A<CD> sep2 -0.559976
+R<GLN>A<CA> R<GLN>A<CG> central_sep1 0.269475
+R<GLN>A<CA> R<GLN>A<CG> central_sep2 0.548958
+R<GLN>A<CA> R<GLN>A<CG> sep1 0.59491
+R<GLN>A<CA> R<GLN>A<CG> sep2 0.58181
+R<GLN>A<CA> R<GLN>A<N> central_sep1 3.20902
+R<GLN>A<CA> R<GLN>A<N> central_sep2 2.13171
+R<GLN>A<CA> R<GLN>A<N> sep1 -2.159
+R<GLN>A<CA> R<GLN>A<N> sep2 1.36476
+R<GLN>A<CA> R<GLN>A<NE2> central_sep1 0.224118
+R<GLN>A<CA> R<GLN>A<NE2> central_sep2 0.286269
+R<GLN>A<CA> R<GLN>A<NE2> sep1 1.34454
+R<GLN>A<CA> R<GLN>A<NE2> sep2 0.294504
+R<GLN>A<CA> R<GLN>A<O> central_sep1 1.10966
+R<GLN>A<CA> R<GLN>A<O> central_sep2 0.0309778
+R<GLN>A<CA> R<GLN>A<O> sep1 -2.19932
+R<GLN>A<CA> R<GLN>A<O> sep2 0.901065
+R<GLN>A<CA> R<GLN>A<OE1> central_sep1 -0.559594
+R<GLN>A<CA> R<GLN>A<OE1> central_sep2 0.141333
+R<GLN>A<CA> R<GLN>A<OE1> sep1 1.03546
+R<GLN>A<CA> R<GLN>A<OE1> sep2 0.220413
+R<GLN>A<CA> R<GLU>A<C> central_sep1 3.98685
+R<GLN>A<CA> R<GLU>A<C> central_sep2 3.10561
+R<GLN>A<CA> R<GLU>A<C> sep1 -2.74488
+R<GLN>A<CA> R<GLU>A<C> sep2 1.58538
+R<GLN>A<CA> R<GLU>A<CA> central_sep1 2.03598
+R<GLN>A<CA> R<GLU>A<CA> central_sep2 0.949647
+R<GLN>A<CA> R<GLU>A<CA> sep1 2.4491
+R<GLN>A<CA> R<GLU>A<CA> sep2 1.31003
+R<GLN>A<CA> R<GLU>A<CB> central_sep1 -1.0546
+R<GLN>A<CA> R<GLU>A<CB> central_sep2 1.0845
+R<GLN>A<CA> R<GLU>A<CB> sep1 1.17647
+R<GLN>A<CA> R<GLU>A<CB> sep2 1.30526
+R<GLN>A<CA> R<GLU>A<CD> central_sep1 0.00855588
+R<GLN>A<CA> R<GLU>A<CD> central_sep2 1.03478
+R<GLN>A<CA> R<GLU>A<CD> sep1 0.567785
+R<GLN>A<CA> R<GLU>A<CD> sep2 0.42436
+R<GLN>A<CA> R<GLU>A<CG> central_sep1 0.607895
+R<GLN>A<CA> R<GLU>A<CG> central_sep2 0.959355
+R<GLN>A<CA> R<GLU>A<CG> sep1 0.689445
+R<GLN>A<CA> R<GLU>A<CG> sep2 1.10259
+R<GLN>A<CA> R<GLU>A<N> central_sep1 3.43335
+R<GLN>A<CA> R<GLU>A<N> central_sep2 2.4863
+R<GLN>A<CA> R<GLU>A<N> sep1 -1.99977
+R<GLN>A<CA> R<GLU>A<N> sep2 1.92399
+R<GLN>A<CA> R<GLU>A<O> central_sep1 1.16469
+R<GLN>A<CA> R<GLU>A<O> central_sep2 0.51889
+R<GLN>A<CA> R<GLU>A<O> sep1 -2.01699
+R<GLN>A<CA> R<GLU>A<O> sep2 1.32414
+R<GLN>A<CA> R<GLU>A<OE1> central_sep1 0.113082
+R<GLN>A<CA> R<GLU>A<OE1> central_sep2 1.37906
+R<GLN>A<CA> R<GLU>A<OE1> sep1 1.43918
+R<GLN>A<CA> R<GLU>A<OE1> sep2 1.02154
+R<GLN>A<CA> R<GLY>A<C> central_sep1 2.46385
+R<GLN>A<CA> R<GLY>A<C> central_sep2 1.29003
+R<GLN>A<CA> R<GLY>A<C> sep1 -2.37703
+R<GLN>A<CA> R<GLY>A<C> sep2 0.463793
+R<GLN>A<CA> R<GLY>A<CA> central_sep1 1.91937
+R<GLN>A<CA> R<GLY>A<CA> central_sep2 0.543656
+R<GLN>A<CA> R<GLY>A<CA> sep1 1.54089
+R<GLN>A<CA> R<GLY>A<CA> sep2 0.573242
+R<GLN>A<CA> R<GLY>A<N> central_sep1 2.11748
+R<GLN>A<CA> R<GLY>A<N> central_sep2 1.51477
+R<GLN>A<CA> R<GLY>A<N> sep1 -1.93956
+R<GLN>A<CA> R<GLY>A<N> sep2 0.934761
+R<GLN>A<CA> R<GLY>A<O> central_sep1 0.922109
+R<GLN>A<CA> R<GLY>A<O> central_sep2 -0.0910745
+R<GLN>A<CA> R<GLY>A<O> sep1 -1.98293
+R<GLN>A<CA> R<GLY>A<O> sep2 0.510968
+R<GLN>A<CA> R<HIS>A<C> central_sep1 2.95827
+R<GLN>A<CA> R<HIS>A<C> central_sep2 2.48419
+R<GLN>A<CA> R<HIS>A<C> sep1 -2.60472
+R<GLN>A<CA> R<HIS>A<C> sep2 0.963555
+R<GLN>A<CA> R<HIS>A<CA> central_sep1 2.32096
+R<GLN>A<CA> R<HIS>A<CA> central_sep2 0.609572
+R<GLN>A<CA> R<HIS>A<CA> sep1 2.38134
+R<GLN>A<CA> R<HIS>A<CA> sep2 1.07193
+R<GLN>A<CA> R<HIS>A<CB> central_sep1 -0.653935
+R<GLN>A<CA> R<HIS>A<CB> central_sep2 0.484454
+R<GLN>A<CA> R<HIS>A<CB> sep1 1.37226
+R<GLN>A<CA> R<HIS>A<CB> sep2 0.504182
+R<GLN>A<CA> R<HIS>A<CD2> central_sep1 0.589182
+R<GLN>A<CA> R<HIS>A<CD2> central_sep2 0.298399
+R<GLN>A<CA> R<HIS>A<CD2> sep1 0.151524
+R<GLN>A<CA> R<HIS>A<CD2> sep2 0.207038
+R<GLN>A<CA> R<HIS>A<CE1> central_sep1 1.30685
+R<GLN>A<CA> R<HIS>A<CE1> central_sep2 0.446199
+R<GLN>A<CA> R<HIS>A<CE1> sep1 1.81361
+R<GLN>A<CA> R<HIS>A<CE1> sep2 0.348093
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+R<GLN>A<CB> R<VAL>A<C> central_sep1 2.99211
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+R<GLN>A<CB> R<VAL>A<C> sep2 0.138587
+R<GLN>A<CB> R<VAL>A<CA> central_sep1 -0.443918
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+R<GLN>A<CB> R<VAL>A<CB> central_sep1 0.260784
+R<GLN>A<CB> R<VAL>A<CB> central_sep2 -0.633123
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+R<GLN>A<CB> R<VAL>A<CG1> central_sep1 0.211671
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+R<GLN>A<CB> R<VAL>A<CG2> sep1 0.986723
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+R<GLN>A<CB> R<VAL>A<N> sep1 -1.23593
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+R<GLN>A<CB> R<VAL>A<O> sep1 0.413034
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+R<GLN>A<CD> R<GLU>A<N> central_sep2 1.83333
+R<GLN>A<CD> R<GLU>A<N> sep1 1.61901
+R<GLN>A<CD> R<GLU>A<N> sep2 0.470494
+R<GLN>A<CD> R<GLU>A<O> central_sep1 0.335681
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+R<GLN>A<CD> R<GLU>A<O> sep1 0.119545
+R<GLN>A<CD> R<GLU>A<O> sep2 0.197203
+R<GLN>A<CD> R<GLU>A<OE1> central_sep1 0.959523
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+R<GLN>A<CD> R<GLY>A<C> central_sep2 0.156027
+R<GLN>A<CD> R<GLY>A<C> sep1 0.16341
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+R<GLN>A<CD> R<GLY>A<CA> central_sep1 0.934262
+R<GLN>A<CD> R<GLY>A<CA> central_sep2 -0.133031
+R<GLN>A<CD> R<GLY>A<CA> sep1 0.932629
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+R<GLN>A<CD> R<GLY>A<N> central_sep1 1.11775
+R<GLN>A<CD> R<GLY>A<N> central_sep2 0.984868
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+R<GLN>A<CD> R<GLY>A<O> central_sep2 0.539244
+R<GLN>A<CD> R<GLY>A<O> sep1 0.448286
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+R<GLN>A<CD> R<HIS>A<C> central_sep1 1.1463
+R<GLN>A<CD> R<HIS>A<C> central_sep2 0.847856
+R<GLN>A<CD> R<HIS>A<C> sep1 0.183696
+R<GLN>A<CD> R<HIS>A<C> sep2 0.433789
+R<GLN>A<CD> R<HIS>A<CA> central_sep1 0.233447
+R<GLN>A<CD> R<HIS>A<CA> central_sep2 0.421794
+R<GLN>A<CD> R<HIS>A<CA> sep1 0.723355
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+R<GLN>A<CD> R<HIS>A<CB> central_sep1 0.141712
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+R<GLN>A<CD> R<HIS>A<CB> sep1 0.745032
+R<GLN>A<CD> R<HIS>A<CB> sep2 -0.991967
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+R<GLN>A<CD> R<HIS>A<CD2> central_sep2 -0.437404
+R<GLN>A<CD> R<HIS>A<CD2> sep1 0.411634
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+R<GLN>A<CD> R<HIS>A<CE1> central_sep1 -0.480693
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+R<GLN>A<CD> R<HIS>A<CE1> sep1 0.18463
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+R<GLN>A<CD> R<HIS>A<CG> central_sep2 -0.922174
+R<GLN>A<CD> R<HIS>A<CG> sep1 0.737544
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+R<GLN>A<CD> R<HIS>A<N> sep1 1.23074
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+R<GLN>A<CD> R<HIS>A<ND1> sep1 0.570425
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+R<GLN>A<CD> R<HIS>A<NE2> sep1 0.0985156
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+R<GLN>A<CD> R<HIS>A<O> central_sep2 0.673642
+R<GLN>A<CD> R<HIS>A<O> sep1 0.563876
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+R<GLN>A<CD> R<ILE>A<C> central_sep2 1.74401
+R<GLN>A<CD> R<ILE>A<C> sep1 0.465495
+R<GLN>A<CD> R<ILE>A<C> sep2 0.440611
+R<GLN>A<CD> R<ILE>A<CA> central_sep1 0.112008
+R<GLN>A<CD> R<ILE>A<CA> central_sep2 1.20965
+R<GLN>A<CD> R<ILE>A<CA> sep1 0.913591
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+R<GLN>A<CD> R<ILE>A<CB> central_sep1 0.252613
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+R<GLN>A<CD> R<ILE>A<CB> sep1 0.697548
+R<GLN>A<CD> R<ILE>A<CB> sep2 -0.952153
+R<GLN>A<CD> R<ILE>A<CD1> central_sep1 0.172388
+R<GLN>A<CD> R<ILE>A<CD1> central_sep2 -0.767034
+R<GLN>A<CD> R<ILE>A<CD1> sep1 0.946586
+R<GLN>A<CD> R<ILE>A<CD1> sep2 -0.96502
+R<GLN>A<CD> R<ILE>A<CG1> central_sep1 0.449232
+R<GLN>A<CD> R<ILE>A<CG1> central_sep2 -0.483348
+R<GLN>A<CD> R<ILE>A<CG1> sep1 1.07784
+R<GLN>A<CD> R<ILE>A<CG1> sep2 -0.878299
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+R<GLN>A<CD> R<ILE>A<CG2> central_sep2 -0.668889
+R<GLN>A<CD> R<ILE>A<CG2> sep1 0.874242
+R<GLN>A<CD> R<ILE>A<CG2> sep2 -0.880908
+R<GLN>A<CD> R<ILE>A<N> central_sep1 1.97813
+R<GLN>A<CD> R<ILE>A<N> central_sep2 2.29519
+R<GLN>A<CD> R<ILE>A<N> sep1 1.82803
+R<GLN>A<CD> R<ILE>A<N> sep2 0.196782
+R<GLN>A<CD> R<ILE>A<O> central_sep1 1.04212
+R<GLN>A<CD> R<ILE>A<O> central_sep2 1.16054
+R<GLN>A<CD> R<ILE>A<O> sep1 0.729017
+R<GLN>A<CD> R<ILE>A<O> sep2 0.23591
+R<GLN>A<CD> R<LEU>A<C> central_sep1 1.65612
+R<GLN>A<CD> R<LEU>A<C> central_sep2 1.49202
+R<GLN>A<CD> R<LEU>A<C> sep1 0.262874
+R<GLN>A<CD> R<LEU>A<C> sep2 0.242689
+R<GLN>A<CD> R<LEU>A<CA> central_sep1 -0.322282
+R<GLN>A<CD> R<LEU>A<CA> central_sep2 0.958781
+R<GLN>A<CD> R<LEU>A<CA> sep1 0.753683
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+R<GLN>A<CD> R<LEU>A<CB> central_sep1 0.25837
+R<GLN>A<CD> R<LEU>A<CB> central_sep2 -0.281884
+R<GLN>A<CD> R<LEU>A<CB> sep1 0.943936
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+R<GLN>A<CD> R<LEU>A<CD1> sep1 0.739238
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+R<GLN>A<CD> R<LEU>A<CD2> central_sep1 -0.163646
+R<GLN>A<CD> R<LEU>A<CD2> central_sep2 -0.817183
+R<GLN>A<CD> R<LEU>A<CD2> sep1 0.602075
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+R<GLN>A<CD> R<LEU>A<CG> sep1 0.58625
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+R<GLN>A<CD> R<LEU>A<N> central_sep1 1.72752
+R<GLN>A<CD> R<LEU>A<N> central_sep2 2.12114
+R<GLN>A<CD> R<LEU>A<N> sep1 1.67588
+R<GLN>A<CD> R<LEU>A<N> sep2 0.3742
+R<GLN>A<CD> R<LEU>A<O> central_sep1 0.731184
+R<GLN>A<CD> R<LEU>A<O> central_sep2 0.969889
+R<GLN>A<CD> R<LEU>A<O> sep1 0.576637
+R<GLN>A<CD> R<LEU>A<O> sep2 0.111541
+R<GLN>A<CD> R<LYS>A<C> central_sep1 1.39793
+R<GLN>A<CD> R<LYS>A<C> central_sep2 1.2845
+R<GLN>A<CD> R<LYS>A<C> sep1 -0.189008
+R<GLN>A<CD> R<LYS>A<C> sep2 0.488465
+R<GLN>A<CD> R<LYS>A<CA> central_sep1 -0.33192
+R<GLN>A<CD> R<LYS>A<CA> central_sep2 0.42726
+R<GLN>A<CD> R<LYS>A<CA> sep1 0.520124
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+R<GLN>A<CD> R<LYS>A<CB> sep1 0.534564
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+R<GLN>A<CD> R<LYS>A<CE> central_sep2 0.177855
+R<GLN>A<CD> R<LYS>A<CE> sep1 0.521021
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+R<GLN>A<CD> R<LYS>A<CG> sep1 0.459253
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+R<GLN>A<CD> R<LYS>A<N> central_sep2 1.82069
+R<GLN>A<CD> R<LYS>A<N> sep1 1.50545
+R<GLN>A<CD> R<LYS>A<N> sep2 0.339587
+R<GLN>A<CD> R<LYS>A<NZ> central_sep1 1.53922
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+R<GLN>A<CD> R<LYS>A<NZ> sep1 0.964572
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+R<GLN>A<CD> R<LYS>A<O> sep1 0.22128
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+R<GLN>A<CD> R<MET>A<C> central_sep1 1.81177
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+R<GLN>A<CD> R<MET>A<C> sep1 0.152016
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+R<GLN>A<CD> R<MET>A<CA> central_sep1 0.267321
+R<GLN>A<CD> R<MET>A<CA> central_sep2 0.715295
+R<GLN>A<CD> R<MET>A<CA> sep1 0.690807
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+R<GLN>A<CD> R<MET>A<CB> central_sep1 0.218656
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+R<GLN>A<CD> R<MET>A<CE> sep1 0.94393
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+R<GLN>A<CD> R<MET>A<CG> sep1 0.592718
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+R<GLN>A<CD> R<MET>A<O> sep1 0.607139
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+R<GLN>A<CD> R<MET>A<SD> sep1 0.834048
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+R<GLN>A<CD> R<PHE>A<C> sep1 0.508663
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+R<GLN>A<CD> R<PHE>A<CA> central_sep1 0.262251
+R<GLN>A<CD> R<PHE>A<CA> central_sep2 0.703071
+R<GLN>A<CD> R<PHE>A<CA> sep1 0.765458
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+R<GLN>A<CD> R<TYR>A<C> sep1 0.443943
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+R<GLN>A<CD> R<TYR>A<CA> central_sep1 0.0689578
+R<GLN>A<CD> R<TYR>A<CA> central_sep2 0.530777
+R<GLN>A<CD> R<TYR>A<CA> sep1 0.716718
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+R<GLN>A<CD> R<TYR>A<CB> central_sep1 0.303053
+R<GLN>A<CD> R<TYR>A<CB> central_sep2 -0.596628
+R<GLN>A<CD> R<TYR>A<CB> sep1 1.09655
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+R<GLN>A<CD> R<TYR>A<CD1> central_sep1 -0.0918959
+R<GLN>A<CD> R<TYR>A<CD1> central_sep2 -0.724697
+R<GLN>A<CD> R<TYR>A<CD1> sep1 0.477282
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+R<GLN>A<CD> R<TYR>A<CE1> central_sep1 -0.495141
+R<GLN>A<CD> R<TYR>A<CE1> central_sep2 -0.760245
+R<GLN>A<CD> R<TYR>A<CE1> sep1 0.292723
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+R<GLN>A<CD> R<TYR>A<CG> central_sep1 1.75531
+R<GLN>A<CD> R<TYR>A<CG> central_sep2 -0.902331
+R<GLN>A<CD> R<TYR>A<CG> sep1 1.39241
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+R<GLN>A<CD> R<TYR>A<CZ> central_sep2 -0.653674
+R<GLN>A<CD> R<TYR>A<CZ> sep1 -0.302236
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+R<GLN>A<CD> R<TYR>A<N> central_sep1 1.54567
+R<GLN>A<CD> R<TYR>A<N> central_sep2 1.50602
+R<GLN>A<CD> R<TYR>A<N> sep1 1.79634
+R<GLN>A<CD> R<TYR>A<N> sep2 0.0655898
+R<GLN>A<CD> R<TYR>A<O> central_sep1 0.707315
+R<GLN>A<CD> R<TYR>A<O> central_sep2 0.973975
+R<GLN>A<CD> R<TYR>A<O> sep1 0.915664
+R<GLN>A<CD> R<TYR>A<O> sep2 -0.0456961
+R<GLN>A<CD> R<TYR>A<OH> central_sep1 -0.00669617
+R<GLN>A<CD> R<TYR>A<OH> central_sep2 -0.186547
+R<GLN>A<CD> R<TYR>A<OH> sep1 0.0644811
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+R<GLN>A<CD> R<VAL>A<C> central_sep1 2.03082
+R<GLN>A<CD> R<VAL>A<C> central_sep2 1.52084
+R<GLN>A<CD> R<VAL>A<C> sep1 0.515781
+R<GLN>A<CD> R<VAL>A<C> sep2 0.460404
+R<GLN>A<CD> R<VAL>A<CA> central_sep1 0.202639
+R<GLN>A<CD> R<VAL>A<CA> central_sep2 0.880384
+R<GLN>A<CD> R<VAL>A<CA> sep1 0.989119
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+R<GLN>A<CD> R<VAL>A<CB> central_sep1 0.243141
+R<GLN>A<CD> R<VAL>A<CB> central_sep2 -0.240045
+R<GLN>A<CD> R<VAL>A<CB> sep1 0.866756
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+R<GLN>A<CD> R<VAL>A<CG1> central_sep1 -0.242627
+R<GLN>A<CD> R<VAL>A<CG1> central_sep2 -0.646673
+R<GLN>A<CD> R<VAL>A<CG1> sep1 0.902869
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+R<GLN>A<CD> R<VAL>A<CG2> central_sep1 0.441012
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+R<GLN>A<CD> R<VAL>A<O> sep1 0.749991
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+R<GLN>A<CD> c<solvent> . -0.289179
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+R<GLN>A<CG> R<GLN>A<CG> sep1 0.385157
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+R<GLN>A<CG> R<GLN>A<N> central_sep1 0.966542
+R<GLN>A<CG> R<GLN>A<N> central_sep2 1.49431
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+R<GLN>A<CG> R<GLN>A<NE2> central_sep2 -0.184097
+R<GLN>A<CG> R<GLN>A<NE2> sep1 1.00879
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+R<GLN>A<CG> R<GLN>A<O> central_sep2 0.0855745
+R<GLN>A<CG> R<GLN>A<O> sep1 0.59083
+R<GLN>A<CG> R<GLN>A<O> sep2 0.271772
+R<GLN>A<CG> R<GLN>A<OE1> central_sep1 -0.486024
+R<GLN>A<CG> R<GLN>A<OE1> central_sep2 -0.485415
+R<GLN>A<CG> R<GLN>A<OE1> sep1 0.526055
+R<GLN>A<CG> R<GLN>A<OE1> sep2 -0.521024
+R<GLN>A<CG> R<GLU>A<C> central_sep1 0.956233
+R<GLN>A<CG> R<GLU>A<C> central_sep2 1.35574
+R<GLN>A<CG> R<GLU>A<C> sep1 -0.406538
+R<GLN>A<CG> R<GLU>A<C> sep2 0.4324
+R<GLN>A<CG> R<GLU>A<CA> central_sep1 0.288208
+R<GLN>A<CG> R<GLU>A<CA> central_sep2 0.894205
+R<GLN>A<CG> R<GLU>A<CA> sep1 0.655019
+R<GLN>A<CG> R<GLU>A<CA> sep2 0.889588
+R<GLN>A<CG> R<GLU>A<CB> central_sep1 0.38134
+R<GLN>A<CG> R<GLU>A<CB> central_sep2 0.216275
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+R<GLN>A<CG> R<GLU>A<CB> sep2 0.404479
+R<GLN>A<CG> R<GLU>A<CD> central_sep1 -0.619954
+R<GLN>A<CG> R<GLU>A<CD> central_sep2 0.00112669
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+R<GLN>A<CG> R<GLU>A<CG> central_sep1 -0.548219
+R<GLN>A<CG> R<GLU>A<CG> central_sep2 0.176896
+R<GLN>A<CG> R<GLU>A<CG> sep1 0.399106
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+R<GLN>A<CG> R<GLU>A<N> central_sep1 0.955593
+R<GLN>A<CG> R<GLU>A<N> central_sep2 2.0161
+R<GLN>A<CG> R<GLU>A<N> sep1 0.244582
+R<GLN>A<CG> R<GLU>A<N> sep2 1.34553
+R<GLN>A<CG> R<GLU>A<O> central_sep1 -1.51193
+R<GLN>A<CG> R<GLU>A<O> central_sep2 0.371476
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+R<GLN>A<N> R<TYR>A<CB> central_sep1 1.4217
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+R<GLN>A<NE2> R<HIS>A<C> sep1 1.12526
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+R<GLN>A<NE2> R<HIS>A<CA> sep1 1.68117
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+R<GLN>A<NE2> R<HIS>A<CB> sep1 1.74959
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+R<GLN>A<NE2> R<HIS>A<CG> sep1 0.919099
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+R<GLN>A<NE2> R<HIS>A<N> central_sep2 0.991932
+R<GLN>A<NE2> R<HIS>A<N> sep1 2.27332
+R<GLN>A<NE2> R<HIS>A<N> sep2 0.655021
+R<GLN>A<NE2> R<HIS>A<ND1> central_sep1 0.404207
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+R<GLN>A<NE2> R<HIS>A<ND1> sep1 1.22674
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+R<GLN>A<NE2> R<HIS>A<NE2> central_sep1 0.0551525
+R<GLN>A<NE2> R<HIS>A<NE2> central_sep2 -0.239955
+R<GLN>A<NE2> R<HIS>A<NE2> sep1 0.819884
+R<GLN>A<NE2> R<HIS>A<NE2> sep2 -0.674643
+R<GLN>A<NE2> R<HIS>A<O> central_sep1 0.00310488
+R<GLN>A<NE2> R<HIS>A<O> central_sep2 -0.421118
+R<GLN>A<NE2> R<HIS>A<O> sep1 1.56188
+R<GLN>A<NE2> R<HIS>A<O> sep2 0.775093
+R<GLN>A<NE2> R<ILE>A<C> central_sep1 1.64767
+R<GLN>A<NE2> R<ILE>A<C> central_sep2 1.77485
+R<GLN>A<NE2> R<ILE>A<C> sep1 1.79181
+R<GLN>A<NE2> R<ILE>A<C> sep2 0.488998
+R<GLN>A<NE2> R<ILE>A<CA> central_sep1 0.832678
+R<GLN>A<NE2> R<ILE>A<CA> central_sep2 0.869594
+R<GLN>A<NE2> R<ILE>A<CA> sep1 2.11793
+R<GLN>A<NE2> R<ILE>A<CA> sep2 0.571576
+R<GLN>A<NE2> R<ILE>A<CB> central_sep1 0.317553
+R<GLN>A<NE2> R<ILE>A<CB> central_sep2 0.165584
+R<GLN>A<NE2> R<ILE>A<CB> sep1 1.80848
+R<GLN>A<NE2> R<ILE>A<CB> sep2 -0.0624678
+R<GLN>A<NE2> R<ILE>A<CD1> central_sep1 0.497079
+R<GLN>A<NE2> R<ILE>A<CD1> central_sep2 -0.151559
+R<GLN>A<NE2> R<ILE>A<CD1> sep1 2.09185
+R<GLN>A<NE2> R<ILE>A<CD1> sep2 0.150526
+R<GLN>A<NE2> R<ILE>A<CG1> central_sep1 0.68745
+R<GLN>A<NE2> R<ILE>A<CG1> central_sep2 0.106752
+R<GLN>A<NE2> R<ILE>A<CG1> sep1 1.93865
+R<GLN>A<NE2> R<ILE>A<CG1> sep2 -0.0234088
+R<GLN>A<NE2> R<ILE>A<CG2> central_sep1 -0.0442045
+R<GLN>A<NE2> R<ILE>A<CG2> central_sep2 -0.167305
+R<GLN>A<NE2> R<ILE>A<CG2> sep1 1.64397
+R<GLN>A<NE2> R<ILE>A<CG2> sep2 0.305228
+R<GLN>A<NE2> R<ILE>A<N> central_sep1 1.99651
+R<GLN>A<NE2> R<ILE>A<N> central_sep2 1.04446
+R<GLN>A<NE2> R<ILE>A<N> sep1 2.4607
+R<GLN>A<NE2> R<ILE>A<N> sep2 0.799913
+R<GLN>A<NE2> R<ILE>A<O> central_sep1 0.393657
+R<GLN>A<NE2> R<ILE>A<O> central_sep2 -0.256257
+R<GLN>A<NE2> R<ILE>A<O> sep1 1.97359
+R<GLN>A<NE2> R<ILE>A<O> sep2 0.884144
+R<GLN>A<NE2> R<LEU>A<C> central_sep1 1.41923
+R<GLN>A<NE2> R<LEU>A<C> central_sep2 1.25481
+R<GLN>A<NE2> R<LEU>A<C> sep1 1.24858
+R<GLN>A<NE2> R<LEU>A<C> sep2 0.0989253
+R<GLN>A<NE2> R<LEU>A<CA> central_sep1 0.538694
+R<GLN>A<NE2> R<LEU>A<CA> central_sep2 0.640761
+R<GLN>A<NE2> R<LEU>A<CA> sep1 2.03435
+R<GLN>A<NE2> R<LEU>A<CA> sep2 0.548623
+R<GLN>A<NE2> R<LEU>A<CB> central_sep1 0.152815
+R<GLN>A<NE2> R<LEU>A<CB> central_sep2 -0.0239511
+R<GLN>A<NE2> R<LEU>A<CB> sep1 1.82212
+R<GLN>A<NE2> R<LEU>A<CB> sep2 0.121481
+R<GLN>A<NE2> R<LEU>A<CD1> central_sep1 0.259796
+R<GLN>A<NE2> R<LEU>A<CD1> central_sep2 -0.0970727
+R<GLN>A<NE2> R<LEU>A<CD1> sep1 1.76149
+R<GLN>A<NE2> R<LEU>A<CD1> sep2 0.151124
+R<GLN>A<NE2> R<LEU>A<CD2> central_sep1 0.0921638
+R<GLN>A<NE2> R<LEU>A<CD2> central_sep2 -0.240698
+R<GLN>A<NE2> R<LEU>A<CD2> sep1 1.27516
+R<GLN>A<NE2> R<LEU>A<CD2> sep2 0.0424116
+R<GLN>A<NE2> R<LEU>A<CG> central_sep1 0.283729
+R<GLN>A<NE2> R<LEU>A<CG> central_sep2 0.3927
+R<GLN>A<NE2> R<LEU>A<CG> sep1 1.41845
+R<GLN>A<NE2> R<LEU>A<CG> sep2 -0.133298
+R<GLN>A<NE2> R<LEU>A<N> central_sep1 1.68765
+R<GLN>A<NE2> R<LEU>A<N> central_sep2 0.984958
+R<GLN>A<NE2> R<LEU>A<N> sep1 2.21859
+R<GLN>A<NE2> R<LEU>A<N> sep2 0.841245
+R<GLN>A<NE2> R<LEU>A<O> central_sep1 0.0953055
+R<GLN>A<NE2> R<LEU>A<O> central_sep2 -0.379979
+R<GLN>A<NE2> R<LEU>A<O> sep1 1.59885
+R<GLN>A<NE2> R<LEU>A<O> sep2 0.76982
+R<GLN>A<NE2> R<LYS>A<C> central_sep1 1.06705
+R<GLN>A<NE2> R<LYS>A<C> central_sep2 1.42363
+R<GLN>A<NE2> R<LYS>A<C> sep1 1.0495
+R<GLN>A<NE2> R<LYS>A<C> sep2 0.283405
+R<GLN>A<NE2> R<LYS>A<CA> central_sep1 0.433248
+R<GLN>A<NE2> R<LYS>A<CA> central_sep2 0.584926
+R<GLN>A<NE2> R<LYS>A<CA> sep1 1.58122
+R<GLN>A<NE2> R<LYS>A<CA> sep2 0.421495
+R<GLN>A<NE2> R<LYS>A<CB> central_sep1 -0.116097
+R<GLN>A<NE2> R<LYS>A<CB> central_sep2 0.19771
+R<GLN>A<NE2> R<LYS>A<CB> sep1 1.31626
+R<GLN>A<NE2> R<LYS>A<CB> sep2 0.292445
+R<GLN>A<NE2> R<LYS>A<CD> central_sep1 -0.192187
+R<GLN>A<NE2> R<LYS>A<CD> central_sep2 -0.0166296
+R<GLN>A<NE2> R<LYS>A<CD> sep1 1.08094
+R<GLN>A<NE2> R<LYS>A<CD> sep2 -0.0354385
+R<GLN>A<NE2> R<LYS>A<CE> central_sep1 -0.160856
+R<GLN>A<NE2> R<LYS>A<CE> central_sep2 0.0425624
+R<GLN>A<NE2> R<LYS>A<CE> sep1 1.23683
+R<GLN>A<NE2> R<LYS>A<CE> sep2 -0.103288
+R<GLN>A<NE2> R<LYS>A<CG> central_sep1 0.00188011
+R<GLN>A<NE2> R<LYS>A<CG> central_sep2 0.256059
+R<GLN>A<NE2> R<LYS>A<CG> sep1 1.21382
+R<GLN>A<NE2> R<LYS>A<CG> sep2 0.183113
+R<GLN>A<NE2> R<LYS>A<N> central_sep1 1.64331
+R<GLN>A<NE2> R<LYS>A<N> central_sep2 1.17333
+R<GLN>A<NE2> R<LYS>A<N> sep1 2.05269
+R<GLN>A<NE2> R<LYS>A<N> sep2 0.937142
+R<GLN>A<NE2> R<LYS>A<NZ> central_sep1 0.535906
+R<GLN>A<NE2> R<LYS>A<NZ> central_sep2 0.185978
+R<GLN>A<NE2> R<LYS>A<NZ> sep1 1.25383
+R<GLN>A<NE2> R<LYS>A<NZ> sep2 -0.146301
+R<GLN>A<NE2> R<LYS>A<O> central_sep1 0.121526
+R<GLN>A<NE2> R<LYS>A<O> central_sep2 -0.166978
+R<GLN>A<NE2> R<LYS>A<O> sep1 1.32565
+R<GLN>A<NE2> R<LYS>A<O> sep2 0.89693
+R<GLN>A<NE2> R<MET>A<C> central_sep1 1.40287
+R<GLN>A<NE2> R<MET>A<C> central_sep2 1.14456
+R<GLN>A<NE2> R<MET>A<C> sep1 1.21588
+R<GLN>A<NE2> R<MET>A<C> sep2 0.120065
+R<GLN>A<NE2> R<MET>A<CA> central_sep1 0.595924
+R<GLN>A<NE2> R<MET>A<CA> central_sep2 0.521081
+R<GLN>A<NE2> R<MET>A<CA> sep1 1.72884
+R<GLN>A<NE2> R<MET>A<CA> sep2 0.30215
+R<GLN>A<NE2> R<MET>A<CB> central_sep1 0.118158
+R<GLN>A<NE2> R<MET>A<CB> central_sep2 -0.134043
+R<GLN>A<NE2> R<MET>A<CB> sep1 1.86924
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+R<GLN>A<NE2> R<MET>A<CE> central_sep1 0.302505
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+R<GLN>A<NE2> R<MET>A<CG> central_sep1 0.236928
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+R<GLN>A<NE2> R<MET>A<CG> sep1 1.55101
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+R<GLN>A<NE2> R<MET>A<N> central_sep1 1.80701
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+R<GLN>A<NE2> R<MET>A<N> sep1 2.29464
+R<GLN>A<NE2> R<MET>A<N> sep2 0.636019
+R<GLN>A<NE2> R<MET>A<O> central_sep1 0.133325
+R<GLN>A<NE2> R<MET>A<O> central_sep2 -0.387753
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+R<GLN>A<NE2> R<MET>A<SD> central_sep1 0.298114
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+R<GLN>A<NE2> R<MET>A<SD> sep1 1.78156
+R<GLN>A<NE2> R<MET>A<SD> sep2 -0.0235418
+R<GLN>A<NE2> R<PHE>A<C> central_sep1 1.24515
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+R<GLN>A<NE2> R<PHE>A<C> sep1 1.33707
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+R<GLN>A<NE2> R<PHE>A<CA> central_sep1 0.584685
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+R<GLN>A<NE2> R<PHE>A<CA> sep1 1.7872
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+R<GLN>A<NE2> R<PHE>A<CB> central_sep1 0.589545
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+R<GLN>A<NE2> R<PHE>A<CD1> central_sep1 0.30531
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+R<GLN>A<NE2> R<PHE>A<CE1> central_sep1 0.354916
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+R<GLN>A<NE2> R<PHE>A<CG> sep1 1.44935
+R<GLN>A<NE2> R<PHE>A<CG> sep2 -0.912261
+R<GLN>A<NE2> R<PHE>A<CZ> central_sep1 0.251774
+R<GLN>A<NE2> R<PHE>A<CZ> central_sep2 -0.277569
+R<GLN>A<NE2> R<PHE>A<CZ> sep1 1.03457
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+R<GLN>A<NE2> R<PHE>A<N> central_sep1 1.73448
+R<GLN>A<NE2> R<PHE>A<N> central_sep2 0.969862
+R<GLN>A<NE2> R<PHE>A<N> sep1 2.30138
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+R<GLN>A<NE2> R<PHE>A<O> central_sep1 0.128163
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+R<GLN>A<NE2> R<PHE>A<O> sep1 1.63066
+R<GLN>A<NE2> R<PHE>A<O> sep2 0.689072
+R<GLN>A<NE2> R<PRO>A<C> central_sep1 0.862544
+R<GLN>A<NE2> R<PRO>A<C> central_sep2 1.13914
+R<GLN>A<NE2> R<PRO>A<C> sep1 1.1081
+R<GLN>A<NE2> R<PRO>A<C> sep2 0.0614847
+R<GLN>A<NE2> R<PRO>A<CA> central_sep1 0.41883
+R<GLN>A<NE2> R<PRO>A<CA> central_sep2 0.171583
+R<GLN>A<NE2> R<PRO>A<CA> sep1 1.66352
+R<GLN>A<NE2> R<PRO>A<CA> sep2 0.122386
+R<GLN>A<NE2> R<PRO>A<CB> central_sep1 0.0570356
+R<GLN>A<NE2> R<PRO>A<CB> central_sep2 -0.333659
+R<GLN>A<NE2> R<PRO>A<CB> sep1 1.28965
+R<GLN>A<NE2> R<PRO>A<CB> sep2 -0.264289
+R<GLN>A<NE2> R<PRO>A<CD> central_sep1 0.249086
+R<GLN>A<NE2> R<PRO>A<CD> central_sep2 0.0265644
+R<GLN>A<NE2> R<PRO>A<CD> sep1 1.54155
+R<GLN>A<NE2> R<PRO>A<CD> sep2 0.0767248
+R<GLN>A<NE2> R<PRO>A<CG> central_sep1 0.439472
+R<GLN>A<NE2> R<PRO>A<CG> central_sep2 -0.370963
+R<GLN>A<NE2> R<PRO>A<CG> sep1 1.22893
+R<GLN>A<NE2> R<PRO>A<CG> sep2 -0.411227
+R<GLN>A<NE2> R<PRO>A<N> central_sep1 0.981421
+R<GLN>A<NE2> R<PRO>A<N> central_sep2 0.887768
+R<GLN>A<NE2> R<PRO>A<N> sep1 1.05512
+R<GLN>A<NE2> R<PRO>A<N> sep2 -0.207228
+R<GLN>A<NE2> R<PRO>A<O> central_sep1 -0.240665
+R<GLN>A<NE2> R<PRO>A<O> central_sep2 -0.476362
+R<GLN>A<NE2> R<PRO>A<O> sep1 1.11654
+R<GLN>A<NE2> R<PRO>A<O> sep2 0.521742
+R<GLN>A<NE2> R<SER>A<C> central_sep1 0.522123
+R<GLN>A<NE2> R<SER>A<C> central_sep2 0.852177
+R<GLN>A<NE2> R<SER>A<C> sep1 0.802463
+R<GLN>A<NE2> R<SER>A<C> sep2 0.0160412
+R<GLN>A<NE2> R<SER>A<CA> central_sep1 0.646427
+R<GLN>A<NE2> R<SER>A<CA> central_sep2 0.263996
+R<GLN>A<NE2> R<SER>A<CA> sep1 1.60819
+R<GLN>A<NE2> R<SER>A<CA> sep2 0.0273733
+R<GLN>A<NE2> R<SER>A<CB> central_sep1 0.212356
+R<GLN>A<NE2> R<SER>A<CB> central_sep2 -0.210979
+R<GLN>A<NE2> R<SER>A<CB> sep1 1.25577
+R<GLN>A<NE2> R<SER>A<CB> sep2 -0.304215
+R<GLN>A<NE2> R<SER>A<N> central_sep1 0.969494
+R<GLN>A<NE2> R<SER>A<N> central_sep2 0.767627
+R<GLN>A<NE2> R<SER>A<N> sep1 2.09983
+R<GLN>A<NE2> R<SER>A<N> sep2 0.432215
+R<GLN>A<NE2> R<SER>A<O> central_sep1 -0.133834
+R<GLN>A<NE2> R<SER>A<O> central_sep2 -0.391056
+R<GLN>A<NE2> R<SER>A<O> sep1 1.24996
+R<GLN>A<NE2> R<SER>A<O> sep2 0.468105
+R<GLN>A<NE2> R<SER>A<OG> central_sep1 -0.358962
+R<GLN>A<NE2> R<SER>A<OG> central_sep2 -0.606088
+R<GLN>A<NE2> R<SER>A<OG> sep1 1.27384
+R<GLN>A<NE2> R<SER>A<OG> sep2 -0.0865349
+R<GLN>A<NE2> R<THR>A<C> central_sep1 0.910976
+R<GLN>A<NE2> R<THR>A<C> central_sep2 0.963136
+R<GLN>A<NE2> R<THR>A<C> sep1 1.29103
+R<GLN>A<NE2> R<THR>A<C> sep2 0.0277842
+R<GLN>A<NE2> R<THR>A<CA> central_sep1 0.657959
+R<GLN>A<NE2> R<THR>A<CA> central_sep2 0.341025
+R<GLN>A<NE2> R<THR>A<CA> sep1 1.69539
+R<GLN>A<NE2> R<THR>A<CA> sep2 0.107373
+R<GLN>A<NE2> R<THR>A<CB> central_sep1 0.396688
+R<GLN>A<NE2> R<THR>A<CB> central_sep2 -0.176495
+R<GLN>A<NE2> R<THR>A<CB> sep1 1.08942
+R<GLN>A<NE2> R<THR>A<CB> sep2 -0.609644
+R<GLN>A<NE2> R<THR>A<CG2> central_sep1 -0.0401201
+R<GLN>A<NE2> R<THR>A<CG2> central_sep2 -0.343118
+R<GLN>A<NE2> R<THR>A<CG2> sep1 1.23964
+R<GLN>A<NE2> R<THR>A<CG2> sep2 -0.14284
+R<GLN>A<NE2> R<THR>A<N> central_sep1 1.00745
+R<GLN>A<NE2> R<THR>A<N> central_sep2 0.828183
+R<GLN>A<NE2> R<THR>A<N> sep1 2.11704
+R<GLN>A<NE2> R<THR>A<N> sep2 0.694653
+R<GLN>A<NE2> R<THR>A<O> central_sep1 -0.00561326
+R<GLN>A<NE2> R<THR>A<O> central_sep2 -0.395952
+R<GLN>A<NE2> R<THR>A<O> sep1 1.44029
+R<GLN>A<NE2> R<THR>A<O> sep2 0.600222
+R<GLN>A<NE2> R<THR>A<OG1> central_sep1 -0.191489
+R<GLN>A<NE2> R<THR>A<OG1> central_sep2 -0.750855
+R<GLN>A<NE2> R<THR>A<OG1> sep1 1.31871
+R<GLN>A<NE2> R<THR>A<OG1> sep2 -0.217313
+R<GLN>A<NE2> R<TRP>A<C> central_sep1 1.06534
+R<GLN>A<NE2> R<TRP>A<C> central_sep2 1.09953
+R<GLN>A<NE2> R<TRP>A<C> sep1 1.17385
+R<GLN>A<NE2> R<TRP>A<C> sep2 0.0508654
+R<GLN>A<NE2> R<TRP>A<CA> central_sep1 0.315285
+R<GLN>A<NE2> R<TRP>A<CA> central_sep2 0.35464
+R<GLN>A<NE2> R<TRP>A<CA> sep1 1.67827
+R<GLN>A<NE2> R<TRP>A<CA> sep2 0.436163
+R<GLN>A<NE2> R<TRP>A<CB> central_sep1 0.467877
+R<GLN>A<NE2> R<TRP>A<CB> central_sep2 -0.409839
+R<GLN>A<NE2> R<TRP>A<CB> sep1 2.04838
+R<GLN>A<NE2> R<TRP>A<CB> sep2 -0.170573
+R<GLN>A<NE2> R<TRP>A<CD1> central_sep1 -0.248852
+R<GLN>A<NE2> R<TRP>A<CD1> central_sep2 -0.415378
+R<GLN>A<NE2> R<TRP>A<CD1> sep1 1.21709
+R<GLN>A<NE2> R<TRP>A<CD1> sep2 -0.506364
+R<GLN>A<NE2> R<TRP>A<CD2> central_sep1 0.619515
+R<GLN>A<NE2> R<TRP>A<CD2> central_sep2 -0.26451
+R<GLN>A<NE2> R<TRP>A<CD2> sep1 1.09032
+R<GLN>A<NE2> R<TRP>A<CD2> sep2 -0.846409
+R<GLN>A<NE2> R<TRP>A<CE2> central_sep1 -0.155779
+R<GLN>A<NE2> R<TRP>A<CE2> central_sep2 -0.335203
+R<GLN>A<NE2> R<TRP>A<CE2> sep1 0.997149
+R<GLN>A<NE2> R<TRP>A<CE2> sep2 -0.974117
+R<GLN>A<NE2> R<TRP>A<CE3> central_sep1 0.345182
+R<GLN>A<NE2> R<TRP>A<CE3> central_sep2 -0.0290791
+R<GLN>A<NE2> R<TRP>A<CE3> sep1 1.8414
+R<GLN>A<NE2> R<TRP>A<CE3> sep2 -0.212419
+R<GLN>A<NE2> R<TRP>A<CG> central_sep1 2.0615
+R<GLN>A<NE2> R<TRP>A<CG> central_sep2 -0.196825
+R<GLN>A<NE2> R<TRP>A<CG> sep1 1.11337
+R<GLN>A<NE2> R<TRP>A<CG> sep2 -1.26594
+R<GLN>A<NE2> R<TRP>A<CH2> central_sep1 0.520777
+R<GLN>A<NE2> R<TRP>A<CH2> central_sep2 -0.548383
+R<GLN>A<NE2> R<TRP>A<CH2> sep1 1.26031
+R<GLN>A<NE2> R<TRP>A<CH2> sep2 -0.81735
+R<GLN>A<NE2> R<TRP>A<CZ2> central_sep1 -0.228533
+R<GLN>A<NE2> R<TRP>A<CZ2> central_sep2 -0.757847
+R<GLN>A<NE2> R<TRP>A<CZ2> sep1 0.762577
+R<GLN>A<NE2> R<TRP>A<CZ2> sep2 -0.975452
+R<GLN>A<NE2> R<TRP>A<CZ3> central_sep1 0.434891
+R<GLN>A<NE2> R<TRP>A<CZ3> central_sep2 -0.349043
+R<GLN>A<NE2> R<TRP>A<CZ3> sep1 1.45511
+R<GLN>A<NE2> R<TRP>A<CZ3> sep2 -0.317972
+R<GLN>A<NE2> R<TRP>A<N> central_sep1 1.70544
+R<GLN>A<NE2> R<TRP>A<N> central_sep2 0.869916
+R<GLN>A<NE2> R<TRP>A<N> sep1 1.90908
+R<GLN>A<NE2> R<TRP>A<N> sep2 0.542072
+R<GLN>A<NE2> R<TRP>A<NE1> central_sep1 -0.461183
+R<GLN>A<NE2> R<TRP>A<NE1> central_sep2 -0.666122
+R<GLN>A<NE2> R<TRP>A<NE1> sep1 0.675247
+R<GLN>A<NE2> R<TRP>A<NE1> sep2 -0.851475
+R<GLN>A<NE2> R<TRP>A<O> central_sep1 -0.227113
+R<GLN>A<NE2> R<TRP>A<O> central_sep2 -0.470326
+R<GLN>A<NE2> R<TRP>A<O> sep1 1.32775
+R<GLN>A<NE2> R<TRP>A<O> sep2 0.77179
+R<GLN>A<NE2> R<TYR>A<C> central_sep1 1.04884
+R<GLN>A<NE2> R<TYR>A<C> central_sep2 1.11346
+R<GLN>A<NE2> R<TYR>A<C> sep1 1.30445
+R<GLN>A<NE2> R<TYR>A<C> sep2 -0.0393028
+R<GLN>A<NE2> R<TYR>A<CA> central_sep1 0.618909
+R<GLN>A<NE2> R<TYR>A<CA> central_sep2 0.474148
+R<GLN>A<NE2> R<TYR>A<CA> sep1 1.86937
+R<GLN>A<NE2> R<TYR>A<CA> sep2 0.477881
+R<GLN>A<NE2> R<TYR>A<CB> central_sep1 0.640812
+R<GLN>A<NE2> R<TYR>A<CB> central_sep2 -0.189588
+R<GLN>A<NE2> R<TYR>A<CB> sep1 2.13588
+R<GLN>A<NE2> R<TYR>A<CB> sep2 -0.0150126
+R<GLN>A<NE2> R<TYR>A<CD1> central_sep1 0.0984278
+R<GLN>A<NE2> R<TYR>A<CD1> central_sep2 -0.12371
+R<GLN>A<NE2> R<TYR>A<CD1> sep1 1.54156
+R<GLN>A<NE2> R<TYR>A<CD1> sep2 -0.222394
+R<GLN>A<NE2> R<TYR>A<CE1> central_sep1 0.000862453
+R<GLN>A<NE2> R<TYR>A<CE1> central_sep2 -0.455073
+R<GLN>A<NE2> R<TYR>A<CE1> sep1 0.825904
+R<GLN>A<NE2> R<TYR>A<CE1> sep2 -0.574781
+R<GLN>A<NE2> R<TYR>A<CG> central_sep1 1.82796
+R<GLN>A<NE2> R<TYR>A<CG> central_sep2 0.22179
+R<GLN>A<NE2> R<TYR>A<CG> sep1 1.16662
+R<GLN>A<NE2> R<TYR>A<CG> sep2 -0.976175
+R<GLN>A<NE2> R<TYR>A<CZ> central_sep1 -0.0902301
+R<GLN>A<NE2> R<TYR>A<CZ> central_sep2 -0.207648
+R<GLN>A<NE2> R<TYR>A<CZ> sep1 0.974397
+R<GLN>A<NE2> R<TYR>A<CZ> sep2 -1.19604
+R<GLN>A<NE2> R<TYR>A<N> central_sep1 1.72869
+R<GLN>A<NE2> R<TYR>A<N> central_sep2 1.00072
+R<GLN>A<NE2> R<TYR>A<N> sep1 2.18179
+R<GLN>A<NE2> R<TYR>A<N> sep2 0.728867
+R<GLN>A<NE2> R<TYR>A<O> central_sep1 0.142529
+R<GLN>A<NE2> R<TYR>A<O> central_sep2 -0.496045
+R<GLN>A<NE2> R<TYR>A<O> sep1 1.58628
+R<GLN>A<NE2> R<TYR>A<O> sep2 0.646967
+R<GLN>A<NE2> R<TYR>A<OH> central_sep1 -0.0917998
+R<GLN>A<NE2> R<TYR>A<OH> central_sep2 -0.96448
+R<GLN>A<NE2> R<TYR>A<OH> sep1 0.933188
+R<GLN>A<NE2> R<TYR>A<OH> sep2 -0.587537
+R<GLN>A<NE2> R<VAL>A<C> central_sep1 1.45711
+R<GLN>A<NE2> R<VAL>A<C> central_sep2 1.54346
+R<GLN>A<NE2> R<VAL>A<C> sep1 1.66366
+R<GLN>A<NE2> R<VAL>A<C> sep2 0.387476
+R<GLN>A<NE2> R<VAL>A<CA> central_sep1 0.909715
+R<GLN>A<NE2> R<VAL>A<CA> central_sep2 0.766466
+R<GLN>A<NE2> R<VAL>A<CA> sep1 2.0376
+R<GLN>A<NE2> R<VAL>A<CA> sep2 0.62622
+R<GLN>A<NE2> R<VAL>A<CB> central_sep1 0.553649
+R<GLN>A<NE2> R<VAL>A<CB> central_sep2 0.151123
+R<GLN>A<NE2> R<VAL>A<CB> sep1 1.73264
+R<GLN>A<NE2> R<VAL>A<CB> sep2 -0.147732
+R<GLN>A<NE2> R<VAL>A<CG1> central_sep1 0.0970558
+R<GLN>A<NE2> R<VAL>A<CG1> central_sep2 -0.154588
+R<GLN>A<NE2> R<VAL>A<CG1> sep1 1.71238
+R<GLN>A<NE2> R<VAL>A<CG1> sep2 0.146299
+R<GLN>A<NE2> R<VAL>A<CG2> central_sep1 0.642912
+R<GLN>A<NE2> R<VAL>A<CG2> central_sep2 -0.113632
+R<GLN>A<NE2> R<VAL>A<CG2> sep1 2.02385
+R<GLN>A<NE2> R<VAL>A<CG2> sep2 0.190882
+R<GLN>A<NE2> R<VAL>A<N> central_sep1 1.78071
+R<GLN>A<NE2> R<VAL>A<N> central_sep2 1.07505
+R<GLN>A<NE2> R<VAL>A<N> sep1 2.38328
+R<GLN>A<NE2> R<VAL>A<N> sep2 0.731894
+R<GLN>A<NE2> R<VAL>A<O> central_sep1 0.309273
+R<GLN>A<NE2> R<VAL>A<O> central_sep2 -0.269108
+R<GLN>A<NE2> R<VAL>A<O> sep1 1.80281
+R<GLN>A<NE2> R<VAL>A<O> sep2 0.881995
+R<GLN>A<NE2> c<solvent> . -0.535555
+R<GLN>A<O> R<GLN>A<O> central_sep1 0.889722
+R<GLN>A<O> R<GLN>A<O> central_sep2 0.707809
+R<GLN>A<O> R<GLN>A<O> sep1 0.431522
+R<GLN>A<O> R<GLN>A<O> sep2 1.04719
+R<GLN>A<O> R<GLN>A<OE1> central_sep1 0.589233
+R<GLN>A<O> R<GLN>A<OE1> central_sep2 0.515716
+R<GLN>A<O> R<GLN>A<OE1> sep1 1.04963
+R<GLN>A<O> R<GLN>A<OE1> sep2 0.354585
+R<GLN>A<O> R<GLU>A<C> central_sep1 -0.692851
+R<GLN>A<O> R<GLU>A<C> central_sep2 2.8604
+R<GLN>A<O> R<GLU>A<C> sep1 -1.49345
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+R<GLN>A<OE1> R<TRP>A<CZ2> sep1 0.324756
+R<GLN>A<OE1> R<TRP>A<CZ2> sep2 -1.2355
+R<GLN>A<OE1> R<TRP>A<CZ3> central_sep1 0.4676
+R<GLN>A<OE1> R<TRP>A<CZ3> central_sep2 -0.168133
+R<GLN>A<OE1> R<TRP>A<CZ3> sep1 1.3206
+R<GLN>A<OE1> R<TRP>A<CZ3> sep2 -0.460057
+R<GLN>A<OE1> R<TRP>A<N> central_sep1 0.685031
+R<GLN>A<OE1> R<TRP>A<N> central_sep2 -0.103708
+R<GLN>A<OE1> R<TRP>A<N> sep1 1.58003
+R<GLN>A<OE1> R<TRP>A<N> sep2 0.435004
+R<GLN>A<OE1> R<TRP>A<NE1> central_sep1 -0.760014
+R<GLN>A<OE1> R<TRP>A<NE1> central_sep2 -1.37925
+R<GLN>A<OE1> R<TRP>A<NE1> sep1 0.738858
+R<GLN>A<OE1> R<TRP>A<NE1> sep2 -0.893716
+R<GLN>A<OE1> R<TRP>A<O> central_sep1 0.64036
+R<GLN>A<OE1> R<TRP>A<O> central_sep2 0.514992
+R<GLN>A<OE1> R<TRP>A<O> sep1 1.29045
+R<GLN>A<OE1> R<TRP>A<O> sep2 0.23802
+R<GLN>A<OE1> R<TYR>A<C> central_sep1 1.3343
+R<GLN>A<OE1> R<TYR>A<C> central_sep2 1.24215
+R<GLN>A<OE1> R<TYR>A<C> sep1 1.55814
+R<GLN>A<OE1> R<TYR>A<C> sep2 0.414545
+R<GLN>A<OE1> R<TYR>A<CA> central_sep1 -0.174254
+R<GLN>A<OE1> R<TYR>A<CA> central_sep2 0.0541485
+R<GLN>A<OE1> R<TYR>A<CA> sep1 1.49071
+R<GLN>A<OE1> R<TYR>A<CA> sep2 0.355339
+R<GLN>A<OE1> R<TYR>A<CB> central_sep1 0.578474
+R<GLN>A<OE1> R<TYR>A<CB> central_sep2 -0.270358
+R<GLN>A<OE1> R<TYR>A<CB> sep1 1.76788
+R<GLN>A<OE1> R<TYR>A<CB> sep2 -0.220587
+R<GLN>A<OE1> R<TYR>A<CD1> central_sep1 -0.0549287
+R<GLN>A<OE1> R<TYR>A<CD1> central_sep2 -0.160373
+R<GLN>A<OE1> R<TYR>A<CD1> sep1 1.36995
+R<GLN>A<OE1> R<TYR>A<CD1> sep2 -0.310306
+R<GLN>A<OE1> R<TYR>A<CE1> central_sep1 0.0609542
+R<GLN>A<OE1> R<TYR>A<CE1> central_sep2 -0.51139
+R<GLN>A<OE1> R<TYR>A<CE1> sep1 0.707546
+R<GLN>A<OE1> R<TYR>A<CE1> sep2 -0.54875
+R<GLN>A<OE1> R<TYR>A<CG> central_sep1 2.34273
+R<GLN>A<OE1> R<TYR>A<CG> central_sep2 0.988189
+R<GLN>A<OE1> R<TYR>A<CG> sep1 1.48368
+R<GLN>A<OE1> R<TYR>A<CG> sep2 -0.667348
+R<GLN>A<OE1> R<TYR>A<CZ> central_sep1 0.687317
+R<GLN>A<OE1> R<TYR>A<CZ> central_sep2 0.571489
+R<GLN>A<OE1> R<TYR>A<CZ> sep1 1.17636
+R<GLN>A<OE1> R<TYR>A<CZ> sep2 -0.834207
+R<GLN>A<OE1> R<TYR>A<N> central_sep1 0.784704
+R<GLN>A<OE1> R<TYR>A<N> central_sep2 -0.0111356
+R<GLN>A<OE1> R<TYR>A<N> sep1 1.8346
+R<GLN>A<OE1> R<TYR>A<N> sep2 0.35393
+R<GLN>A<OE1> R<TYR>A<O> central_sep1 0.88023
+R<GLN>A<OE1> R<TYR>A<O> central_sep2 0.521541
+R<GLN>A<OE1> R<TYR>A<O> sep1 1.47604
+R<GLN>A<OE1> R<TYR>A<O> sep2 0.310067
+R<GLN>A<OE1> R<TYR>A<OH> central_sep1 0.17157
+R<GLN>A<OE1> R<TYR>A<OH> central_sep2 -0.985319
+R<GLN>A<OE1> R<TYR>A<OH> sep1 0.785165
+R<GLN>A<OE1> R<TYR>A<OH> sep2 -0.682932
+R<GLN>A<OE1> R<VAL>A<C> central_sep1 1.77586
+R<GLN>A<OE1> R<VAL>A<C> central_sep2 1.65212
+R<GLN>A<OE1> R<VAL>A<C> sep1 1.95295
+R<GLN>A<OE1> R<VAL>A<C> sep2 0.900938
+R<GLN>A<OE1> R<VAL>A<CA> central_sep1 0.0648367
+R<GLN>A<OE1> R<VAL>A<CA> central_sep2 0.258301
+R<GLN>A<OE1> R<VAL>A<CA> sep1 1.65053
+R<GLN>A<OE1> R<VAL>A<CA> sep2 0.573491
+R<GLN>A<OE1> R<VAL>A<CB> central_sep1 0.571283
+R<GLN>A<OE1> R<VAL>A<CB> central_sep2 -0.0865257
+R<GLN>A<OE1> R<VAL>A<CB> sep1 1.59208
+R<GLN>A<OE1> R<VAL>A<CB> sep2 -0.371466
+R<GLN>A<OE1> R<VAL>A<CG1> central_sep1 0.433969
+R<GLN>A<OE1> R<VAL>A<CG1> central_sep2 -0.185247
+R<GLN>A<OE1> R<VAL>A<CG1> sep1 1.29063
+R<GLN>A<OE1> R<VAL>A<CG1> sep2 -0.0614534
+R<GLN>A<OE1> R<VAL>A<CG2> central_sep1 0.551217
+R<GLN>A<OE1> R<VAL>A<CG2> central_sep2 -0.180018
+R<GLN>A<OE1> R<VAL>A<CG2> sep1 1.74007
+R<GLN>A<OE1> R<VAL>A<CG2> sep2 -0.0914518
+R<GLN>A<OE1> R<VAL>A<N> central_sep1 1.33268
+R<GLN>A<OE1> R<VAL>A<N> central_sep2 -0.0182542
+R<GLN>A<OE1> R<VAL>A<N> sep1 2.12551
+R<GLN>A<OE1> R<VAL>A<N> sep2 0.64374
+R<GLN>A<OE1> R<VAL>A<O> central_sep1 1.07653
+R<GLN>A<OE1> R<VAL>A<O> central_sep2 0.616992
+R<GLN>A<OE1> R<VAL>A<O> sep1 1.79753
+R<GLN>A<OE1> R<VAL>A<O> sep2 0.410262
+R<GLN>A<OE1> c<solvent> . -0.509974
+R<GLU>A<C> R<GLU>A<C> central_sep1 4.74725
+R<GLU>A<C> R<GLU>A<C> central_sep2 4.09082
+R<GLU>A<C> R<GLU>A<C> sep1 -2.71502
+R<GLU>A<C> R<GLU>A<C> sep2 2.26827
+R<GLU>A<C> R<GLU>A<CA> central_sep1 3.97321
+R<GLU>A<C> R<GLU>A<CA> central_sep2 2.95794
+R<GLU>A<C> R<GLU>A<CA> sep1 -2.86078
+R<GLU>A<C> R<GLU>A<CA> sep2 1.60495
+R<GLU>A<C> R<GLU>A<CB> central_sep1 2.55893
+R<GLU>A<C> R<GLU>A<CB> central_sep2 2.44448
+R<GLU>A<C> R<GLU>A<CB> sep1 0.188895
+R<GLU>A<C> R<GLU>A<CB> sep2 1.21864
+R<GLU>A<C> R<GLU>A<CD> central_sep1 1.91373
+R<GLU>A<C> R<GLU>A<CD> central_sep2 2.61733
+R<GLU>A<C> R<GLU>A<CD> sep1 -0.264542
+R<GLU>A<C> R<GLU>A<CD> sep2 1.79149
+R<GLU>A<C> R<GLU>A<CG> central_sep1 1.36077
+R<GLU>A<C> R<GLU>A<CG> central_sep2 2.01211
+R<GLU>A<C> R<GLU>A<CG> sep1 -0.248641
+R<GLU>A<C> R<GLU>A<CG> sep2 1.08127
+R<GLU>A<C> R<GLU>A<N> central_sep1 -0.860942
+R<GLU>A<C> R<GLU>A<N> central_sep2 3.54787
+R<GLU>A<C> R<GLU>A<N> sep1 -1.70335
+R<GLU>A<C> R<GLU>A<N> sep2 2.44515
+R<GLU>A<C> R<GLU>A<O> central_sep1 -0.810439
+R<GLU>A<C> R<GLU>A<O> central_sep2 3.13709
+R<GLU>A<C> R<GLU>A<O> sep1 -1.67988
+R<GLU>A<C> R<GLU>A<O> sep2 2.03615
+R<GLU>A<C> R<GLU>A<OE1> central_sep1 2.16236
+R<GLU>A<C> R<GLU>A<OE1> central_sep2 3.27144
+R<GLU>A<C> R<GLU>A<OE1> sep1 1.38592
+R<GLU>A<C> R<GLU>A<OE1> sep2 2.04342
+R<GLU>A<C> R<GLY>A<C> central_sep1 4.14069
+R<GLU>A<C> R<GLY>A<C> central_sep2 2.7735
+R<GLU>A<C> R<GLY>A<C> sep1 -1.90224
+R<GLU>A<C> R<GLY>A<C> sep2 1.4947
+R<GLU>A<C> R<GLY>A<CA> central_sep1 3.11742
+R<GLU>A<C> R<GLY>A<CA> central_sep2 1.39367
+R<GLU>A<C> R<GLY>A<CA> sep1 -1.74446
+R<GLU>A<C> R<GLY>A<CA> sep2 0.312739
+R<GLU>A<C> R<GLY>A<N> central_sep1 -0.303224
+R<GLU>A<C> R<GLY>A<N> central_sep2 2.22575
+R<GLU>A<C> R<GLY>A<N> sep1 -1.77497
+R<GLU>A<C> R<GLY>A<N> sep2 1.05662
+R<GLU>A<C> R<GLY>A<O> central_sep1 -0.26399
+R<GLU>A<C> R<GLY>A<O> central_sep2 2.1283
+R<GLU>A<C> R<GLY>A<O> sep1 -1.37941
+R<GLU>A<C> R<GLY>A<O> sep2 1.33392
+R<GLU>A<C> R<HIS>A<C> central_sep1 4.16979
+R<GLU>A<C> R<HIS>A<C> central_sep2 3.66908
+R<GLU>A<C> R<HIS>A<C> sep1 -2.26506
+R<GLU>A<C> R<HIS>A<C> sep2 2.25704
+R<GLU>A<C> R<HIS>A<CA> central_sep1 3.98948
+R<GLU>A<C> R<HIS>A<CA> central_sep2 3.31847
+R<GLU>A<C> R<HIS>A<CA> sep1 -2.59516
+R<GLU>A<C> R<HIS>A<CA> sep2 1.41617
+R<GLU>A<C> R<HIS>A<CB> central_sep1 2.21442
+R<GLU>A<C> R<HIS>A<CB> central_sep2 1.42392
+R<GLU>A<C> R<HIS>A<CB> sep1 0.0616911
+R<GLU>A<C> R<HIS>A<CB> sep2 0.383818
+R<GLU>A<C> R<HIS>A<CD2> central_sep1 0.065839
+R<GLU>A<C> R<HIS>A<CD2> central_sep2 0.945634
+R<GLU>A<C> R<HIS>A<CD2> sep1 -0.274641
+R<GLU>A<C> R<HIS>A<CD2> sep2 0.0477826
+R<GLU>A<C> R<HIS>A<CE1> central_sep1 1.7016
+R<GLU>A<C> R<HIS>A<CE1> central_sep2 0.852916
+R<GLU>A<C> R<HIS>A<CE1> sep1 1.67687
+R<GLU>A<C> R<HIS>A<CE1> sep2 0.0521364
+R<GLU>A<C> R<HIS>A<CG> central_sep1 0.329102
+R<GLU>A<C> R<HIS>A<CG> central_sep2 1.16998
+R<GLU>A<C> R<HIS>A<CG> sep1 -1.62215
+R<GLU>A<C> R<HIS>A<CG> sep2 0.480452
+R<GLU>A<C> R<HIS>A<N> central_sep1 -0.598358
+R<GLU>A<C> R<HIS>A<N> central_sep2 3.09244
+R<GLU>A<C> R<HIS>A<N> sep1 -1.63431
+R<GLU>A<C> R<HIS>A<N> sep2 1.76315
+R<GLU>A<C> R<HIS>A<ND1> central_sep1 0.218083
+R<GLU>A<C> R<HIS>A<ND1> central_sep2 1.40336
+R<GLU>A<C> R<HIS>A<ND1> sep1 -0.282701
+R<GLU>A<C> R<HIS>A<ND1> sep2 0.347888
+R<GLU>A<C> R<HIS>A<NE2> central_sep1 2.52856
+R<GLU>A<C> R<HIS>A<NE2> central_sep2 1.24791
+R<GLU>A<C> R<HIS>A<NE2> sep1 2.31797
+R<GLU>A<C> R<HIS>A<NE2> sep2 0.266156
+R<GLU>A<C> R<HIS>A<O> central_sep1 -0.721694
+R<GLU>A<C> R<HIS>A<O> central_sep2 2.40931
+R<GLU>A<C> R<HIS>A<O> sep1 -1.27683
+R<GLU>A<C> R<HIS>A<O> sep2 1.43739
+R<GLU>A<C> R<ILE>A<C> central_sep1 4.79145
+R<GLU>A<C> R<ILE>A<C> central_sep2 4.73344
+R<GLU>A<C> R<ILE>A<C> sep1 -2.91409
+R<GLU>A<C> R<ILE>A<C> sep2 3.72752
+R<GLU>A<C> R<ILE>A<CA> central_sep1 4.60248
+R<GLU>A<C> R<ILE>A<CA> central_sep2 3.61563
+R<GLU>A<C> R<ILE>A<CA> sep1 -2.8937
+R<GLU>A<C> R<ILE>A<CA> sep2 1.44818
+R<GLU>A<C> R<ILE>A<CB> central_sep1 2.25712
+R<GLU>A<C> R<ILE>A<CB> central_sep2 1.75121
+R<GLU>A<C> R<ILE>A<CB> sep1 0.0999797
+R<GLU>A<C> R<ILE>A<CB> sep2 0.146099
+R<GLU>A<C> R<ILE>A<CD1> central_sep1 0.89981
+R<GLU>A<C> R<ILE>A<CD1> central_sep2 0.282522
+R<GLU>A<C> R<ILE>A<CD1> sep1 0.0361709
+R<GLU>A<C> R<ILE>A<CD1> sep2 -0.0728813
+R<GLU>A<C> R<ILE>A<CG1> central_sep1 0.534051
+R<GLU>A<C> R<ILE>A<CG1> central_sep2 0.884397
+R<GLU>A<C> R<ILE>A<CG1> sep1 -1.10413
+R<GLU>A<C> R<ILE>A<CG1> sep2 0.0603709
+R<GLU>A<C> R<ILE>A<CG2> central_sep1 0.373236
+R<GLU>A<C> R<ILE>A<CG2> central_sep2 0.768674
+R<GLU>A<C> R<ILE>A<CG2> sep1 -0.164191
+R<GLU>A<C> R<ILE>A<CG2> sep2 -0.0790308
+R<GLU>A<C> R<ILE>A<N> central_sep1 -0.434653
+R<GLU>A<C> R<ILE>A<N> central_sep2 3.99012
+R<GLU>A<C> R<ILE>A<N> sep1 -2.0277
+R<GLU>A<C> R<ILE>A<N> sep2 2.41423
+R<GLU>A<C> R<ILE>A<O> central_sep1 -1.0243
+R<GLU>A<C> R<ILE>A<O> central_sep2 3.07899
+R<GLU>A<C> R<ILE>A<O> sep1 -1.40786
+R<GLU>A<C> R<ILE>A<O> sep2 1.68661
+R<GLU>A<C> R<LEU>A<C> central_sep1 4.03904
+R<GLU>A<C> R<LEU>A<C> central_sep2 4.71822
+R<GLU>A<C> R<LEU>A<C> sep1 -2.70433
+R<GLU>A<C> R<LEU>A<C> sep2 2.81277
+R<GLU>A<C> R<LEU>A<CA> central_sep1 3.93871
+R<GLU>A<C> R<LEU>A<CA> central_sep2 3.07514
+R<GLU>A<C> R<LEU>A<CA> sep1 -2.88999
+R<GLU>A<C> R<LEU>A<CA> sep2 1.71202
+R<GLU>A<C> R<LEU>A<CB> central_sep1 1.80714
+R<GLU>A<C> R<LEU>A<CB> central_sep2 1.77441
+R<GLU>A<C> R<LEU>A<CB> sep1 0.349908
+R<GLU>A<C> R<LEU>A<CB> sep2 0.600373
+R<GLU>A<C> R<LEU>A<CD1> central_sep1 0.825142
+R<GLU>A<C> R<LEU>A<CD1> central_sep2 0.167462
+R<GLU>A<C> R<LEU>A<CD1> sep1 0.457414
+R<GLU>A<C> R<LEU>A<CD1> sep2 -0.187154
+R<GLU>A<C> R<LEU>A<CD2> central_sep1 1.09234
+R<GLU>A<C> R<LEU>A<CD2> central_sep2 0.325191
+R<GLU>A<C> R<LEU>A<CD2> sep1 0.32216
+R<GLU>A<C> R<LEU>A<CD2> sep2 0.0217802
+R<GLU>A<C> R<LEU>A<CG> central_sep1 0.264304
+R<GLU>A<C> R<LEU>A<CG> central_sep2 1.4244
+R<GLU>A<C> R<LEU>A<CG> sep1 -0.941224
+R<GLU>A<C> R<LEU>A<CG> sep2 0.465514
+R<GLU>A<C> R<LEU>A<N> central_sep1 -0.734908
+R<GLU>A<C> R<LEU>A<N> central_sep2 3.32006
+R<GLU>A<C> R<LEU>A<N> sep1 -2.10238
+R<GLU>A<C> R<LEU>A<N> sep2 2.49356
+R<GLU>A<C> R<LEU>A<O> central_sep1 -1.06306
+R<GLU>A<C> R<LEU>A<O> central_sep2 2.90262
+R<GLU>A<C> R<LEU>A<O> sep1 -1.53592
+R<GLU>A<C> R<LEU>A<O> sep2 1.73026
+R<GLU>A<C> R<LYS>A<C> central_sep1 4.08867
+R<GLU>A<C> R<LYS>A<C> central_sep2 4.01402
+R<GLU>A<C> R<LYS>A<C> sep1 -2.70333
+R<GLU>A<C> R<LYS>A<C> sep2 2.6954
+R<GLU>A<C> R<LYS>A<CA> central_sep1 3.48704
+R<GLU>A<C> R<LYS>A<CA> central_sep2 2.07364
+R<GLU>A<C> R<LYS>A<CA> sep1 -2.8795
+R<GLU>A<C> R<LYS>A<CA> sep2 1.19762
+R<GLU>A<C> R<LYS>A<CB> central_sep1 1.7377
+R<GLU>A<C> R<LYS>A<CB> central_sep2 1.24974
+R<GLU>A<C> R<LYS>A<CB> sep1 -0.25057
+R<GLU>A<C> R<LYS>A<CB> sep2 0.177636
+R<GLU>A<C> R<LYS>A<CD> central_sep1 1.41498
+R<GLU>A<C> R<LYS>A<CD> central_sep2 0.905036
+R<GLU>A<C> R<LYS>A<CD> sep1 -0.132296
+R<GLU>A<C> R<LYS>A<CD> sep2 0.0927897
+R<GLU>A<C> R<LYS>A<CE> central_sep1 1.47873
+R<GLU>A<C> R<LYS>A<CE> central_sep2 1.33063
+R<GLU>A<C> R<LYS>A<CE> sep1 0.718708
+R<GLU>A<C> R<LYS>A<CE> sep2 0.121331
+R<GLU>A<C> R<LYS>A<CG> central_sep1 0.510952
+R<GLU>A<C> R<LYS>A<CG> central_sep2 0.830699
+R<GLU>A<C> R<LYS>A<CG> sep1 -0.824316
+R<GLU>A<C> R<LYS>A<CG> sep2 -0.0109342
+R<GLU>A<C> R<LYS>A<N> central_sep1 -1.12951
+R<GLU>A<C> R<LYS>A<N> central_sep2 2.62572
+R<GLU>A<C> R<LYS>A<N> sep1 -1.88558
+R<GLU>A<C> R<LYS>A<N> sep2 1.50632
+R<GLU>A<C> R<LYS>A<NZ> central_sep1 2.27809
+R<GLU>A<C> R<LYS>A<NZ> central_sep2 1.91713
+R<GLU>A<C> R<LYS>A<NZ> sep1 2.03834
+R<GLU>A<C> R<LYS>A<NZ> sep2 0.343526
+R<GLU>A<C> R<LYS>A<O> central_sep1 -0.890713
+R<GLU>A<C> R<LYS>A<O> central_sep2 2.96605
+R<GLU>A<C> R<LYS>A<O> sep1 -1.70833
+R<GLU>A<C> R<LYS>A<O> sep2 1.62717
+R<GLU>A<C> R<MET>A<C> central_sep1 4.81051
+R<GLU>A<C> R<MET>A<C> central_sep2 3.94653
+R<GLU>A<C> R<MET>A<C> sep1 -2.61002
+R<GLU>A<C> R<MET>A<C> sep2 2.45387
+R<GLU>A<C> R<MET>A<CA> central_sep1 4.2175
+R<GLU>A<C> R<MET>A<CA> central_sep2 3.10924
+R<GLU>A<C> R<MET>A<CA> sep1 -2.75589
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+R<GLU>A<C> R<MET>A<CB> central_sep1 2.29928
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+R<GLU>A<C> R<MET>A<CB> sep1 0.00811848
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+R<GLU>A<C> R<MET>A<CE> central_sep1 0.358309
+R<GLU>A<C> R<MET>A<CE> central_sep2 0.246198
+R<GLU>A<C> R<MET>A<CE> sep1 1.1926
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+R<GLU>A<C> R<MET>A<CG> central_sep1 0.751394
+R<GLU>A<C> R<MET>A<CG> central_sep2 0.927321
+R<GLU>A<C> R<MET>A<CG> sep1 -0.490399
+R<GLU>A<C> R<MET>A<CG> sep2 0.127928
+R<GLU>A<C> R<MET>A<N> central_sep1 -0.544442
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+R<GLU>A<C> R<MET>A<N> sep1 -1.92055
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+R<GLU>A<C> R<MET>A<O> sep1 -1.53498
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+R<GLU>A<C> R<MET>A<SD> central_sep1 0.567839
+R<GLU>A<C> R<MET>A<SD> central_sep2 0.317498
+R<GLU>A<C> R<MET>A<SD> sep1 0.48414
+R<GLU>A<C> R<MET>A<SD> sep2 0.0258567
+R<GLU>A<C> R<PHE>A<C> central_sep1 3.00113
+R<GLU>A<C> R<PHE>A<C> central_sep2 4.56879
+R<GLU>A<C> R<PHE>A<C> sep1 -2.59145
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+R<GLU>A<C> R<PHE>A<CA> central_sep1 3.82707
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+R<GLU>A<C> R<PHE>A<CD1> central_sep1 -0.457898
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+R<GLU>A<C> R<PHE>A<CE1> central_sep1 0.836752
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+R<GLU>A<C> R<PHE>A<CE1> sep1 1.66378
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+R<GLU>A<C> R<PHE>A<CG> central_sep1 1.30901
+R<GLU>A<C> R<PHE>A<CG> central_sep2 1.54526
+R<GLU>A<C> R<PHE>A<CG> sep1 -1.65401
+R<GLU>A<C> R<PHE>A<CG> sep2 0.813969
+R<GLU>A<C> R<PHE>A<CZ> central_sep1 1.90962
+R<GLU>A<C> R<PHE>A<CZ> central_sep2 0.0999365
+R<GLU>A<C> R<PHE>A<CZ> sep1 2.59811
+R<GLU>A<C> R<PHE>A<CZ> sep2 -0.275738
+R<GLU>A<C> R<PHE>A<N> central_sep1 -0.68645
+R<GLU>A<C> R<PHE>A<N> central_sep2 3.43247
+R<GLU>A<C> R<PHE>A<N> sep1 -1.98259
+R<GLU>A<C> R<PHE>A<N> sep2 2.13302
+R<GLU>A<C> R<PHE>A<O> central_sep1 -0.916492
+R<GLU>A<C> R<PHE>A<O> central_sep2 2.84936
+R<GLU>A<C> R<PHE>A<O> sep1 -1.36306
+R<GLU>A<C> R<PHE>A<O> sep2 1.60008
+R<GLU>A<C> R<PRO>A<C> central_sep1 3.11814
+R<GLU>A<C> R<PRO>A<C> central_sep2 3.99721
+R<GLU>A<C> R<PRO>A<C> sep1 -2.43474
+R<GLU>A<C> R<PRO>A<C> sep2 2.56893
+R<GLU>A<C> R<PRO>A<CA> central_sep1 3.40419
+R<GLU>A<C> R<PRO>A<CA> central_sep2 1.98376
+R<GLU>A<C> R<PRO>A<CA> sep1 -2.02804
+R<GLU>A<C> R<PRO>A<CA> sep2 0.643854
+R<GLU>A<C> R<PRO>A<CB> central_sep1 1.85855
+R<GLU>A<C> R<PRO>A<CB> central_sep2 0.871701
+R<GLU>A<C> R<PRO>A<CB> sep1 1.51973
+R<GLU>A<C> R<PRO>A<CB> sep2 0.146374
+R<GLU>A<C> R<PRO>A<CD> central_sep1 -0.360763
+R<GLU>A<C> R<PRO>A<CD> central_sep2 1.37976
+R<GLU>A<C> R<PRO>A<CD> sep1 -0.698045
+R<GLU>A<C> R<PRO>A<CD> sep2 0.428477
+R<GLU>A<C> R<PRO>A<CG> central_sep1 1.83524
+R<GLU>A<C> R<PRO>A<CG> central_sep2 0.660322
+R<GLU>A<C> R<PRO>A<CG> sep1 2.34612
+R<GLU>A<C> R<PRO>A<CG> sep2 0.0157452
+R<GLU>A<C> R<PRO>A<N> central_sep1 1.26871
+R<GLU>A<C> R<PRO>A<N> central_sep2 1.54365
+R<GLU>A<C> R<PRO>A<N> sep1 -0.955909
+R<GLU>A<C> R<PRO>A<N> sep2 1.44465
+R<GLU>A<C> R<PRO>A<O> central_sep1 -1.07686
+R<GLU>A<C> R<PRO>A<O> central_sep2 3.09942
+R<GLU>A<C> R<PRO>A<O> sep1 -2.01709
+R<GLU>A<C> R<PRO>A<O> sep2 1.82001
+R<GLU>A<C> R<SER>A<C> central_sep1 4.70359
+R<GLU>A<C> R<SER>A<C> central_sep2 3.30779
+R<GLU>A<C> R<SER>A<C> sep1 -2.18552
+R<GLU>A<C> R<SER>A<C> sep2 2.19062
+R<GLU>A<C> R<SER>A<CA> central_sep1 4.08836
+R<GLU>A<C> R<SER>A<CA> central_sep2 2.55329
+R<GLU>A<C> R<SER>A<CA> sep1 -2.36043
+R<GLU>A<C> R<SER>A<CA> sep2 0.836409
+R<GLU>A<C> R<SER>A<CB> central_sep1 2.49264
+R<GLU>A<C> R<SER>A<CB> central_sep2 1.32924
+R<GLU>A<C> R<SER>A<CB> sep1 0.0905633
+R<GLU>A<C> R<SER>A<CB> sep2 0.28481
+R<GLU>A<C> R<SER>A<N> central_sep1 -0.4624
+R<GLU>A<C> R<SER>A<N> central_sep2 3.03269
+R<GLU>A<C> R<SER>A<N> sep1 -1.46633
+R<GLU>A<C> R<SER>A<N> sep2 1.70664
+R<GLU>A<C> R<SER>A<O> central_sep1 -0.59943
+R<GLU>A<C> R<SER>A<O> central_sep2 2.69697
+R<GLU>A<C> R<SER>A<O> sep1 -1.38872
+R<GLU>A<C> R<SER>A<O> sep2 1.6883
+R<GLU>A<C> R<SER>A<OG> central_sep1 2.05424
+R<GLU>A<C> R<SER>A<OG> central_sep2 1.7462
+R<GLU>A<C> R<SER>A<OG> sep1 0.53665
+R<GLU>A<C> R<SER>A<OG> sep2 0.731409
+R<GLU>A<C> R<THR>A<C> central_sep1 5.01517
+R<GLU>A<C> R<THR>A<C> central_sep2 4.32713
+R<GLU>A<C> R<THR>A<C> sep1 -2.42066
+R<GLU>A<C> R<THR>A<C> sep2 2.44065
+R<GLU>A<C> R<THR>A<CA> central_sep1 4.22914
+R<GLU>A<C> R<THR>A<CA> central_sep2 3.24031
+R<GLU>A<C> R<THR>A<CA> sep1 -2.61477
+R<GLU>A<C> R<THR>A<CA> sep2 1.40876
+R<GLU>A<C> R<THR>A<CB> central_sep1 2.33256
+R<GLU>A<C> R<THR>A<CB> central_sep2 1.54511
+R<GLU>A<C> R<THR>A<CB> sep1 0.191756
+R<GLU>A<C> R<THR>A<CB> sep2 0.256283
+R<GLU>A<C> R<THR>A<CG2> central_sep1 0.927023
+R<GLU>A<C> R<THR>A<CG2> central_sep2 0.895
+R<GLU>A<C> R<THR>A<CG2> sep1 -0.23253
+R<GLU>A<C> R<THR>A<CG2> sep2 -0.00256001
+R<GLU>A<C> R<THR>A<N> central_sep1 -0.349395
+R<GLU>A<C> R<THR>A<N> central_sep2 3.62636
+R<GLU>A<C> R<THR>A<N> sep1 -1.49688
+R<GLU>A<C> R<THR>A<N> sep2 2.28498
+R<GLU>A<C> R<THR>A<O> central_sep1 -0.785586
+R<GLU>A<C> R<THR>A<O> central_sep2 2.49992
+R<GLU>A<C> R<THR>A<O> sep1 -1.29165
+R<GLU>A<C> R<THR>A<O> sep2 1.6628
+R<GLU>A<C> R<THR>A<OG1> central_sep1 1.97071
+R<GLU>A<C> R<THR>A<OG1> central_sep2 1.50535
+R<GLU>A<C> R<THR>A<OG1> sep1 -0.0133314
+R<GLU>A<C> R<THR>A<OG1> sep2 0.652093
+R<GLU>A<C> R<TRP>A<C> central_sep1 3.71636
+R<GLU>A<C> R<TRP>A<C> central_sep2 4.80187
+R<GLU>A<C> R<TRP>A<C> sep1 -2.63303
+R<GLU>A<C> R<TRP>A<C> sep2 2.92988
+R<GLU>A<C> R<TRP>A<CA> central_sep1 3.74198
+R<GLU>A<C> R<TRP>A<CA> central_sep2 2.93489
+R<GLU>A<C> R<TRP>A<CA> sep1 -2.73883
+R<GLU>A<C> R<TRP>A<CA> sep2 1.35629
+R<GLU>A<C> R<TRP>A<CB> central_sep1 1.77784
+R<GLU>A<C> R<TRP>A<CB> central_sep2 1.16727
+R<GLU>A<C> R<TRP>A<CB> sep1 0.0117419
+R<GLU>A<C> R<TRP>A<CB> sep2 0.0827873
+R<GLU>A<C> R<TRP>A<CD1> central_sep1 -0.560657
+R<GLU>A<C> R<TRP>A<CD1> central_sep2 0.417866
+R<GLU>A<C> R<TRP>A<CD1> sep1 -0.475731
+R<GLU>A<C> R<TRP>A<CD1> sep2 -0.24038
+R<GLU>A<C> R<TRP>A<CD2> central_sep1 -0.173726
+R<GLU>A<C> R<TRP>A<CD2> central_sep2 1.52322
+R<GLU>A<C> R<TRP>A<CD2> sep1 -0.132094
+R<GLU>A<C> R<TRP>A<CD2> sep2 0.899699
+R<GLU>A<C> R<TRP>A<CE2> central_sep1 0.440243
+R<GLU>A<C> R<TRP>A<CE2> central_sep2 1.58586
+R<GLU>A<C> R<TRP>A<CE2> sep1 1.24598
+R<GLU>A<C> R<TRP>A<CE2> sep2 0.173014
+R<GLU>A<C> R<TRP>A<CE3> central_sep1 -0.242855
+R<GLU>A<C> R<TRP>A<CE3> central_sep2 -0.28791
+R<GLU>A<C> R<TRP>A<CE3> sep1 0.783205
+R<GLU>A<C> R<TRP>A<CE3> sep2 0.168237
+R<GLU>A<C> R<TRP>A<CG> central_sep1 1.6532
+R<GLU>A<C> R<TRP>A<CG> central_sep2 1.50692
+R<GLU>A<C> R<TRP>A<CG> sep1 -0.891997
+R<GLU>A<C> R<TRP>A<CG> sep2 0.688421
+R<GLU>A<C> R<TRP>A<CH2> central_sep1 2.35041
+R<GLU>A<C> R<TRP>A<CH2> central_sep2 -0.0290282
+R<GLU>A<C> R<TRP>A<CH2> sep1 3.19247
+R<GLU>A<C> R<TRP>A<CH2> sep2 -0.575096
+R<GLU>A<C> R<TRP>A<CZ2> central_sep1 2.03241
+R<GLU>A<C> R<TRP>A<CZ2> central_sep2 -0.108883
+R<GLU>A<C> R<TRP>A<CZ2> sep1 2.91153
+R<GLU>A<C> R<TRP>A<CZ2> sep2 -0.569632
+R<GLU>A<C> R<TRP>A<CZ3> central_sep1 1.36193
+R<GLU>A<C> R<TRP>A<CZ3> central_sep2 -0.0724955
+R<GLU>A<C> R<TRP>A<CZ3> sep1 2.16332
+R<GLU>A<C> R<TRP>A<CZ3> sep2 -0.432592
+R<GLU>A<C> R<TRP>A<N> central_sep1 -0.677482
+R<GLU>A<C> R<TRP>A<N> central_sep2 2.38601
+R<GLU>A<C> R<TRP>A<N> sep1 -1.79102
+R<GLU>A<C> R<TRP>A<N> sep2 1.93209
+R<GLU>A<C> R<TRP>A<NE1> central_sep1 1.69607
+R<GLU>A<C> R<TRP>A<NE1> central_sep2 0.807679
+R<GLU>A<C> R<TRP>A<NE1> sep1 1.71456
+R<GLU>A<C> R<TRP>A<NE1> sep2 -0.0528923
+R<GLU>A<C> R<TRP>A<O> central_sep1 -0.956992
+R<GLU>A<C> R<TRP>A<O> central_sep2 3.18313
+R<GLU>A<C> R<TRP>A<O> sep1 -1.4045
+R<GLU>A<C> R<TRP>A<O> sep2 2.15938
+R<GLU>A<C> R<TYR>A<C> central_sep1 3.6068
+R<GLU>A<C> R<TYR>A<C> central_sep2 4.15269
+R<GLU>A<C> R<TYR>A<C> sep1 -2.47295
+R<GLU>A<C> R<TYR>A<C> sep2 2.87341
+R<GLU>A<C> R<TYR>A<CA> central_sep1 3.86408
+R<GLU>A<C> R<TYR>A<CA> central_sep2 2.64323
+R<GLU>A<C> R<TYR>A<CA> sep1 -2.63091
+R<GLU>A<C> R<TYR>A<CA> sep2 1.09478
+R<GLU>A<C> R<TYR>A<CB> central_sep1 2.09178
+R<GLU>A<C> R<TYR>A<CB> central_sep2 1.20913
+R<GLU>A<C> R<TYR>A<CB> sep1 0.0119331
+R<GLU>A<C> R<TYR>A<CB> sep2 0.178242
+R<GLU>A<C> R<TYR>A<CD1> central_sep1 -0.49839
+R<GLU>A<C> R<TYR>A<CD1> central_sep2 0.114435
+R<GLU>A<C> R<TYR>A<CD1> sep1 -0.368986
+R<GLU>A<C> R<TYR>A<CD1> sep2 -0.188355
+R<GLU>A<C> R<TYR>A<CE1> central_sep1 0.74998
+R<GLU>A<C> R<TYR>A<CE1> central_sep2 0.384744
+R<GLU>A<C> R<TYR>A<CE1> sep1 1.53149
+R<GLU>A<C> R<TYR>A<CE1> sep2 -0.16047
+R<GLU>A<C> R<TYR>A<CG> central_sep1 1.19036
+R<GLU>A<C> R<TYR>A<CG> central_sep2 1.37135
+R<GLU>A<C> R<TYR>A<CG> sep1 -1.62888
+R<GLU>A<C> R<TYR>A<CG> sep2 0.483024
+R<GLU>A<C> R<TYR>A<CZ> central_sep1 1.12375
+R<GLU>A<C> R<TYR>A<CZ> central_sep2 0.801171
+R<GLU>A<C> R<TYR>A<CZ> sep1 1.6561
+R<GLU>A<C> R<TYR>A<CZ> sep2 -0.156614
+R<GLU>A<C> R<TYR>A<N> central_sep1 -0.690503
+R<GLU>A<C> R<TYR>A<N> central_sep2 3.1599
+R<GLU>A<C> R<TYR>A<N> sep1 -1.84441
+R<GLU>A<C> R<TYR>A<N> sep2 2.23682
+R<GLU>A<C> R<TYR>A<O> central_sep1 -0.810464
+R<GLU>A<C> R<TYR>A<O> central_sep2 3.0858
+R<GLU>A<C> R<TYR>A<O> sep1 -1.29894
+R<GLU>A<C> R<TYR>A<O> sep2 1.65439
+R<GLU>A<C> R<TYR>A<OH> central_sep1 3.09041
+R<GLU>A<C> R<TYR>A<OH> central_sep2 0.900533
+R<GLU>A<C> R<TYR>A<OH> sep1 3.68471
+R<GLU>A<C> R<TYR>A<OH> sep2 0.0118911
+R<GLU>A<C> R<VAL>A<C> central_sep1 5.22083
+R<GLU>A<C> R<VAL>A<C> central_sep2 4.69965
+R<GLU>A<C> R<VAL>A<C> sep1 -2.81261
+R<GLU>A<C> R<VAL>A<C> sep2 3.56144
+R<GLU>A<C> R<VAL>A<CA> central_sep1 4.48
+R<GLU>A<C> R<VAL>A<CA> central_sep2 3.43728
+R<GLU>A<C> R<VAL>A<CA> sep1 -2.79684
+R<GLU>A<C> R<VAL>A<CA> sep2 1.53443
+R<GLU>A<C> R<VAL>A<CB> central_sep1 2.12011
+R<GLU>A<C> R<VAL>A<CB> central_sep2 1.31482
+R<GLU>A<C> R<VAL>A<CB> sep1 0.13544
+R<GLU>A<C> R<VAL>A<CB> sep2 -0.171026
+R<GLU>A<C> R<VAL>A<CG1> central_sep1 0.305384
+R<GLU>A<C> R<VAL>A<CG1> central_sep2 0.592949
+R<GLU>A<C> R<VAL>A<CG1> sep1 -0.244117
+R<GLU>A<C> R<VAL>A<CG1> sep2 -0.196534
+R<GLU>A<C> R<VAL>A<CG2> central_sep1 0.815281
+R<GLU>A<C> R<VAL>A<CG2> central_sep2 0.576495
+R<GLU>A<C> R<VAL>A<CG2> sep1 -0.687601
+R<GLU>A<C> R<VAL>A<CG2> sep2 -0.0428264
+R<GLU>A<C> R<VAL>A<N> central_sep1 -0.222146
+R<GLU>A<C> R<VAL>A<N> central_sep2 3.54426
+R<GLU>A<C> R<VAL>A<N> sep1 -1.8324
+R<GLU>A<C> R<VAL>A<N> sep2 2.447
+R<GLU>A<C> R<VAL>A<O> central_sep1 -0.885535
+R<GLU>A<C> R<VAL>A<O> central_sep2 2.8459
+R<GLU>A<C> R<VAL>A<O> sep1 -1.34086
+R<GLU>A<C> R<VAL>A<O> sep2 1.76766
+R<GLU>A<C> c<solvent> . 1.80406
+R<GLU>A<CA> R<GLU>A<CA> central_sep1 2.23196
+R<GLU>A<CA> R<GLU>A<CA> central_sep2 1.15199
+R<GLU>A<CA> R<GLU>A<CA> sep1 2.42687
+R<GLU>A<CA> R<GLU>A<CA> sep2 1.98813
+R<GLU>A<CA> R<GLU>A<CB> central_sep1 -1.16307
+R<GLU>A<CA> R<GLU>A<CB> central_sep2 1.50198
+R<GLU>A<CA> R<GLU>A<CB> sep1 1.04156
+R<GLU>A<CA> R<GLU>A<CB> sep2 1.49998
+R<GLU>A<CA> R<GLU>A<CD> central_sep1 -0.0125721
+R<GLU>A<CA> R<GLU>A<CD> central_sep2 1.16188
+R<GLU>A<CA> R<GLU>A<CD> sep1 0.498709
+R<GLU>A<CA> R<GLU>A<CD> sep2 0.775609
+R<GLU>A<CA> R<GLU>A<CG> central_sep1 0.584766
+R<GLU>A<CA> R<GLU>A<CG> central_sep2 1.30831
+R<GLU>A<CA> R<GLU>A<CG> sep1 0.50471
+R<GLU>A<CA> R<GLU>A<CG> sep2 1.45474
+R<GLU>A<CA> R<GLU>A<N> central_sep1 3.33995
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+R<GLU>A<CG> R<HIS>A<CE1> sep1 0.88226
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+R<GLU>A<CG> R<HIS>A<ND1> sep1 0.601313
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+R<GLU>A<OE1> R<THR>A<C> sep1 1.93244
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+R<GLU>A<OE1> R<THR>A<CA> central_sep1 0.571977
+R<GLU>A<OE1> R<THR>A<CA> central_sep2 0.885841
+R<GLU>A<OE1> R<THR>A<CA> sep1 1.8266
+R<GLU>A<OE1> R<THR>A<CA> sep2 0.578659
+R<GLU>A<OE1> R<THR>A<CB> central_sep1 -0.251711
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+R<GLU>A<OE1> R<THR>A<CB> sep1 0.971605
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+R<GLU>A<OE1> R<THR>A<CG2> sep1 1.03129
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+R<GLU>A<OE1> R<THR>A<N> sep1 1.97398
+R<GLU>A<OE1> R<THR>A<N> sep2 0.836468
+R<GLU>A<OE1> R<THR>A<O> central_sep1 1.4886
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+R<GLU>A<OE1> R<THR>A<O> sep1 1.68706
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+R<GLU>A<OE1> R<THR>A<OG1> central_sep1 0.133505
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+R<GLU>A<OE1> R<THR>A<OG1> sep1 1.03928
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+R<GLU>A<OE1> R<TRP>A<C> sep1 2.23953
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+R<GLU>A<OE1> R<TRP>A<CA> central_sep1 0.247543
+R<GLU>A<OE1> R<TRP>A<CA> central_sep2 1.37014
+R<GLU>A<OE1> R<TRP>A<CA> sep1 1.78465
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+R<GLU>A<OE1> R<TRP>A<CB> central_sep1 0.691868
+R<GLU>A<OE1> R<TRP>A<CB> central_sep2 0.255733
+R<GLU>A<OE1> R<TRP>A<CB> sep1 2.05601
+R<GLU>A<OE1> R<TRP>A<CB> sep2 0.359681
+R<GLU>A<OE1> R<TRP>A<CD1> central_sep1 0.0439582
+R<GLU>A<OE1> R<TRP>A<CD1> central_sep2 0.26245
+R<GLU>A<OE1> R<TRP>A<CD1> sep1 1.18956
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+R<GLU>A<OE1> R<TRP>A<CD2> sep1 2.74503
+R<GLU>A<OE1> R<TRP>A<CD2> sep2 0.454984
+R<GLU>A<OE1> R<TRP>A<CE2> central_sep1 2.60738
+R<GLU>A<OE1> R<TRP>A<CE2> central_sep2 2.04805
+R<GLU>A<OE1> R<TRP>A<CE2> sep1 2.10149
+R<GLU>A<OE1> R<TRP>A<CE2> sep2 0.226403
+R<GLU>A<OE1> R<TRP>A<CE3> central_sep1 1.08219
+R<GLU>A<OE1> R<TRP>A<CE3> central_sep2 0.934494
+R<GLU>A<OE1> R<TRP>A<CE3> sep1 2.33146
+R<GLU>A<OE1> R<TRP>A<CE3> sep2 0.576933
+R<GLU>A<OE1> R<TRP>A<CG> central_sep1 3.43699
+R<GLU>A<OE1> R<TRP>A<CG> central_sep2 2.2059
+R<GLU>A<OE1> R<TRP>A<CG> sep1 2.10337
+R<GLU>A<OE1> R<TRP>A<CG> sep2 0.107956
+R<GLU>A<OE1> R<TRP>A<CH2> central_sep1 1.86998
+R<GLU>A<OE1> R<TRP>A<CH2> central_sep2 0.11912
+R<GLU>A<OE1> R<TRP>A<CH2> sep1 1.80707
+R<GLU>A<OE1> R<TRP>A<CH2> sep2 -0.564299
+R<GLU>A<OE1> R<TRP>A<CZ2> central_sep1 0.683121
+R<GLU>A<OE1> R<TRP>A<CZ2> central_sep2 -0.403522
+R<GLU>A<OE1> R<TRP>A<CZ2> sep1 0.974293
+R<GLU>A<OE1> R<TRP>A<CZ2> sep2 -0.905025
+R<GLU>A<OE1> R<TRP>A<CZ3> central_sep1 1.06849
+R<GLU>A<OE1> R<TRP>A<CZ3> central_sep2 0.567013
+R<GLU>A<OE1> R<TRP>A<CZ3> sep1 1.85065
+R<GLU>A<OE1> R<TRP>A<CZ3> sep2 0.031871
+R<GLU>A<OE1> R<TRP>A<N> central_sep1 1.09749
+R<GLU>A<OE1> R<TRP>A<N> central_sep2 0.661104
+R<GLU>A<OE1> R<TRP>A<N> sep1 2.03801
+R<GLU>A<OE1> R<TRP>A<N> sep2 0.731441
+R<GLU>A<OE1> R<TRP>A<NE1> central_sep1 -0.519996
+R<GLU>A<OE1> R<TRP>A<NE1> central_sep2 -1.20538
+R<GLU>A<OE1> R<TRP>A<NE1> sep1 0.991922
+R<GLU>A<OE1> R<TRP>A<NE1> sep2 -0.626895
+R<GLU>A<OE1> R<TRP>A<O> central_sep1 1.69368
+R<GLU>A<OE1> R<TRP>A<O> central_sep2 1.4991
+R<GLU>A<OE1> R<TRP>A<O> sep1 1.81985
+R<GLU>A<OE1> R<TRP>A<O> sep2 0.944236
+R<GLU>A<OE1> R<TYR>A<C> central_sep1 2.21401
+R<GLU>A<OE1> R<TYR>A<C> central_sep2 2.4481
+R<GLU>A<OE1> R<TYR>A<C> sep1 2.12807
+R<GLU>A<OE1> R<TYR>A<C> sep2 1.52865
+R<GLU>A<OE1> R<TYR>A<CA> central_sep1 0.426348
+R<GLU>A<OE1> R<TYR>A<CA> central_sep2 1.09094
+R<GLU>A<OE1> R<TYR>A<CA> sep1 1.8855
+R<GLU>A<OE1> R<TYR>A<CA> sep2 1.09192
+R<GLU>A<OE1> R<TYR>A<CB> central_sep1 0.745337
+R<GLU>A<OE1> R<TYR>A<CB> central_sep2 0.405062
+R<GLU>A<OE1> R<TYR>A<CB> sep1 1.98596
+R<GLU>A<OE1> R<TYR>A<CB> sep2 0.397007
+R<GLU>A<OE1> R<TYR>A<CD1> central_sep1 0.414398
+R<GLU>A<OE1> R<TYR>A<CD1> central_sep2 0.651717
+R<GLU>A<OE1> R<TYR>A<CD1> sep1 1.76005
+R<GLU>A<OE1> R<TYR>A<CD1> sep2 0.242827
+R<GLU>A<OE1> R<TYR>A<CE1> central_sep1 0.359789
+R<GLU>A<OE1> R<TYR>A<CE1> central_sep2 -0.5816
+R<GLU>A<OE1> R<TYR>A<CE1> sep1 1.18624
+R<GLU>A<OE1> R<TYR>A<CE1> sep2 -0.371724
+R<GLU>A<OE1> R<TYR>A<CG> central_sep1 3.80082
+R<GLU>A<OE1> R<TYR>A<CG> central_sep2 2.10119
+R<GLU>A<OE1> R<TYR>A<CG> sep1 2.11655
+R<GLU>A<OE1> R<TYR>A<CG> sep2 0.118723
+R<GLU>A<OE1> R<TYR>A<CZ> central_sep1 1.55899
+R<GLU>A<OE1> R<TYR>A<CZ> central_sep2 1.67272
+R<GLU>A<OE1> R<TYR>A<CZ> sep1 1.54708
+R<GLU>A<OE1> R<TYR>A<CZ> sep2 -0.61158
+R<GLU>A<OE1> R<TYR>A<N> central_sep1 1.15851
+R<GLU>A<OE1> R<TYR>A<N> central_sep2 0.643432
+R<GLU>A<OE1> R<TYR>A<N> sep1 2.13227
+R<GLU>A<OE1> R<TYR>A<N> sep2 0.970057
+R<GLU>A<OE1> R<TYR>A<O> central_sep1 1.75917
+R<GLU>A<OE1> R<TYR>A<O> central_sep2 1.51598
+R<GLU>A<OE1> R<TYR>A<O> sep1 1.85777
+R<GLU>A<OE1> R<TYR>A<O> sep2 1.17833
+R<GLU>A<OE1> R<TYR>A<OH> central_sep1 0.14846
+R<GLU>A<OE1> R<TYR>A<OH> central_sep2 -1.30659
+R<GLU>A<OE1> R<TYR>A<OH> sep1 1.24263
+R<GLU>A<OE1> R<TYR>A<OH> sep2 -0.755768
+R<GLU>A<OE1> R<VAL>A<C> central_sep1 2.65677
+R<GLU>A<OE1> R<VAL>A<C> central_sep2 2.7003
+R<GLU>A<OE1> R<VAL>A<C> sep1 2.3085
+R<GLU>A<OE1> R<VAL>A<C> sep2 1.71855
+R<GLU>A<OE1> R<VAL>A<CA> central_sep1 0.717129
+R<GLU>A<OE1> R<VAL>A<CA> central_sep2 1.3701
+R<GLU>A<OE1> R<VAL>A<CA> sep1 1.9017
+R<GLU>A<OE1> R<VAL>A<CA> sep2 1.11786
+R<GLU>A<OE1> R<VAL>A<CB> central_sep1 0.864615
+R<GLU>A<OE1> R<VAL>A<CB> central_sep2 0.628723
+R<GLU>A<OE1> R<VAL>A<CB> sep1 1.77326
+R<GLU>A<OE1> R<VAL>A<CB> sep2 0.111082
+R<GLU>A<OE1> R<VAL>A<CG1> central_sep1 0.517811
+R<GLU>A<OE1> R<VAL>A<CG1> central_sep2 0.454397
+R<GLU>A<OE1> R<VAL>A<CG1> sep1 1.5383
+R<GLU>A<OE1> R<VAL>A<CG1> sep2 0.265297
+R<GLU>A<OE1> R<VAL>A<CG2> central_sep1 0.86608
+R<GLU>A<OE1> R<VAL>A<CG2> central_sep2 0.472661
+R<GLU>A<OE1> R<VAL>A<CG2> sep1 1.93625
+R<GLU>A<OE1> R<VAL>A<CG2> sep2 0.239178
+R<GLU>A<OE1> R<VAL>A<N> central_sep1 1.37256
+R<GLU>A<OE1> R<VAL>A<N> central_sep2 0.849197
+R<GLU>A<OE1> R<VAL>A<N> sep1 2.17391
+R<GLU>A<OE1> R<VAL>A<N> sep2 1.05028
+R<GLU>A<OE1> R<VAL>A<O> central_sep1 1.63826
+R<GLU>A<OE1> R<VAL>A<O> central_sep2 1.43216
+R<GLU>A<OE1> R<VAL>A<O> sep1 1.82169
+R<GLU>A<OE1> R<VAL>A<O> sep2 1.14119
+R<GLU>A<OE1> c<solvent> . -0.661627
+R<GLY>A<C> R<GLY>A<C> central_sep1 2.02935
+R<GLY>A<C> R<GLY>A<C> central_sep2 0.154217
+R<GLY>A<C> R<GLY>A<C> sep1 -1.28874
+R<GLY>A<C> R<GLY>A<C> sep2 0.19708
+R<GLY>A<C> R<GLY>A<CA> central_sep1 1.38031
+R<GLY>A<C> R<GLY>A<CA> central_sep2 0.105069
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+R<GLY>A<C> R<THR>A<N> central_sep1 -0.118505
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+R<GLY>A<C> R<THR>A<N> sep1 -1.40556
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+R<GLY>A<C> R<THR>A<O> central_sep1 0.0354371
+R<GLY>A<C> R<THR>A<O> central_sep2 1.30689
+R<GLY>A<C> R<THR>A<O> sep1 -1.57711
+R<GLY>A<C> R<THR>A<O> sep2 0.326052
+R<GLY>A<C> R<THR>A<OG1> central_sep1 0.907058
+R<GLY>A<C> R<THR>A<OG1> central_sep2 0.27498
+R<GLY>A<C> R<THR>A<OG1> sep1 -0.481297
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+R<GLY>A<C> R<TRP>A<C> central_sep1 3.04008
+R<GLY>A<C> R<TRP>A<C> central_sep2 2.33952
+R<GLY>A<C> R<TRP>A<C> sep1 -2.19601
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+R<GLY>A<C> R<TRP>A<CA> sep1 -2.49735
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+R<GLY>A<C> R<TRP>A<CG> central_sep1 0.834726
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+R<GLY>A<C> R<TYR>A<C> central_sep2 2.00999
+R<GLY>A<C> R<TYR>A<C> sep1 -2.15641
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+R<GLY>A<C> R<TYR>A<CA> central_sep2 1.12686
+R<GLY>A<C> R<TYR>A<CA> sep1 -2.46635
+R<GLY>A<C> R<TYR>A<CA> sep2 0.208977
+R<GLY>A<C> R<TYR>A<CB> central_sep1 0.783419
+R<GLY>A<C> R<TYR>A<CB> central_sep2 0.0429553
+R<GLY>A<C> R<TYR>A<CB> sep1 -0.0785399
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+R<GLY>A<C> R<TYR>A<CD1> central_sep1 -0.636729
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+R<GLY>A<C> R<TYR>A<CZ> sep1 0.920145
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+R<GLY>A<C> R<TYR>A<N> sep1 -1.36794
+R<GLY>A<C> R<TYR>A<N> sep2 0.762705
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+R<GLY>A<C> R<TYR>A<O> sep2 0.354739
+R<GLY>A<C> R<TYR>A<OH> central_sep1 1.47629
+R<GLY>A<C> R<TYR>A<OH> central_sep2 0.00491748
+R<GLY>A<C> R<TYR>A<OH> sep1 2.39706
+R<GLY>A<C> R<TYR>A<OH> sep2 -0.696612
+R<GLY>A<C> R<VAL>A<C> central_sep1 3.66199
+R<GLY>A<C> R<VAL>A<C> central_sep2 3.12382
+R<GLY>A<C> R<VAL>A<C> sep1 -2.37017
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+R<GLY>A<C> R<VAL>A<CA> central_sep1 2.23771
+R<GLY>A<C> R<VAL>A<CA> central_sep2 1.62522
+R<GLY>A<C> R<VAL>A<CA> sep1 -2.47119
+R<GLY>A<C> R<VAL>A<CA> sep2 0.30595
+R<GLY>A<C> R<VAL>A<CB> central_sep1 0.786841
+R<GLY>A<C> R<VAL>A<CB> central_sep2 0.0231039
+R<GLY>A<C> R<VAL>A<CB> sep1 0.238411
+R<GLY>A<C> R<VAL>A<CB> sep2 -0.854293
+R<GLY>A<C> R<VAL>A<CG1> central_sep1 0.0828621
+R<GLY>A<C> R<VAL>A<CG1> central_sep2 -0.302496
+R<GLY>A<C> R<VAL>A<CG1> sep1 -0.0310485
+R<GLY>A<C> R<VAL>A<CG1> sep2 -0.697968
+R<GLY>A<C> R<VAL>A<CG2> central_sep1 0.537295
+R<GLY>A<C> R<VAL>A<CG2> central_sep2 -0.251421
+R<GLY>A<C> R<VAL>A<CG2> sep1 -0.627245
+R<GLY>A<C> R<VAL>A<CG2> sep2 -0.600061
+R<GLY>A<C> R<VAL>A<N> central_sep1 0.27916
+R<GLY>A<C> R<VAL>A<N> central_sep2 1.73668
+R<GLY>A<C> R<VAL>A<N> sep1 -1.22217
+R<GLY>A<C> R<VAL>A<N> sep2 0.546238
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+R<GLY>A<C> R<VAL>A<O> central_sep2 1.44446
+R<GLY>A<C> R<VAL>A<O> sep1 -1.22909
+R<GLY>A<C> R<VAL>A<O> sep2 0.259086
+R<GLY>A<C> c<solvent> . 1.11007
+R<GLY>A<CA> R<GLY>A<CA> central_sep1 1.45793
+R<GLY>A<CA> R<GLY>A<CA> central_sep2 -0.433677
+R<GLY>A<CA> R<GLY>A<CA> sep1 2.29172
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+R<GLY>A<CA> R<GLY>A<N> central_sep2 0.23134
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+R<GLY>A<CA> R<GLY>A<O> central_sep1 0.513014
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+R<GLY>A<CA> R<GLY>A<O> sep2 -0.00597487
+R<GLY>A<CA> R<HIS>A<C> central_sep1 2.86384
+R<GLY>A<CA> R<HIS>A<C> central_sep2 0.872082
+R<GLY>A<CA> R<HIS>A<C> sep1 -1.839
+R<GLY>A<CA> R<HIS>A<C> sep2 -0.154608
+R<GLY>A<CA> R<HIS>A<CA> central_sep1 1.87013
+R<GLY>A<CA> R<HIS>A<CA> central_sep2 0.38368
+R<GLY>A<CA> R<HIS>A<CA> sep1 1.8269
+R<GLY>A<CA> R<HIS>A<CA> sep2 0.380971
+R<GLY>A<CA> R<HIS>A<CB> central_sep1 0.660054
+R<GLY>A<CA> R<HIS>A<CB> central_sep2 -0.256162
+R<GLY>A<CA> R<HIS>A<CB> sep1 2.0625
+R<GLY>A<CA> R<HIS>A<CB> sep2 0.0166153
+R<GLY>A<CA> R<HIS>A<CD2> central_sep1 0.761995
+R<GLY>A<CA> R<HIS>A<CD2> central_sep2 -0.339724
+R<GLY>A<CA> R<HIS>A<CD2> sep1 0.577133
+R<GLY>A<CA> R<HIS>A<CD2> sep2 -0.123761
+R<GLY>A<CA> R<HIS>A<CE1> central_sep1 0.444482
+R<GLY>A<CA> R<HIS>A<CE1> central_sep2 -0.449816
+R<GLY>A<CA> R<HIS>A<CE1> sep1 1.16457
+R<GLY>A<CA> R<HIS>A<CE1> sep2 -0.312731
+R<GLY>A<CA> R<HIS>A<CG> central_sep1 1.66434
+R<GLY>A<CA> R<HIS>A<CG> central_sep2 -0.596104
+R<GLY>A<CA> R<HIS>A<CG> sep1 1.5462
+R<GLY>A<CA> R<HIS>A<CG> sep2 -1.15412
+R<GLY>A<CA> R<HIS>A<N> central_sep1 2.32967
+R<GLY>A<CA> R<HIS>A<N> central_sep2 0.8997
+R<GLY>A<CA> R<HIS>A<N> sep1 -1.49799
+R<GLY>A<CA> R<HIS>A<N> sep2 0.753255
+R<GLY>A<CA> R<HIS>A<ND1> central_sep1 0.887436
+R<GLY>A<CA> R<HIS>A<ND1> central_sep2 -0.179115
+R<GLY>A<CA> R<HIS>A<ND1> sep1 0.478425
+R<GLY>A<CA> R<HIS>A<ND1> sep2 -0.619398
+R<GLY>A<CA> R<HIS>A<NE2> central_sep1 0.71907
+R<GLY>A<CA> R<HIS>A<NE2> central_sep2 -0.224653
+R<GLY>A<CA> R<HIS>A<NE2> sep1 1.13132
+R<GLY>A<CA> R<HIS>A<NE2> sep2 -0.634051
+R<GLY>A<CA> R<HIS>A<O> central_sep1 0.551226
+R<GLY>A<CA> R<HIS>A<O> central_sep2 -0.485727
+R<GLY>A<CA> R<HIS>A<O> sep1 -1.46838
+R<GLY>A<CA> R<HIS>A<O> sep2 0.457887
+R<GLY>A<CA> R<ILE>A<C> central_sep1 3.41614
+R<GLY>A<CA> R<ILE>A<C> central_sep2 1.74738
+R<GLY>A<CA> R<ILE>A<C> sep1 -1.86134
+R<GLY>A<CA> R<ILE>A<C> sep2 0.2276
+R<GLY>A<CA> R<ILE>A<CA> central_sep1 2.02895
+R<GLY>A<CA> R<ILE>A<CA> central_sep2 0.394769
+R<GLY>A<CA> R<ILE>A<CA> sep1 2.03499
+R<GLY>A<CA> R<ILE>A<CA> sep2 0.700079
+R<GLY>A<CA> R<ILE>A<CB> central_sep1 0.21209
+R<GLY>A<CA> R<ILE>A<CB> central_sep2 -0.215141
+R<GLY>A<CA> R<ILE>A<CB> sep1 2.10893
+R<GLY>A<CA> R<ILE>A<CB> sep2 -0.0551388
+R<GLY>A<CA> R<ILE>A<CD1> central_sep1 0.81795
+R<GLY>A<CA> R<ILE>A<CD1> central_sep2 -0.607172
+R<GLY>A<CA> R<ILE>A<CD1> sep1 2.20415
+R<GLY>A<CA> R<ILE>A<CD1> sep2 0.33258
+R<GLY>A<CA> R<ILE>A<CG1> central_sep1 0.947457
+R<GLY>A<CA> R<ILE>A<CG1> central_sep2 -0.376524
+R<GLY>A<CA> R<ILE>A<CG1> sep1 1.44007
+R<GLY>A<CA> R<ILE>A<CG1> sep2 0.0224576
+R<GLY>A<CA> R<ILE>A<CG2> central_sep1 0.582788
+R<GLY>A<CA> R<ILE>A<CG2> central_sep2 -0.579058
+R<GLY>A<CA> R<ILE>A<CG2> sep1 1.24391
+R<GLY>A<CA> R<ILE>A<CG2> sep2 0.612631
+R<GLY>A<CA> R<ILE>A<N> central_sep1 3.09602
+R<GLY>A<CA> R<ILE>A<N> central_sep2 1.29631
+R<GLY>A<CA> R<ILE>A<N> sep1 -1.59541
+R<GLY>A<CA> R<ILE>A<N> sep2 0.905355
+R<GLY>A<CA> R<ILE>A<O> central_sep1 0.39874
+R<GLY>A<CA> R<ILE>A<O> central_sep2 -0.340025
+R<GLY>A<CA> R<ILE>A<O> sep1 -1.35248
+R<GLY>A<CA> R<ILE>A<O> sep2 0.196894
+R<GLY>A<CA> R<LEU>A<C> central_sep1 3.18452
+R<GLY>A<CA> R<LEU>A<C> central_sep2 1.31714
+R<GLY>A<CA> R<LEU>A<C> sep1 -1.69062
+R<GLY>A<CA> R<LEU>A<C> sep2 0.0146137
+R<GLY>A<CA> R<LEU>A<CA> central_sep1 1.76817
+R<GLY>A<CA> R<LEU>A<CA> central_sep2 0.516488
+R<GLY>A<CA> R<LEU>A<CA> sep1 1.79142
+R<GLY>A<CA> R<LEU>A<CA> sep2 0.705933
+R<GLY>A<CA> R<LEU>A<CB> central_sep1 0.206605
+R<GLY>A<CA> R<LEU>A<CB> central_sep2 -0.232418
+R<GLY>A<CA> R<LEU>A<CB> sep1 1.98308
+R<GLY>A<CA> R<LEU>A<CB> sep2 0.349079
+R<GLY>A<CA> R<LEU>A<CD1> central_sep1 0.688745
+R<GLY>A<CA> R<LEU>A<CD1> central_sep2 -0.595061
+R<GLY>A<CA> R<LEU>A<CD1> sep1 2.17258
+R<GLY>A<CA> R<LEU>A<CD1> sep2 0.311016
+R<GLY>A<CA> R<LEU>A<CD2> central_sep1 1.31584
+R<GLY>A<CA> R<LEU>A<CD2> central_sep2 -0.576294
+R<GLY>A<CA> R<LEU>A<CD2> sep1 2.15339
+R<GLY>A<CA> R<LEU>A<CD2> sep2 0.363258
+R<GLY>A<CA> R<LEU>A<CG> central_sep1 0.704176
+R<GLY>A<CA> R<LEU>A<CG> central_sep2 0.0540669
+R<GLY>A<CA> R<LEU>A<CG> sep1 0.954962
+R<GLY>A<CA> R<LEU>A<CG> sep2 -0.134855
+R<GLY>A<CA> R<LEU>A<N> central_sep1 2.98758
+R<GLY>A<CA> R<LEU>A<N> central_sep2 1.19172
+R<GLY>A<CA> R<LEU>A<N> sep1 -1.33763
+R<GLY>A<CA> R<LEU>A<N> sep2 0.985171
+R<GLY>A<CA> R<LEU>A<O> central_sep1 0.622345
+R<GLY>A<CA> R<LEU>A<O> central_sep2 -0.236731
+R<GLY>A<CA> R<LEU>A<O> sep1 -1.35446
+R<GLY>A<CA> R<LEU>A<O> sep2 0.445791
+R<GLY>A<CA> R<LYS>A<C> central_sep1 3.18543
+R<GLY>A<CA> R<LYS>A<C> central_sep2 1.19307
+R<GLY>A<CA> R<LYS>A<C> sep1 -1.73431
+R<GLY>A<CA> R<LYS>A<C> sep2 0.168386
+R<GLY>A<CA> R<LYS>A<CA> central_sep1 1.94831
+R<GLY>A<CA> R<LYS>A<CA> central_sep2 0.656232
+R<GLY>A<CA> R<LYS>A<CA> sep1 1.41049
+R<GLY>A<CA> R<LYS>A<CA> sep2 0.737024
+R<GLY>A<CA> R<LYS>A<CB> central_sep1 0.558775
+R<GLY>A<CA> R<LYS>A<CB> central_sep2 0.0594534
+R<GLY>A<CA> R<LYS>A<CB> sep1 1.96293
+R<GLY>A<CA> R<LYS>A<CB> sep2 0.505792
+R<GLY>A<CA> R<LYS>A<CD> central_sep1 0.848865
+R<GLY>A<CA> R<LYS>A<CD> central_sep2 0.0969684
+R<GLY>A<CA> R<LYS>A<CD> sep1 1.43312
+R<GLY>A<CA> R<LYS>A<CD> sep2 0.190135
+R<GLY>A<CA> R<LYS>A<CE> central_sep1 0.969176
+R<GLY>A<CA> R<LYS>A<CE> central_sep2 0.16722
+R<GLY>A<CA> R<LYS>A<CE> sep1 1.75206
+R<GLY>A<CA> R<LYS>A<CE> sep2 0.0811485
+R<GLY>A<CA> R<LYS>A<CG> central_sep1 1.09554
+R<GLY>A<CA> R<LYS>A<CG> central_sep2 0.0712221
+R<GLY>A<CA> R<LYS>A<CG> sep1 0.695689
+R<GLY>A<CA> R<LYS>A<CG> sep2 0.427777
+R<GLY>A<CA> R<LYS>A<N> central_sep1 2.8359
+R<GLY>A<CA> R<LYS>A<N> central_sep2 1.21529
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+R<ILE>A<C> R<PHE>A<CD1> sep1 -0.713031
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+R<ILE>A<C> R<PHE>A<CE1> central_sep1 0.957572
+R<ILE>A<C> R<PHE>A<CE1> central_sep2 0.18073
+R<ILE>A<C> R<PHE>A<CE1> sep1 1.65615
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+R<ILE>A<C> R<PHE>A<CZ> central_sep2 0.175381
+R<ILE>A<C> R<PHE>A<CZ> sep1 2.56688
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+R<ILE>A<C> R<PRO>A<C> central_sep2 6.14063
+R<ILE>A<C> R<PRO>A<C> sep1 -2.8944
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+R<ILE>A<C> R<PRO>A<CA> central_sep1 3.50757
+R<ILE>A<C> R<PRO>A<CA> central_sep2 2.38715
+R<ILE>A<C> R<PRO>A<CA> sep1 -2.68948
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+R<ILE>A<C> R<PRO>A<CB> central_sep2 0.90915
+R<ILE>A<C> R<PRO>A<CB> sep1 0.780432
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+R<ILE>A<C> R<PRO>A<CD> sep1 -0.745138
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+R<ILE>A<C> R<PRO>A<CG> sep1 2.29655
+R<ILE>A<C> R<PRO>A<CG> sep2 0.212262
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+R<ILE>A<C> R<PRO>A<N> central_sep2 2.32669
+R<ILE>A<C> R<PRO>A<N> sep1 -1.29727
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+R<ILE>A<C> R<PRO>A<O> sep1 -1.59777
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+R<ILE>A<C> R<SER>A<C> sep1 -2.6427
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+R<ILE>A<C> R<SER>A<CB> sep1 -0.433375
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+R<ILE>A<C> R<SER>A<N> sep1 -1.72029
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+R<ILE>A<C> R<SER>A<O> central_sep1 -0.475855
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+R<ILE>A<C> R<SER>A<O> sep1 -1.30622
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+R<ILE>A<C> R<SER>A<OG> central_sep1 2.17098
+R<ILE>A<C> R<SER>A<OG> central_sep2 1.45321
+R<ILE>A<C> R<SER>A<OG> sep1 0.019311
+R<ILE>A<C> R<SER>A<OG> sep2 0.38188
+R<ILE>A<C> R<THR>A<C> central_sep1 4.79346
+R<ILE>A<C> R<THR>A<C> central_sep2 5.33384
+R<ILE>A<C> R<THR>A<C> sep1 -2.66482
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+R<ILE>A<C> R<THR>A<CA> central_sep1 4.76426
+R<ILE>A<C> R<THR>A<CA> central_sep2 3.4111
+R<ILE>A<C> R<THR>A<CA> sep1 -2.9361
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+R<ILE>A<C> R<THR>A<CB> central_sep1 2.65831
+R<ILE>A<C> R<THR>A<CB> central_sep2 1.72071
+R<ILE>A<C> R<THR>A<CB> sep1 -0.354102
+R<ILE>A<C> R<THR>A<CB> sep2 -0.22394
+R<ILE>A<C> R<THR>A<CG2> central_sep1 0.223199
+R<ILE>A<C> R<THR>A<CG2> central_sep2 0.524474
+R<ILE>A<C> R<THR>A<CG2> sep1 -0.949968
+R<ILE>A<C> R<THR>A<CG2> sep2 -0.642109
+R<ILE>A<C> R<THR>A<N> central_sep1 -0.0477255
+R<ILE>A<C> R<THR>A<N> central_sep2 3.46987
+R<ILE>A<C> R<THR>A<N> sep1 -1.57597
+R<ILE>A<C> R<THR>A<N> sep2 2.2279
+R<ILE>A<C> R<THR>A<O> central_sep1 -0.606712
+R<ILE>A<C> R<THR>A<O> central_sep2 3.01716
+R<ILE>A<C> R<THR>A<O> sep1 -1.10753
+R<ILE>A<C> R<THR>A<O> sep2 1.69802
+R<ILE>A<C> R<THR>A<OG1> central_sep1 2.35338
+R<ILE>A<C> R<THR>A<OG1> central_sep2 1.50293
+R<ILE>A<C> R<THR>A<OG1> sep1 -0.658512
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+R<ILE>A<C> R<TRP>A<C> central_sep1 5.31971
+R<ILE>A<C> R<TRP>A<C> central_sep2 3.97362
+R<ILE>A<C> R<TRP>A<C> sep1 -2.54885
+R<ILE>A<C> R<TRP>A<C> sep2 5.1373
+R<ILE>A<C> R<TRP>A<CA> central_sep1 5.43743
+R<ILE>A<C> R<TRP>A<CA> central_sep2 4.92911
+R<ILE>A<C> R<TRP>A<CA> sep1 -2.65201
+R<ILE>A<C> R<TRP>A<CA> sep2 1.06265
+R<ILE>A<C> R<TRP>A<CB> central_sep1 2.83404
+R<ILE>A<C> R<TRP>A<CB> central_sep2 1.22253
+R<ILE>A<C> R<TRP>A<CB> sep1 0.0665101
+R<ILE>A<C> R<TRP>A<CB> sep2 -0.335557
+R<ILE>A<C> R<TRP>A<CD1> central_sep1 -0.531973
+R<ILE>A<C> R<TRP>A<CD1> central_sep2 0.688835
+R<ILE>A<C> R<TRP>A<CD1> sep1 -0.377395
+R<ILE>A<C> R<TRP>A<CD1> sep2 -0.50754
+R<ILE>A<C> R<TRP>A<CD2> central_sep1 -0.0572599
+R<ILE>A<C> R<TRP>A<CD2> central_sep2 2.67869
+R<ILE>A<C> R<TRP>A<CD2> sep1 -0.538737
+R<ILE>A<C> R<TRP>A<CD2> sep2 1.15301
+R<ILE>A<C> R<TRP>A<CE2> central_sep1 1.02291
+R<ILE>A<C> R<TRP>A<CE2> central_sep2 1.98455
+R<ILE>A<C> R<TRP>A<CE2> sep1 1.41892
+R<ILE>A<C> R<TRP>A<CE2> sep2 0.779884
+R<ILE>A<C> R<TRP>A<CE3> central_sep1 -0.360722
+R<ILE>A<C> R<TRP>A<CE3> central_sep2 -1.1522
+R<ILE>A<C> R<TRP>A<CE3> sep1 0.534747
+R<ILE>A<C> R<TRP>A<CE3> sep2 -0.486989
+R<ILE>A<C> R<TRP>A<CG> central_sep1 3.01298
+R<ILE>A<C> R<TRP>A<CG> central_sep2 2.02158
+R<ILE>A<C> R<TRP>A<CG> sep1 -1.05506
+R<ILE>A<C> R<TRP>A<CG> sep2 0.473208
+R<ILE>A<C> R<TRP>A<CH2> central_sep1 3.30074
+R<ILE>A<C> R<TRP>A<CH2> central_sep2 0.00359569
+R<ILE>A<C> R<TRP>A<CH2> sep1 3.90352
+R<ILE>A<C> R<TRP>A<CH2> sep2 -0.808536
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+R<ILE>A<C> R<TRP>A<CZ2> central_sep2 0.31931
+R<ILE>A<C> R<TRP>A<CZ2> sep1 3.9863
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+R<ILE>A<C> R<TRP>A<N> sep1 -1.45858
+R<ILE>A<C> R<TRP>A<N> sep2 2.03468
+R<ILE>A<C> R<TRP>A<NE1> central_sep1 2.54544
+R<ILE>A<C> R<TRP>A<NE1> central_sep2 1.10278
+R<ILE>A<C> R<TRP>A<NE1> sep1 2.05414
+R<ILE>A<C> R<TRP>A<NE1> sep2 0.0940039
+R<ILE>A<C> R<TRP>A<O> central_sep1 -0.739016
+R<ILE>A<C> R<TRP>A<O> central_sep2 2.48921
+R<ILE>A<C> R<TRP>A<O> sep1 -0.983121
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+R<ILE>A<C> R<TYR>A<C> central_sep1 4.56728
+R<ILE>A<C> R<TYR>A<C> central_sep2 5.75602
+R<ILE>A<C> R<TYR>A<C> sep1 -2.53643
+R<ILE>A<C> R<TYR>A<C> sep2 2.53754
+R<ILE>A<C> R<TYR>A<CA> central_sep1 4.61136
+R<ILE>A<C> R<TYR>A<CA> central_sep2 3.1666
+R<ILE>A<C> R<TYR>A<CA> sep1 -2.81776
+R<ILE>A<C> R<TYR>A<CA> sep2 1.16628
+R<ILE>A<C> R<TYR>A<CB> central_sep1 2.83332
+R<ILE>A<C> R<TYR>A<CB> central_sep2 1.14222
+R<ILE>A<C> R<TYR>A<CB> sep1 -0.271166
+R<ILE>A<C> R<TYR>A<CB> sep2 -0.41636
+R<ILE>A<C> R<TYR>A<CD1> central_sep1 -0.557674
+R<ILE>A<C> R<TYR>A<CD1> central_sep2 -0.175515
+R<ILE>A<C> R<TYR>A<CD1> sep1 -0.703458
+R<ILE>A<C> R<TYR>A<CD1> sep2 -0.626797
+R<ILE>A<C> R<TYR>A<CE1> central_sep1 1.04421
+R<ILE>A<C> R<TYR>A<CE1> central_sep2 0.512878
+R<ILE>A<C> R<TYR>A<CE1> sep1 1.79473
+R<ILE>A<C> R<TYR>A<CE1> sep2 -0.332205
+R<ILE>A<C> R<TYR>A<CG> central_sep1 1.97045
+R<ILE>A<C> R<TYR>A<CG> central_sep2 2.18959
+R<ILE>A<C> R<TYR>A<CG> sep1 -1.89396
+R<ILE>A<C> R<TYR>A<CG> sep2 0.648424
+R<ILE>A<C> R<TYR>A<CZ> central_sep1 1.1728
+R<ILE>A<C> R<TYR>A<CZ> central_sep2 1.68166
+R<ILE>A<C> R<TYR>A<CZ> sep1 1.69216
+R<ILE>A<C> R<TYR>A<CZ> sep2 0.379556
+R<ILE>A<C> R<TYR>A<N> central_sep1 -0.21294
+R<ILE>A<C> R<TYR>A<N> central_sep2 4.83812
+R<ILE>A<C> R<TYR>A<N> sep1 -1.55827
+R<ILE>A<C> R<TYR>A<N> sep2 1.99109
+R<ILE>A<C> R<TYR>A<O> central_sep1 -0.580014
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+R<ILE>A<C> R<TYR>A<O> sep1 -0.886978
+R<ILE>A<C> R<TYR>A<O> sep2 1.63691
+R<ILE>A<C> R<TYR>A<OH> central_sep1 3.54417
+R<ILE>A<C> R<TYR>A<OH> central_sep2 1.27728
+R<ILE>A<C> R<TYR>A<OH> sep1 4.5951
+R<ILE>A<C> R<TYR>A<OH> sep2 0.188722
+R<ILE>A<C> R<VAL>A<C> central_sep1 4.44873
+R<ILE>A<C> R<VAL>A<C> central_sep2 6.33231
+R<ILE>A<C> R<VAL>A<C> sep1 -2.68673
+R<ILE>A<C> R<VAL>A<C> sep2 3.74027
+R<ILE>A<C> R<VAL>A<CA> central_sep1 5.76431
+R<ILE>A<C> R<VAL>A<CA> central_sep2 3.65717
+R<ILE>A<C> R<VAL>A<CA> sep1 -2.86752
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+R<ILE>A<C> R<VAL>A<CB> central_sep1 2.71519
+R<ILE>A<C> R<VAL>A<CB> central_sep2 1.20694
+R<ILE>A<C> R<VAL>A<CB> sep1 0.234075
+R<ILE>A<C> R<VAL>A<CB> sep2 -0.705048
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+R<ILE>A<C> R<VAL>A<CG1> central_sep2 0.58561
+R<ILE>A<C> R<VAL>A<CG1> sep1 -0.792153
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+R<ILE>A<C> R<VAL>A<CG2> central_sep1 0.920459
+R<ILE>A<C> R<VAL>A<CG2> central_sep2 0.430374
+R<ILE>A<C> R<VAL>A<CG2> sep1 -1.04768
+R<ILE>A<C> R<VAL>A<CG2> sep2 -0.639506
+R<ILE>A<C> R<VAL>A<N> central_sep1 0.344555
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+R<ILE>A<C> R<VAL>A<N> sep1 -1.12742
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+R<ILE>A<C> R<VAL>A<O> central_sep1 -0.507764
+R<ILE>A<C> R<VAL>A<O> central_sep2 3.18032
+R<ILE>A<C> R<VAL>A<O> sep1 -0.828681
+R<ILE>A<C> R<VAL>A<O> sep2 1.62135
+R<ILE>A<C> c<solvent> . 2.51899
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+R<ILE>A<CA> R<ILE>A<CA> central_sep2 -0.617972
+R<ILE>A<CA> R<ILE>A<CA> sep1 3.62642
+R<ILE>A<CA> R<ILE>A<CA> sep2 0.235003
+R<ILE>A<CA> R<ILE>A<CB> central_sep1 -1.55092
+R<ILE>A<CA> R<ILE>A<CB> central_sep2 -1.27402
+R<ILE>A<CA> R<ILE>A<CB> sep1 1.05734
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+R<ILE>A<CA> R<ILE>A<CD1> central_sep2 -0.801665
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+R<ILE>A<CA> R<ILE>A<CG1> central_sep1 0.0483752
+R<ILE>A<CA> R<ILE>A<CG1> central_sep2 -0.465025
+R<ILE>A<CA> R<ILE>A<CG1> sep1 1.36175
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+R<ILE>A<CA> R<ILE>A<CG2> central_sep2 -0.334203
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+R<ILE>A<CA> R<ILE>A<CG2> sep2 -0.0501605
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+R<ILE>A<CA> R<ILE>A<N> central_sep2 1.55076
+R<ILE>A<CA> R<ILE>A<N> sep1 -2.35063
+R<ILE>A<CA> R<ILE>A<N> sep2 0.615662
+R<ILE>A<CA> R<ILE>A<O> central_sep1 0.89189
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+R<ILE>A<CA> R<ILE>A<O> sep1 -2.10005
+R<ILE>A<CA> R<ILE>A<O> sep2 -0.0988952
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+R<ILE>A<CA> R<LEU>A<C> central_sep2 2.78338
+R<ILE>A<CA> R<LEU>A<C> sep1 -2.6049
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+R<ILE>A<CA> R<LEU>A<CA> central_sep1 1.85434
+R<ILE>A<CA> R<LEU>A<CA> central_sep2 0.279281
+R<ILE>A<CA> R<LEU>A<CA> sep1 3.58983
+R<ILE>A<CA> R<LEU>A<CA> sep2 0.645955
+R<ILE>A<CA> R<LEU>A<CB> central_sep1 -1.23816
+R<ILE>A<CA> R<LEU>A<CB> central_sep2 -0.137151
+R<ILE>A<CA> R<LEU>A<CB> sep1 1.26728
+R<ILE>A<CA> R<LEU>A<CB> sep2 0.516259
+R<ILE>A<CA> R<LEU>A<CD1> central_sep1 -0.419358
+R<ILE>A<CA> R<LEU>A<CD1> central_sep2 -0.634378
+R<ILE>A<CA> R<LEU>A<CD1> sep1 1.51786
+R<ILE>A<CA> R<LEU>A<CD1> sep2 -0.280606
+R<ILE>A<CA> R<LEU>A<CD2> central_sep1 1.18307
+R<ILE>A<CA> R<LEU>A<CD2> central_sep2 -0.58522
+R<ILE>A<CA> R<LEU>A<CD2> sep1 1.44269
+R<ILE>A<CA> R<LEU>A<CD2> sep2 -0.226972
+R<ILE>A<CA> R<LEU>A<CG> central_sep1 -0.431613
+R<ILE>A<CA> R<LEU>A<CG> central_sep2 0.636067
+R<ILE>A<CA> R<LEU>A<CG> sep1 0.711578
+R<ILE>A<CA> R<LEU>A<CG> sep2 0.288686
+R<ILE>A<CA> R<LEU>A<N> central_sep1 2.74997
+R<ILE>A<CA> R<LEU>A<N> central_sep2 1.71406
+R<ILE>A<CA> R<LEU>A<N> sep1 -2.04661
+R<ILE>A<CA> R<LEU>A<N> sep2 0.77592
+R<ILE>A<CA> R<LEU>A<O> central_sep1 1.42561
+R<ILE>A<CA> R<LEU>A<O> central_sep2 -1.17119
+R<ILE>A<CA> R<LEU>A<O> sep1 -1.88299
+R<ILE>A<CA> R<LEU>A<O> sep2 0.302345
+R<ILE>A<CA> R<LYS>A<C> central_sep1 3.69268
+R<ILE>A<CA> R<LYS>A<C> central_sep2 2.80105
+R<ILE>A<CA> R<LYS>A<C> sep1 -2.90993
+R<ILE>A<CA> R<LYS>A<C> sep2 1.14238
+R<ILE>A<CA> R<LYS>A<CA> central_sep1 1.79817
+R<ILE>A<CA> R<LYS>A<CA> central_sep2 0.683742
+R<ILE>A<CA> R<LYS>A<CA> sep1 2.99568
+R<ILE>A<CA> R<LYS>A<CA> sep2 0.984432
+R<ILE>A<CA> R<LYS>A<CB> central_sep1 -0.586022
+R<ILE>A<CA> R<LYS>A<CB> central_sep2 0.826542
+R<ILE>A<CA> R<LYS>A<CB> sep1 1.25229
+R<ILE>A<CA> R<LYS>A<CB> sep2 1.03647
+R<ILE>A<CA> R<LYS>A<CD> central_sep1 0.424365
+R<ILE>A<CA> R<LYS>A<CD> central_sep2 0.872044
+R<ILE>A<CA> R<LYS>A<CD> sep1 0.989731
+R<ILE>A<CA> R<LYS>A<CD> sep2 0.562997
+R<ILE>A<CA> R<LYS>A<CE> central_sep1 1.25575
+R<ILE>A<CA> R<LYS>A<CE> central_sep2 1.39438
+R<ILE>A<CA> R<LYS>A<CE> sep1 2.38104
+R<ILE>A<CA> R<LYS>A<CE> sep2 0.712635
+R<ILE>A<CA> R<LYS>A<CG> central_sep1 0.804917
+R<ILE>A<CA> R<LYS>A<CG> central_sep2 0.83563
+R<ILE>A<CA> R<LYS>A<CG> sep1 1.03418
+R<ILE>A<CA> R<LYS>A<CG> sep2 0.782068
+R<ILE>A<CA> R<LYS>A<N> central_sep1 3.27662
+R<ILE>A<CA> R<LYS>A<N> central_sep2 2.1827
+R<ILE>A<CA> R<LYS>A<N> sep1 -2.36384
+R<ILE>A<CA> R<LYS>A<N> sep2 1.5762
+R<ILE>A<CA> R<LYS>A<NZ> central_sep1 2.54763
+R<ILE>A<CA> R<LYS>A<NZ> central_sep2 2.01041
+R<ILE>A<CA> R<LYS>A<NZ> sep1 2.86535
+R<ILE>A<CA> R<LYS>A<NZ> sep2 0.945897
+R<ILE>A<CA> R<LYS>A<O> central_sep1 0.936111
+R<ILE>A<CA> R<LYS>A<O> central_sep2 -0.634016
+R<ILE>A<CA> R<LYS>A<O> sep1 -2.14672
+R<ILE>A<CA> R<LYS>A<O> sep2 0.747921
+R<ILE>A<CA> R<MET>A<C> central_sep1 3.80337
+R<ILE>A<CA> R<MET>A<C> central_sep2 3.30297
+R<ILE>A<CA> R<MET>A<C> sep1 -2.7152
+R<ILE>A<CA> R<MET>A<C> sep2 0.895678
+R<ILE>A<CA> R<MET>A<CA> central_sep1 1.63693
+R<ILE>A<CA> R<MET>A<CA> central_sep2 -0.04441
+R<ILE>A<CA> R<MET>A<CA> sep1 3.48467
+R<ILE>A<CA> R<MET>A<CA> sep2 0.500334
+R<ILE>A<CA> R<MET>A<CB> central_sep1 -1.08155
+R<ILE>A<CA> R<MET>A<CB> central_sep2 0.0449124
+R<ILE>A<CA> R<MET>A<CB> sep1 1.20427
+R<ILE>A<CA> R<MET>A<CB> sep2 0.465208
+R<ILE>A<CA> R<MET>A<CE> central_sep1 -0.0302308
+R<ILE>A<CA> R<MET>A<CE> central_sep2 -0.399418
+R<ILE>A<CA> R<MET>A<CE> sep1 2.21941
+R<ILE>A<CA> R<MET>A<CE> sep2 -0.176353
+R<ILE>A<CA> R<MET>A<CG> central_sep1 0.0499467
+R<ILE>A<CA> R<MET>A<CG> central_sep2 0.0577721
+R<ILE>A<CA> R<MET>A<CG> sep1 1.13446
+R<ILE>A<CA> R<MET>A<CG> sep2 0.216504
+R<ILE>A<CA> R<MET>A<N> central_sep1 2.47313
+R<ILE>A<CA> R<MET>A<N> central_sep2 1.8941
+R<ILE>A<CA> R<MET>A<N> sep1 -1.94543
+R<ILE>A<CA> R<MET>A<N> sep2 1.10267
+R<ILE>A<CA> R<MET>A<O> central_sep1 1.08027
+R<ILE>A<CA> R<MET>A<O> central_sep2 -1.01474
+R<ILE>A<CA> R<MET>A<O> sep1 -2.00122
+R<ILE>A<CA> R<MET>A<O> sep2 0.520737
+R<ILE>A<CA> R<MET>A<SD> central_sep1 -0.478861
+R<ILE>A<CA> R<MET>A<SD> central_sep2 -0.645496
+R<ILE>A<CA> R<MET>A<SD> sep1 1.31114
+R<ILE>A<CA> R<MET>A<SD> sep2 -0.295171
+R<ILE>A<CA> R<PHE>A<C> central_sep1 3.57317
+R<ILE>A<CA> R<PHE>A<C> central_sep2 2.77724
+R<ILE>A<CA> R<PHE>A<C> sep1 -2.6883
+R<ILE>A<CA> R<PHE>A<C> sep2 0.835134
+R<ILE>A<CA> R<PHE>A<CA> central_sep1 1.68031
+R<ILE>A<CA> R<PHE>A<CA> central_sep2 -0.0168872
+R<ILE>A<CA> R<PHE>A<CA> sep1 3.50289
+R<ILE>A<CA> R<PHE>A<CA> sep2 0.219852
+R<ILE>A<CA> R<PHE>A<CB> central_sep1 -0.767312
+R<ILE>A<CA> R<PHE>A<CB> central_sep2 -0.262055
+R<ILE>A<CA> R<PHE>A<CB> sep1 1.48901
+R<ILE>A<CA> R<PHE>A<CB> sep2 0.220236
+R<ILE>A<CA> R<PHE>A<CD1> central_sep1 -0.0908607
+R<ILE>A<CA> R<PHE>A<CD1> central_sep2 -0.0560662
+R<ILE>A<CA> R<PHE>A<CD1> sep1 0.0160588
+R<ILE>A<CA> R<PHE>A<CD1> sep2 -0.259342
+R<ILE>A<CA> R<PHE>A<CE1> central_sep1 1.19715
+R<ILE>A<CA> R<PHE>A<CE1> central_sep2 -0.510809
+R<ILE>A<CA> R<PHE>A<CE1> sep1 1.70845
+R<ILE>A<CA> R<PHE>A<CE1> sep2 -0.464541
+R<ILE>A<CA> R<PHE>A<CG> central_sep1 1.08103
+R<ILE>A<CA> R<PHE>A<CG> central_sep2 0.703345
+R<ILE>A<CA> R<PHE>A<CG> sep1 1.37902
+R<ILE>A<CA> R<PHE>A<CG> sep2 -0.383868
+R<ILE>A<CA> R<PHE>A<CZ> central_sep1 1.94625
+R<ILE>A<CA> R<PHE>A<CZ> central_sep2 -0.677899
+R<ILE>A<CA> R<PHE>A<CZ> sep1 2.77612
+R<ILE>A<CA> R<PHE>A<CZ> sep2 -0.563142
+R<ILE>A<CA> R<PHE>A<N> central_sep1 2.9328
+R<ILE>A<CA> R<PHE>A<N> central_sep2 2.07119
+R<ILE>A<CA> R<PHE>A<N> sep1 -2.1302
+R<ILE>A<CA> R<PHE>A<N> sep2 1.11278
+R<ILE>A<CA> R<PHE>A<O> central_sep1 1.1541
+R<ILE>A<CA> R<PHE>A<O> central_sep2 -1.21637
+R<ILE>A<CA> R<PHE>A<O> sep1 -1.98219
+R<ILE>A<CA> R<PHE>A<O> sep2 0.30198
+R<ILE>A<CA> R<PRO>A<C> central_sep1 2.46849
+R<ILE>A<CA> R<PRO>A<C> central_sep2 3.10605
+R<ILE>A<CA> R<PRO>A<C> sep1 -2.58835
+R<ILE>A<CA> R<PRO>A<C> sep2 1.59009
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+R<LEU>A<C> R<TRP>A<CZ3> central_sep2 -0.619943
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+R<LEU>A<C> R<TRP>A<NE1> central_sep1 1.34819
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+R<LEU>A<C> R<TRP>A<NE1> sep1 1.75882
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+R<LEU>A<C> R<TYR>A<C> central_sep1 3.77338
+R<LEU>A<C> R<TYR>A<C> central_sep2 3.78983
+R<LEU>A<C> R<TYR>A<C> sep1 -2.46414
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+R<LEU>A<C> R<TYR>A<CA> central_sep1 3.88461
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+R<LEU>A<C> R<TYR>A<CA> sep1 -2.53653
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+R<LEU>A<C> R<TYR>A<CB> central_sep1 1.66909
+R<LEU>A<C> R<TYR>A<CB> central_sep2 0.701966
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+R<LEU>A<C> R<TYR>A<OH> sep1 3.93941
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+R<LEU>A<C> c<solvent> . 2.13035
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+R<LEU>A<CA> R<MET>A<N> sep1 -1.98196
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+R<LEU>A<CA> R<PHE>A<C> central_sep2 2.91842
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+R<LEU>A<CA> R<PHE>A<CA> central_sep1 1.71086
+R<LEU>A<CA> R<PHE>A<CA> central_sep2 0.16102
+R<LEU>A<CA> R<PHE>A<CA> sep1 3.27191
+R<LEU>A<CA> R<PHE>A<CA> sep2 0.661242
+R<LEU>A<CA> R<PHE>A<CB> central_sep1 -1.09092
+R<LEU>A<CA> R<PHE>A<CB> central_sep2 0.022112
+R<LEU>A<CA> R<PHE>A<CB> sep1 1.16703
+R<LEU>A<CA> R<PHE>A<CB> sep2 0.226507
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+R<LEU>A<CA> R<PHE>A<CD1> central_sep2 -0.207265
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+R<LEU>A<CA> R<PHE>A<CE1> central_sep1 0.967188
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+R<LEU>A<CA> R<PHE>A<CG> central_sep2 0.841475
+R<LEU>A<CA> R<PHE>A<CG> sep1 1.12626
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+R<LEU>A<CA> R<PHE>A<CZ> central_sep1 1.57911
+R<LEU>A<CA> R<PHE>A<CZ> central_sep2 -0.678312
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+R<LEU>A<CA> R<PHE>A<N> central_sep2 2.46631
+R<LEU>A<CA> R<PHE>A<N> sep1 -2.09334
+R<LEU>A<CA> R<PHE>A<N> sep2 1.60857
+R<LEU>A<CA> R<PHE>A<O> central_sep1 0.933231
+R<LEU>A<CA> R<PHE>A<O> central_sep2 -0.828773
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+R<LEU>A<CA> R<PHE>A<O> sep2 0.365207
+R<LEU>A<CA> R<PRO>A<C> central_sep1 2.731
+R<LEU>A<CA> R<PRO>A<C> central_sep2 3.18404
+R<LEU>A<CA> R<PRO>A<C> sep1 -2.72814
+R<LEU>A<CA> R<PRO>A<C> sep2 1.73217
+R<LEU>A<CA> R<PRO>A<CA> central_sep1 0.446395
+R<LEU>A<CA> R<PRO>A<CA> central_sep2 0.546718
+R<LEU>A<CA> R<PRO>A<CA> sep1 2.36346
+R<LEU>A<CA> R<PRO>A<CA> sep2 0.848204
+R<LEU>A<CA> R<PRO>A<CB> central_sep1 1.8571
+R<LEU>A<CA> R<PRO>A<CB> central_sep2 0.433971
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+R<LEU>A<CA> R<PRO>A<CB> sep2 0.431851
+R<LEU>A<CA> R<PRO>A<CD> central_sep1 -2.35687
+R<LEU>A<CA> R<PRO>A<CD> central_sep2 0.796576
+R<LEU>A<CA> R<PRO>A<CD> sep1 1.30254
+R<LEU>A<CA> R<PRO>A<CD> sep2 0.811896
+R<LEU>A<CA> R<PRO>A<CG> central_sep1 1.59833
+R<LEU>A<CA> R<PRO>A<CG> central_sep2 0.285301
+R<LEU>A<CA> R<PRO>A<CG> sep1 2.13011
+R<LEU>A<CA> R<PRO>A<CG> sep2 0.291901
+R<LEU>A<CA> R<PRO>A<N> central_sep1 3.27874
+R<LEU>A<CA> R<PRO>A<N> central_sep2 2.98213
+R<LEU>A<CA> R<PRO>A<N> sep1 -1.62506
+R<LEU>A<CA> R<PRO>A<N> sep2 1.34132
+R<LEU>A<CA> R<PRO>A<O> central_sep1 2.84505
+R<LEU>A<CA> R<PRO>A<O> central_sep2 0.513627
+R<LEU>A<CA> R<PRO>A<O> sep1 -2.03154
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+R<LEU>A<CA> R<SER>A<C> central_sep1 3.771
+R<LEU>A<CA> R<SER>A<C> central_sep2 2.64823
+R<LEU>A<CA> R<SER>A<C> sep1 -2.81467
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+R<LEU>A<CA> R<SER>A<CA> central_sep1 2.45745
+R<LEU>A<CA> R<SER>A<CA> central_sep2 0.671216
+R<LEU>A<CA> R<SER>A<CA> sep1 3.64665
+R<LEU>A<CA> R<SER>A<CA> sep2 0.886809
+R<LEU>A<CA> R<SER>A<CB> central_sep1 -0.0680742
+R<LEU>A<CA> R<SER>A<CB> central_sep2 0.564777
+R<LEU>A<CA> R<SER>A<CB> sep1 1.53171
+R<LEU>A<CA> R<SER>A<CB> sep2 0.641355
+R<LEU>A<CA> R<SER>A<N> central_sep1 3.05785
+R<LEU>A<CA> R<SER>A<N> central_sep2 2.18186
+R<LEU>A<CA> R<SER>A<N> sep1 -2.38374
+R<LEU>A<CA> R<SER>A<N> sep2 1.53927
+R<LEU>A<CA> R<SER>A<O> central_sep1 1.44523
+R<LEU>A<CA> R<SER>A<O> central_sep2 -0.331183
+R<LEU>A<CA> R<SER>A<O> sep1 -2.08472
+R<LEU>A<CA> R<SER>A<O> sep2 0.714237
+R<LEU>A<CA> R<SER>A<OG> central_sep1 0.094904
+R<LEU>A<CA> R<SER>A<OG> central_sep2 0.457653
+R<LEU>A<CA> R<SER>A<OG> sep1 1.03967
+R<LEU>A<CA> R<SER>A<OG> sep2 0.626344
+R<LEU>A<CA> R<THR>A<C> central_sep1 4.63679
+R<LEU>A<CA> R<THR>A<C> central_sep2 2.4985
+R<LEU>A<CA> R<THR>A<C> sep1 -2.9583
+R<LEU>A<CA> R<THR>A<C> sep2 1.16726
+R<LEU>A<CA> R<THR>A<CA> central_sep1 2.18582
+R<LEU>A<CA> R<THR>A<CA> central_sep2 0.504047
+R<LEU>A<CA> R<THR>A<CA> sep1 3.83429
+R<LEU>A<CA> R<THR>A<CA> sep2 0.901648
+R<LEU>A<CA> R<THR>A<CB> central_sep1 -0.692625
+R<LEU>A<CA> R<THR>A<CB> central_sep2 0.6354
+R<LEU>A<CA> R<THR>A<CB> sep1 1.4481
+R<LEU>A<CA> R<THR>A<CB> sep2 0.540479
+R<LEU>A<CA> R<THR>A<CG2> central_sep1 0.936921
+R<LEU>A<CA> R<THR>A<CG2> central_sep2 0.274494
+R<LEU>A<CA> R<THR>A<CG2> sep1 1.46534
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+R<LYS>A<NZ> R<TYR>A<O> central_sep1 0.80809
+R<LYS>A<NZ> R<TYR>A<O> central_sep2 -0.198451
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+R<LYS>A<NZ> R<TYR>A<O> sep2 0.567646
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+R<LYS>A<NZ> R<VAL>A<C> sep1 3.13152
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+R<LYS>A<NZ> R<VAL>A<CA> sep2 0.944531
+R<LYS>A<NZ> R<VAL>A<CB> central_sep1 2.19916
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+R<LYS>A<NZ> R<VAL>A<CB> sep1 2.72307
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+R<LYS>A<NZ> R<VAL>A<CG1> central_sep1 1.44631
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+R<LYS>A<NZ> R<VAL>A<CG1> sep2 0.828141
+R<LYS>A<NZ> R<VAL>A<CG2> central_sep1 1.79512
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+R<LYS>A<NZ> R<VAL>A<CG2> sep2 0.886036
+R<LYS>A<NZ> R<VAL>A<N> central_sep1 3.11091
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+R<LYS>A<O> R<MET>A<CA> central_sep1 0.978732
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+R<LYS>A<O> R<MET>A<CE> central_sep1 0.455662
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+R<LYS>A<O> R<MET>A<CE> sep2 0.733148
+R<LYS>A<O> R<MET>A<CG> central_sep1 -1.12026
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+R<LYS>A<O> R<MET>A<SD> central_sep1 0.975995
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+R<LYS>A<O> R<MET>A<SD> sep2 0.542166
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+R<LYS>A<O> R<PHE>A<C> sep1 -1.13995
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+R<LYS>A<O> R<PHE>A<CA> central_sep1 0.765333
+R<LYS>A<O> R<PHE>A<CA> central_sep2 -0.532293
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+R<LYS>A<O> R<PHE>A<CB> central_sep1 -1.12179
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+R<LYS>A<O> R<PHE>A<CB> sep1 0.488317
+R<LYS>A<O> R<PHE>A<CB> sep2 -0.0686239
+R<LYS>A<O> R<PHE>A<CD1> central_sep1 -0.381392
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+R<LYS>A<O> R<PHE>A<CD1> sep1 0.79827
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+R<LYS>A<O> R<PHE>A<CE1> central_sep1 0.726476
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+R<LYS>A<O> R<PHE>A<CE1> sep1 1.40745
+R<LYS>A<O> R<PHE>A<CE1> sep2 0.210053
+R<LYS>A<O> R<PHE>A<CG> central_sep1 0.500604
+R<LYS>A<O> R<PHE>A<CG> central_sep2 1.99906
+R<LYS>A<O> R<PHE>A<CG> sep1 0.401059
+R<LYS>A<O> R<PHE>A<CG> sep2 0.367917
+R<LYS>A<O> R<PHE>A<CZ> central_sep1 1.71198
+R<LYS>A<O> R<PHE>A<CZ> central_sep2 -0.059369
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+R<LYS>A<O> R<PHE>A<CZ> sep2 0.146535
+R<LYS>A<O> R<PHE>A<N> central_sep1 -1.50749
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+R<PHE>A<O> R<VAL>A<CB> sep1 0.524619
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+R<PHE>A<O> R<VAL>A<O> central_sep1 0.714474
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+R<PHE>A<O> c<solvent> . 0.828803
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+R<PRO>A<C> R<SER>A<OG> sep1 0.815895
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+R<PRO>A<C> R<THR>A<CA> sep1 -2.61108
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+R<PRO>A<C> R<THR>A<CB> sep1 0.495996
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+R<PRO>A<C> R<THR>A<N> sep1 -1.61865
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+R<PRO>A<C> R<THR>A<O> sep1 -1.82499
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+R<PRO>A<C> R<THR>A<OG1> sep1 0.336874
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+R<PRO>A<C> R<TRP>A<CB> sep1 0.080688
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+R<PRO>A<C> R<TRP>A<CD2> sep1 -0.20725
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+R<PRO>A<C> R<TRP>A<CE2> central_sep2 0.918488
+R<PRO>A<C> R<TRP>A<CE2> sep1 2.37196
+R<PRO>A<C> R<TRP>A<CE2> sep2 0.276524
+R<PRO>A<C> R<TRP>A<CE3> central_sep1 0.26861
+R<PRO>A<C> R<TRP>A<CE3> central_sep2 0.147118
+R<PRO>A<C> R<TRP>A<CE3> sep1 0.898154
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+R<PRO>A<C> R<TRP>A<CZ2> central_sep2 -0.0298593
+R<PRO>A<C> R<TRP>A<CZ2> sep1 2.61194
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+R<PRO>A<C> R<TRP>A<CZ3> central_sep2 -0.0668705
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+R<PRO>A<C> R<TRP>A<N> sep1 -1.83876
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+R<PRO>A<C> R<TRP>A<NE1> central_sep1 1.25104
+R<PRO>A<C> R<TRP>A<NE1> central_sep2 -0.0391368
+R<PRO>A<C> R<TRP>A<NE1> sep1 1.46841
+R<PRO>A<C> R<TRP>A<NE1> sep2 -0.647996
+R<PRO>A<C> R<TRP>A<O> central_sep1 -1.22771
+R<PRO>A<C> R<TRP>A<O> central_sep2 2.91938
+R<PRO>A<C> R<TRP>A<O> sep1 -1.57054
+R<PRO>A<C> R<TRP>A<O> sep2 1.73621
+R<PRO>A<C> R<TYR>A<C> central_sep1 2.56927
+R<PRO>A<C> R<TYR>A<C> central_sep2 4.48414
+R<PRO>A<C> R<TYR>A<C> sep1 -2.48188
+R<PRO>A<C> R<TYR>A<C> sep2 2.47913
+R<PRO>A<C> R<TYR>A<CA> central_sep1 1.45021
+R<PRO>A<C> R<TYR>A<CA> central_sep2 2.43316
+R<PRO>A<C> R<TYR>A<CA> sep1 -2.66729
+R<PRO>A<C> R<TYR>A<CA> sep2 0.974448
+R<PRO>A<C> R<TYR>A<CB> central_sep1 2.37514
+R<PRO>A<C> R<TYR>A<CB> central_sep2 0.874
+R<PRO>A<C> R<TYR>A<CB> sep1 -0.0361788
+R<PRO>A<C> R<TYR>A<CB> sep2 -0.102189
+R<PRO>A<C> R<TYR>A<CD1> central_sep1 -0.171733
+R<PRO>A<C> R<TYR>A<CD1> central_sep2 0.184574
+R<PRO>A<C> R<TYR>A<CD1> sep1 -0.292828
+R<PRO>A<C> R<TYR>A<CD1> sep2 -0.434007
+R<PRO>A<C> R<TYR>A<CE1> central_sep1 1.16434
+R<PRO>A<C> R<TYR>A<CE1> central_sep2 0.36998
+R<PRO>A<C> R<TYR>A<CE1> sep1 1.59357
+R<PRO>A<C> R<TYR>A<CE1> sep2 -0.362041
+R<PRO>A<C> R<TYR>A<CG> central_sep1 1.47703
+R<PRO>A<C> R<TYR>A<CG> central_sep2 0.897365
+R<PRO>A<C> R<TYR>A<CG> sep1 -1.37907
+R<PRO>A<C> R<TYR>A<CG> sep2 0.0183493
+R<PRO>A<C> R<TYR>A<CZ> central_sep1 2.86743
+R<PRO>A<C> R<TYR>A<CZ> central_sep2 0.995149
+R<PRO>A<C> R<TYR>A<CZ> sep1 2.31311
+R<PRO>A<C> R<TYR>A<CZ> sep2 0.145635
+R<PRO>A<C> R<TYR>A<N> central_sep1 -0.749868
+R<PRO>A<C> R<TYR>A<N> central_sep2 2.78274
+R<PRO>A<C> R<TYR>A<N> sep1 -1.70593
+R<PRO>A<C> R<TYR>A<N> sep2 1.78435
+R<PRO>A<C> R<TYR>A<O> central_sep1 -1.26368
+R<PRO>A<C> R<TYR>A<O> central_sep2 2.55622
+R<PRO>A<C> R<TYR>A<O> sep1 -1.7082
+R<PRO>A<C> R<TYR>A<O> sep2 1.31167
+R<PRO>A<C> R<TYR>A<OH> central_sep1 3.18568
+R<PRO>A<C> R<TYR>A<OH> central_sep2 0.752386
+R<PRO>A<C> R<TYR>A<OH> sep1 3.49893
+R<PRO>A<C> R<TYR>A<OH> sep2 -0.0143659
+R<PRO>A<C> R<VAL>A<C> central_sep1 3.08188
+R<PRO>A<C> R<VAL>A<C> central_sep2 4.48336
+R<PRO>A<C> R<VAL>A<C> sep1 -2.90485
+R<PRO>A<C> R<VAL>A<C> sep2 2.87883
+R<PRO>A<C> R<VAL>A<CA> central_sep1 2.20845
+R<PRO>A<C> R<VAL>A<CA> central_sep2 2.87704
+R<PRO>A<C> R<VAL>A<CA> sep1 -2.76249
+R<PRO>A<C> R<VAL>A<CA> sep2 1.36212
+R<PRO>A<C> R<VAL>A<CB> central_sep1 2.10473
+R<PRO>A<C> R<VAL>A<CB> central_sep2 1.40802
+R<PRO>A<C> R<VAL>A<CB> sep1 0.211164
+R<PRO>A<C> R<VAL>A<CB> sep2 0.0962358
+R<PRO>A<C> R<VAL>A<CG1> central_sep1 1.14347
+R<PRO>A<C> R<VAL>A<CG1> central_sep2 0.731082
+R<PRO>A<C> R<VAL>A<CG1> sep1 0.228149
+R<PRO>A<C> R<VAL>A<CG1> sep2 -0.0900478
+R<PRO>A<C> R<VAL>A<CG2> central_sep1 0.914744
+R<PRO>A<C> R<VAL>A<CG2> central_sep2 0.678883
+R<PRO>A<C> R<VAL>A<CG2> sep1 -0.499761
+R<PRO>A<C> R<VAL>A<CG2> sep2 -0.0135579
+R<PRO>A<C> R<VAL>A<N> central_sep1 -0.449503
+R<PRO>A<C> R<VAL>A<N> central_sep2 3.1116
+R<PRO>A<C> R<VAL>A<N> sep1 -1.67658
+R<PRO>A<C> R<VAL>A<N> sep2 1.93306
+R<PRO>A<C> R<VAL>A<O> central_sep1 -1.47896
+R<PRO>A<C> R<VAL>A<O> central_sep2 2.90393
+R<PRO>A<C> R<VAL>A<O> sep1 -1.80039
+R<PRO>A<C> R<VAL>A<O> sep2 1.49762
+R<PRO>A<C> c<solvent> . 1.84162
+R<PRO>A<CA> R<PRO>A<CA> central_sep1 -0.432529
+R<PRO>A<CA> R<PRO>A<CA> central_sep2 0.134283
+R<PRO>A<CA> R<PRO>A<CA> sep1 1.72389
+R<PRO>A<CA> R<PRO>A<CA> sep2 0.269595
+R<PRO>A<CA> R<PRO>A<CB> central_sep1 0.965918
+R<PRO>A<CA> R<PRO>A<CB> central_sep2 -0.0773382
+R<PRO>A<CA> R<PRO>A<CB> sep1 0.560025
+R<PRO>A<CA> R<PRO>A<CB> sep2 -0.00768307
+R<PRO>A<CA> R<PRO>A<CD> central_sep1 -2.07792
+R<PRO>A<CA> R<PRO>A<CD> central_sep2 0.0963637
+R<PRO>A<CA> R<PRO>A<CD> sep1 1.70917
+R<PRO>A<CA> R<PRO>A<CD> sep2 0.373208
+R<PRO>A<CA> R<PRO>A<CG> central_sep1 0.989271
+R<PRO>A<CA> R<PRO>A<CG> central_sep2 -0.106901
+R<PRO>A<CA> R<PRO>A<CG> sep1 1.97021
+R<PRO>A<CA> R<PRO>A<CG> sep2 -0.023907
+R<PRO>A<CA> R<PRO>A<N> central_sep1 2.52124
+R<PRO>A<CA> R<PRO>A<N> central_sep2 1.01942
+R<PRO>A<CA> R<PRO>A<N> sep1 -1.05105
+R<PRO>A<CA> R<PRO>A<N> sep2 -0.384841
+R<PRO>A<CA> R<PRO>A<O> central_sep1 0.86553
+R<PRO>A<CA> R<PRO>A<O> central_sep2 -0.232708
+R<PRO>A<CA> R<PRO>A<O> sep1 -1.5824
+R<PRO>A<CA> R<PRO>A<O> sep2 0.237624
+R<PRO>A<CA> R<SER>A<C> central_sep1 3.0065
+R<PRO>A<CA> R<SER>A<C> central_sep2 1.44661
+R<PRO>A<CA> R<SER>A<C> sep1 -2.32638
+R<PRO>A<CA> R<SER>A<C> sep2 0.21478
+R<PRO>A<CA> R<SER>A<CA> central_sep1 0.0313922
+R<PRO>A<CA> R<SER>A<CA> central_sep2 0.333973
+R<PRO>A<CA> R<SER>A<CA> sep1 2.15959
+R<PRO>A<CA> R<SER>A<CA> sep2 0.28601
+R<PRO>A<CA> R<SER>A<CB> central_sep1 0.380793
+R<PRO>A<CA> R<SER>A<CB> central_sep2 0.087865
+R<PRO>A<CA> R<SER>A<CB> sep1 1.14481
+R<PRO>A<CA> R<SER>A<CB> sep2 0.138018
+R<PRO>A<CA> R<SER>A<N> central_sep1 2.20356
+R<PRO>A<CA> R<SER>A<N> central_sep2 1.45935
+R<PRO>A<CA> R<SER>A<N> sep1 -2.21381
+R<PRO>A<CA> R<SER>A<N> sep2 0.788941
+R<PRO>A<CA> R<SER>A<O> central_sep1 0.405637
+R<PRO>A<CA> R<SER>A<O> central_sep2 -0.286013
+R<PRO>A<CA> R<SER>A<O> sep1 -1.60465
+R<PRO>A<CA> R<SER>A<O> sep2 0.405911
+R<PRO>A<CA> R<SER>A<OG> central_sep1 0.23007
+R<PRO>A<CA> R<SER>A<OG> central_sep2 -0.146533
+R<PRO>A<CA> R<SER>A<OG> sep1 1.12006
+R<PRO>A<CA> R<SER>A<OG> sep2 0.0641002
+R<PRO>A<CA> R<THR>A<C> central_sep1 2.9604
+R<PRO>A<CA> R<THR>A<C> central_sep2 1.43495
+R<PRO>A<CA> R<THR>A<C> sep1 -2.59271
+R<PRO>A<CA> R<THR>A<C> sep2 0.13907
+R<PRO>A<CA> R<THR>A<CA> central_sep1 0.252268
+R<PRO>A<CA> R<THR>A<CA> central_sep2 0.0487343
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+R<SER>A<C> R<TRP>A<CD1> sep2 -0.625548
+R<SER>A<C> R<TRP>A<CD2> central_sep1 -0.504581
+R<SER>A<C> R<TRP>A<CD2> central_sep2 0.582318
+R<SER>A<C> R<TRP>A<CD2> sep1 -0.24714
+R<SER>A<C> R<TRP>A<CD2> sep2 0.321068
+R<SER>A<C> R<TRP>A<CE2> central_sep1 0.055886
+R<SER>A<C> R<TRP>A<CE2> central_sep2 0.373685
+R<SER>A<C> R<TRP>A<CE2> sep1 1.1147
+R<SER>A<C> R<TRP>A<CE2> sep2 -0.160455
+R<SER>A<C> R<TRP>A<CE3> central_sep1 -0.677343
+R<SER>A<C> R<TRP>A<CE3> central_sep2 -0.739224
+R<SER>A<C> R<TRP>A<CE3> sep1 0.41672
+R<SER>A<C> R<TRP>A<CE3> sep2 -0.322462
+R<SER>A<C> R<TRP>A<CG> central_sep1 1.32503
+R<SER>A<C> R<TRP>A<CG> central_sep2 0.568949
+R<SER>A<C> R<TRP>A<CG> sep1 -1.09973
+R<SER>A<C> R<TRP>A<CG> sep2 -0.112535
+R<SER>A<C> R<TRP>A<CH2> central_sep1 2.05793
+R<SER>A<C> R<TRP>A<CH2> central_sep2 -0.711083
+R<SER>A<C> R<TRP>A<CH2> sep1 2.93268
+R<SER>A<C> R<TRP>A<CH2> sep2 -0.600461
+R<SER>A<C> R<TRP>A<CZ2> central_sep1 1.73608
+R<SER>A<C> R<TRP>A<CZ2> central_sep2 -0.505974
+R<SER>A<C> R<TRP>A<CZ2> sep1 2.8657
+R<SER>A<C> R<TRP>A<CZ2> sep2 -0.881562
+R<SER>A<C> R<TRP>A<CZ3> central_sep1 0.744798
+R<SER>A<C> R<TRP>A<CZ3> central_sep2 -0.487832
+R<SER>A<C> R<TRP>A<CZ3> sep1 1.93701
+R<SER>A<C> R<TRP>A<CZ3> sep2 -0.774667
+R<SER>A<C> R<TRP>A<N> central_sep1 -0.778901
+R<SER>A<C> R<TRP>A<N> central_sep2 2.49158
+R<SER>A<C> R<TRP>A<N> sep1 -1.73759
+R<SER>A<C> R<TRP>A<N> sep2 1.40577
+R<SER>A<C> R<TRP>A<NE1> central_sep1 0.910331
+R<SER>A<C> R<TRP>A<NE1> central_sep2 -0.240836
+R<SER>A<C> R<TRP>A<NE1> sep1 1.40227
+R<SER>A<C> R<TRP>A<NE1> sep2 -0.710537
+R<SER>A<C> R<TRP>A<O> central_sep1 -0.657419
+R<SER>A<C> R<TRP>A<O> central_sep2 2.08772
+R<SER>A<C> R<TRP>A<O> sep1 -1.53852
+R<SER>A<C> R<TRP>A<O> sep2 1.31778
+R<SER>A<C> R<TYR>A<C> central_sep1 3.82886
+R<SER>A<C> R<TYR>A<C> central_sep2 3.87122
+R<SER>A<C> R<TYR>A<C> sep1 -2.38306
+R<SER>A<C> R<TYR>A<C> sep2 2.02952
+R<SER>A<C> R<TYR>A<CA> central_sep1 3.50262
+R<SER>A<C> R<TYR>A<CA> central_sep2 2.31509
+R<SER>A<C> R<TYR>A<CA> sep1 -2.70116
+R<SER>A<C> R<TYR>A<CA> sep2 0.741368
+R<SER>A<C> R<TYR>A<CB> central_sep1 2.14089
+R<SER>A<C> R<TYR>A<CB> central_sep2 0.484079
+R<SER>A<C> R<TYR>A<CB> sep1 -0.370227
+R<SER>A<C> R<TYR>A<CB> sep2 -0.191168
+R<SER>A<C> R<TYR>A<CD1> central_sep1 -0.61527
+R<SER>A<C> R<TYR>A<CD1> central_sep2 -0.211049
+R<SER>A<C> R<TYR>A<CD1> sep1 -0.452369
+R<SER>A<C> R<TYR>A<CD1> sep2 -0.518789
+R<SER>A<C> R<TYR>A<CE1> central_sep1 0.49187
+R<SER>A<C> R<TYR>A<CE1> central_sep2 -0.0272725
+R<SER>A<C> R<TYR>A<CE1> sep1 1.40219
+R<SER>A<C> R<TYR>A<CE1> sep2 -0.468009
+R<SER>A<C> R<TYR>A<CG> central_sep1 0.679897
+R<SER>A<C> R<TYR>A<CG> central_sep2 0.391327
+R<SER>A<C> R<TYR>A<CG> sep1 -1.52935
+R<SER>A<C> R<TYR>A<CG> sep2 -0.138775
+R<SER>A<C> R<TYR>A<CZ> central_sep1 0.674332
+R<SER>A<C> R<TYR>A<CZ> central_sep2 0.291329
+R<SER>A<C> R<TYR>A<CZ> sep1 1.6172
+R<SER>A<C> R<TYR>A<CZ> sep2 -0.300536
+R<SER>A<C> R<TYR>A<N> central_sep1 -0.882025
+R<SER>A<C> R<TYR>A<N> central_sep2 2.393
+R<SER>A<C> R<TYR>A<N> sep1 -1.83584
+R<SER>A<C> R<TYR>A<N> sep2 1.65075
+R<SER>A<C> R<TYR>A<O> central_sep1 -0.637022
+R<SER>A<C> R<TYR>A<O> central_sep2 2.10331
+R<SER>A<C> R<TYR>A<O> sep1 -1.39154
+R<SER>A<C> R<TYR>A<O> sep2 0.969464
+R<SER>A<C> R<TYR>A<OH> central_sep1 2.69537
+R<SER>A<C> R<TYR>A<OH> central_sep2 0.337641
+R<SER>A<C> R<TYR>A<OH> sep1 3.57276
+R<SER>A<C> R<TYR>A<OH> sep2 -0.191499
+R<SER>A<C> R<VAL>A<C> central_sep1 4.84907
+R<SER>A<C> R<VAL>A<C> central_sep2 4.84524
+R<SER>A<C> R<VAL>A<C> sep1 -2.53174
+R<SER>A<C> R<VAL>A<C> sep2 2.5542
+R<SER>A<C> R<VAL>A<CA> central_sep1 3.80191
+R<SER>A<C> R<VAL>A<CA> central_sep2 2.46268
+R<SER>A<C> R<VAL>A<CA> sep1 -2.70191
+R<SER>A<C> R<VAL>A<CA> sep2 0.92828
+R<SER>A<C> R<VAL>A<CB> central_sep1 2.19366
+R<SER>A<C> R<VAL>A<CB> central_sep2 0.727114
+R<SER>A<C> R<VAL>A<CB> sep1 0.0226371
+R<SER>A<C> R<VAL>A<CB> sep2 -0.384923
+R<SER>A<C> R<VAL>A<CG1> central_sep1 0.451133
+R<SER>A<C> R<VAL>A<CG1> central_sep2 0.251531
+R<SER>A<C> R<VAL>A<CG1> sep1 -0.231326
+R<SER>A<C> R<VAL>A<CG1> sep2 -0.453268
+R<SER>A<C> R<VAL>A<CG2> central_sep1 0.696284
+R<SER>A<C> R<VAL>A<CG2> central_sep2 0.160159
+R<SER>A<C> R<VAL>A<CG2> sep1 -0.71023
+R<SER>A<C> R<VAL>A<CG2> sep2 -0.291936
+R<SER>A<C> R<VAL>A<N> central_sep1 -0.322299
+R<SER>A<C> R<VAL>A<N> central_sep2 2.76531
+R<SER>A<C> R<VAL>A<N> sep1 -1.63831
+R<SER>A<C> R<VAL>A<N> sep2 1.4837
+R<SER>A<C> R<VAL>A<O> central_sep1 -0.587251
+R<SER>A<C> R<VAL>A<O> central_sep2 1.7644
+R<SER>A<C> R<VAL>A<O> sep1 -1.33155
+R<SER>A<C> R<VAL>A<O> sep2 0.820046
+R<SER>A<C> c<solvent> . 1.73647
+R<SER>A<CA> R<SER>A<CA> central_sep1 1.77736
+R<SER>A<CA> R<SER>A<CA> central_sep2 -0.0598985
+R<SER>A<CA> R<SER>A<CA> sep1 2.93159
+R<SER>A<CA> R<SER>A<CA> sep2 0.171051
+R<SER>A<CA> R<SER>A<CB> central_sep1 0.25832
+R<SER>A<CA> R<SER>A<CB> central_sep2 0.0325049
+R<SER>A<CA> R<SER>A<CB> sep1 1.81104
+R<SER>A<CA> R<SER>A<CB> sep2 -0.037878
+R<SER>A<CA> R<SER>A<N> central_sep1 3.04124
+R<SER>A<CA> R<SER>A<N> central_sep2 1.00436
+R<SER>A<CA> R<SER>A<N> sep1 -2.18335
+R<SER>A<CA> R<SER>A<N> sep2 0.726995
+R<SER>A<CA> R<SER>A<O> central_sep1 1.38263
+R<SER>A<CA> R<SER>A<O> central_sep2 -0.379694
+R<SER>A<CA> R<SER>A<O> sep1 -2.05185
+R<SER>A<CA> R<SER>A<O> sep2 0.356784
+R<SER>A<CA> R<SER>A<OG> central_sep1 0.439195
+R<SER>A<CA> R<SER>A<OG> central_sep2 -0.121894
+R<SER>A<CA> R<SER>A<OG> sep1 0.995497
+R<SER>A<CA> R<SER>A<OG> sep2 -0.123862
+R<SER>A<CA> R<THR>A<C> central_sep1 4.45214
+R<SER>A<CA> R<THR>A<C> central_sep2 1.96141
+R<SER>A<CA> R<THR>A<C> sep1 -2.59875
+R<SER>A<CA> R<THR>A<C> sep2 0.321152
+R<SER>A<CA> R<THR>A<CA> central_sep1 1.4725
+R<SER>A<CA> R<THR>A<CA> central_sep2 -0.162015
+R<SER>A<CA> R<THR>A<CA> sep1 3.53125
+R<SER>A<CA> R<THR>A<CA> sep2 0.364938
+R<SER>A<CA> R<THR>A<CB> central_sep1 -0.226439
+R<SER>A<CA> R<THR>A<CB> central_sep2 0.152862
+R<SER>A<CA> R<THR>A<CB> sep1 1.74093
+R<SER>A<CA> R<THR>A<CB> sep2 -0.154894
+R<SER>A<CA> R<THR>A<CG2> central_sep1 1.28649
+R<SER>A<CA> R<THR>A<CG2> central_sep2 -0.0687886
+R<SER>A<CA> R<THR>A<CG2> sep1 1.27601
+R<SER>A<CA> R<THR>A<CG2> sep2 0.13766
+R<SER>A<CA> R<THR>A<N> central_sep1 3.28629
+R<SER>A<CA> R<THR>A<N> central_sep2 1.35618
+R<SER>A<CA> R<THR>A<N> sep1 -2.19984
+R<SER>A<CA> R<THR>A<N> sep2 0.950219
+R<SER>A<CA> R<THR>A<O> central_sep1 1.3387
+R<SER>A<CA> R<THR>A<O> central_sep2 -0.446619
+R<SER>A<CA> R<THR>A<O> sep1 -1.93597
+R<SER>A<CA> R<THR>A<O> sep2 0.33577
+R<SER>A<CA> R<THR>A<OG1> central_sep1 0.297501
+R<SER>A<CA> R<THR>A<OG1> central_sep2 -0.0638964
+R<SER>A<CA> R<THR>A<OG1> sep1 1.06478
+R<SER>A<CA> R<THR>A<OG1> sep2 -0.070328
+R<SER>A<CA> R<TRP>A<C> central_sep1 3.60124
+R<SER>A<CA> R<TRP>A<C> central_sep2 2.69762
+R<SER>A<CA> R<TRP>A<C> sep1 -2.58577
+R<SER>A<CA> R<TRP>A<C> sep2 0.649791
+R<SER>A<CA> R<TRP>A<CA> central_sep1 1.26458
+R<SER>A<CA> R<TRP>A<CA> central_sep2 0.161036
+R<SER>A<CA> R<TRP>A<CA> sep1 2.79102
+R<SER>A<CA> R<TRP>A<CA> sep2 0.655882
+R<SER>A<CA> R<TRP>A<CB> central_sep1 -0.0588717
+R<SER>A<CA> R<TRP>A<CB> central_sep2 0.133284
+R<SER>A<CA> R<TRP>A<CB> sep1 1.86884
+R<SER>A<CA> R<TRP>A<CB> sep2 0.129664
+R<SER>A<CA> R<TRP>A<CD1> central_sep1 0.195604
+R<SER>A<CA> R<TRP>A<CD1> central_sep2 -0.219233
+R<SER>A<CA> R<TRP>A<CD1> sep1 -0.0932145
+R<SER>A<CA> R<TRP>A<CD1> sep2 -0.315372
+R<SER>A<CA> R<TRP>A<CD2> central_sep1 1.0226
+R<SER>A<CA> R<TRP>A<CD2> central_sep2 -0.274997
+R<SER>A<CA> R<TRP>A<CD2> sep1 0.827819
+R<SER>A<CA> R<TRP>A<CD2> sep2 -0.8315
+R<SER>A<CA> R<TRP>A<CE2> central_sep1 0.705456
+R<SER>A<CA> R<TRP>A<CE2> central_sep2 -0.276179
+R<SER>A<CA> R<TRP>A<CE2> sep1 1.10822
+R<SER>A<CA> R<TRP>A<CE2> sep2 -0.700934
+R<SER>A<CA> R<TRP>A<CE3> central_sep1 -0.884315
+R<SER>A<CA> R<TRP>A<CE3> central_sep2 -0.367306
+R<SER>A<CA> R<TRP>A<CE3> sep1 1.24728
+R<SER>A<CA> R<TRP>A<CE3> sep2 -0.302637
+R<SER>A<CA> R<TRP>A<CG> central_sep1 1.72546
+R<SER>A<CA> R<TRP>A<CG> central_sep2 -0.163881
+R<SER>A<CA> R<TRP>A<CG> sep1 1.38591
+R<SER>A<CA> R<TRP>A<CG> sep2 -1.11806
+R<SER>A<CA> R<TRP>A<CH2> central_sep1 1.25958
+R<SER>A<CA> R<TRP>A<CH2> central_sep2 -0.548105
+R<SER>A<CA> R<TRP>A<CH2> sep1 2.45782
+R<SER>A<CA> R<TRP>A<CH2> sep2 -0.5344
+R<SER>A<CA> R<TRP>A<CZ2> central_sep1 0.851919
+R<SER>A<CA> R<TRP>A<CZ2> central_sep2 -0.621088
+R<SER>A<CA> R<TRP>A<CZ2> sep1 2.02375
+R<SER>A<CA> R<TRP>A<CZ2> sep2 -0.497102
+R<SER>A<CA> R<TRP>A<CZ3> central_sep1 0.887143
+R<SER>A<CA> R<TRP>A<CZ3> central_sep2 -0.655096
+R<SER>A<CA> R<TRP>A<CZ3> sep1 0.862785
+R<SER>A<CA> R<TRP>A<CZ3> sep2 -0.548018
+R<SER>A<CA> R<TRP>A<N> central_sep1 2.71022
+R<SER>A<CA> R<TRP>A<N> central_sep2 1.45001
+R<SER>A<CA> R<TRP>A<N> sep1 -2.26255
+R<SER>A<CA> R<TRP>A<N> sep2 0.726968
+R<SER>A<CA> R<TRP>A<NE1> central_sep1 0.654079
+R<SER>A<CA> R<TRP>A<NE1> central_sep2 0.02574
+R<SER>A<CA> R<TRP>A<NE1> sep1 1.48163
+R<SER>A<CA> R<TRP>A<NE1> sep2 -0.58394
+R<SER>A<CA> R<TRP>A<O> central_sep1 1.01051
+R<SER>A<CA> R<TRP>A<O> central_sep2 -0.608309
+R<SER>A<CA> R<TRP>A<O> sep1 -1.96455
+R<SER>A<CA> R<TRP>A<O> sep2 0.40929
+R<SER>A<CA> R<TYR>A<C> central_sep1 3.17278
+R<SER>A<CA> R<TYR>A<C> central_sep2 2.0213
+R<SER>A<CA> R<TYR>A<C> sep1 -2.61015
+R<SER>A<CA> R<TYR>A<C> sep2 0.641245
+R<SER>A<CA> R<TYR>A<CA> central_sep1 1.92363
+R<SER>A<CA> R<TYR>A<CA> central_sep2 0.274291
+R<SER>A<CA> R<TYR>A<CA> sep1 3.58668
+R<SER>A<CA> R<TYR>A<CA> sep2 0.545331
+R<SER>A<CA> R<TYR>A<CB> central_sep1 -0.0609141
+R<SER>A<CA> R<TYR>A<CB> central_sep2 0.0349596
+R<SER>A<CA> R<TYR>A<CB> sep1 1.7856
+R<SER>A<CA> R<TYR>A<CB> sep2 0.180068
+R<SER>A<CA> R<TYR>A<CD1> central_sep1 0.337301
+R<SER>A<CA> R<TYR>A<CD1> central_sep2 -0.278624
+R<SER>A<CA> R<TYR>A<CD1> sep1 -0.0304849
+R<SER>A<CA> R<TYR>A<CD1> sep2 -0.322852
+R<SER>A<CA> R<TYR>A<CE1> central_sep1 0.648907
+R<SER>A<CA> R<TYR>A<CE1> central_sep2 -0.222492
+R<SER>A<CA> R<TYR>A<CE1> sep1 1.27175
+R<SER>A<CA> R<TYR>A<CE1> sep2 -0.341742
+R<SER>A<CA> R<TYR>A<CG> central_sep1 1.3461
+R<SER>A<CA> R<TYR>A<CG> central_sep2 -0.195072
+R<SER>A<CA> R<TYR>A<CG> sep1 1.8455
+R<SER>A<CA> R<TYR>A<CG> sep2 -0.960932
+R<SER>A<CA> R<TYR>A<CZ> central_sep1 0.233255
+R<SER>A<CA> R<TYR>A<CZ> central_sep2 -0.101402
+R<SER>A<CA> R<TYR>A<CZ> sep1 1.18645
+R<SER>A<CA> R<TYR>A<CZ> sep2 -0.833847
+R<SER>A<CA> R<TYR>A<N> central_sep1 2.5055
+R<SER>A<CA> R<TYR>A<N> central_sep2 1.51851
+R<SER>A<CA> R<TYR>A<N> sep1 -2.13382
+R<SER>A<CA> R<TYR>A<N> sep2 0.961896
+R<SER>A<CA> R<TYR>A<O> central_sep1 0.859457
+R<SER>A<CA> R<TYR>A<O> central_sep2 -0.676338
+R<SER>A<CA> R<TYR>A<O> sep1 -1.98495
+R<SER>A<CA> R<TYR>A<O> sep2 0.318815
+R<SER>A<CA> R<TYR>A<OH> central_sep1 1.36185
+R<SER>A<CA> R<TYR>A<OH> central_sep2 -0.378377
+R<SER>A<CA> R<TYR>A<OH> sep1 2.14226
+R<SER>A<CA> R<TYR>A<OH> sep2 -0.319417
+R<SER>A<CA> R<VAL>A<C> central_sep1 4.46167
+R<SER>A<CA> R<VAL>A<C> central_sep2 2.6859
+R<SER>A<CA> R<VAL>A<C> sep1 -2.73869
+R<SER>A<CA> R<VAL>A<C> sep2 0.625821
+R<SER>A<CA> R<VAL>A<CA> central_sep1 1.98595
+R<SER>A<CA> R<VAL>A<CA> central_sep2 0.344427
+R<SER>A<CA> R<VAL>A<CA> sep1 3.91556
+R<SER>A<CA> R<VAL>A<CA> sep2 0.685794
+R<SER>A<CA> R<VAL>A<CB> central_sep1 -0.629876
+R<SER>A<CA> R<VAL>A<CB> central_sep2 0.111973
+R<SER>A<CA> R<VAL>A<CB> sep1 1.67919
+R<SER>A<CA> R<VAL>A<CB> sep2 -0.0150601
+R<SER>A<CA> R<VAL>A<CG1> central_sep1 1.4249
+R<SER>A<CA> R<VAL>A<CG1> central_sep2 -0.107102
+R<SER>A<CA> R<VAL>A<CG1> sep1 1.00615
+R<SER>A<CA> R<VAL>A<CG1> sep2 0.231106
+R<SER>A<CA> R<VAL>A<CG2> central_sep1 0.601933
+R<SER>A<CA> R<VAL>A<CG2> central_sep2 -0.205085
+R<SER>A<CA> R<VAL>A<CG2> sep1 1.31728
+R<SER>A<CA> R<VAL>A<CG2> sep2 0.18408
+R<SER>A<CA> R<VAL>A<N> central_sep1 2.68342
+R<SER>A<CA> R<VAL>A<N> central_sep2 1.54529
+R<SER>A<CA> R<VAL>A<N> sep1 -2.24762
+R<SER>A<CA> R<VAL>A<N> sep2 0.889382
+R<SER>A<CA> R<VAL>A<O> central_sep1 0.932814
+R<SER>A<CA> R<VAL>A<O> central_sep2 -0.741372
+R<SER>A<CA> R<VAL>A<O> sep1 -1.98467
+R<SER>A<CA> R<VAL>A<O> sep2 0.238688
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+R<SER>A<OG> R<TRP>A<CH2> central_sep1 2.1299
+R<SER>A<OG> R<TRP>A<CH2> central_sep2 -0.191744
+R<SER>A<OG> R<TRP>A<CH2> sep1 2.00083
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+R<SER>A<OG> R<TRP>A<CZ2> central_sep1 1.2976
+R<SER>A<OG> R<TRP>A<CZ2> central_sep2 -0.444975
+R<SER>A<OG> R<TRP>A<CZ2> sep1 1.34351
+R<SER>A<OG> R<TRP>A<CZ2> sep2 -0.771741
+R<SER>A<OG> R<TRP>A<CZ3> central_sep1 1.26559
+R<SER>A<OG> R<TRP>A<CZ3> central_sep2 -0.0704851
+R<SER>A<OG> R<TRP>A<CZ3> sep1 1.38622
+R<SER>A<OG> R<TRP>A<CZ3> sep2 -0.236737
+R<SER>A<OG> R<TRP>A<N> central_sep1 -0.80966
+R<SER>A<OG> R<TRP>A<N> central_sep2 0.135937
+R<SER>A<OG> R<TRP>A<N> sep1 -0.27853
+R<SER>A<OG> R<TRP>A<N> sep2 0.593168
+R<SER>A<OG> R<TRP>A<NE1> central_sep1 -0.0494368
+R<SER>A<OG> R<TRP>A<NE1> central_sep2 -1.40725
+R<SER>A<OG> R<TRP>A<NE1> sep1 0.754218
+R<SER>A<OG> R<TRP>A<NE1> sep2 -0.570075
+R<SER>A<OG> R<TRP>A<O> central_sep1 -0.710738
+R<SER>A<OG> R<TRP>A<O> central_sep2 0.0270729
+R<SER>A<OG> R<TRP>A<O> sep1 1.00491
+R<SER>A<OG> R<TRP>A<O> sep2 0.25593
+R<SER>A<OG> R<TYR>A<C> central_sep1 1.69207
+R<SER>A<OG> R<TYR>A<C> central_sep2 1.07097
+R<SER>A<OG> R<TYR>A<C> sep1 -0.0286532
+R<SER>A<OG> R<TYR>A<C> sep2 0.194961
+R<SER>A<OG> R<TYR>A<CA> central_sep1 -0.0498668
+R<SER>A<OG> R<TYR>A<CA> central_sep2 0.141613
+R<SER>A<OG> R<TYR>A<CA> sep1 0.79326
+R<SER>A<OG> R<TYR>A<CA> sep2 0.180603
+R<SER>A<OG> R<TYR>A<CB> central_sep1 -0.414582
+R<SER>A<OG> R<TYR>A<CB> central_sep2 -0.478742
+R<SER>A<OG> R<TYR>A<CB> sep1 1.32335
+R<SER>A<OG> R<TYR>A<CB> sep2 0.0559164
+R<SER>A<OG> R<TYR>A<CD1> central_sep1 -0.337347
+R<SER>A<OG> R<TYR>A<CD1> central_sep2 -0.176163
+R<SER>A<OG> R<TYR>A<CD1> sep1 1.24043
+R<SER>A<OG> R<TYR>A<CD1> sep2 -0.136796
+R<SER>A<OG> R<TYR>A<CE1> central_sep1 0.34091
+R<SER>A<OG> R<TYR>A<CE1> central_sep2 -0.37652
+R<SER>A<OG> R<TYR>A<CE1> sep1 1.02351
+R<SER>A<OG> R<TYR>A<CE1> sep2 -0.456696
+R<SER>A<OG> R<TYR>A<CG> central_sep1 2.25533
+R<SER>A<OG> R<TYR>A<CG> central_sep2 1.65368
+R<SER>A<OG> R<TYR>A<CG> sep1 1.59808
+R<SER>A<OG> R<TYR>A<CG> sep2 -0.471841
+R<SER>A<OG> R<TYR>A<CZ> central_sep1 0.746431
+R<SER>A<OG> R<TYR>A<CZ> central_sep2 1.07329
+R<SER>A<OG> R<TYR>A<CZ> sep1 0.792943
+R<SER>A<OG> R<TYR>A<CZ> sep2 -0.647327
+R<SER>A<OG> R<TYR>A<N> central_sep1 -0.89143
+R<SER>A<OG> R<TYR>A<N> central_sep2 0.119774
+R<SER>A<OG> R<TYR>A<N> sep1 -0.158881
+R<SER>A<OG> R<TYR>A<N> sep2 0.481141
+R<SER>A<OG> R<TYR>A<O> central_sep1 -0.663226
+R<SER>A<OG> R<TYR>A<O> central_sep2 0.00530552
+R<SER>A<OG> R<TYR>A<O> sep1 1.04168
+R<SER>A<OG> R<TYR>A<O> sep2 0.214468
+R<SER>A<OG> R<TYR>A<OH> central_sep1 1.3272
+R<SER>A<OG> R<TYR>A<OH> central_sep2 -0.745673
+R<SER>A<OG> R<TYR>A<OH> sep1 1.44826
+R<SER>A<OG> R<TYR>A<OH> sep2 -0.500444
+R<SER>A<OG> R<VAL>A<C> central_sep1 2.23151
+R<SER>A<OG> R<VAL>A<C> central_sep2 1.48143
+R<SER>A<OG> R<VAL>A<C> sep1 -0.102705
+R<SER>A<OG> R<VAL>A<C> sep2 0.333104
+R<SER>A<OG> R<VAL>A<CA> central_sep1 0.478664
+R<SER>A<OG> R<VAL>A<CA> central_sep2 0.310089
+R<SER>A<OG> R<VAL>A<CA> sep1 1.33921
+R<SER>A<OG> R<VAL>A<CA> sep2 0.57442
+R<SER>A<OG> R<VAL>A<CB> central_sep1 -0.233203
+R<SER>A<OG> R<VAL>A<CB> central_sep2 -0.385986
+R<SER>A<OG> R<VAL>A<CB> sep1 1.29331
+R<SER>A<OG> R<VAL>A<CB> sep2 -0.338076
+R<SER>A<OG> R<VAL>A<CG1> central_sep1 0.0743942
+R<SER>A<OG> R<VAL>A<CG1> central_sep2 -0.20479
+R<SER>A<OG> R<VAL>A<CG1> sep1 1.69338
+R<SER>A<OG> R<VAL>A<CG1> sep2 -0.139563
+R<SER>A<OG> R<VAL>A<CG2> central_sep1 -0.1049
+R<SER>A<OG> R<VAL>A<CG2> central_sep2 -0.246124
+R<SER>A<OG> R<VAL>A<CG2> sep1 1.55069
+R<SER>A<OG> R<VAL>A<CG2> sep2 0.00178172
+R<SER>A<OG> R<VAL>A<N> central_sep1 -0.534942
+R<SER>A<OG> R<VAL>A<N> central_sep2 0.0864894
+R<SER>A<OG> R<VAL>A<N> sep1 -0.0564388
+R<SER>A<OG> R<VAL>A<N> sep2 0.604511
+R<SER>A<OG> R<VAL>A<O> central_sep1 -0.42636
+R<SER>A<OG> R<VAL>A<O> central_sep2 0.136129
+R<SER>A<OG> R<VAL>A<O> sep1 1.10092
+R<SER>A<OG> R<VAL>A<O> sep2 0.227349
+R<SER>A<OG> c<solvent> . -0.144232
+R<THR>A<C> R<THR>A<C> central_sep1 3.39951
+R<THR>A<C> R<THR>A<C> central_sep2 2.86665
+R<THR>A<C> R<THR>A<C> sep1 -2.42954
+R<THR>A<C> R<THR>A<C> sep2 1.9012
+R<THR>A<C> R<THR>A<CA> central_sep1 3.77408
+R<THR>A<C> R<THR>A<CA> central_sep2 2.37576
+R<THR>A<C> R<THR>A<CA> sep1 -2.73619
+R<THR>A<C> R<THR>A<CA> sep2 0.578481
+R<THR>A<C> R<THR>A<CB> central_sep1 2.29292
+R<THR>A<C> R<THR>A<CB> central_sep2 0.843044
+R<THR>A<C> R<THR>A<CB> sep1 -0.120783
+R<THR>A<C> R<THR>A<CB> sep2 -0.332518
+R<THR>A<C> R<THR>A<CG2> central_sep1 0.65695
+R<THR>A<C> R<THR>A<CG2> central_sep2 0.181506
+R<THR>A<C> R<THR>A<CG2> sep1 -0.555202
+R<THR>A<C> R<THR>A<CG2> sep2 -0.411657
+R<THR>A<C> R<THR>A<N> central_sep1 -0.43626
+R<THR>A<C> R<THR>A<N> central_sep2 2.85905
+R<THR>A<C> R<THR>A<N> sep1 -1.55435
+R<THR>A<C> R<THR>A<N> sep2 1.59341
+R<THR>A<C> R<THR>A<O> central_sep1 -0.41485
+R<THR>A<C> R<THR>A<O> central_sep2 1.97049
+R<THR>A<C> R<THR>A<O> sep1 -1.28222
+R<THR>A<C> R<THR>A<O> sep2 0.76445
+R<THR>A<C> R<THR>A<OG1> central_sep1 1.55515
+R<THR>A<C> R<THR>A<OG1> central_sep2 0.649113
+R<THR>A<C> R<THR>A<OG1> sep1 -0.332321
+R<THR>A<C> R<THR>A<OG1> sep2 0.0633299
+R<THR>A<C> R<TRP>A<C> central_sep1 3.58741
+R<THR>A<C> R<TRP>A<C> central_sep2 3.40273
+R<THR>A<C> R<TRP>A<C> sep1 -2.58373
+R<THR>A<C> R<TRP>A<C> sep2 2.74333
+R<THR>A<C> R<TRP>A<CA> central_sep1 4.35797
+R<THR>A<C> R<TRP>A<CA> central_sep2 2.26797
+R<THR>A<C> R<TRP>A<CA> sep1 -2.87492
+R<THR>A<C> R<TRP>A<CA> sep2 0.72149
+R<THR>A<C> R<TRP>A<CB> central_sep1 2.0383
+R<THR>A<C> R<TRP>A<CB> central_sep2 0.756325
+R<THR>A<C> R<TRP>A<CB> sep1 -0.234437
+R<THR>A<C> R<TRP>A<CB> sep2 -0.384879
+R<THR>A<C> R<TRP>A<CD1> central_sep1 -0.922501
+R<THR>A<C> R<TRP>A<CD1> central_sep2 -0.247688
+R<THR>A<C> R<TRP>A<CD1> sep1 -0.705132
+R<THR>A<C> R<TRP>A<CD1> sep2 -0.58233
+R<THR>A<C> R<TRP>A<CD2> central_sep1 -0.36734
+R<THR>A<C> R<TRP>A<CD2> central_sep2 1.17182
+R<THR>A<C> R<TRP>A<CD2> sep1 -0.400765
+R<THR>A<C> R<TRP>A<CD2> sep2 0.827541
+R<THR>A<C> R<TRP>A<CE2> central_sep1 0.324685
+R<THR>A<C> R<TRP>A<CE2> central_sep2 0.589146
+R<THR>A<C> R<TRP>A<CE2> sep1 1.47014
+R<THR>A<C> R<TRP>A<CE2> sep2 0.00361769
+R<THR>A<C> R<TRP>A<CE3> central_sep1 -0.917522
+R<THR>A<C> R<TRP>A<CE3> central_sep2 -1.08375
+R<THR>A<C> R<TRP>A<CE3> sep1 0.467396
+R<THR>A<C> R<TRP>A<CE3> sep2 -0.434177
+R<THR>A<C> R<TRP>A<CG> central_sep1 1.58603
+R<THR>A<C> R<TRP>A<CG> central_sep2 0.607823
+R<THR>A<C> R<TRP>A<CG> sep1 -1.35848
+R<THR>A<C> R<TRP>A<CG> sep2 0.261477
+R<THR>A<C> R<TRP>A<CH2> central_sep1 2.18483
+R<THR>A<C> R<TRP>A<CH2> central_sep2 -0.571984
+R<THR>A<C> R<TRP>A<CH2> sep1 2.67159
+R<THR>A<C> R<TRP>A<CH2> sep2 -0.772127
+R<THR>A<C> R<TRP>A<CZ2> central_sep1 1.70869
+R<THR>A<C> R<TRP>A<CZ2> central_sep2 -0.439979
+R<THR>A<C> R<TRP>A<CZ2> sep1 3.28373
+R<THR>A<C> R<TRP>A<CZ2> sep2 -0.784836
+R<THR>A<C> R<TRP>A<CZ3> central_sep1 0.741825
+R<THR>A<C> R<TRP>A<CZ3> central_sep2 -0.543154
+R<THR>A<C> R<TRP>A<CZ3> sep1 1.61988
+R<THR>A<C> R<TRP>A<CZ3> sep2 -0.99714
+R<THR>A<C> R<TRP>A<N> central_sep1 -0.544414
+R<THR>A<C> R<TRP>A<N> central_sep2 3.32632
+R<THR>A<C> R<TRP>A<N> sep1 -1.58561
+R<THR>A<C> R<TRP>A<N> sep2 1.24981
+R<THR>A<C> R<TRP>A<NE1> central_sep1 1.33535
+R<THR>A<C> R<TRP>A<NE1> central_sep2 -0.182345
+R<THR>A<C> R<TRP>A<NE1> sep1 1.48451
+R<THR>A<C> R<TRP>A<NE1> sep2 -0.566442
+R<THR>A<C> R<TRP>A<O> central_sep1 -0.456153
+R<THR>A<C> R<TRP>A<O> central_sep2 2.37438
+R<THR>A<C> R<TRP>A<O> sep1 -1.33306
+R<THR>A<C> R<TRP>A<O> sep2 1.24425
+R<THR>A<C> R<TYR>A<C> central_sep1 3.91102
+R<THR>A<C> R<TYR>A<C> central_sep2 3.57753
+R<THR>A<C> R<TYR>A<C> sep1 -2.4352
+R<THR>A<C> R<TYR>A<C> sep2 2.06511
+R<THR>A<C> R<TYR>A<CA> central_sep1 4.09625
+R<THR>A<C> R<TYR>A<CA> central_sep2 2.4629
+R<THR>A<C> R<TYR>A<CA> sep1 -2.78279
+R<THR>A<C> R<TYR>A<CA> sep2 0.604419
+R<THR>A<C> R<TYR>A<CB> central_sep1 1.82014
+R<THR>A<C> R<TYR>A<CB> central_sep2 0.507561
+R<THR>A<C> R<TYR>A<CB> sep1 -0.342607
+R<THR>A<C> R<TYR>A<CB> sep2 -0.306648
+R<THR>A<C> R<TYR>A<CD1> central_sep1 -0.768709
+R<THR>A<C> R<TYR>A<CD1> central_sep2 -0.353058
+R<THR>A<C> R<TYR>A<CD1> sep1 -0.6847
+R<THR>A<C> R<TYR>A<CD1> sep2 -0.614321
+R<THR>A<C> R<TYR>A<CE1> central_sep1 0.576391
+R<THR>A<C> R<TYR>A<CE1> central_sep2 -0.0237307
+R<THR>A<C> R<TYR>A<CE1> sep1 1.32444
+R<THR>A<C> R<TYR>A<CE1> sep2 -0.379616
+R<THR>A<C> R<TYR>A<CG> central_sep1 0.975903
+R<THR>A<C> R<TYR>A<CG> central_sep2 0.742451
+R<THR>A<C> R<TYR>A<CG> sep1 -1.94081
+R<THR>A<C> R<TYR>A<CG> sep2 -0.0845778
+R<THR>A<C> R<TYR>A<CZ> central_sep1 1.16126
+R<THR>A<C> R<TYR>A<CZ> central_sep2 0.666615
+R<THR>A<C> R<TYR>A<CZ> sep1 1.59503
+R<THR>A<C> R<TYR>A<CZ> sep2 -0.0193604
+R<THR>A<C> R<TYR>A<N> central_sep1 -0.528991
+R<THR>A<C> R<TYR>A<N> central_sep2 2.73623
+R<THR>A<C> R<TYR>A<N> sep1 -1.59527
+R<THR>A<C> R<TYR>A<N> sep2 1.71519
+R<THR>A<C> R<TYR>A<O> central_sep1 -0.350628
+R<THR>A<C> R<TYR>A<O> central_sep2 2.06104
+R<THR>A<C> R<TYR>A<O> sep1 -1.2024
+R<THR>A<C> R<TYR>A<O> sep2 1.0558
+R<THR>A<C> R<TYR>A<OH> central_sep1 3.14144
+R<THR>A<C> R<TYR>A<OH> central_sep2 0.555982
+R<THR>A<C> R<TYR>A<OH> sep1 3.47322
+R<THR>A<C> R<TYR>A<OH> sep2 -0.136209
+R<THR>A<C> R<VAL>A<C> central_sep1 4.59724
+R<THR>A<C> R<VAL>A<C> central_sep2 3.67051
+R<THR>A<C> R<VAL>A<C> sep1 -2.66291
+R<THR>A<C> R<VAL>A<C> sep2 2.48734
+R<THR>A<C> R<VAL>A<CA> central_sep1 4.44183
+R<THR>A<C> R<VAL>A<CA> central_sep2 2.62594
+R<THR>A<C> R<VAL>A<CA> sep1 -2.94164
+R<THR>A<C> R<VAL>A<CA> sep2 0.810006
+R<THR>A<C> R<VAL>A<CB> central_sep1 2.19958
+R<THR>A<C> R<VAL>A<CB> central_sep2 0.609093
+R<THR>A<C> R<VAL>A<CB> sep1 0.0542634
+R<THR>A<C> R<VAL>A<CB> sep2 -0.560782
+R<THR>A<C> R<VAL>A<CG1> central_sep1 0.306604
+R<THR>A<C> R<VAL>A<CG1> central_sep2 0.0484482
+R<THR>A<C> R<VAL>A<CG1> sep1 -0.567388
+R<THR>A<C> R<VAL>A<CG1> sep2 -0.603598
+R<THR>A<C> R<VAL>A<CG2> central_sep1 0.707029
+R<THR>A<C> R<VAL>A<CG2> central_sep2 -0.0203819
+R<THR>A<C> R<VAL>A<CG2> sep1 -1.05295
+R<THR>A<C> R<VAL>A<CG2> sep2 -0.398536
+R<THR>A<C> R<VAL>A<N> central_sep1 0.0991086
+R<THR>A<C> R<VAL>A<N> central_sep2 3.07998
+R<THR>A<C> R<VAL>A<N> sep1 -1.41202
+R<THR>A<C> R<VAL>A<N> sep2 1.64283
+R<THR>A<C> R<VAL>A<O> central_sep1 -0.279991
+R<THR>A<C> R<VAL>A<O> central_sep2 2.39453
+R<THR>A<C> R<VAL>A<O> sep1 -1.12395
+R<THR>A<C> R<VAL>A<O> sep2 0.84043
+R<THR>A<C> c<solvent> . 1.92461
+R<THR>A<CA> R<THR>A<CA> central_sep1 1.01676
+R<THR>A<CA> R<THR>A<CA> central_sep2 -0.827195
+R<THR>A<CA> R<THR>A<CA> sep1 3.49098
+R<THR>A<CA> R<THR>A<CA> sep2 0.251521
+R<THR>A<CA> R<THR>A<CB> central_sep1 -0.334814
+R<THR>A<CA> R<THR>A<CB> central_sep2 -0.00450779
+R<THR>A<CA> R<THR>A<CB> sep1 1.82889
+R<THR>A<CA> R<THR>A<CB> sep2 -0.176724
+R<THR>A<CA> R<THR>A<CG2> central_sep1 1.40078
+R<THR>A<CA> R<THR>A<CG2> central_sep2 -0.0181425
+R<THR>A<CA> R<THR>A<CG2> sep1 1.32317
+R<THR>A<CA> R<THR>A<CG2> sep2 0.174239
+R<THR>A<CA> R<THR>A<N> central_sep1 3.39217
+R<THR>A<CA> R<THR>A<N> central_sep2 1.33042
+R<THR>A<CA> R<THR>A<N> sep1 -2.25354
+R<THR>A<CA> R<THR>A<N> sep2 0.94299
+R<THR>A<CA> R<THR>A<O> central_sep1 1.26193
+R<THR>A<CA> R<THR>A<O> central_sep2 -0.771108
+R<THR>A<CA> R<THR>A<O> sep1 -2.06914
+R<THR>A<CA> R<THR>A<O> sep2 0.56319
+R<THR>A<CA> R<THR>A<OG1> central_sep1 0.531025
+R<THR>A<CA> R<THR>A<OG1> central_sep2 -0.00648583
+R<THR>A<CA> R<THR>A<OG1> sep1 1.21452
+R<THR>A<CA> R<THR>A<OG1> sep2 -0.0413776
+R<THR>A<CA> R<TRP>A<C> central_sep1 3.19044
+R<THR>A<CA> R<TRP>A<C> central_sep2 4.1718
+R<THR>A<CA> R<TRP>A<C> sep1 -2.76338
+R<THR>A<CA> R<TRP>A<C> sep2 0.985405
+R<THR>A<CA> R<TRP>A<CA> central_sep1 2.27755
+R<THR>A<CA> R<TRP>A<CA> central_sep2 0.402673
+R<THR>A<CA> R<TRP>A<CA> sep1 3.60549
+R<THR>A<CA> R<TRP>A<CA> sep2 0.641856
+R<THR>A<CA> R<TRP>A<CB> central_sep1 -0.236763
+R<THR>A<CA> R<TRP>A<CB> central_sep2 0.2367
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+R<THR>A<CB> c<solvent> . 0.0451396
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+R<TRP>A<C> R<TRP>A<CE2> central_sep1 0.583264
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+R<TRP>A<C> R<TRP>A<CE2> sep1 1.11287
+R<TRP>A<C> R<TRP>A<CE2> sep2 0.265501
+R<TRP>A<C> R<TRP>A<CE3> central_sep1 -0.675723
+R<TRP>A<C> R<TRP>A<CE3> central_sep2 -1.59882
+R<TRP>A<C> R<TRP>A<CE3> sep1 0.5092
+R<TRP>A<C> R<TRP>A<CE3> sep2 -1.00066
+R<TRP>A<C> R<TRP>A<CG> central_sep1 1.09133
+R<TRP>A<C> R<TRP>A<CG> central_sep2 1.27048
+R<TRP>A<C> R<TRP>A<CG> sep1 -1.11433
+R<TRP>A<C> R<TRP>A<CG> sep2 -0.351792
+R<TRP>A<C> R<TRP>A<CH2> central_sep1 2.87073
+R<TRP>A<C> R<TRP>A<CH2> central_sep2 -0.864323
+R<TRP>A<C> R<TRP>A<CH2> sep1 4.0258
+R<TRP>A<C> R<TRP>A<CH2> sep2 -1.17372
+R<TRP>A<C> R<TRP>A<CZ2> central_sep1 1.97936
+R<TRP>A<C> R<TRP>A<CZ2> central_sep2 -0.630411
+R<TRP>A<C> R<TRP>A<CZ2> sep1 2.76168
+R<TRP>A<C> R<TRP>A<CZ2> sep2 -0.884107
+R<TRP>A<C> R<TRP>A<CZ3> central_sep1 0.96123
+R<TRP>A<C> R<TRP>A<CZ3> central_sep2 -1.37178
+R<TRP>A<C> R<TRP>A<CZ3> sep1 1.82231
+R<TRP>A<C> R<TRP>A<CZ3> sep2 -1.37056
+R<TRP>A<C> R<TRP>A<N> central_sep1 -0.869068
+R<TRP>A<C> R<TRP>A<N> central_sep2 3.61179
+R<TRP>A<C> R<TRP>A<N> sep1 -1.88692
+R<TRP>A<C> R<TRP>A<N> sep2 1.62169
+R<TRP>A<C> R<TRP>A<NE1> central_sep1 1.52302
+R<TRP>A<C> R<TRP>A<NE1> central_sep2 -0.184905
+R<TRP>A<C> R<TRP>A<NE1> sep1 1.74491
+R<TRP>A<C> R<TRP>A<NE1> sep2 -1.3228
+R<TRP>A<C> R<TRP>A<O> central_sep1 -0.896188
+R<TRP>A<C> R<TRP>A<O> central_sep2 1.61347
+R<TRP>A<C> R<TRP>A<O> sep1 -1.11611
+R<TRP>A<C> R<TRP>A<O> sep2 0.591419
+R<TRP>A<C> R<TYR>A<C> central_sep1 4.42169
+R<TRP>A<C> R<TYR>A<C> central_sep2 3.5604
+R<TRP>A<C> R<TYR>A<C> sep1 -2.4767
+R<TRP>A<C> R<TYR>A<C> sep2 2.4131
+R<TRP>A<C> R<TYR>A<CA> central_sep1 3.09674
+R<TRP>A<C> R<TYR>A<CA> central_sep2 1.99725
+R<TRP>A<C> R<TYR>A<CA> sep1 -2.70518
+R<TRP>A<C> R<TYR>A<CA> sep2 0.717786
+R<TRP>A<C> R<TYR>A<CB> central_sep1 1.87424
+R<TRP>A<C> R<TYR>A<CB> central_sep2 0.369689
+R<TRP>A<C> R<TYR>A<CB> sep1 -0.266365
+R<TRP>A<C> R<TYR>A<CB> sep2 -0.446942
+R<TRP>A<C> R<TYR>A<CD1> central_sep1 -0.892914
+R<TRP>A<C> R<TYR>A<CD1> central_sep2 -0.371776
+R<TRP>A<C> R<TYR>A<CD1> sep1 -0.59868
+R<TRP>A<C> R<TYR>A<CD1> sep2 -0.865392
+R<TRP>A<C> R<TYR>A<CE1> central_sep1 0.901507
+R<TRP>A<C> R<TYR>A<CE1> central_sep2 -0.0372614
+R<TRP>A<C> R<TYR>A<CE1> sep1 1.61681
+R<TRP>A<C> R<TYR>A<CE1> sep2 -0.538366
+R<TRP>A<C> R<TYR>A<CG> central_sep1 1.20329
+R<TRP>A<C> R<TYR>A<CG> central_sep2 0.924578
+R<TRP>A<C> R<TYR>A<CG> sep1 -1.93634
+R<TRP>A<C> R<TYR>A<CG> sep2 -0.0855114
+R<TRP>A<C> R<TYR>A<CZ> central_sep1 1.57163
+R<TRP>A<C> R<TYR>A<CZ> central_sep2 0.503154
+R<TRP>A<C> R<TYR>A<CZ> sep1 2.12385
+R<TRP>A<C> R<TYR>A<CZ> sep2 0.0278634
+R<TRP>A<C> R<TYR>A<N> central_sep1 -0.603702
+R<TRP>A<C> R<TYR>A<N> central_sep2 4.62972
+R<TRP>A<C> R<TYR>A<N> sep1 -1.62556
+R<TRP>A<C> R<TYR>A<N> sep2 1.79005
+R<TRP>A<C> R<TYR>A<O> central_sep1 -0.765823
+R<TRP>A<C> R<TYR>A<O> central_sep2 1.84056
+R<TRP>A<C> R<TYR>A<O> sep1 -1.1845
+R<TRP>A<C> R<TYR>A<O> sep2 0.935501
+R<TRP>A<C> R<TYR>A<OH> central_sep1 3.19331
+R<TRP>A<C> R<TYR>A<OH> central_sep2 0.336357
+R<TRP>A<C> R<TYR>A<OH> sep1 4.1806
+R<TRP>A<C> R<TYR>A<OH> sep2 -0.0989732
+R<TRP>A<C> R<VAL>A<C> central_sep2 4.56477
+R<TRP>A<C> R<VAL>A<C> sep1 -2.49397
+R<TRP>A<C> R<VAL>A<C> sep2 3.66212
+R<TRP>A<C> R<VAL>A<CA> central_sep1 4.19788
+R<TRP>A<C> R<VAL>A<CA> central_sep2 3.41581
+R<TRP>A<C> R<VAL>A<CA> sep1 -2.59048
+R<TRP>A<C> R<VAL>A<CA> sep2 1.09526
+R<TRP>A<C> R<VAL>A<CB> central_sep1 1.38462
+R<TRP>A<C> R<VAL>A<CB> central_sep2 0.831512
+R<TRP>A<C> R<VAL>A<CB> sep1 0.00297216
+R<TRP>A<C> R<VAL>A<CB> sep2 -0.71361
+R<TRP>A<C> R<VAL>A<CG1> central_sep1 0.225725
+R<TRP>A<C> R<VAL>A<CG1> central_sep2 0.305449
+R<TRP>A<C> R<VAL>A<CG1> sep1 -0.378425
+R<TRP>A<C> R<VAL>A<CG1> sep2 -0.604275
+R<TRP>A<C> R<VAL>A<CG2> central_sep1 0.294362
+R<TRP>A<C> R<VAL>A<CG2> central_sep2 -0.036316
+R<TRP>A<C> R<VAL>A<CG2> sep1 -0.815898
+R<TRP>A<C> R<VAL>A<CG2> sep2 -0.597938
+R<TRP>A<C> R<VAL>A<N> central_sep1 -0.337833
+R<TRP>A<C> R<VAL>A<N> central_sep2 3.41488
+R<TRP>A<C> R<VAL>A<N> sep1 -1.43859
+R<TRP>A<C> R<VAL>A<N> sep2 1.79176
+R<TRP>A<C> R<VAL>A<O> central_sep1 -0.520525
+R<TRP>A<C> R<VAL>A<O> central_sep2 2.59222
+R<TRP>A<C> R<VAL>A<O> sep1 -0.879804
+R<TRP>A<C> R<VAL>A<O> sep2 1.42332
+R<TRP>A<C> c<solvent> . 2.30258
+R<TRP>A<CA> R<TRP>A<CA> central_sep1 0.339693
+R<TRP>A<CA> R<TRP>A<CA> central_sep2 -0.768655
+R<TRP>A<CA> R<TRP>A<CA> sep1 1.7768
+R<TRP>A<CA> R<TRP>A<CA> sep2 0.11435
+R<TRP>A<CA> R<TRP>A<CB> central_sep1 -1.13537
+R<TRP>A<CA> R<TRP>A<CB> central_sep2 -0.690256
+R<TRP>A<CA> R<TRP>A<CB> sep1 1.36355
+R<TRP>A<CA> R<TRP>A<CB> sep2 -0.0297194
+R<TRP>A<CA> R<TRP>A<CD1> central_sep1 -0.252624
+R<TRP>A<CA> R<TRP>A<CD1> central_sep2 -0.845282
+R<TRP>A<CA> R<TRP>A<CD1> sep1 0.453523
+R<TRP>A<CA> R<TRP>A<CD1> sep2 -0.362857
+R<TRP>A<CA> R<TRP>A<CD2> central_sep1 -0.0686188
+R<TRP>A<CA> R<TRP>A<CD2> central_sep2 -0.42784
+R<TRP>A<CA> R<TRP>A<CD2> sep1 0.134817
+R<TRP>A<CA> R<TRP>A<CD2> sep2 -1.38291
+R<TRP>A<CA> R<TRP>A<CE2> central_sep1 -0.21659
+R<TRP>A<CA> R<TRP>A<CE2> central_sep2 -0.572185
+R<TRP>A<CA> R<TRP>A<CE2> sep1 1.00252
+R<TRP>A<CA> R<TRP>A<CE2> sep2 -1.38832
+R<TRP>A<CA> R<TRP>A<CE3> central_sep1 -1.46419
+R<TRP>A<CA> R<TRP>A<CE3> central_sep2 -0.967275
+R<TRP>A<CA> R<TRP>A<CE3> sep1 0.600177
+R<TRP>A<CA> R<TRP>A<CE3> sep2 -0.951186
+R<TRP>A<CA> R<TRP>A<CG> central_sep1 0.800569
+R<TRP>A<CA> R<TRP>A<CG> central_sep2 -0.222682
+R<TRP>A<CA> R<TRP>A<CG> sep1 0.338803
+R<TRP>A<CA> R<TRP>A<CG> sep2 -2.05507
+R<TRP>A<CA> R<TRP>A<CH2> central_sep1 1.36213
+R<TRP>A<CA> R<TRP>A<CH2> central_sep2 -1.06658
+R<TRP>A<CA> R<TRP>A<CH2> sep1 2.39266
+R<TRP>A<CA> R<TRP>A<CH2> sep2 -0.900519
+R<TRP>A<CA> R<TRP>A<CZ2> central_sep1 0.907392
+R<TRP>A<CA> R<TRP>A<CZ2> central_sep2 -0.979087
+R<TRP>A<CA> R<TRP>A<CZ2> sep1 2.38564
+R<TRP>A<CA> R<TRP>A<CZ2> sep2 -0.774164
+R<TRP>A<CA> R<TRP>A<CZ3> central_sep1 0.593357
+R<TRP>A<CA> R<TRP>A<CZ3> central_sep2 -1.21304
+R<TRP>A<CA> R<TRP>A<CZ3> sep1 0.431442
+R<TRP>A<CA> R<TRP>A<CZ3> sep2 -0.800397
+R<TRP>A<CA> R<TRP>A<N> central_sep1 2.39836
+R<TRP>A<CA> R<TRP>A<N> central_sep2 0.662778
+R<TRP>A<CA> R<TRP>A<N> sep1 -2.14307
+R<TRP>A<CA> R<TRP>A<N> sep2 0.892914
+R<TRP>A<CA> R<TRP>A<NE1> central_sep1 0.480948
+R<TRP>A<CA> R<TRP>A<NE1> central_sep2 -0.368134
+R<TRP>A<CA> R<TRP>A<NE1> sep1 1.64816
+R<TRP>A<CA> R<TRP>A<NE1> sep2 -0.671542
+R<TRP>A<CA> R<TRP>A<O> central_sep1 1.12936
+R<TRP>A<CA> R<TRP>A<O> central_sep2 -1.24077
+R<TRP>A<CA> R<TRP>A<O> sep1 -1.97952
+R<TRP>A<CA> R<TRP>A<O> sep2 -0.431678
+R<TRP>A<CA> R<TYR>A<C> central_sep1 3.1091
+R<TRP>A<CA> R<TYR>A<C> central_sep2 2.77292
+R<TRP>A<CA> R<TYR>A<C> sep1 -2.79508
+R<TRP>A<CA> R<TYR>A<C> sep2 0.528123
+R<TRP>A<CA> R<TYR>A<CA> central_sep1 0.55946
+R<TRP>A<CA> R<TYR>A<CA> central_sep2 -0.586191
+R<TRP>A<CA> R<TYR>A<CA> sep1 3.12064
+R<TRP>A<CA> R<TYR>A<CA> sep2 0.315905
+R<TRP>A<CA> R<TYR>A<CB> central_sep1 -0.850041
+R<TRP>A<CA> R<TYR>A<CB> central_sep2 -0.398318
+R<TRP>A<CA> R<TYR>A<CB> sep1 1.26109
+R<TRP>A<CA> R<TYR>A<CB> sep2 -0.148816
+R<TRP>A<CA> R<TYR>A<CD1> central_sep1 -0.216126
+R<TRP>A<CA> R<TYR>A<CD1> central_sep2 -0.499112
+R<TRP>A<CA> R<TYR>A<CD1> sep1 -0.204191
+R<TRP>A<CA> R<TYR>A<CD1> sep2 -0.346634
+R<TRP>A<CA> R<TYR>A<CE1> central_sep1 0.727656
+R<TRP>A<CA> R<TYR>A<CE1> central_sep2 -0.391854
+R<TRP>A<CA> R<TYR>A<CE1> sep1 1.29547
+R<TRP>A<CA> R<TYR>A<CE1> sep2 -0.362074
+R<TRP>A<CA> R<TYR>A<CG> central_sep1 1.70683
+R<TRP>A<CA> R<TYR>A<CG> central_sep2 -0.212807
+R<TRP>A<CA> R<TYR>A<CG> sep1 1.40472
+R<TRP>A<CA> R<TYR>A<CG> sep2 -1.14191
+R<TRP>A<CA> R<TYR>A<CZ> central_sep1 0.944372
+R<TRP>A<CA> R<TYR>A<CZ> central_sep2 -0.0181352
+R<TRP>A<CA> R<TYR>A<CZ> sep1 1.51414
+R<TRP>A<CA> R<TYR>A<CZ> sep2 -1.19245
+R<TRP>A<CA> R<TYR>A<N> central_sep1 2.25532
+R<TRP>A<CA> R<TYR>A<N> central_sep2 1.45801
+R<TRP>A<CA> R<TYR>A<N> sep1 -2.22237
+R<TRP>A<CA> R<TYR>A<N> sep2 0.924216
+R<TRP>A<CA> R<TYR>A<O> central_sep1 0.67475
+R<TRP>A<CA> R<TYR>A<O> central_sep2 -1.45276
+R<TRP>A<CA> R<TYR>A<O> sep1 -2.06594
+R<TRP>A<CA> R<TYR>A<O> sep2 0.181874
+R<TRP>A<CA> R<TYR>A<OH> central_sep1 1.85842
+R<TRP>A<CA> R<TYR>A<OH> central_sep2 -0.351256
+R<TRP>A<CA> R<TYR>A<OH> sep1 2.54444
+R<TRP>A<CA> R<TYR>A<OH> sep2 -0.150556
+R<TRP>A<CA> R<VAL>A<C> central_sep2 3.51015
+R<TRP>A<CA> R<VAL>A<C> sep1 -2.79026
+R<TRP>A<CA> R<VAL>A<C> sep2 0.948465
+R<TRP>A<CA> R<VAL>A<CA> central_sep1 1.26979
+R<TRP>A<CA> R<VAL>A<CA> central_sep2 -0.0676477
+R<TRP>A<CA> R<VAL>A<CA> sep1 3.82219
+R<TRP>A<CA> R<VAL>A<CA> sep2 0.690527
+R<TRP>A<CA> R<VAL>A<CB> central_sep1 -1.03412
+R<TRP>A<CA> R<VAL>A<CB> central_sep2 -0.451796
+R<TRP>A<CA> R<VAL>A<CB> sep1 1.17597
+R<TRP>A<CA> R<VAL>A<CB> sep2 0.104775
+R<TRP>A<CA> R<VAL>A<CG1> central_sep1 0.82276
+R<TRP>A<CA> R<VAL>A<CG1> central_sep2 -0.113602
+R<TRP>A<CA> R<VAL>A<CG1> sep1 1.32272
+R<TRP>A<CA> R<VAL>A<CG1> sep2 0.227315
+R<TRP>A<CA> R<VAL>A<CG2> central_sep1 -0.124248
+R<TRP>A<CA> R<VAL>A<CG2> central_sep2 -0.329585
+R<TRP>A<CA> R<VAL>A<CG2> sep1 1.34915
+R<TRP>A<CA> R<VAL>A<CG2> sep2 0.273091
+R<TRP>A<CA> R<VAL>A<N> central_sep1 2.72472
+R<TRP>A<CA> R<VAL>A<N> central_sep2 1.32945
+R<TRP>A<CA> R<VAL>A<N> sep1 -2.2359
+R<TRP>A<CA> R<VAL>A<N> sep2 0.244134
+R<TRP>A<CA> R<VAL>A<O> central_sep1 0.791216
+R<TRP>A<CA> R<VAL>A<O> central_sep2 -1.21435
+R<TRP>A<CA> R<VAL>A<O> sep1 -1.93859
+R<TRP>A<CA> R<VAL>A<O> sep2 0.164966
+R<TRP>A<CA> c<solvent> . 1.598
+R<TRP>A<CB> R<TRP>A<CB> central_sep1 -0.755957
+R<TRP>A<CB> R<TRP>A<CB> central_sep2 -1.78098
+R<TRP>A<CB> R<TRP>A<CB> sep1 1.39059
+R<TRP>A<CB> R<TRP>A<CB> sep2 -0.533617
+R<TRP>A<CB> R<TRP>A<CD1> central_sep1 -0.540169
+R<TRP>A<CB> R<TRP>A<CD1> central_sep2 -1.32231
+R<TRP>A<CB> R<TRP>A<CD1> sep1 0.821914
+R<TRP>A<CB> R<TRP>A<CD1> sep2 -1.06659
+R<TRP>A<CB> R<TRP>A<CD2> central_sep1 -0.507183
+R<TRP>A<CB> R<TRP>A<CD2> central_sep2 -1.52136
+R<TRP>A<CB> R<TRP>A<CD2> sep1 -0.251285
+R<TRP>A<CB> R<TRP>A<CD2> sep2 -1.99986
+R<TRP>A<CB> R<TRP>A<CE2> central_sep1 -1.23748
+R<TRP>A<CB> R<TRP>A<CE2> central_sep2 -1.49964
+R<TRP>A<CB> R<TRP>A<CE2> sep1 -0.303037
+R<TRP>A<CB> R<TRP>A<CE2> sep2 -2.0258
+R<TRP>A<CB> R<TRP>A<CE3> central_sep1 -1.14799
+R<TRP>A<CB> R<TRP>A<CE3> central_sep2 -2.09785
+R<TRP>A<CB> R<TRP>A<CE3> sep1 0.504418
+R<TRP>A<CB> R<TRP>A<CE3> sep2 -1.35373
+R<TRP>A<CB> R<TRP>A<CG> central_sep1 0.716074
+R<TRP>A<CB> R<TRP>A<CG> central_sep2 -1.09249
+R<TRP>A<CB> R<TRP>A<CG> sep1 0.0423014
+R<TRP>A<CB> R<TRP>A<CG> sep2 -2.3215
+R<TRP>A<CB> R<TRP>A<CH2> central_sep1 0.105479
+R<TRP>A<CB> R<TRP>A<CH2> central_sep2 -2.0748
+R<TRP>A<CB> R<TRP>A<CH2> sep1 1.06091
+R<TRP>A<CB> R<TRP>A<CH2> sep2 -1.85478
+R<TRP>A<CB> R<TRP>A<CZ2> central_sep1 -0.329783
+R<TRP>A<CB> R<TRP>A<CZ2> central_sep2 -1.76937
+R<TRP>A<CB> R<TRP>A<CZ2> sep1 1.36626
+R<TRP>A<CB> R<TRP>A<CZ2> sep2 -1.53798
+R<TRP>A<CB> R<TRP>A<CZ3> central_sep1 -0.655332
+R<TRP>A<CB> R<TRP>A<CZ3> central_sep2 -2.08009
+R<TRP>A<CB> R<TRP>A<CZ3> sep1 0.778855
+R<TRP>A<CB> R<TRP>A<CZ3> sep2 -1.89918
+R<TRP>A<CB> R<TRP>A<N> central_sep1 1.13319
+R<TRP>A<CB> R<TRP>A<N> central_sep2 0.362695
+R<TRP>A<CB> R<TRP>A<N> sep1 -1.02277
+R<TRP>A<CB> R<TRP>A<N> sep2 0.286607
+R<TRP>A<CB> R<TRP>A<NE1> central_sep1 -0.557155
+R<TRP>A<CB> R<TRP>A<NE1> central_sep2 -1.09448
+R<TRP>A<CB> R<TRP>A<NE1> sep1 0.682999
+R<TRP>A<CB> R<TRP>A<NE1> sep2 -1.38822
+R<TRP>A<CB> R<TRP>A<O> central_sep1 -1.61698
+R<TRP>A<CB> R<TRP>A<O> central_sep2 -0.874582
+R<TRP>A<CB> R<TRP>A<O> sep1 0.432307
+R<TRP>A<CB> R<TRP>A<O> sep2 -0.771257
+R<TRP>A<CB> R<TYR>A<C> central_sep1 1.32058
+R<TRP>A<CB> R<TYR>A<C> central_sep2 0.596299
+R<TRP>A<CB> R<TYR>A<C> sep1 -0.359846
+R<TRP>A<CB> R<TYR>A<C> sep2 -0.823395
+R<TRP>A<CB> R<TYR>A<CA> central_sep1 -0.925269
+R<TRP>A<CB> R<TYR>A<CA> central_sep2 -0.230345
+R<TRP>A<CB> R<TYR>A<CA> sep1 1.01611
+R<TRP>A<CB> R<TYR>A<CA> sep2 0.258699
+R<TRP>A<CB> R<TYR>A<CB> central_sep1 -0.242862
+R<TRP>A<CB> R<TYR>A<CB> central_sep2 -1.53025
+R<TRP>A<CB> R<TYR>A<CB> sep1 1.8671
+R<TRP>A<CB> R<TYR>A<CB> sep2 -0.758156
+R<TRP>A<CB> R<TYR>A<CD1> central_sep1 -0.451029
+R<TRP>A<CB> R<TYR>A<CD1> central_sep2 -1.38706
+R<TRP>A<CB> R<TYR>A<CD1> sep1 1.00077
+R<TRP>A<CB> R<TYR>A<CD1> sep2 -0.987987
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+R<TRP>A<CB> R<TYR>A<CE1> sep1 1.20812
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+R<TRP>A<CB> R<TYR>A<CG> sep1 0.752685
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+R<TRP>A<CB> R<TYR>A<CZ> sep1 0.0853622
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+R<TRP>A<CB> R<TYR>A<N> central_sep1 1.22
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+R<TRP>A<CB> R<TYR>A<N> sep1 -1.22335
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+R<TRP>A<CB> R<TYR>A<O> sep1 0.373458
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+R<TRP>A<CB> R<TYR>A<OH> sep1 2.0224
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+R<TRP>A<CB> R<VAL>A<C> central_sep2 1.23737
+R<TRP>A<CB> R<VAL>A<C> sep1 -0.159743
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+R<TRP>A<CB> R<VAL>A<CA> sep1 1.76891
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+R<TRP>A<CB> R<VAL>A<CB> sep1 1.54077
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+R<TRP>A<CB> R<VAL>A<CG1> sep1 1.73113
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+R<TRP>A<CD1> R<TRP>A<CD2> sep1 0.498078
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+R<TRP>A<CD1> R<TRP>A<CZ3> sep1 0.769807
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+R<TRP>A<CD1> R<TRP>A<O> sep1 0.770321
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+R<TRP>A<CD1> R<TYR>A<CA> sep1 0.253509
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+R<TRP>A<CD1> R<TYR>A<CD1> sep1 1.18998
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+R<TRP>A<CD1> R<TYR>A<CG> sep1 0.575864
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+R<TRP>A<CD1> R<TYR>A<CZ> sep1 0.712665
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+R<TRP>A<CD1> R<TYR>A<O> sep1 0.965588
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+R<TRP>A<CD1> R<TYR>A<OH> central_sep1 0.689929
+R<TRP>A<CD1> R<TYR>A<OH> central_sep2 -0.745934
+R<TRP>A<CD1> R<TYR>A<OH> sep1 1.78454
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+R<TRP>A<CD1> R<VAL>A<C> central_sep2 0.247012
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+R<TRP>A<CD1> R<VAL>A<CA> central_sep2 0.230879
+R<TRP>A<CD1> R<VAL>A<CA> sep1 0.563073
+R<TRP>A<CD1> R<VAL>A<CA> sep2 0.107915
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+R<TRP>A<CD1> R<VAL>A<CB> sep1 0.998091
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+R<TRP>A<CD1> R<VAL>A<CG2> sep1 1.44661
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+R<TRP>A<CD1> R<VAL>A<N> sep1 0.540265
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+R<TRP>A<CD2> R<TRP>A<CD2> central_sep2 -1.04681
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+R<TRP>A<CD2> R<TRP>A<CE2> central_sep2 -0.334276
+R<TRP>A<CD2> R<TRP>A<CE2> sep1 2.10838
+R<TRP>A<CD2> R<TRP>A<CE2> sep2 -1.30623
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+R<TRP>A<CD2> R<TRP>A<CE3> central_sep2 -2.06791
+R<TRP>A<CD2> R<TRP>A<CE3> sep1 0.295829
+R<TRP>A<CD2> R<TRP>A<CE3> sep2 -2.13626
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+R<TRP>A<CD2> R<TRP>A<CG> central_sep2 -1.47419
+R<TRP>A<CD2> R<TRP>A<CG> sep1 2.36991
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+R<TRP>A<CD2> R<TRP>A<CH2> central_sep2 -1.6874
+R<TRP>A<CD2> R<TRP>A<CH2> sep1 1.1815
+R<TRP>A<CD2> R<TRP>A<CH2> sep2 -2.28159
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+R<TRP>A<CD2> R<TRP>A<CZ2> central_sep2 -1.4409
+R<TRP>A<CD2> R<TRP>A<CZ2> sep1 0.731459
+R<TRP>A<CD2> R<TRP>A<CZ2> sep2 -2.21424
+R<TRP>A<CD2> R<TRP>A<CZ3> central_sep1 -0.631087
+R<TRP>A<CD2> R<TRP>A<CZ3> central_sep2 -1.64461
+R<TRP>A<CD2> R<TRP>A<CZ3> sep1 0.303404
+R<TRP>A<CD2> R<TRP>A<CZ3> sep2 -2.10045
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+R<TRP>A<CD2> R<TRP>A<N> central_sep2 0.326194
+R<TRP>A<CD2> R<TRP>A<N> sep1 0.0197951
+R<TRP>A<CD2> R<TRP>A<N> sep2 -0.460673
+R<TRP>A<CD2> R<TRP>A<NE1> central_sep1 -0.0827654
+R<TRP>A<CD2> R<TRP>A<NE1> central_sep2 -1.45204
+R<TRP>A<CD2> R<TRP>A<NE1> sep1 0.939374
+R<TRP>A<CD2> R<TRP>A<NE1> sep2 -1.83951
+R<TRP>A<CD2> R<TRP>A<O> central_sep1 -0.0990869
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+R<TRP>A<CD2> R<TRP>A<O> sep1 0.700233
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+R<TRP>A<CD2> R<TYR>A<C> central_sep1 -0.259675
+R<TRP>A<CD2> R<TYR>A<C> central_sep2 0.705285
+R<TRP>A<CD2> R<TYR>A<C> sep1 -0.213306
+R<TRP>A<CD2> R<TYR>A<C> sep2 -0.0331645
+R<TRP>A<CD2> R<TYR>A<CA> central_sep1 0.242175
+R<TRP>A<CD2> R<TYR>A<CA> central_sep2 -0.219556
+R<TRP>A<CD2> R<TYR>A<CA> sep1 0.561315
+R<TRP>A<CD2> R<TYR>A<CA> sep2 -1.12674
+R<TRP>A<CD2> R<TYR>A<CB> central_sep1 -0.539767
+R<TRP>A<CD2> R<TYR>A<CB> central_sep2 -1.41533
+R<TRP>A<CD2> R<TYR>A<CB> sep1 0.0543647
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+R<TRP>A<CD2> R<TYR>A<CD1> central_sep1 -0.930703
+R<TRP>A<CD2> R<TYR>A<CD1> central_sep2 -1.58173
+R<TRP>A<CD2> R<TYR>A<CD1> sep1 0.380024
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+R<TRP>A<CD2> R<TYR>A<CE1> central_sep1 0.536319
+R<TRP>A<CD2> R<TYR>A<CE1> central_sep2 -0.532387
+R<TRP>A<CD2> R<TYR>A<CE1> sep1 1.02332
+R<TRP>A<CD2> R<TYR>A<CE1> sep2 -1.34453
+R<TRP>A<CD2> R<TYR>A<CG> central_sep1 1.49045
+R<TRP>A<CD2> R<TYR>A<CG> central_sep2 -1.21705
+R<TRP>A<CD2> R<TYR>A<CG> sep1 1.77347
+R<TRP>A<CD2> R<TYR>A<CG> sep2 -1.87822
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+R<TRP>A<CD2> R<TYR>A<CZ> sep1 2.33698
+R<TRP>A<CD2> R<TYR>A<CZ> sep2 -0.482454
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+R<TRP>A<CD2> R<TYR>A<O> sep1 0.512175
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+R<TRP>A<CD2> R<TYR>A<OH> central_sep1 1.68333
+R<TRP>A<CD2> R<TYR>A<OH> central_sep2 0.456451
+R<TRP>A<CD2> R<TYR>A<OH> sep1 1.59416
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+R<TRP>A<CD2> R<VAL>A<C> central_sep1 -0.314957
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+R<TRP>A<CD2> R<VAL>A<C> sep1 -0.658283
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+R<TRP>A<CD2> R<VAL>A<CA> central_sep1 0.248281
+R<TRP>A<CD2> R<VAL>A<CA> central_sep2 0.885207
+R<TRP>A<CD2> R<VAL>A<CA> sep1 1.21194
+R<TRP>A<CD2> R<VAL>A<CA> sep2 -0.137672
+R<TRP>A<CD2> R<VAL>A<CB> central_sep1 0.0104052
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+R<TRP>A<CD2> R<VAL>A<CB> sep1 0.405361
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+R<TRP>A<CD2> R<VAL>A<CG1> central_sep2 -1.15455
+R<TRP>A<CD2> R<VAL>A<CG1> sep1 0.409267
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+R<TRP>A<CD2> R<VAL>A<CG2> central_sep1 -0.108666
+R<TRP>A<CD2> R<VAL>A<CG2> central_sep2 -1.3278
+R<TRP>A<CD2> R<VAL>A<CG2> sep1 0.391145
+R<TRP>A<CD2> R<VAL>A<CG2> sep2 -1.66203
+R<TRP>A<CD2> R<VAL>A<N> central_sep1 0.025259
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+R<TRP>A<CD2> R<VAL>A<N> sep1 0.216294
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+R<TRP>A<CD2> R<VAL>A<O> central_sep1 0.780304
+R<TRP>A<CD2> R<VAL>A<O> central_sep2 1.25357
+R<TRP>A<CD2> R<VAL>A<O> sep1 0.560287
+R<TRP>A<CD2> R<VAL>A<O> sep2 0.750018
+R<TRP>A<CD2> c<solvent> . 1.36838
+R<TRP>A<CE2> R<TRP>A<CE2> central_sep1 1.62194
+R<TRP>A<CE2> R<TRP>A<CE2> central_sep2 -0.747225
+R<TRP>A<CE2> R<TRP>A<CE2> sep1 1.2167
+R<TRP>A<CE2> R<TRP>A<CE2> sep2 -1.34006
+R<TRP>A<CE2> R<TRP>A<CE3> central_sep1 -1.19883
+R<TRP>A<CE2> R<TRP>A<CE3> central_sep2 -1.86518
+R<TRP>A<CE2> R<TRP>A<CE3> sep1 -0.227444
+R<TRP>A<CE2> R<TRP>A<CE3> sep2 -2.24015
+R<TRP>A<CE2> R<TRP>A<CG> central_sep1 0.960052
+R<TRP>A<CE2> R<TRP>A<CG> central_sep2 -1.31711
+R<TRP>A<CE2> R<TRP>A<CG> sep1 1.12164
+R<TRP>A<CE2> R<TRP>A<CG> sep2 -1.70824
+R<TRP>A<CE2> R<TRP>A<CH2> central_sep1 1.12369
+R<TRP>A<CE2> R<TRP>A<CH2> central_sep2 -1.2753
+R<TRP>A<CE2> R<TRP>A<CH2> sep1 0.854456
+R<TRP>A<CE2> R<TRP>A<CH2> sep2 -2.30952
+R<TRP>A<CE2> R<TRP>A<CZ2> central_sep1 0.908033
+R<TRP>A<CE2> R<TRP>A<CZ2> central_sep2 -1.2431
+R<TRP>A<CE2> R<TRP>A<CZ2> sep1 0.902327
+R<TRP>A<CE2> R<TRP>A<CZ2> sep2 -2.11306
+R<TRP>A<CE2> R<TRP>A<CZ3> central_sep1 -0.354788
+R<TRP>A<CE2> R<TRP>A<CZ3> central_sep2 -1.35081
+R<TRP>A<CE2> R<TRP>A<CZ3> sep1 0.0764616
+R<TRP>A<CE2> R<TRP>A<CZ3> sep2 -2.19253
+R<TRP>A<CE2> R<TRP>A<N> central_sep1 1.40532
+R<TRP>A<CE2> R<TRP>A<N> central_sep2 -0.169662
+R<TRP>A<CE2> R<TRP>A<N> sep1 1.3262
+R<TRP>A<CE2> R<TRP>A<N> sep2 -0.78101
+R<TRP>A<CE2> R<TRP>A<NE1> central_sep1 0.066677
+R<TRP>A<CE2> R<TRP>A<NE1> central_sep2 -1.16268
+R<TRP>A<CE2> R<TRP>A<NE1> sep1 0.877317
+R<TRP>A<CE2> R<TRP>A<NE1> sep2 -1.97509
+R<TRP>A<CE2> R<TRP>A<O> central_sep1 0.724804
+R<TRP>A<CE2> R<TRP>A<O> central_sep2 1.22621
+R<TRP>A<CE2> R<TRP>A<O> sep1 0.860541
+R<TRP>A<CE2> R<TRP>A<O> sep2 0.347645
+R<TRP>A<CE2> R<TYR>A<C> central_sep1 1.02406
+R<TRP>A<CE2> R<TYR>A<C> central_sep2 0.556219
+R<TRP>A<CE2> R<TYR>A<C> sep1 1.05575
+R<TRP>A<CE2> R<TYR>A<C> sep2 -0.369325
+R<TRP>A<CE2> R<TYR>A<CA> central_sep1 0.924591
+R<TRP>A<CE2> R<TYR>A<CA> central_sep2 -0.322772
+R<TRP>A<CE2> R<TYR>A<CA> sep1 1.37076
+R<TRP>A<CE2> R<TYR>A<CA> sep2 -1.1332
+R<TRP>A<CE2> R<TYR>A<CB> central_sep1 -1.07688
+R<TRP>A<CE2> R<TYR>A<CB> central_sep2 -1.4437
+R<TRP>A<CE2> R<TYR>A<CB> sep1 -0.224122
+R<TRP>A<CE2> R<TYR>A<CB> sep2 -1.88051
+R<TRP>A<CE2> R<TYR>A<CD1> central_sep1 -0.883387
+R<TRP>A<CE2> R<TYR>A<CD1> central_sep2 -1.4157
+R<TRP>A<CE2> R<TYR>A<CD1> sep1 0.354214
+R<TRP>A<CE2> R<TYR>A<CD1> sep2 -1.87865
+R<TRP>A<CE2> R<TYR>A<CE1> central_sep1 0.202206
+R<TRP>A<CE2> R<TYR>A<CE1> central_sep2 -0.405697
+R<TRP>A<CE2> R<TYR>A<CE1> sep1 1.02498
+R<TRP>A<CE2> R<TYR>A<CE1> sep2 -1.66582
+R<TRP>A<CE2> R<TYR>A<CG> central_sep1 0.899432
+R<TRP>A<CE2> R<TYR>A<CG> central_sep2 -1.1637
+R<TRP>A<CE2> R<TYR>A<CG> sep1 1.06142
+R<TRP>A<CE2> R<TYR>A<CG> sep2 -1.75533
+R<TRP>A<CE2> R<TYR>A<CZ> central_sep1 1.69163
+R<TRP>A<CE2> R<TYR>A<CZ> central_sep2 0.338753
+R<TRP>A<CE2> R<TYR>A<CZ> sep1 1.17388
+R<TRP>A<CE2> R<TYR>A<CZ> sep2 -0.553432
+R<TRP>A<CE2> R<TYR>A<N> central_sep1 2.04154
+R<TRP>A<CE2> R<TYR>A<N> central_sep2 0.515317
+R<TRP>A<CE2> R<TYR>A<N> sep1 1.73423
+R<TRP>A<CE2> R<TYR>A<N> sep2 -0.185946
+R<TRP>A<CE2> R<TYR>A<O> central_sep1 0.924605
+R<TRP>A<CE2> R<TYR>A<O> central_sep2 1.48289
+R<TRP>A<CE2> R<TYR>A<O> sep1 0.878126
+R<TRP>A<CE2> R<TYR>A<O> sep2 0.258677
+R<TRP>A<CE2> R<TYR>A<OH> central_sep1 2.69234
+R<TRP>A<CE2> R<TYR>A<OH> central_sep2 0.955376
+R<TRP>A<CE2> R<TYR>A<OH> sep1 2.17493
+R<TRP>A<CE2> R<TYR>A<OH> sep2 -0.827054
+R<TRP>A<CE2> R<VAL>A<C> central_sep1 0.578871
+R<TRP>A<CE2> R<VAL>A<C> central_sep2 1.64362
+R<TRP>A<CE2> R<VAL>A<C> sep1 1.52773
+R<TRP>A<CE2> R<VAL>A<C> sep2 0.63528
+R<TRP>A<CE2> R<VAL>A<CA> central_sep1 0.941287
+R<TRP>A<CE2> R<VAL>A<CA> central_sep2 0.483519
+R<TRP>A<CE2> R<VAL>A<CA> sep1 1.52326
+R<TRP>A<CE2> R<VAL>A<CA> sep2 -0.193259
+R<TRP>A<CE2> R<VAL>A<CB> central_sep1 -0.384118
+R<TRP>A<CE2> R<VAL>A<CB> central_sep2 -1.17632
+R<TRP>A<CE2> R<VAL>A<CB> sep1 0.614963
+R<TRP>A<CE2> R<VAL>A<CB> sep2 -1.38975
+R<TRP>A<CE2> R<VAL>A<CG1> central_sep1 -0.672765
+R<TRP>A<CE2> R<VAL>A<CG1> central_sep2 -1.07567
+R<TRP>A<CE2> R<VAL>A<CG1> sep1 0.376705
+R<TRP>A<CE2> R<VAL>A<CG1> sep2 -1.64792
+R<TRP>A<CE2> R<VAL>A<CG2> central_sep1 -0.648804
+R<TRP>A<CE2> R<VAL>A<CG2> central_sep2 -1.19303
+R<TRP>A<CE2> R<VAL>A<CG2> sep1 0.722966
+R<TRP>A<CE2> R<VAL>A<CG2> sep2 -1.76997
+R<TRP>A<CE2> R<VAL>A<N> central_sep1 2.41696
+R<TRP>A<CE2> R<VAL>A<N> central_sep2 1.12206
+R<TRP>A<CE2> R<VAL>A<N> sep1 2.22782
+R<TRP>A<CE2> R<VAL>A<N> sep2 0.258003
+R<TRP>A<CE2> R<VAL>A<O> central_sep1 0.868266
+R<TRP>A<CE2> R<VAL>A<O> central_sep2 1.89633
+R<TRP>A<CE2> R<VAL>A<O> sep1 1.49319
+R<TRP>A<CE2> R<VAL>A<O> sep2 0.667176
+R<TRP>A<CE2> c<solvent> . 1.32701
+R<TRP>A<CE3> R<TRP>A<CE3> central_sep1 -1.15868
+R<TRP>A<CE3> R<TRP>A<CE3> central_sep2 -1.94357
+R<TRP>A<CE3> R<TRP>A<CE3> sep1 0.166671
+R<TRP>A<CE3> R<TRP>A<CE3> sep2 -1.85965
+R<TRP>A<CE3> R<TRP>A<CG> central_sep1 -0.853299
+R<TRP>A<CE3> R<TRP>A<CG> central_sep2 -1.57328
+R<TRP>A<CE3> R<TRP>A<CG> sep1 -0.838829
+R<TRP>A<CE3> R<TRP>A<CG> sep2 -2.74577
+R<TRP>A<CE3> R<TRP>A<CH2> central_sep1 -0.20795
+R<TRP>A<CE3> R<TRP>A<CH2> central_sep2 -1.78692
+R<TRP>A<CE3> R<TRP>A<CH2> sep1 1.03551
+R<TRP>A<CE3> R<TRP>A<CH2> sep2 -1.92236
+R<TRP>A<CE3> R<TRP>A<CZ2> central_sep1 -0.612188
+R<TRP>A<CE3> R<TRP>A<CZ2> central_sep2 -1.60489
+R<TRP>A<CE3> R<TRP>A<CZ2> sep1 0.817826
+R<TRP>A<CE3> R<TRP>A<CZ2> sep2 -1.81001
+R<TRP>A<CE3> R<TRP>A<CZ3> central_sep1 -0.907829
+R<TRP>A<CE3> R<TRP>A<CZ3> central_sep2 -1.73291
+R<TRP>A<CE3> R<TRP>A<CZ3> sep1 0.714194
+R<TRP>A<CE3> R<TRP>A<CZ3> sep2 -2.02612
+R<TRP>A<CE3> R<TRP>A<N> central_sep1 -0.723097
+R<TRP>A<CE3> R<TRP>A<N> central_sep2 -0.604282
+R<TRP>A<CE3> R<TRP>A<N> sep1 0.380911
+R<TRP>A<CE3> R<TRP>A<N> sep2 -0.400295
+R<TRP>A<CE3> R<TRP>A<NE1> central_sep1 -0.660573
+R<TRP>A<CE3> R<TRP>A<NE1> central_sep2 -1.19295
+R<TRP>A<CE3> R<TRP>A<NE1> sep1 0.765375
+R<TRP>A<CE3> R<TRP>A<NE1> sep2 -1.55822
+R<TRP>A<CE3> R<TRP>A<O> central_sep1 -0.232478
+R<TRP>A<CE3> R<TRP>A<O> central_sep2 -0.581815
+R<TRP>A<CE3> R<TRP>A<O> sep1 1.02019
+R<TRP>A<CE3> R<TRP>A<O> sep2 -0.295392
+R<TRP>A<CE3> R<TYR>A<C> central_sep1 -0.760281
+R<TRP>A<CE3> R<TYR>A<C> central_sep2 -1.83279
+R<TRP>A<CE3> R<TYR>A<C> sep1 0.323229
+R<TRP>A<CE3> R<TYR>A<C> sep2 -0.958636
+R<TRP>A<CE3> R<TYR>A<CA> central_sep1 -1.31418
+R<TRP>A<CE3> R<TYR>A<CA> central_sep2 -0.59978
+R<TRP>A<CE3> R<TYR>A<CA> sep1 0.826527
+R<TRP>A<CE3> R<TYR>A<CA> sep2 -0.695412
+R<TRP>A<CE3> R<TYR>A<CB> central_sep1 -0.991395
+R<TRP>A<CE3> R<TYR>A<CB> central_sep2 -1.98699
+R<TRP>A<CE3> R<TYR>A<CB> sep1 0.535731
+R<TRP>A<CE3> R<TYR>A<CB> sep2 -1.34107
+R<TRP>A<CE3> R<TYR>A<CD1> central_sep1 -0.995851
+R<TRP>A<CE3> R<TYR>A<CD1> central_sep2 -1.3915
+R<TRP>A<CE3> R<TYR>A<CD1> sep1 0.519791
+R<TRP>A<CE3> R<TYR>A<CD1> sep2 -1.47799
+R<TRP>A<CE3> R<TYR>A<CE1> central_sep1 -0.638366
+R<TRP>A<CE3> R<TYR>A<CE1> central_sep2 -0.950017
+R<TRP>A<CE3> R<TYR>A<CE1> sep1 1.22962
+R<TRP>A<CE3> R<TYR>A<CE1> sep2 -1.13693
+R<TRP>A<CE3> R<TYR>A<CG> central_sep1 -0.497648
+R<TRP>A<CE3> R<TYR>A<CG> central_sep2 -1.74771
+R<TRP>A<CE3> R<TYR>A<CG> sep1 -0.334606
+R<TRP>A<CE3> R<TYR>A<CG> sep2 -2.51661
+R<TRP>A<CE3> R<TYR>A<CZ> central_sep1 -0.38942
+R<TRP>A<CE3> R<TYR>A<CZ> central_sep2 -0.936693
+R<TRP>A<CE3> R<TYR>A<CZ> sep1 0.416683
+R<TRP>A<CE3> R<TYR>A<CZ> sep2 -1.52818
+R<TRP>A<CE3> R<TYR>A<N> central_sep1 -0.593866
+R<TRP>A<CE3> R<TYR>A<N> central_sep2 -0.481018
+R<TRP>A<CE3> R<TYR>A<N> sep1 0.572865
+R<TRP>A<CE3> R<TYR>A<N> sep2 -0.649248
+R<TRP>A<CE3> R<TYR>A<O> central_sep1 -0.351775
+R<TRP>A<CE3> R<TYR>A<O> central_sep2 -0.733593
+R<TRP>A<CE3> R<TYR>A<O> sep1 1.01671
+R<TRP>A<CE3> R<TYR>A<O> sep2 -0.386716
+R<TRP>A<CE3> R<TYR>A<OH> central_sep1 0.396709
+R<TRP>A<CE3> R<TYR>A<OH> central_sep2 -0.619023
+R<TRP>A<CE3> R<TYR>A<OH> sep1 2.29308
+R<TRP>A<CE3> R<TYR>A<OH> sep2 -0.517139
+R<TRP>A<CE3> R<VAL>A<C> central_sep1 -0.642375
+R<TRP>A<CE3> R<VAL>A<C> central_sep2 -1.19904
+R<TRP>A<CE3> R<VAL>A<C> sep1 0.394026
+R<TRP>A<CE3> R<VAL>A<C> sep2 -0.753753
+R<TRP>A<CE3> R<VAL>A<CA> central_sep1 -1.10547
+R<TRP>A<CE3> R<VAL>A<CA> central_sep2 -0.0249128
+R<TRP>A<CE3> R<VAL>A<CA> sep1 1.01982
+R<TRP>A<CE3> R<VAL>A<CA> sep2 -0.243973
+R<TRP>A<CE3> R<VAL>A<CB> central_sep1 -1.05747
+R<TRP>A<CE3> R<VAL>A<CB> central_sep2 -1.16228
+R<TRP>A<CE3> R<VAL>A<CB> sep1 0.932936
+R<TRP>A<CE3> R<VAL>A<CB> sep2 -1.24865
+R<TRP>A<CE3> R<VAL>A<CG1> central_sep1 -0.655342
+R<TRP>A<CE3> R<VAL>A<CG1> central_sep2 -1.37631
+R<TRP>A<CE3> R<VAL>A<CG1> sep1 1.27784
+R<TRP>A<CE3> R<VAL>A<CG1> sep2 -0.971799
+R<TRP>A<CE3> R<VAL>A<CG2> central_sep1 -0.91834
+R<TRP>A<CE3> R<VAL>A<CG2> central_sep2 -1.35792
+R<TRP>A<CE3> R<VAL>A<CG2> sep1 1.26882
+R<TRP>A<CE3> R<VAL>A<CG2> sep2 -1.13726
+R<TRP>A<CE3> R<VAL>A<N> central_sep1 -0.134029
+R<TRP>A<CE3> R<VAL>A<N> central_sep2 -0.0054719
+R<TRP>A<CE3> R<VAL>A<N> sep1 0.817233
+R<TRP>A<CE3> R<VAL>A<N> sep2 0.155913
+R<TRP>A<CE3> R<VAL>A<O> central_sep1 0.0563911
+R<TRP>A<CE3> R<VAL>A<O> central_sep2 -0.35258
+R<TRP>A<CE3> R<VAL>A<O> sep1 1.38602
+R<TRP>A<CE3> R<VAL>A<O> sep2 -0.088522
+R<TRP>A<CE3> c<solvent> . 1.30254
+R<TRP>A<CG> R<TRP>A<CG> central_sep1 1.04697
+R<TRP>A<CG> R<TRP>A<CG> central_sep2 -2.21677
+R<TRP>A<CG> R<TRP>A<CG> sep1 3.05969
+R<TRP>A<CG> R<TRP>A<CG> sep2 -1.95304
+R<TRP>A<CG> R<TRP>A<CH2> central_sep1 0.191882
+R<TRP>A<CG> R<TRP>A<CH2> central_sep2 -1.72158
+R<TRP>A<CG> R<TRP>A<CH2> sep1 0.78397
+R<TRP>A<CG> R<TRP>A<CH2> sep2 -2.89665
+R<TRP>A<CG> R<TRP>A<CZ2> central_sep1 -0.0261793
+R<TRP>A<CG> R<TRP>A<CZ2> central_sep2 -1.50786
+R<TRP>A<CG> R<TRP>A<CZ2> sep1 -0.15192
+R<TRP>A<CG> R<TRP>A<CZ2> sep2 -2.83808
+R<TRP>A<CG> R<TRP>A<CZ3> central_sep1 -0.126011
+R<TRP>A<CG> R<TRP>A<CZ3> central_sep2 -1.57792
+R<TRP>A<CG> R<TRP>A<CZ3> sep1 -0.255856
+R<TRP>A<CG> R<TRP>A<CZ3> sep2 -2.83501
+R<TRP>A<CG> R<TRP>A<N> central_sep1 -1.26422
+R<TRP>A<CG> R<TRP>A<N> central_sep2 0.820533
+R<TRP>A<CG> R<TRP>A<N> sep1 -0.912785
+R<TRP>A<CG> R<TRP>A<N> sep2 -0.156996
+R<TRP>A<CG> R<TRP>A<NE1> central_sep1 0.602014
+R<TRP>A<CG> R<TRP>A<NE1> central_sep2 -1.06632
+R<TRP>A<CG> R<TRP>A<NE1> sep1 0.254906
+R<TRP>A<CG> R<TRP>A<NE1> sep2 -2.1839
+R<TRP>A<CG> R<TRP>A<O> central_sep1 -0.236819
+R<TRP>A<CG> R<TRP>A<O> central_sep2 0.905415
+R<TRP>A<CG> R<TRP>A<O> sep1 0.177569
+R<TRP>A<CG> R<TRP>A<O> sep2 -0.401015
+R<TRP>A<CG> R<TYR>A<C> central_sep1 0.889
+R<TRP>A<CG> R<TYR>A<C> central_sep2 0.950131
+R<TRP>A<CG> R<TYR>A<C> sep1 -1.06661
+R<TRP>A<CG> R<TYR>A<C> sep2 -0.11119
+R<TRP>A<CG> R<TYR>A<CA> central_sep1 0.407411
+R<TRP>A<CG> R<TYR>A<CA> central_sep2 0.20701
+R<TRP>A<CG> R<TYR>A<CA> sep1 0.795324
+R<TRP>A<CG> R<TYR>A<CA> sep2 -1.51456
+R<TRP>A<CG> R<TYR>A<CB> central_sep1 0.488739
+R<TRP>A<CG> R<TYR>A<CB> central_sep2 -0.910678
+R<TRP>A<CG> R<TYR>A<CB> sep1 0.306125
+R<TRP>A<CG> R<TYR>A<CB> sep2 -2.12539
+R<TRP>A<CG> R<TYR>A<CD1> central_sep1 0.136198
+R<TRP>A<CG> R<TYR>A<CD1> central_sep2 -1.25225
+R<TRP>A<CG> R<TYR>A<CD1> sep1 -0.112169
+R<TRP>A<CG> R<TYR>A<CD1> sep2 -2.33275
+R<TRP>A<CG> R<TYR>A<CE1> central_sep1 1.4853
+R<TRP>A<CG> R<TYR>A<CE1> central_sep2 -0.83163
+R<TRP>A<CG> R<TYR>A<CE1> sep1 0.562974
+R<TRP>A<CG> R<TYR>A<CE1> sep2 -2.0506
+R<TRP>A<CG> R<TYR>A<CG> central_sep1 1.48605
+R<TRP>A<CG> R<TYR>A<CG> central_sep2 -1.55404
+R<TRP>A<CG> R<TYR>A<CG> sep1 1.47884
+R<TRP>A<CG> R<TYR>A<CG> sep2 -2.23732
+R<TRP>A<CG> R<TYR>A<CZ> central_sep1 0.893321
+R<TRP>A<CG> R<TYR>A<CZ> central_sep2 -0.830576
+R<TRP>A<CG> R<TYR>A<CZ> sep1 0.74375
+R<TRP>A<CG> R<TYR>A<CZ> sep2 -1.48391
+R<TRP>A<CG> R<TYR>A<N> central_sep1 -0.754924
+R<TRP>A<CG> R<TYR>A<N> central_sep2 1.25329
+R<TRP>A<CG> R<TYR>A<N> sep1 -0.453367
+R<TRP>A<CG> R<TYR>A<N> sep2 -0.114036
+R<TRP>A<CG> R<TYR>A<O> central_sep1 -0.0677681
+R<TRP>A<CG> R<TYR>A<O> central_sep2 1.0685
+R<TRP>A<CG> R<TYR>A<O> sep1 0.017584
+R<TRP>A<CG> R<TYR>A<O> sep2 -0.588185
+R<TRP>A<CG> R<TYR>A<OH> central_sep1 1.97928
+R<TRP>A<CG> R<TYR>A<OH> central_sep2 0.0544519
+R<TRP>A<CG> R<TYR>A<OH> sep1 0.678342
+R<TRP>A<CG> R<TYR>A<OH> sep2 -1.68991
+R<TRP>A<CG> R<VAL>A<C> central_sep1 1.69034
+R<TRP>A<CG> R<VAL>A<C> central_sep2 1.70578
+R<TRP>A<CG> R<VAL>A<C> sep1 -1.25313
+R<TRP>A<CG> R<VAL>A<C> sep2 0.140259
+R<TRP>A<CG> R<VAL>A<CA> central_sep1 0.583203
+R<TRP>A<CG> R<VAL>A<CA> central_sep2 0.441861
+R<TRP>A<CG> R<VAL>A<CA> sep1 1.26851
+R<TRP>A<CG> R<VAL>A<CA> sep2 -0.152737
+R<TRP>A<CG> R<VAL>A<CB> central_sep1 0.630204
+R<TRP>A<CG> R<VAL>A<CB> central_sep2 -0.864557
+R<TRP>A<CG> R<VAL>A<CB> sep1 0.6962
+R<TRP>A<CG> R<VAL>A<CB> sep2 -2.09283
+R<TRP>A<CG> R<VAL>A<CG1> central_sep1 1.10035
+R<TRP>A<CG> R<VAL>A<CG1> central_sep2 -0.877136
+R<TRP>A<CG> R<VAL>A<CG1> sep1 0.311412
+R<TRP>A<CG> R<VAL>A<CG1> sep2 -2.24104
+R<TRP>A<CG> R<VAL>A<CG2> central_sep1 1.32292
+R<TRP>A<CG> R<VAL>A<CG2> central_sep2 -0.998051
+R<TRP>A<CG> R<VAL>A<CG2> sep1 0.641433
+R<TRP>A<CG> R<VAL>A<CG2> sep2 -2.37975
+R<TRP>A<CG> R<VAL>A<N> central_sep1 0.285305
+R<TRP>A<CG> R<VAL>A<N> central_sep2 1.6667
+R<TRP>A<CG> R<VAL>A<N> sep1 -0.86513
+R<TRP>A<CG> R<VAL>A<N> sep2 0.477177
+R<TRP>A<CG> R<VAL>A<O> central_sep1 0.0152549
+R<TRP>A<CG> R<VAL>A<O> central_sep2 1.89842
+R<TRP>A<CG> R<VAL>A<O> sep1 0.175338
+R<TRP>A<CG> R<VAL>A<O> sep2 -0.156321
+R<TRP>A<CG> c<solvent> . 1.56957
+R<TRP>A<CH2> R<TRP>A<CH2> central_sep1 0.743315
+R<TRP>A<CH2> R<TRP>A<CH2> central_sep2 -2.21152
+R<TRP>A<CH2> R<TRP>A<CH2> sep1 1.45516
+R<TRP>A<CH2> R<TRP>A<CH2> sep2 -2.35372
+R<TRP>A<CH2> R<TRP>A<CZ2> central_sep1 0.575211
+R<TRP>A<CH2> R<TRP>A<CZ2> central_sep2 -1.88894
+R<TRP>A<CH2> R<TRP>A<CZ2> sep1 1.57537
+R<TRP>A<CH2> R<TRP>A<CZ2> sep2 -1.96627
+R<TRP>A<CH2> R<TRP>A<CZ3> central_sep1 0.203405
+R<TRP>A<CH2> R<TRP>A<CZ3> central_sep2 -1.98119
+R<TRP>A<CH2> R<TRP>A<CZ3> sep1 0.434711
+R<TRP>A<CH2> R<TRP>A<CZ3> sep2 -2.12329
+R<TRP>A<CH2> R<TRP>A<N> central_sep1 2.79127
+R<TRP>A<CH2> R<TRP>A<N> central_sep2 -0.49403
+R<TRP>A<CH2> R<TRP>A<N> sep1 2.56564
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+R<TRP>A<CH2> R<TRP>A<NE1> central_sep1 0.606232
+R<TRP>A<CH2> R<TRP>A<NE1> central_sep2 -1.14269
+R<TRP>A<CH2> R<TRP>A<NE1> sep1 1.21953
+R<TRP>A<CH2> R<TRP>A<NE1> sep2 -1.76726
+R<TRP>A<CH2> R<TRP>A<O> central_sep1 3.03075
+R<TRP>A<CH2> R<TRP>A<O> central_sep2 -0.808922
+R<TRP>A<CH2> R<TRP>A<O> sep1 3.52093
+R<TRP>A<CH2> R<TRP>A<O> sep2 -0.758859
+R<TRP>A<CH2> R<TYR>A<C> central_sep1 2.29601
+R<TRP>A<CH2> R<TYR>A<C> central_sep2 -0.729749
+R<TRP>A<CH2> R<TYR>A<C> sep1 2.9291
+R<TRP>A<CH2> R<TYR>A<C> sep2 -1.18372
+R<TRP>A<CH2> R<TYR>A<CA> central_sep1 1.58458
+R<TRP>A<CH2> R<TYR>A<CA> central_sep2 -0.934317
+R<TRP>A<CH2> R<TYR>A<CA> sep1 2.84366
+R<TRP>A<CH2> R<TYR>A<CA> sep2 -0.686179
+R<TRP>A<CH2> R<TYR>A<CB> central_sep1 0.27109
+R<TRP>A<CH2> R<TYR>A<CB> central_sep2 -1.85159
+R<TRP>A<CH2> R<TYR>A<CB> sep1 1.38478
+R<TRP>A<CH2> R<TYR>A<CB> sep2 -1.612
+R<TRP>A<CH2> R<TYR>A<CD1> central_sep1 0.302666
+R<TRP>A<CH2> R<TYR>A<CD1> central_sep2 -1.56823
+R<TRP>A<CH2> R<TYR>A<CD1> sep1 1.30905
+R<TRP>A<CH2> R<TYR>A<CD1> sep2 -1.67341
+R<TRP>A<CH2> R<TYR>A<CE1> central_sep1 0.454124
+R<TRP>A<CH2> R<TYR>A<CE1> central_sep2 -1.38152
+R<TRP>A<CH2> R<TYR>A<CE1> sep1 0.910854
+R<TRP>A<CH2> R<TYR>A<CE1> sep2 -1.49478
+R<TRP>A<CH2> R<TYR>A<CG> central_sep1 0.486289
+R<TRP>A<CH2> R<TYR>A<CG> central_sep2 -1.72724
+R<TRP>A<CH2> R<TYR>A<CG> sep1 0.45059
+R<TRP>A<CH2> R<TYR>A<CG> sep2 -2.76277
+R<TRP>A<CH2> R<TYR>A<CZ> central_sep1 1.11667
+R<TRP>A<CH2> R<TYR>A<CZ> central_sep2 -1.11729
+R<TRP>A<CH2> R<TYR>A<CZ> sep1 1.40399
+R<TRP>A<CH2> R<TYR>A<CZ> sep2 -2.0795
+R<TRP>A<CH2> R<TYR>A<N> central_sep1 2.83322
+R<TRP>A<CH2> R<TYR>A<N> central_sep2 -0.219038
+R<TRP>A<CH2> R<TYR>A<N> sep1 3.0834
+R<TRP>A<CH2> R<TYR>A<N> sep2 -0.705759
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+R<TRP>A<CH2> R<TYR>A<O> central_sep2 -0.591672
+R<TRP>A<CH2> R<TYR>A<O> sep1 3.1627
+R<TRP>A<CH2> R<TYR>A<O> sep2 -0.621919
+R<TRP>A<CH2> R<TYR>A<OH> central_sep1 1.64214
+R<TRP>A<CH2> R<TYR>A<OH> central_sep2 -0.89218
+R<TRP>A<CH2> R<TYR>A<OH> sep1 1.57674
+R<TRP>A<CH2> R<TYR>A<OH> sep2 -1.0465
+R<TRP>A<CH2> R<VAL>A<C> central_sep1 3.0527
+R<TRP>A<CH2> R<VAL>A<C> central_sep2 -0.294018
+R<TRP>A<CH2> R<VAL>A<C> sep1 3.81587
+R<TRP>A<CH2> R<VAL>A<C> sep2 -0.849036
+R<TRP>A<CH2> R<VAL>A<CA> central_sep1 2.51757
+R<TRP>A<CH2> R<VAL>A<CA> central_sep2 -0.533009
+R<TRP>A<CH2> R<VAL>A<CA> sep1 3.78553
+R<TRP>A<CH2> R<VAL>A<CA> sep2 -0.469626
+R<TRP>A<CH2> R<VAL>A<CB> central_sep1 1.40461
+R<TRP>A<CH2> R<VAL>A<CB> central_sep2 -1.15644
+R<TRP>A<CH2> R<VAL>A<CB> sep1 1.74355
+R<TRP>A<CH2> R<VAL>A<CB> sep2 -1.56726
+R<TRP>A<CH2> R<VAL>A<CG1> central_sep1 0.96868
+R<TRP>A<CH2> R<VAL>A<CG1> central_sep2 -1.57503
+R<TRP>A<CH2> R<VAL>A<CG1> sep1 1.45606
+R<TRP>A<CH2> R<VAL>A<CG1> sep2 -1.18137
+R<TRP>A<CH2> R<VAL>A<CG2> central_sep1 0.791084
+R<TRP>A<CH2> R<VAL>A<CG2> central_sep2 -1.57078
+R<TRP>A<CH2> R<VAL>A<CG2> sep1 1.51797
+R<TRP>A<CH2> R<VAL>A<CG2> sep2 -1.2095
+R<TRP>A<CH2> R<VAL>A<N> central_sep1 3.38849
+R<TRP>A<CH2> R<VAL>A<N> central_sep2 0.372682
+R<TRP>A<CH2> R<VAL>A<N> sep1 3.83295
+R<TRP>A<CH2> R<VAL>A<N> sep2 -0.0634631
+R<TRP>A<CH2> R<VAL>A<O> central_sep1 2.77079
+R<TRP>A<CH2> R<VAL>A<O> central_sep2 -0.233813
+R<TRP>A<CH2> R<VAL>A<O> sep1 3.62311
+R<TRP>A<CH2> R<VAL>A<O> sep2 -0.142801
+R<TRP>A<CH2> c<solvent> . 0.473928
+R<TRP>A<CZ2> R<TRP>A<CZ2> central_sep1 0.678504
+R<TRP>A<CZ2> R<TRP>A<CZ2> central_sep2 -1.74864
+R<TRP>A<CZ2> R<TRP>A<CZ2> sep1 1.81688
+R<TRP>A<CZ2> R<TRP>A<CZ2> sep2 -1.84721
+R<TRP>A<CZ2> R<TRP>A<CZ3> central_sep1 0.0120594
+R<TRP>A<CZ2> R<TRP>A<CZ3> central_sep2 -1.67281
+R<TRP>A<CZ2> R<TRP>A<CZ3> sep1 0.569699
+R<TRP>A<CZ2> R<TRP>A<CZ3> sep2 -1.79756
+R<TRP>A<CZ2> R<TRP>A<N> central_sep1 2.15934
+R<TRP>A<CZ2> R<TRP>A<N> central_sep2 -0.443148
+R<TRP>A<CZ2> R<TRP>A<N> sep1 2.46919
+R<TRP>A<CZ2> R<TRP>A<N> sep2 -0.569335
+R<TRP>A<CZ2> R<TRP>A<NE1> central_sep1 0.550179
+R<TRP>A<CZ2> R<TRP>A<NE1> central_sep2 -1.05509
+R<TRP>A<CZ2> R<TRP>A<NE1> sep1 1.39748
+R<TRP>A<CZ2> R<TRP>A<NE1> sep2 -1.72095
+R<TRP>A<CZ2> R<TRP>A<O> central_sep1 1.04272
+R<TRP>A<CZ2> R<TRP>A<O> central_sep2 -0.829146
+R<TRP>A<CZ2> R<TRP>A<O> sep1 2.80564
+R<TRP>A<CZ2> R<TRP>A<O> sep2 -0.821208
+R<TRP>A<CZ2> R<TYR>A<C> central_sep1 2.24085
+R<TRP>A<CZ2> R<TYR>A<C> central_sep2 -0.661396
+R<TRP>A<CZ2> R<TYR>A<C> sep1 2.92004
+R<TRP>A<CZ2> R<TYR>A<C> sep2 -0.829291
+R<TRP>A<CZ2> R<TYR>A<CA> central_sep1 1.59206
+R<TRP>A<CZ2> R<TYR>A<CA> central_sep2 -0.902896
+R<TRP>A<CZ2> R<TYR>A<CA> sep1 2.56259
+R<TRP>A<CZ2> R<TYR>A<CA> sep2 -0.476128
+R<TRP>A<CZ2> R<TYR>A<CB> central_sep1 -0.136111
+R<TRP>A<CZ2> R<TYR>A<CB> central_sep2 -1.56977
+R<TRP>A<CZ2> R<TYR>A<CB> sep1 1.45992
+R<TRP>A<CZ2> R<TYR>A<CB> sep2 -1.20725
+R<TRP>A<CZ2> R<TYR>A<CD1> central_sep1 -0.086216
+R<TRP>A<CZ2> R<TYR>A<CD1> central_sep2 -1.32073
+R<TRP>A<CZ2> R<TYR>A<CD1> sep1 1.15638
+R<TRP>A<CZ2> R<TYR>A<CD1> sep2 -1.48924
+R<TRP>A<CZ2> R<TYR>A<CE1> central_sep1 0.482258
+R<TRP>A<CZ2> R<TYR>A<CE1> central_sep2 -1.25301
+R<TRP>A<CZ2> R<TYR>A<CE1> sep1 1.23393
+R<TRP>A<CZ2> R<TYR>A<CE1> sep2 -1.43199
+R<TRP>A<CZ2> R<TYR>A<CG> central_sep1 -0.0395285
+R<TRP>A<CZ2> R<TYR>A<CG> central_sep2 -1.49119
+R<TRP>A<CZ2> R<TYR>A<CG> sep1 0.114846
+R<TRP>A<CZ2> R<TYR>A<CG> sep2 -2.70613
+R<TRP>A<CZ2> R<TYR>A<CZ> central_sep1 1.05792
+R<TRP>A<CZ2> R<TYR>A<CZ> central_sep2 -1.2206
+R<TRP>A<CZ2> R<TYR>A<CZ> sep1 1.53425
+R<TRP>A<CZ2> R<TYR>A<CZ> sep2 -2.03458
+R<TRP>A<CZ2> R<TYR>A<N> central_sep1 2.30943
+R<TRP>A<CZ2> R<TYR>A<N> central_sep2 -0.00954932
+R<TRP>A<CZ2> R<TYR>A<N> sep1 2.81603
+R<TRP>A<CZ2> R<TYR>A<N> sep2 -0.234155
+R<TRP>A<CZ2> R<TYR>A<O> central_sep1 1.54803
+R<TRP>A<CZ2> R<TYR>A<O> central_sep2 -0.619722
+R<TRP>A<CZ2> R<TYR>A<O> sep1 2.38575
+R<TRP>A<CZ2> R<TYR>A<O> sep2 -0.450692
+R<TRP>A<CZ2> R<TYR>A<OH> central_sep1 1.31683
+R<TRP>A<CZ2> R<TYR>A<OH> central_sep2 -0.988445
+R<TRP>A<CZ2> R<TYR>A<OH> sep1 1.97461
+R<TRP>A<CZ2> R<TYR>A<OH> sep2 -1.12516
+R<TRP>A<CZ2> R<VAL>A<C> central_sep1 2.9712
+R<TRP>A<CZ2> R<VAL>A<C> central_sep2 0.0695808
+R<TRP>A<CZ2> R<VAL>A<C> sep1 3.84662
+R<TRP>A<CZ2> R<VAL>A<C> sep2 -0.556624
+R<TRP>A<CZ2> R<VAL>A<CA> central_sep1 1.86986
+R<TRP>A<CZ2> R<VAL>A<CA> central_sep2 -0.344136
+R<TRP>A<CZ2> R<VAL>A<CA> sep1 3.27237
+R<TRP>A<CZ2> R<VAL>A<CA> sep2 -0.117777
+R<TRP>A<CZ2> R<VAL>A<CB> central_sep1 0.373784
+R<TRP>A<CZ2> R<VAL>A<CB> central_sep2 -0.981543
+R<TRP>A<CZ2> R<VAL>A<CB> sep1 1.50289
+R<TRP>A<CZ2> R<VAL>A<CB> sep2 -1.23989
+R<TRP>A<CZ2> R<VAL>A<CG1> central_sep1 0.2662
+R<TRP>A<CZ2> R<VAL>A<CG1> central_sep2 -1.23323
+R<TRP>A<CZ2> R<VAL>A<CG1> sep1 1.47439
+R<TRP>A<CZ2> R<VAL>A<CG1> sep2 -0.899228
+R<TRP>A<CZ2> R<VAL>A<CG2> central_sep1 0.261594
+R<TRP>A<CZ2> R<VAL>A<CG2> central_sep2 -1.19763
+R<TRP>A<CZ2> R<VAL>A<CG2> sep1 1.44563
+R<TRP>A<CZ2> R<VAL>A<CG2> sep2 -0.978256
+R<TRP>A<CZ2> R<VAL>A<N> central_sep1 3.0092
+R<TRP>A<CZ2> R<VAL>A<N> central_sep2 0.427625
+R<TRP>A<CZ2> R<VAL>A<N> sep1 3.50369
+R<TRP>A<CZ2> R<VAL>A<N> sep2 0.200619
+R<TRP>A<CZ2> R<VAL>A<O> central_sep1 2.23175
+R<TRP>A<CZ2> R<VAL>A<O> central_sep2 -0.360398
+R<TRP>A<CZ2> R<VAL>A<O> sep1 2.92429
+R<TRP>A<CZ2> R<VAL>A<O> sep2 -0.116812
+R<TRP>A<CZ2> c<solvent> . 0.387086
+R<TRP>A<CZ3> R<TRP>A<CZ3> central_sep1 -0.684118
+R<TRP>A<CZ3> R<TRP>A<CZ3> central_sep2 -2.04029
+R<TRP>A<CZ3> R<TRP>A<CZ3> sep1 0.415043
+R<TRP>A<CZ3> R<TRP>A<CZ3> sep2 -2.2566
+R<TRP>A<CZ3> R<TRP>A<N> central_sep1 0.401066
+R<TRP>A<CZ3> R<TRP>A<N> central_sep2 -0.760887
+R<TRP>A<CZ3> R<TRP>A<N> sep1 1.45251
+R<TRP>A<CZ3> R<TRP>A<N> sep2 -0.829366
+R<TRP>A<CZ3> R<TRP>A<NE1> central_sep1 -0.24619
+R<TRP>A<CZ3> R<TRP>A<NE1> central_sep2 -1.26914
+R<TRP>A<CZ3> R<TRP>A<NE1> sep1 0.297761
+R<TRP>A<CZ3> R<TRP>A<NE1> sep2 -1.63826
+R<TRP>A<CZ3> R<TRP>A<O> central_sep1 0.962785
+R<TRP>A<CZ3> R<TRP>A<O> central_sep2 -1.09548
+R<TRP>A<CZ3> R<TRP>A<O> sep1 2.38513
+R<TRP>A<CZ3> R<TRP>A<O> sep2 -0.829047
+R<TRP>A<CZ3> R<TYR>A<C> central_sep1 0.566397
+R<TRP>A<CZ3> R<TYR>A<C> central_sep2 -1.15946
+R<TRP>A<CZ3> R<TYR>A<C> sep1 1.5097
+R<TRP>A<CZ3> R<TYR>A<C> sep2 -1.62255
+R<TRP>A<CZ3> R<TYR>A<CA> central_sep1 0.79159
+R<TRP>A<CZ3> R<TYR>A<CA> central_sep2 -1.12711
+R<TRP>A<CZ3> R<TYR>A<CA> sep1 0.634032
+R<TRP>A<CZ3> R<TYR>A<CA> sep2 -0.973876
+R<TRP>A<CZ3> R<TYR>A<CB> central_sep1 -0.521307
+R<TRP>A<CZ3> R<TYR>A<CB> central_sep2 -1.89482
+R<TRP>A<CZ3> R<TYR>A<CB> sep1 0.954712
+R<TRP>A<CZ3> R<TYR>A<CB> sep2 -1.66094
+R<TRP>A<CZ3> R<TYR>A<CD1> central_sep1 -0.606032
+R<TRP>A<CZ3> R<TYR>A<CD1> central_sep2 -1.47487
+R<TRP>A<CZ3> R<TYR>A<CD1> sep1 0.828396
+R<TRP>A<CZ3> R<TYR>A<CD1> sep2 -1.69694
+R<TRP>A<CZ3> R<TYR>A<CE1> central_sep1 -0.501675
+R<TRP>A<CZ3> R<TYR>A<CE1> central_sep2 -1.20367
+R<TRP>A<CZ3> R<TYR>A<CE1> sep1 0.657966
+R<TRP>A<CZ3> R<TYR>A<CE1> sep2 -1.43839
+R<TRP>A<CZ3> R<TYR>A<CG> central_sep1 -0.0747253
+R<TRP>A<CZ3> R<TYR>A<CG> central_sep2 -1.52742
+R<TRP>A<CZ3> R<TYR>A<CG> sep1 -0.289126
+R<TRP>A<CZ3> R<TYR>A<CG> sep2 -2.6486
+R<TRP>A<CZ3> R<TYR>A<CZ> central_sep1 -0.111319
+R<TRP>A<CZ3> R<TYR>A<CZ> central_sep2 -0.954527
+R<TRP>A<CZ3> R<TYR>A<CZ> sep1 0.333399
+R<TRP>A<CZ3> R<TYR>A<CZ> sep2 -1.79811
+R<TRP>A<CZ3> R<TYR>A<N> central_sep1 0.853516
+R<TRP>A<CZ3> R<TYR>A<N> central_sep2 -0.425401
+R<TRP>A<CZ3> R<TYR>A<N> sep1 1.78538
+R<TRP>A<CZ3> R<TYR>A<N> sep2 -0.532301
+R<TRP>A<CZ3> R<TYR>A<O> central_sep1 0.803588
+R<TRP>A<CZ3> R<TYR>A<O> central_sep2 -0.686055
+R<TRP>A<CZ3> R<TYR>A<O> sep1 2.29354
+R<TRP>A<CZ3> R<TYR>A<O> sep2 -0.543697
+R<TRP>A<CZ3> R<TYR>A<OH> central_sep1 0.826005
+R<TRP>A<CZ3> R<TYR>A<OH> central_sep2 -0.714882
+R<TRP>A<CZ3> R<TYR>A<OH> sep1 0.959024
+R<TRP>A<CZ3> R<TYR>A<OH> sep2 -0.818591
+R<TRP>A<CZ3> R<VAL>A<C> central_sep1 1.77448
+R<TRP>A<CZ3> R<VAL>A<C> central_sep2 -0.458672
+R<TRP>A<CZ3> R<VAL>A<C> sep1 2.03078
+R<TRP>A<CZ3> R<VAL>A<C> sep2 -1.11876
+R<TRP>A<CZ3> R<VAL>A<CA> central_sep1 1.30186
+R<TRP>A<CZ3> R<VAL>A<CA> central_sep2 -0.570784
+R<TRP>A<CZ3> R<VAL>A<CA> sep1 1.04353
+R<TRP>A<CZ3> R<VAL>A<CA> sep2 -0.584837
+R<TRP>A<CZ3> R<VAL>A<CB> central_sep1 0.582568
+R<TRP>A<CZ3> R<VAL>A<CB> central_sep2 -1.19595
+R<TRP>A<CZ3> R<VAL>A<CB> sep1 0.957391
+R<TRP>A<CZ3> R<VAL>A<CB> sep2 -1.61443
+R<TRP>A<CZ3> R<VAL>A<CG1> central_sep1 -0.0938965
+R<TRP>A<CZ3> R<VAL>A<CG1> central_sep2 -1.50176
+R<TRP>A<CZ3> R<VAL>A<CG1> sep1 1.12148
+R<TRP>A<CZ3> R<VAL>A<CG1> sep2 -1.2146
+R<TRP>A<CZ3> R<VAL>A<CG2> central_sep1 -0.0406708
+R<TRP>A<CZ3> R<VAL>A<CG2> central_sep2 -1.59971
+R<TRP>A<CZ3> R<VAL>A<CG2> sep1 0.68681
+R<TRP>A<CZ3> R<VAL>A<CG2> sep2 -1.16936
+R<TRP>A<CZ3> R<VAL>A<N> central_sep1 1.96922
+R<TRP>A<CZ3> R<VAL>A<N> central_sep2 0.0687794
+R<TRP>A<CZ3> R<VAL>A<N> sep1 2.17196
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+R<TRP>A<CZ3> R<VAL>A<O> central_sep2 -0.428476
+R<TRP>A<CZ3> R<VAL>A<O> sep1 3.12955
+R<TRP>A<CZ3> R<VAL>A<O> sep2 0.095308
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+R<TRP>A<N> R<TRP>A<N> central_sep2 1.72159
+R<TRP>A<N> R<TRP>A<N> sep1 -2.29472
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+R<TRP>A<N> R<TRP>A<NE1> sep1 1.5743
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+R<TRP>A<N> R<TRP>A<O> sep1 0.0856357
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+R<TRP>A<N> R<TYR>A<C> sep1 -1.64951
+R<TRP>A<N> R<TYR>A<C> sep2 1.22454
+R<TRP>A<N> R<TYR>A<CA> central_sep1 2.44919
+R<TRP>A<N> R<TYR>A<CA> central_sep2 1.33606
+R<TRP>A<N> R<TYR>A<CA> sep1 -2.33024
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+R<TRP>A<N> R<TYR>A<CB> central_sep1 1.3571
+R<TRP>A<N> R<TYR>A<CB> central_sep2 0.4756
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+R<TRP>A<N> R<TYR>A<CD1> central_sep2 0.401549
+R<TRP>A<N> R<TYR>A<CD1> sep1 0.0981114
+R<TRP>A<N> R<TYR>A<CD1> sep2 0.0293718
+R<TRP>A<N> R<TYR>A<CE1> central_sep1 1.41472
+R<TRP>A<N> R<TYR>A<CE1> central_sep2 0.191383
+R<TRP>A<N> R<TYR>A<CE1> sep1 2.09892
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+R<TRP>A<N> R<TYR>A<CG> central_sep1 0.165142
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+R<TRP>A<N> R<TYR>A<CG> sep1 -0.619135
+R<TRP>A<N> R<TYR>A<CG> sep2 0.164872
+R<TRP>A<N> R<TYR>A<CZ> central_sep1 2.52147
+R<TRP>A<N> R<TYR>A<CZ> central_sep2 0.246397
+R<TRP>A<N> R<TYR>A<CZ> sep1 1.96278
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+R<TRP>A<N> R<TYR>A<N> central_sep1 1.84463
+R<TRP>A<N> R<TYR>A<N> central_sep2 1.20839
+R<TRP>A<N> R<TYR>A<N> sep1 -2.20962
+R<TRP>A<N> R<TYR>A<N> sep2 0.881199
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+R<TRP>A<N> R<TYR>A<O> central_sep2 -1.72391
+R<TRP>A<N> R<TYR>A<O> sep1 0.302523
+R<TRP>A<N> R<TYR>A<O> sep2 0.383056
+R<TRP>A<N> R<TYR>A<OH> central_sep1 2.39079
+R<TRP>A<N> R<TYR>A<OH> central_sep2 -0.260679
+R<TRP>A<N> R<TYR>A<OH> sep1 3.42996
+R<TRP>A<N> R<TYR>A<OH> sep2 0.0791022
+R<TRP>A<N> R<VAL>A<C> central_sep1 -0.0373548
+R<TRP>A<N> R<VAL>A<C> central_sep2 4.37994
+R<TRP>A<N> R<VAL>A<C> sep1 -1.43383
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+R<TRP>A<N> R<VAL>A<CA> central_sep1 2.70419
+R<TRP>A<N> R<VAL>A<CA> central_sep2 1.95225
+R<TRP>A<N> R<VAL>A<CA> sep1 -2.19926
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+R<TRP>A<N> R<VAL>A<CB> central_sep1 1.98163
+R<TRP>A<N> R<VAL>A<CB> central_sep2 0.916676
+R<TRP>A<N> R<VAL>A<CB> sep1 -1.37696
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+R<TRP>A<N> R<VAL>A<CG1> central_sep1 0.233395
+R<TRP>A<N> R<VAL>A<CG1> central_sep2 0.52019
+R<TRP>A<N> R<VAL>A<CG1> sep1 -0.416537
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+R<TRP>A<N> R<VAL>A<CG2> central_sep2 0.628617
+R<TRP>A<N> R<VAL>A<CG2> sep1 1.24783
+R<TRP>A<N> R<VAL>A<CG2> sep2 0.451858
+R<TRP>A<N> R<VAL>A<N> central_sep1 2.48584
+R<TRP>A<N> R<VAL>A<N> central_sep2 1.8531
+R<TRP>A<N> R<VAL>A<N> sep1 -1.84166
+R<TRP>A<N> R<VAL>A<N> sep2 1.02844
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+R<TRP>A<N> R<VAL>A<O> sep1 0.312942
+R<TRP>A<N> R<VAL>A<O> sep2 0.57441
+R<TRP>A<N> c<solvent> . 1.89879
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+R<TRP>A<NE1> R<TRP>A<NE1> central_sep2 -0.945752
+R<TRP>A<NE1> R<TRP>A<NE1> sep1 0.745754
+R<TRP>A<NE1> R<TRP>A<NE1> sep2 -1.44811
+R<TRP>A<NE1> R<TRP>A<O> central_sep1 0.0591388
+R<TRP>A<NE1> R<TRP>A<O> central_sep2 -1.39171
+R<TRP>A<NE1> R<TRP>A<O> sep1 0.959537
+R<TRP>A<NE1> R<TRP>A<O> sep2 -0.595792
+R<TRP>A<NE1> R<TYR>A<C> central_sep1 0.820065
+R<TRP>A<NE1> R<TYR>A<C> central_sep2 -0.142813
+R<TRP>A<NE1> R<TYR>A<C> sep1 1.56702
+R<TRP>A<NE1> R<TYR>A<C> sep2 -0.856885
+R<TRP>A<NE1> R<TYR>A<CA> central_sep1 0.624155
+R<TRP>A<NE1> R<TYR>A<CA> central_sep2 -0.195155
+R<TRP>A<NE1> R<TYR>A<CA> sep1 1.58246
+R<TRP>A<NE1> R<TYR>A<CA> sep2 -0.53419
+R<TRP>A<NE1> R<TYR>A<CB> central_sep1 -0.375137
+R<TRP>A<NE1> R<TYR>A<CB> central_sep2 -0.894807
+R<TRP>A<NE1> R<TYR>A<CB> sep1 0.903152
+R<TRP>A<NE1> R<TYR>A<CB> sep2 -1.08676
+R<TRP>A<NE1> R<TYR>A<CD1> central_sep1 -0.0313767
+R<TRP>A<NE1> R<TYR>A<CD1> central_sep2 -0.911624
+R<TRP>A<NE1> R<TYR>A<CD1> sep1 0.88435
+R<TRP>A<NE1> R<TYR>A<CD1> sep2 -1.06638
+R<TRP>A<NE1> R<TYR>A<CE1> central_sep1 0.46766
+R<TRP>A<NE1> R<TYR>A<CE1> central_sep2 -0.907124
+R<TRP>A<NE1> R<TYR>A<CE1> sep1 0.801995
+R<TRP>A<NE1> R<TYR>A<CE1> sep2 -1.45772
+R<TRP>A<NE1> R<TYR>A<CG> central_sep1 1.78416
+R<TRP>A<NE1> R<TYR>A<CG> central_sep2 -1.0692
+R<TRP>A<NE1> R<TYR>A<CG> sep1 0.335055
+R<TRP>A<NE1> R<TYR>A<CG> sep2 -1.89409
+R<TRP>A<NE1> R<TYR>A<CZ> central_sep1 0.0910603
+R<TRP>A<NE1> R<TYR>A<CZ> central_sep2 -0.77999
+R<TRP>A<NE1> R<TYR>A<CZ> sep1 1.12134
+R<TRP>A<NE1> R<TYR>A<CZ> sep2 -1.83549
+R<TRP>A<NE1> R<TYR>A<N> central_sep1 2.06248
+R<TRP>A<NE1> R<TYR>A<N> central_sep2 0.209447
+R<TRP>A<NE1> R<TYR>A<N> sep1 1.95706
+R<TRP>A<NE1> R<TYR>A<N> sep2 -0.0571771
+R<TRP>A<NE1> R<TYR>A<O> central_sep1 0.0328305
+R<TRP>A<NE1> R<TYR>A<O> central_sep2 -1.21336
+R<TRP>A<NE1> R<TYR>A<O> sep1 1.14855
+R<TRP>A<NE1> R<TYR>A<O> sep2 -0.220243
+R<TRP>A<NE1> R<TYR>A<OH> central_sep1 0.706542
+R<TRP>A<NE1> R<TYR>A<OH> central_sep2 -1.39019
+R<TRP>A<NE1> R<TYR>A<OH> sep1 1.41489
+R<TRP>A<NE1> R<TYR>A<OH> sep2 -1.03846
+R<TRP>A<NE1> R<VAL>A<C> central_sep1 2.32294
+R<TRP>A<NE1> R<VAL>A<C> central_sep2 0.742559
+R<TRP>A<NE1> R<VAL>A<C> sep1 1.94802
+R<TRP>A<NE1> R<VAL>A<C> sep2 -0.169921
+R<TRP>A<NE1> R<VAL>A<CA> central_sep1 0.9421
+R<TRP>A<NE1> R<VAL>A<CA> central_sep2 0.290988
+R<TRP>A<NE1> R<VAL>A<CA> sep1 2.55577
+R<TRP>A<NE1> R<VAL>A<CA> sep2 0.141993
+R<TRP>A<NE1> R<VAL>A<CB> central_sep1 -0.10922
+R<TRP>A<NE1> R<VAL>A<CB> central_sep2 -0.605495
+R<TRP>A<NE1> R<VAL>A<CB> sep1 0.666352
+R<TRP>A<NE1> R<VAL>A<CB> sep2 -1.04083
+R<TRP>A<NE1> R<VAL>A<CG1> central_sep1 -0.0789099
+R<TRP>A<NE1> R<VAL>A<CG1> central_sep2 -0.6941
+R<TRP>A<NE1> R<VAL>A<CG1> sep1 1.12939
+R<TRP>A<NE1> R<VAL>A<CG1> sep2 -0.814038
+R<TRP>A<NE1> R<VAL>A<CG2> central_sep1 0.103387
+R<TRP>A<NE1> R<VAL>A<CG2> central_sep2 -0.659741
+R<TRP>A<NE1> R<VAL>A<CG2> sep1 1.1688
+R<TRP>A<NE1> R<VAL>A<CG2> sep2 -0.799357
+R<TRP>A<NE1> R<VAL>A<N> central_sep1 2.63767
+R<TRP>A<NE1> R<VAL>A<N> central_sep2 0.828935
+R<TRP>A<NE1> R<VAL>A<N> sep1 2.28005
+R<TRP>A<NE1> R<VAL>A<N> sep2 0.207951
+R<TRP>A<NE1> R<VAL>A<O> central_sep1 0.274544
+R<TRP>A<NE1> R<VAL>A<O> central_sep2 -0.804452
+R<TRP>A<NE1> R<VAL>A<O> sep1 1.35878
+R<TRP>A<NE1> R<VAL>A<O> sep2 0.0294807
+R<TRP>A<NE1> c<solvent> . 0.293238
+R<TRP>A<O> R<TRP>A<O> central_sep1 0.77176
+R<TRP>A<O> R<TRP>A<O> central_sep2 -0.211043
+R<TRP>A<O> R<TRP>A<O> sep1 1.00406
+R<TRP>A<O> R<TRP>A<O> sep2 0.207201
+R<TRP>A<O> R<TYR>A<C> central_sep1 -0.809557
+R<TRP>A<O> R<TYR>A<C> central_sep2 1.84867
+R<TRP>A<O> R<TYR>A<C> sep1 -1.14536
+R<TRP>A<O> R<TYR>A<C> sep2 0.87843
+R<TRP>A<O> R<TYR>A<CA> central_sep1 0.997597
+R<TRP>A<O> R<TYR>A<CA> central_sep2 -1.05589
+R<TRP>A<O> R<TYR>A<CA> sep1 -2.01183
+R<TRP>A<O> R<TYR>A<CA> sep2 0.30373
+R<TRP>A<O> R<TYR>A<CB> central_sep1 -1.46173
+R<TRP>A<O> R<TYR>A<CB> central_sep2 -0.612954
+R<TRP>A<O> R<TYR>A<CB> sep1 0.3495
+R<TRP>A<O> R<TYR>A<CB> sep2 -0.747139
+R<TRP>A<O> R<TYR>A<CD1> central_sep1 -0.635886
+R<TRP>A<O> R<TYR>A<CD1> central_sep2 -0.545751
+R<TRP>A<O> R<TYR>A<CD1> sep1 0.694157
+R<TRP>A<O> R<TYR>A<CD1> sep2 -0.094431
+R<TRP>A<O> R<TYR>A<CE1> central_sep1 0.600054
+R<TRP>A<O> R<TYR>A<CE1> central_sep2 -0.419299
+R<TRP>A<O> R<TYR>A<CE1> sep1 1.41455
+R<TRP>A<O> R<TYR>A<CE1> sep2 -0.144177
+R<TRP>A<O> R<TYR>A<CG> central_sep1 0.455259
+R<TRP>A<O> R<TYR>A<CG> central_sep2 1.90831
+R<TRP>A<O> R<TYR>A<CG> sep1 -0.41699
+R<TRP>A<O> R<TYR>A<CG> sep2 -0.173167
+R<TRP>A<O> R<TYR>A<CZ> central_sep1 1.54395
+R<TRP>A<O> R<TYR>A<CZ> central_sep2 1.21192
+R<TRP>A<O> R<TYR>A<CZ> sep1 1.30323
+R<TRP>A<O> R<TYR>A<CZ> sep2 0.00945464
+R<TRP>A<O> R<TYR>A<N> central_sep1 -2.03166
+R<TRP>A<O> R<TYR>A<N> central_sep2 -1.58828
+R<TRP>A<O> R<TYR>A<N> sep1 0.214114
+R<TRP>A<O> R<TYR>A<N> sep2 0.379961
+R<TRP>A<O> R<TYR>A<O> central_sep1 0.808423
+R<TRP>A<O> R<TYR>A<O> central_sep2 0.0854456
+R<TRP>A<O> R<TYR>A<O> sep1 1.01872
+R<TRP>A<O> R<TYR>A<O> sep2 0.491243
+R<TRP>A<O> R<TYR>A<OH> central_sep1 1.83539
+R<TRP>A<O> R<TYR>A<OH> central_sep2 -0.590847
+R<TRP>A<O> R<TYR>A<OH> sep1 2.79725
+R<TRP>A<O> R<TYR>A<OH> sep2 -0.210808
+R<TRP>A<O> R<VAL>A<C> central_sep1 -0.531215
+R<TRP>A<O> R<VAL>A<C> central_sep2 2.63123
+R<TRP>A<O> R<VAL>A<C> sep1 -0.824457
+R<TRP>A<O> R<VAL>A<C> sep2 1.70673
+R<TRP>A<O> R<VAL>A<CA> central_sep1 1.2709
+R<TRP>A<O> R<VAL>A<CA> central_sep2 -1.05022
+R<TRP>A<O> R<VAL>A<CA> sep1 -1.92694
+R<TRP>A<O> R<VAL>A<CA> sep2 0.43562
+R<TRP>A<O> R<VAL>A<CB> central_sep1 -1.38526
+R<TRP>A<O> R<VAL>A<CB> central_sep2 -0.354725
+R<TRP>A<O> R<VAL>A<CB> sep1 0.55457
+R<TRP>A<O> R<VAL>A<CB> sep2 -0.905075
+R<TRP>A<O> R<VAL>A<CG1> central_sep1 -0.307472
+R<TRP>A<O> R<VAL>A<CG1> central_sep2 -0.278834
+R<TRP>A<O> R<VAL>A<CG1> sep1 1.21961
+R<TRP>A<O> R<VAL>A<CG1> sep2 0.460902
+R<TRP>A<O> R<VAL>A<CG2> central_sep1 -0.780795
+R<TRP>A<O> R<VAL>A<CG2> central_sep2 -0.118695
+R<TRP>A<O> R<VAL>A<CG2> sep1 0.761248
+R<TRP>A<O> R<VAL>A<CG2> sep2 0.171633
+R<TRP>A<O> R<VAL>A<N> central_sep1 -1.78522
+R<TRP>A<O> R<VAL>A<N> central_sep2 -1.78022
+R<TRP>A<O> R<VAL>A<N> sep1 0.258421
+R<TRP>A<O> R<VAL>A<N> sep2 1.10307
+R<TRP>A<O> R<VAL>A<O> central_sep1 0.764664
+R<TRP>A<O> R<VAL>A<O> central_sep2 0.0757999
+R<TRP>A<O> R<VAL>A<O> sep1 1.11016
+R<TRP>A<O> R<VAL>A<O> sep2 0.786182
+R<TRP>A<O> c<solvent> . 0.796365
+R<TYR>A<C> R<TYR>A<C> central_sep1 4.11354
+R<TYR>A<C> R<TYR>A<C> central_sep2 2.17371
+R<TYR>A<C> R<TYR>A<C> sep1 -2.54497
+R<TYR>A<C> R<TYR>A<C> sep2 2.34784
+R<TYR>A<C> R<TYR>A<CA> central_sep1 3.05459
+R<TYR>A<C> R<TYR>A<CA> central_sep2 2.04753
+R<TYR>A<C> R<TYR>A<CA> sep1 -2.86125
+R<TYR>A<C> R<TYR>A<CA> sep2 0.547836
+R<TYR>A<C> R<TYR>A<CB> central_sep1 1.59799
+R<TYR>A<C> R<TYR>A<CB> central_sep2 0.230475
+R<TYR>A<C> R<TYR>A<CB> sep1 -0.518233
+R<TYR>A<C> R<TYR>A<CB> sep2 -0.773033
+R<TYR>A<C> R<TYR>A<CD1> central_sep1 -0.771667
+R<TYR>A<C> R<TYR>A<CD1> central_sep2 -0.468476
+R<TYR>A<C> R<TYR>A<CD1> sep1 -0.650862
+R<TYR>A<C> R<TYR>A<CD1> sep2 -0.884206
+R<TYR>A<C> R<TYR>A<CE1> central_sep1 0.564962
+R<TYR>A<C> R<TYR>A<CE1> central_sep2 -0.183154
+R<TYR>A<C> R<TYR>A<CE1> sep1 1.3904
+R<TYR>A<C> R<TYR>A<CE1> sep2 -0.684407
+R<TYR>A<C> R<TYR>A<CG> central_sep1 0.54798
+R<TYR>A<C> R<TYR>A<CG> central_sep2 1.06651
+R<TYR>A<C> R<TYR>A<CG> sep1 -1.89636
+R<TYR>A<C> R<TYR>A<CG> sep2 -0.165798
+R<TYR>A<C> R<TYR>A<CZ> central_sep1 0.810595
+R<TYR>A<C> R<TYR>A<CZ> central_sep2 0.464343
+R<TYR>A<C> R<TYR>A<CZ> sep1 1.72695
+R<TYR>A<C> R<TYR>A<CZ> sep2 -0.206661
+R<TYR>A<C> R<TYR>A<N> central_sep1 -0.523674
+R<TYR>A<C> R<TYR>A<N> central_sep2 2.2664
+R<TYR>A<C> R<TYR>A<N> sep1 -1.66209
+R<TYR>A<C> R<TYR>A<N> sep2 1.55289
+R<TYR>A<C> R<TYR>A<O> central_sep1 -0.692768
+R<TYR>A<C> R<TYR>A<O> central_sep2 1.79287
+R<TYR>A<C> R<TYR>A<O> sep1 -1.30606
+R<TYR>A<C> R<TYR>A<O> sep2 0.829885
+R<TYR>A<C> R<TYR>A<OH> central_sep1 2.96586
+R<TYR>A<C> R<TYR>A<OH> central_sep2 0.469611
+R<TYR>A<C> R<TYR>A<OH> sep1 3.6805
+R<TYR>A<C> R<TYR>A<OH> sep2 -0.320216
+R<TYR>A<C> R<VAL>A<C> central_sep1 4.20521
+R<TYR>A<C> R<VAL>A<C> central_sep2 4.90456
+R<TYR>A<C> R<VAL>A<C> sep1 -2.45221
+R<TYR>A<C> R<VAL>A<C> sep2 2.84679
+R<TYR>A<C> R<VAL>A<CA> central_sep1 3.80314
+R<TYR>A<C> R<VAL>A<CA> central_sep2 3.13725
+R<TYR>A<C> R<VAL>A<CA> sep1 -2.66763
+R<TYR>A<C> R<VAL>A<CA> sep2 0.655397
+R<TYR>A<C> R<VAL>A<CB> central_sep1 1.86639
+R<TYR>A<C> R<VAL>A<CB> central_sep2 0.736931
+R<TYR>A<C> R<VAL>A<CB> sep1 0.0928994
+R<TYR>A<C> R<VAL>A<CB> sep2 -0.680317
+R<TYR>A<C> R<VAL>A<CG1> central_sep1 0.161969
+R<TYR>A<C> R<VAL>A<CG1> central_sep2 0.11538
+R<TYR>A<C> R<VAL>A<CG1> sep1 -0.495575
+R<TYR>A<C> R<VAL>A<CG1> sep2 -0.787909
+R<TYR>A<C> R<VAL>A<CG2> central_sep1 0.341019
+R<TYR>A<C> R<VAL>A<CG2> central_sep2 -0.139491
+R<TYR>A<C> R<VAL>A<CG2> sep1 -0.928641
+R<TYR>A<C> R<VAL>A<CG2> sep2 -0.670569
+R<TYR>A<C> R<VAL>A<N> central_sep1 0.0643068
+R<TYR>A<C> R<VAL>A<N> central_sep2 2.7924
+R<TYR>A<C> R<VAL>A<N> sep1 -1.36585
+R<TYR>A<C> R<VAL>A<N> sep2 1.78665
+R<TYR>A<C> R<VAL>A<O> central_sep1 -0.547878
+R<TYR>A<C> R<VAL>A<O> central_sep2 2.87874
+R<TYR>A<C> R<VAL>A<O> sep1 -0.778317
+R<TYR>A<C> R<VAL>A<O> sep2 1.13718
+R<TYR>A<C> c<solvent> . 2.17883
+R<TYR>A<CA> R<TYR>A<CA> central_sep1 1.35047
+R<TYR>A<CA> R<TYR>A<CA> central_sep2 -0.502086
+R<TYR>A<CA> R<TYR>A<CA> sep1 3.21093
+R<TYR>A<CA> R<TYR>A<CA> sep2 0.13616
+R<TYR>A<CA> R<TYR>A<CB> central_sep1 -0.65205
+R<TYR>A<CA> R<TYR>A<CB> central_sep2 -0.400476
+R<TYR>A<CA> R<TYR>A<CB> sep1 1.3432
+R<TYR>A<CA> R<TYR>A<CB> sep2 -0.0756286
+R<TYR>A<CA> R<TYR>A<CD1> central_sep1 -0.193316
+R<TYR>A<CA> R<TYR>A<CD1> central_sep2 -0.568349
+R<TYR>A<CA> R<TYR>A<CD1> sep1 -0.152724
+R<TYR>A<CA> R<TYR>A<CD1> sep2 -0.505346
+R<TYR>A<CA> R<TYR>A<CE1> central_sep1 0.746603
+R<TYR>A<CA> R<TYR>A<CE1> central_sep2 -0.514823
+R<TYR>A<CA> R<TYR>A<CE1> sep1 1.24488
+R<TYR>A<CA> R<TYR>A<CE1> sep2 -0.427957
+R<TYR>A<CA> R<TYR>A<CG> central_sep1 0.849766
+R<TYR>A<CA> R<TYR>A<CG> central_sep2 -0.1095
+R<TYR>A<CA> R<TYR>A<CG> sep1 1.16669
+R<TYR>A<CA> R<TYR>A<CG> sep2 -1.32871
+R<TYR>A<CA> R<TYR>A<CZ> central_sep1 0.78631
+R<TYR>A<CA> R<TYR>A<CZ> central_sep2 -0.514392
+R<TYR>A<CA> R<TYR>A<CZ> sep1 1.41149
+R<TYR>A<CA> R<TYR>A<CZ> sep2 -1.14931
+R<TYR>A<CA> R<TYR>A<N> central_sep1 2.03879
+R<TYR>A<CA> R<TYR>A<N> central_sep2 1.08976
+R<TYR>A<CA> R<TYR>A<N> sep1 -2.39537
+R<TYR>A<CA> R<TYR>A<N> sep2 0.670063
+R<TYR>A<CA> R<TYR>A<O> central_sep1 0.815969
+R<TYR>A<CA> R<TYR>A<O> central_sep2 -1.34364
+R<TYR>A<CA> R<TYR>A<O> sep1 -2.16932
+R<TYR>A<CA> R<TYR>A<O> sep2 0.149032
+R<TYR>A<CA> R<TYR>A<OH> central_sep1 1.4271
+R<TYR>A<CA> R<TYR>A<OH> central_sep2 -0.600855
+R<TYR>A<CA> R<TYR>A<OH> sep1 2.66634
+R<TYR>A<CA> R<TYR>A<OH> sep2 -0.301052
+R<TYR>A<CA> R<VAL>A<C> central_sep1 4.84399
+R<TYR>A<CA> R<VAL>A<C> central_sep2 3.05357
+R<TYR>A<CA> R<VAL>A<C> sep1 -2.79842
+R<TYR>A<CA> R<VAL>A<C> sep2 0.984856
+R<TYR>A<CA> R<VAL>A<CA> central_sep1 1.8026
+R<TYR>A<CA> R<VAL>A<CA> central_sep2 0.0339305
+R<TYR>A<CA> R<VAL>A<CA> sep1 3.50947
+R<TYR>A<CA> R<VAL>A<CA> sep2 0.364165
+R<TYR>A<CA> R<VAL>A<CB> central_sep1 -0.692172
+R<TYR>A<CA> R<VAL>A<CB> central_sep2 -0.264407
+R<TYR>A<CA> R<VAL>A<CB> sep1 1.41329
+R<TYR>A<CA> R<VAL>A<CB> sep2 -0.0604062
+R<TYR>A<CA> R<VAL>A<CG1> central_sep1 1.03304
+R<TYR>A<CA> R<VAL>A<CG1> central_sep2 -0.268336
+R<TYR>A<CA> R<VAL>A<CG1> sep1 1.39174
+R<TYR>A<CA> R<VAL>A<CG1> sep2 0.161595
+R<TYR>A<CA> R<VAL>A<CG2> central_sep1 0.316256
+R<TYR>A<CA> R<VAL>A<CG2> central_sep2 -0.401438
+R<TYR>A<CA> R<VAL>A<CG2> sep1 1.41204
+R<TYR>A<CA> R<VAL>A<CG2> sep2 0.241825
+R<TYR>A<CA> R<VAL>A<N> central_sep1 2.46209
+R<TYR>A<CA> R<VAL>A<N> central_sep2 1.20217
+R<TYR>A<CA> R<VAL>A<N> sep1 -2.31437
+R<TYR>A<CA> R<VAL>A<N> sep2 0.291428
+R<TYR>A<CA> R<VAL>A<O> central_sep1 0.802164
+R<TYR>A<CA> R<VAL>A<O> central_sep2 -1.21667
+R<TYR>A<CA> R<VAL>A<O> sep1 -1.99323
+R<TYR>A<CA> R<VAL>A<O> sep2 0.340674
+R<TYR>A<CA> c<solvent> . 1.53348
+R<TYR>A<CB> R<TYR>A<CB> central_sep1 -0.261177
+R<TYR>A<CB> R<TYR>A<CB> central_sep2 -1.6337
+R<TYR>A<CB> R<TYR>A<CB> sep1 1.65778
+R<TYR>A<CB> R<TYR>A<CB> sep2 -0.855319
+R<TYR>A<CB> R<TYR>A<CD1> central_sep1 -0.51074
+R<TYR>A<CB> R<TYR>A<CD1> central_sep2 -1.43351
+R<TYR>A<CB> R<TYR>A<CD1> sep1 0.83305
+R<TYR>A<CB> R<TYR>A<CD1> sep2 -1.16677
+R<TYR>A<CB> R<TYR>A<CE1> central_sep1 -0.655165
+R<TYR>A<CB> R<TYR>A<CE1> central_sep2 -1.31959
+R<TYR>A<CB> R<TYR>A<CE1> sep1 1.0064
+R<TYR>A<CB> R<TYR>A<CE1> sep2 -1.13555
+R<TYR>A<CB> R<TYR>A<CG> central_sep1 0.550933
+R<TYR>A<CB> R<TYR>A<CG> central_sep2 -1.35538
+R<TYR>A<CB> R<TYR>A<CG> sep1 0.507071
+R<TYR>A<CB> R<TYR>A<CG> sep2 -2.44604
+R<TYR>A<CB> R<TYR>A<CZ> central_sep1 -0.756731
+R<TYR>A<CB> R<TYR>A<CZ> central_sep2 -1.40427
+R<TYR>A<CB> R<TYR>A<CZ> sep1 0.0205364
+R<TYR>A<CB> R<TYR>A<CZ> sep2 -1.8255
+R<TYR>A<CB> R<TYR>A<N> central_sep1 1.28654
+R<TYR>A<CB> R<TYR>A<N> central_sep2 0.471072
+R<TYR>A<CB> R<TYR>A<N> sep1 -1.36997
+R<TYR>A<CB> R<TYR>A<N> sep2 0.161549
+R<TYR>A<CB> R<TYR>A<O> central_sep1 -1.39177
+R<TYR>A<CB> R<TYR>A<O> central_sep2 -0.7253
+R<TYR>A<CB> R<TYR>A<O> sep1 0.223487
+R<TYR>A<CB> R<TYR>A<O> sep2 -0.937164
+R<TYR>A<CB> R<TYR>A<OH> central_sep1 0.78044
+R<TYR>A<CB> R<TYR>A<OH> central_sep2 -1.02061
+R<TYR>A<CB> R<TYR>A<OH> sep1 1.55867
+R<TYR>A<CB> R<TYR>A<OH> sep2 -0.906937
+R<TYR>A<CB> R<VAL>A<C> central_sep1 2.32046
+R<TYR>A<CB> R<VAL>A<C> central_sep2 0.921886
+R<TYR>A<CB> R<VAL>A<C> sep1 -0.220159
+R<TYR>A<CB> R<VAL>A<C> sep2 -0.486839
+R<TYR>A<CB> R<VAL>A<CA> central_sep1 -0.523203
+R<TYR>A<CB> R<VAL>A<CA> central_sep2 -0.228437
+R<TYR>A<CB> R<VAL>A<CA> sep1 1.61871
+R<TYR>A<CB> R<VAL>A<CA> sep2 0.297057
+R<TYR>A<CB> R<VAL>A<CB> central_sep1 0.0631377
+R<TYR>A<CB> R<VAL>A<CB> central_sep2 -1.41732
+R<TYR>A<CB> R<VAL>A<CB> sep1 1.59492
+R<TYR>A<CB> R<VAL>A<CB> sep2 -0.857059
+R<TYR>A<CB> R<VAL>A<CG1> central_sep1 -0.0775203
+R<TYR>A<CB> R<VAL>A<CG1> central_sep2 -1.42639
+R<TYR>A<CB> R<VAL>A<CG1> sep1 1.61882
+R<TYR>A<CB> R<VAL>A<CG1> sep2 -0.513616
+R<TYR>A<CB> R<VAL>A<CG2> central_sep1 -0.475152
+R<TYR>A<CB> R<VAL>A<CG2> central_sep2 -1.42631
+R<TYR>A<CB> R<VAL>A<CG2> sep1 1.5819
+R<TYR>A<CB> R<VAL>A<CG2> sep2 -0.496839
+R<TYR>A<CB> R<VAL>A<N> central_sep1 1.70187
+R<TYR>A<CB> R<VAL>A<N> central_sep2 0.749158
+R<TYR>A<CB> R<VAL>A<N> sep1 -1.10596
+R<TYR>A<CB> R<VAL>A<N> sep2 0.551803
+R<TYR>A<CB> R<VAL>A<O> central_sep1 -1.10056
+R<TYR>A<CB> R<VAL>A<O> central_sep2 -0.352351
+R<TYR>A<CB> R<VAL>A<O> sep1 0.524154
+R<TYR>A<CB> R<VAL>A<O> sep2 -0.810227
+R<TYR>A<CB> c<solvent> . 0.917591
+R<TYR>A<CD1> R<TYR>A<CD1> central_sep1 -0.846264
+R<TYR>A<CD1> R<TYR>A<CD1> central_sep2 -1.37519
+R<TYR>A<CD1> R<TYR>A<CD1> sep1 0.849041
+R<TYR>A<CD1> R<TYR>A<CD1> sep2 -1.46781
+R<TYR>A<CD1> R<TYR>A<CE1> central_sep1 -0.351681
+R<TYR>A<CD1> R<TYR>A<CE1> central_sep2 -1.19885
+R<TYR>A<CD1> R<TYR>A<CE1> sep1 0.837513
+R<TYR>A<CD1> R<TYR>A<CE1> sep2 -1.31702
+R<TYR>A<CD1> R<TYR>A<CG> central_sep1 -0.172689
+R<TYR>A<CD1> R<TYR>A<CG> central_sep2 -1.42932
+R<TYR>A<CD1> R<TYR>A<CG> sep1 -0.175124
+R<TYR>A<CD1> R<TYR>A<CG> sep2 -2.3399
+R<TYR>A<CD1> R<TYR>A<CZ> central_sep1 -0.632435
+R<TYR>A<CD1> R<TYR>A<CZ> central_sep2 -1.23571
+R<TYR>A<CD1> R<TYR>A<CZ> sep1 0.295338
+R<TYR>A<CD1> R<TYR>A<CZ> sep2 -1.77002
+R<TYR>A<CD1> R<TYR>A<N> central_sep1 0.0142357
+R<TYR>A<CD1> R<TYR>A<N> central_sep2 0.3714
+R<TYR>A<CD1> R<TYR>A<N> sep1 0.0249999
+R<TYR>A<CD1> R<TYR>A<N> sep2 -0.0720253
+R<TYR>A<CD1> R<TYR>A<O> central_sep1 -0.688065
+R<TYR>A<CD1> R<TYR>A<O> central_sep2 -0.647818
+R<TYR>A<CD1> R<TYR>A<O> sep1 0.769829
+R<TYR>A<CD1> R<TYR>A<O> sep2 -0.101023
+R<TYR>A<CD1> R<TYR>A<OH> central_sep1 0.209501
+R<TYR>A<CD1> R<TYR>A<OH> central_sep2 -0.876415
+R<TYR>A<CD1> R<TYR>A<OH> sep1 1.71171
+R<TYR>A<CD1> R<TYR>A<OH> sep2 -0.881146
+R<TYR>A<CD1> R<VAL>A<C> central_sep1 -0.701152
+R<TYR>A<CD1> R<VAL>A<C> central_sep2 -0.280588
+R<TYR>A<CD1> R<VAL>A<C> sep1 -0.778217
+R<TYR>A<CD1> R<VAL>A<C> sep2 -0.662231
+R<TYR>A<CD1> R<VAL>A<CA> central_sep1 0.311687
+R<TYR>A<CD1> R<VAL>A<CA> central_sep2 -0.0398209
+R<TYR>A<CD1> R<VAL>A<CA> sep1 0.00712649
+R<TYR>A<CD1> R<VAL>A<CA> sep2 -0.22065
+R<TYR>A<CD1> R<VAL>A<CB> central_sep1 -0.0304625
+R<TYR>A<CD1> R<VAL>A<CB> central_sep2 -0.963469
+R<TYR>A<CD1> R<VAL>A<CB> sep1 1.08699
+R<TYR>A<CD1> R<VAL>A<CB> sep2 -1.26545
+R<TYR>A<CD1> R<VAL>A<CG1> central_sep1 -0.0835306
+R<TYR>A<CD1> R<VAL>A<CG1> central_sep2 -1.2824
+R<TYR>A<CD1> R<VAL>A<CG1> sep1 1.20173
+R<TYR>A<CD1> R<VAL>A<CG1> sep2 -0.965266
+R<TYR>A<CD1> R<VAL>A<CG2> central_sep1 -0.135563
+R<TYR>A<CD1> R<VAL>A<CG2> central_sep2 -1.31951
+R<TYR>A<CD1> R<VAL>A<CG2> sep1 1.08242
+R<TYR>A<CD1> R<VAL>A<CG2> sep2 -1.01485
+R<TYR>A<CD1> R<VAL>A<N> central_sep1 0.393337
+R<TYR>A<CD1> R<VAL>A<N> central_sep2 0.674364
+R<TYR>A<CD1> R<VAL>A<N> sep1 0.130845
+R<TYR>A<CD1> R<VAL>A<N> sep2 0.235157
+R<TYR>A<CD1> R<VAL>A<O> central_sep1 -0.572646
+R<TYR>A<CD1> R<VAL>A<O> central_sep2 -0.552639
+R<TYR>A<CD1> R<VAL>A<O> sep1 0.780093
+R<TYR>A<CD1> R<VAL>A<O> sep2 0.0792328
+R<TYR>A<CD1> c<solvent> . 0.756829
+R<TYR>A<CE1> R<TYR>A<CE1> central_sep1 -0.308511
+R<TYR>A<CE1> R<TYR>A<CE1> central_sep2 -1.14964
+R<TYR>A<CE1> R<TYR>A<CE1> sep1 0.737591
+R<TYR>A<CE1> R<TYR>A<CE1> sep2 -1.34508
+R<TYR>A<CE1> R<TYR>A<CG> central_sep1 1.10397
+R<TYR>A<CE1> R<TYR>A<CG> central_sep2 -0.934621
+R<TYR>A<CE1> R<TYR>A<CG> sep1 0.275197
+R<TYR>A<CE1> R<TYR>A<CG> sep2 -2.17519
+R<TYR>A<CE1> R<TYR>A<CZ> central_sep1 0.0585609
+R<TYR>A<CE1> R<TYR>A<CZ> central_sep2 -0.737563
+R<TYR>A<CE1> R<TYR>A<CZ> sep1 0.67418
+R<TYR>A<CE1> R<TYR>A<CZ> sep2 -1.68366
+R<TYR>A<CE1> R<TYR>A<N> central_sep1 1.39332
+R<TYR>A<CE1> R<TYR>A<N> central_sep2 0.148999
+R<TYR>A<CE1> R<TYR>A<N> sep1 1.98807
+R<TYR>A<CE1> R<TYR>A<N> sep2 -0.123119
+R<TYR>A<CE1> R<TYR>A<O> central_sep1 0.409253
+R<TYR>A<CE1> R<TYR>A<O> central_sep2 -0.503053
+R<TYR>A<CE1> R<TYR>A<O> sep1 1.20252
+R<TYR>A<CE1> R<TYR>A<O> sep2 -0.0422512
+R<TYR>A<CE1> R<TYR>A<OH> central_sep1 1.19596
+R<TYR>A<CE1> R<TYR>A<OH> central_sep2 -0.878838
+R<TYR>A<CE1> R<TYR>A<OH> sep1 0.915605
+R<TYR>A<CE1> R<TYR>A<OH> sep2 -0.999825
+R<TYR>A<CE1> R<VAL>A<C> central_sep1 1.00733
+R<TYR>A<CE1> R<VAL>A<C> central_sep2 0.415644
+R<TYR>A<CE1> R<VAL>A<C> sep1 1.72576
+R<TYR>A<CE1> R<VAL>A<C> sep2 -0.307216
+R<TYR>A<CE1> R<VAL>A<CA> central_sep1 1.31686
+R<TYR>A<CE1> R<VAL>A<CA> central_sep2 0.0154723
+R<TYR>A<CE1> R<VAL>A<CA> sep1 1.89539
+R<TYR>A<CE1> R<VAL>A<CA> sep2 -0.102387
+R<TYR>A<CE1> R<VAL>A<CB> central_sep1 0.128765
+R<TYR>A<CE1> R<VAL>A<CB> central_sep2 -0.981689
+R<TYR>A<CE1> R<VAL>A<CB> sep1 0.805404
+R<TYR>A<CE1> R<VAL>A<CB> sep2 -1.27854
+R<TYR>A<CE1> R<VAL>A<CG1> central_sep1 -0.150008
+R<TYR>A<CE1> R<VAL>A<CG1> central_sep2 -1.16762
+R<TYR>A<CE1> R<VAL>A<CG1> sep1 1.29121
+R<TYR>A<CE1> R<VAL>A<CG1> sep2 -0.830546
+R<TYR>A<CE1> R<VAL>A<CG2> central_sep1 -0.0913295
+R<TYR>A<CE1> R<VAL>A<CG2> central_sep2 -1.24079
+R<TYR>A<CE1> R<VAL>A<CG2> sep1 1.45444
+R<TYR>A<CE1> R<VAL>A<CG2> sep2 -0.794133
+R<TYR>A<CE1> R<VAL>A<N> central_sep1 2.00111
+R<TYR>A<CE1> R<VAL>A<N> central_sep2 0.723044
+R<TYR>A<CE1> R<VAL>A<N> sep1 2.13822
+R<TYR>A<CE1> R<VAL>A<N> sep2 0.259729
+R<TYR>A<CE1> R<VAL>A<O> central_sep1 0.522858
+R<TYR>A<CE1> R<VAL>A<O> central_sep2 -0.201063
+R<TYR>A<CE1> R<VAL>A<O> sep1 1.49362
+R<TYR>A<CE1> R<VAL>A<O> sep2 0.251082
+R<TYR>A<CE1> c<solvent> . 0.356394
+R<TYR>A<CG> R<TYR>A<CG> central_sep1 1.30718
+R<TYR>A<CG> R<TYR>A<CG> central_sep2 -2.07769
+R<TYR>A<CG> R<TYR>A<CG> sep1 1.67356
+R<TYR>A<CG> R<TYR>A<CG> sep2 -2.39308
+R<TYR>A<CG> R<TYR>A<CZ> central_sep1 0.396979
+R<TYR>A<CG> R<TYR>A<CZ> central_sep2 -0.929649
+R<TYR>A<CG> R<TYR>A<CZ> sep1 0.224615
+R<TYR>A<CG> R<TYR>A<CZ> sep2 -1.8527
+R<TYR>A<CG> R<TYR>A<N> central_sep1 0.379109
+R<TYR>A<CG> R<TYR>A<N> central_sep2 1.28183
+R<TYR>A<CG> R<TYR>A<N> sep1 -0.842827
+R<TYR>A<CG> R<TYR>A<N> sep2 -0.000626869
+R<TYR>A<CG> R<TYR>A<O> central_sep1 0.308892
+R<TYR>A<CG> R<TYR>A<O> central_sep2 1.39706
+R<TYR>A<CG> R<TYR>A<O> sep1 -0.0673457
+R<TYR>A<CG> R<TYR>A<O> sep2 -0.507736
+R<TYR>A<CG> R<TYR>A<OH> central_sep1 1.46494
+R<TYR>A<CG> R<TYR>A<OH> central_sep2 0.395624
+R<TYR>A<CG> R<TYR>A<OH> sep1 0.326667
+R<TYR>A<CG> R<TYR>A<OH> sep2 -1.67832
+R<TYR>A<CG> R<VAL>A<C> central_sep1 1.97878
+R<TYR>A<CG> R<VAL>A<C> central_sep2 1.4675
+R<TYR>A<CG> R<VAL>A<C> sep1 -2.02388
+R<TYR>A<CG> R<VAL>A<C> sep2 0.487432
+R<TYR>A<CG> R<VAL>A<CA> central_sep1 1.83222
+R<TYR>A<CG> R<VAL>A<CA> central_sep2 0.722106
+R<TYR>A<CG> R<VAL>A<CA> sep1 1.70307
+R<TYR>A<CG> R<VAL>A<CA> sep2 -0.522329
+R<TYR>A<CG> R<VAL>A<CB> central_sep1 1.09709
+R<TYR>A<CG> R<VAL>A<CB> central_sep2 -0.525587
+R<TYR>A<CG> R<VAL>A<CB> sep1 0.951161
+R<TYR>A<CG> R<VAL>A<CB> sep2 -2.02162
+R<TYR>A<CG> R<VAL>A<CG1> central_sep1 1.21393
+R<TYR>A<CG> R<VAL>A<CG1> central_sep2 -1.07788
+R<TYR>A<CG> R<VAL>A<CG1> sep1 0.486155
+R<TYR>A<CG> R<VAL>A<CG1> sep2 -2.24653
+R<TYR>A<CG> R<VAL>A<CG2> central_sep1 1.18852
+R<TYR>A<CG> R<VAL>A<CG2> central_sep2 -1.11902
+R<TYR>A<CG> R<VAL>A<CG2> sep1 0.841938
+R<TYR>A<CG> R<VAL>A<CG2> sep2 -2.3277
+R<TYR>A<CG> R<VAL>A<N> central_sep1 0.547832
+R<TYR>A<CG> R<VAL>A<N> central_sep2 2.36291
+R<TYR>A<CG> R<VAL>A<N> sep1 -1.02043
+R<TYR>A<CG> R<VAL>A<N> sep2 0.703275
+R<TYR>A<CG> R<VAL>A<O> central_sep1 0.641311
+R<TYR>A<CG> R<VAL>A<O> central_sep2 1.62445
+R<TYR>A<CG> R<VAL>A<O> sep1 0.0387452
+R<TYR>A<CG> R<VAL>A<O> sep2 -0.0201126
+R<TYR>A<CG> c<solvent> . 1.40794
+R<TYR>A<CZ> R<TYR>A<CZ> central_sep1 2.78726
+R<TYR>A<CZ> R<TYR>A<CZ> central_sep2 0.0636982
+R<TYR>A<CZ> R<TYR>A<CZ> sep1 2.23512
+R<TYR>A<CZ> R<TYR>A<CZ> sep2 -0.986274
+R<TYR>A<CZ> R<TYR>A<N> central_sep1 2.43982
+R<TYR>A<CZ> R<TYR>A<N> central_sep2 0.282776
+R<TYR>A<CZ> R<TYR>A<N> sep1 2.01268
+R<TYR>A<CZ> R<TYR>A<N> sep2 -0.439086
+R<TYR>A<CZ> R<TYR>A<O> central_sep1 1.13462
+R<TYR>A<CZ> R<TYR>A<O> central_sep2 0.98944
+R<TYR>A<CZ> R<TYR>A<O> sep1 1.1592
+R<TYR>A<CZ> R<TYR>A<O> sep2 -0.0913219
+R<TYR>A<CZ> R<TYR>A<OH> central_sep1 2.18578
+R<TYR>A<CZ> R<TYR>A<OH> central_sep2 0.36659
+R<TYR>A<CZ> R<TYR>A<OH> sep1 1.66155
+R<TYR>A<CZ> R<TYR>A<OH> sep2 -1.26921
+R<TYR>A<CZ> R<VAL>A<C> central_sep1 1.33093
+R<TYR>A<CZ> R<VAL>A<C> central_sep2 1.49524
+R<TYR>A<CZ> R<VAL>A<C> sep1 1.8383
+R<TYR>A<CZ> R<VAL>A<C> sep2 0.393146
+R<TYR>A<CZ> R<VAL>A<CA> central_sep1 1.63529
+R<TYR>A<CZ> R<VAL>A<CA> central_sep2 0.17371
+R<TYR>A<CZ> R<VAL>A<CA> sep1 2.21268
+R<TYR>A<CZ> R<VAL>A<CA> sep2 -0.37721
+R<TYR>A<CZ> R<VAL>A<CB> central_sep1 0.114488
+R<TYR>A<CZ> R<VAL>A<CB> central_sep2 -1.11317
+R<TYR>A<CZ> R<VAL>A<CB> sep1 0.841693
+R<TYR>A<CZ> R<VAL>A<CB> sep2 -1.55019
+R<TYR>A<CZ> R<VAL>A<CG1> central_sep1 -0.564156
+R<TYR>A<CZ> R<VAL>A<CG1> central_sep2 -1.08359
+R<TYR>A<CZ> R<VAL>A<CG1> sep1 0.653011
+R<TYR>A<CZ> R<VAL>A<CG1> sep2 -1.58527
+R<TYR>A<CZ> R<VAL>A<CG2> central_sep1 -0.386107
+R<TYR>A<CZ> R<VAL>A<CG2> central_sep2 -1.12222
+R<TYR>A<CZ> R<VAL>A<CG2> sep1 0.847254
+R<TYR>A<CZ> R<VAL>A<CG2> sep2 -1.60174
+R<TYR>A<CZ> R<VAL>A<N> central_sep1 3.27566
+R<TYR>A<CZ> R<VAL>A<N> central_sep2 1.16308
+R<TYR>A<CZ> R<VAL>A<N> sep1 2.12634
+R<TYR>A<CZ> R<VAL>A<N> sep2 0.283379
+R<TYR>A<CZ> R<VAL>A<O> central_sep1 0.949806
+R<TYR>A<CZ> R<VAL>A<O> central_sep2 1.23723
+R<TYR>A<CZ> R<VAL>A<O> sep1 1.37467
+R<TYR>A<CZ> R<VAL>A<O> sep2 0.321443
+R<TYR>A<CZ> c<solvent> . 0.819711
+R<TYR>A<N> R<TYR>A<N> central_sep1 1.5405
+R<TYR>A<N> R<TYR>A<N> central_sep2 1.07068
+R<TYR>A<N> R<TYR>A<N> sep1 -2.33389
+R<TYR>A<N> R<TYR>A<N> sep2 0.780966
+R<TYR>A<N> R<TYR>A<O> central_sep1 -1.9425
+R<TYR>A<N> R<TYR>A<O> central_sep2 -1.7449
+R<TYR>A<N> R<TYR>A<O> sep1 0.17479
+R<TYR>A<N> R<TYR>A<O> sep2 0.528182
+R<TYR>A<N> R<TYR>A<OH> central_sep1 2.29009
+R<TYR>A<N> R<TYR>A<OH> central_sep2 -0.154306
+R<TYR>A<N> R<TYR>A<OH> sep1 3.20658
+R<TYR>A<N> R<TYR>A<OH> sep2 -0.171775
+R<TYR>A<N> R<VAL>A<C> central_sep1 -0.026074
+R<TYR>A<N> R<VAL>A<C> central_sep2 5.18241
+R<TYR>A<N> R<VAL>A<C> sep1 -1.35508
+R<TYR>A<N> R<VAL>A<C> sep2 1.95785
+R<TYR>A<N> R<VAL>A<CA> central_sep1 2.76712
+R<TYR>A<N> R<VAL>A<CA> central_sep2 1.58234
+R<TYR>A<N> R<VAL>A<CA> sep1 -2.22391
+R<TYR>A<N> R<VAL>A<CA> sep2 1.12932
+R<TYR>A<N> R<VAL>A<CB> central_sep1 2.08536
+R<TYR>A<N> R<VAL>A<CB> central_sep2 0.679386
+R<TYR>A<N> R<VAL>A<CB> sep1 -1.31028
+R<TYR>A<N> R<VAL>A<CB> sep2 0.480354
+R<TYR>A<N> R<VAL>A<CG1> central_sep1 0.25094
+R<TYR>A<N> R<VAL>A<CG1> central_sep2 0.40166
+R<TYR>A<N> R<VAL>A<CG1> sep1 -0.522834
+R<TYR>A<N> R<VAL>A<CG1> sep2 0.358522
+R<TYR>A<N> R<VAL>A<CG2> central_sep1 0.943271
+R<TYR>A<N> R<VAL>A<CG2> central_sep2 0.649404
+R<TYR>A<N> R<VAL>A<CG2> sep1 1.1825
+R<TYR>A<N> R<VAL>A<CG2> sep2 0.36686
+R<TYR>A<N> R<VAL>A<N> central_sep1 2.22571
+R<TYR>A<N> R<VAL>A<N> central_sep2 1.6152
+R<TYR>A<N> R<VAL>A<N> sep1 -1.84925
+R<TYR>A<N> R<VAL>A<N> sep2 0.885662
+R<TYR>A<N> R<VAL>A<O> central_sep1 -1.66912
+R<TYR>A<N> R<VAL>A<O> central_sep2 -1.87144
+R<TYR>A<N> R<VAL>A<O> sep1 0.277394
+R<TYR>A<N> R<VAL>A<O> sep2 0.559811
+R<TYR>A<N> c<solvent> . 1.96321
+R<TYR>A<O> R<TYR>A<O> central_sep1 0.603341
+R<TYR>A<O> R<TYR>A<O> central_sep2 -0.0333433
+R<TYR>A<O> R<TYR>A<O> sep1 0.782837
+R<TYR>A<O> R<TYR>A<O> sep2 0.539879
+R<TYR>A<O> R<TYR>A<OH> central_sep1 1.70975
+R<TYR>A<O> R<TYR>A<OH> central_sep2 -0.579971
+R<TYR>A<O> R<TYR>A<OH> sep1 2.49627
+R<TYR>A<O> R<TYR>A<OH> sep2 -0.192849
+R<TYR>A<O> R<VAL>A<C> central_sep1 -0.369941
+R<TYR>A<O> R<VAL>A<C> central_sep2 2.67669
+R<TYR>A<O> R<VAL>A<C> sep1 -0.776766
+R<TYR>A<O> R<VAL>A<C> sep2 1.46212
+R<TYR>A<O> R<VAL>A<CA> central_sep1 0.959591
+R<TYR>A<O> R<VAL>A<CA> central_sep2 -1.27577
+R<TYR>A<O> R<VAL>A<CA> sep1 -1.98556
+R<TYR>A<O> R<VAL>A<CA> sep2 0.36596
+R<TYR>A<O> R<VAL>A<CB> central_sep1 -1.20939
+R<TYR>A<O> R<VAL>A<CB> central_sep2 -0.445214
+R<TYR>A<O> R<VAL>A<CB> sep1 0.524205
+R<TYR>A<O> R<VAL>A<CB> sep2 -1.14678
+R<TYR>A<O> R<VAL>A<CG1> central_sep1 -0.347935
+R<TYR>A<O> R<VAL>A<CG1> central_sep2 -0.3762
+R<TYR>A<O> R<VAL>A<CG1> sep1 1.21813
+R<TYR>A<O> R<VAL>A<CG1> sep2 0.211269
+R<TYR>A<O> R<VAL>A<CG2> central_sep1 -0.735952
+R<TYR>A<O> R<VAL>A<CG2> central_sep2 -0.17193
+R<TYR>A<O> R<VAL>A<CG2> sep1 0.726877
+R<TYR>A<O> R<VAL>A<CG2> sep2 -0.0514444
+R<TYR>A<O> R<VAL>A<N> central_sep1 -1.66006
+R<TYR>A<O> R<VAL>A<N> central_sep2 -1.94569
+R<TYR>A<O> R<VAL>A<N> sep1 0.125469
+R<TYR>A<O> R<VAL>A<N> sep2 0.73496
+R<TYR>A<O> R<VAL>A<O> central_sep1 0.750456
+R<TYR>A<O> R<VAL>A<O> central_sep2 -0.0618113
+R<TYR>A<O> R<VAL>A<O> sep1 1.24968
+R<TYR>A<O> R<VAL>A<O> sep2 0.694338
+R<TYR>A<O> c<solvent> . 0.825499
+R<TYR>A<OH> R<TYR>A<OH> central_sep1 1.06582
+R<TYR>A<OH> R<TYR>A<OH> central_sep2 -1.17216
+R<TYR>A<OH> R<TYR>A<OH> sep1 2.00909
+R<TYR>A<OH> R<TYR>A<OH> sep2 -0.853562
+R<TYR>A<OH> R<VAL>A<C> central_sep1 3.68379
+R<TYR>A<OH> R<VAL>A<C> central_sep2 1.22264
+R<TYR>A<OH> R<VAL>A<C> sep1 4.7696
+R<TYR>A<OH> R<VAL>A<C> sep2 0.216505
+R<TYR>A<OH> R<VAL>A<CA> central_sep1 2.36419
+R<TYR>A<OH> R<VAL>A<CA> central_sep2 -0.0799454
+R<TYR>A<OH> R<VAL>A<CA> sep1 3.42712
+R<TYR>A<OH> R<VAL>A<CA> sep2 0.040714
+R<TYR>A<OH> R<VAL>A<CB> central_sep1 1.01824
+R<TYR>A<OH> R<VAL>A<CB> central_sep2 -0.630126
+R<TYR>A<OH> R<VAL>A<CB> sep1 1.32299
+R<TYR>A<OH> R<VAL>A<CB> sep2 -1.05422
+R<TYR>A<OH> R<VAL>A<CG1> central_sep1 1.23241
+R<TYR>A<OH> R<VAL>A<CG1> central_sep2 -0.807707
+R<TYR>A<OH> R<VAL>A<CG1> sep1 1.22534
+R<TYR>A<OH> R<VAL>A<CG1> sep2 -0.541095
+R<TYR>A<OH> R<VAL>A<CG2> central_sep1 1.50451
+R<TYR>A<OH> R<VAL>A<CG2> central_sep2 -0.777107
+R<TYR>A<OH> R<VAL>A<CG2> sep1 1.13244
+R<TYR>A<OH> R<VAL>A<CG2> sep2 -0.588383
+R<TYR>A<OH> R<VAL>A<N> central_sep1 2.42622
+R<TYR>A<OH> R<VAL>A<N> central_sep2 0.21528
+R<TYR>A<OH> R<VAL>A<N> sep1 3.42043
+R<TYR>A<OH> R<VAL>A<N> sep2 0.291729
+R<TYR>A<OH> R<VAL>A<O> central_sep1 2.2454
+R<TYR>A<OH> R<VAL>A<O> central_sep2 -0.284764
+R<TYR>A<OH> R<VAL>A<O> sep1 2.82169
+R<TYR>A<OH> R<VAL>A<O> sep2 0.0348697
+R<TYR>A<OH> c<solvent> . -0.109114
+R<VAL>A<C> R<VAL>A<C> central_sep1 6.08213
+R<VAL>A<C> R<VAL>A<C> central_sep2 4.06916
+R<VAL>A<C> R<VAL>A<C> sep1 -2.70037
+R<VAL>A<C> R<VAL>A<C> sep2 2.89622
+R<VAL>A<C> R<VAL>A<CA> central_sep1 4.1216
+R<VAL>A<C> R<VAL>A<CA> central_sep2 3.28091
+R<VAL>A<C> R<VAL>A<CA> sep1 -2.99111
+R<VAL>A<C> R<VAL>A<CA> sep2 1.01591
+R<VAL>A<C> R<VAL>A<CB> central_sep1 2.68787
+R<VAL>A<C> R<VAL>A<CB> central_sep2 1.14998
+R<VAL>A<C> R<VAL>A<CB> sep1 0.120808
+R<VAL>A<C> R<VAL>A<CB> sep2 -0.863342
+R<VAL>A<C> R<VAL>A<CG1> central_sep1 -0.0877349
+R<VAL>A<C> R<VAL>A<CG1> central_sep2 0.264976
+R<VAL>A<C> R<VAL>A<CG1> sep1 -0.924303
+R<VAL>A<C> R<VAL>A<CG1> sep2 -0.975716
+R<VAL>A<C> R<VAL>A<CG2> central_sep1 0.770511
+R<VAL>A<C> R<VAL>A<CG2> central_sep2 0.164975
+R<VAL>A<C> R<VAL>A<CG2> sep1 -1.24848
+R<VAL>A<C> R<VAL>A<CG2> sep2 -0.772209
+R<VAL>A<C> R<VAL>A<N> central_sep1 0.505458
+R<VAL>A<C> R<VAL>A<N> central_sep2 4.29018
+R<VAL>A<C> R<VAL>A<N> sep1 -1.149
+R<VAL>A<C> R<VAL>A<N> sep2 2.22636
+R<VAL>A<C> R<VAL>A<O> central_sep1 -0.382893
+R<VAL>A<C> R<VAL>A<O> central_sep2 3.07614
+R<VAL>A<C> R<VAL>A<O> sep1 -0.758153
+R<VAL>A<C> R<VAL>A<O> sep2 1.37662
+R<VAL>A<C> c<solvent> . 2.38596
+R<VAL>A<CA> R<VAL>A<CA> central_sep1 1.04763
+R<VAL>A<CA> R<VAL>A<CA> central_sep2 -0.888724
+R<VAL>A<CA> R<VAL>A<CA> sep1 3.82888
+R<VAL>A<CA> R<VAL>A<CA> sep2 0.171998
+R<VAL>A<CA> R<VAL>A<CB> central_sep1 -0.892095
+R<VAL>A<CA> R<VAL>A<CB> central_sep2 -1.00329
+R<VAL>A<CA> R<VAL>A<CB> sep1 1.28568
+R<VAL>A<CA> R<VAL>A<CB> sep2 -0.194508
+R<VAL>A<CA> R<VAL>A<CG1> central_sep1 1.39934
+R<VAL>A<CA> R<VAL>A<CG1> central_sep2 -0.484416
+R<VAL>A<CA> R<VAL>A<CG1> sep1 1.38894
+R<VAL>A<CA> R<VAL>A<CG1> sep2 0.00798969
+R<VAL>A<CA> R<VAL>A<CG2> central_sep1 0.336524
+R<VAL>A<CA> R<VAL>A<CG2> central_sep2 -0.586687
+R<VAL>A<CA> R<VAL>A<CG2> sep1 1.33952
+R<VAL>A<CA> R<VAL>A<CG2> sep2 -0.063585
+R<VAL>A<CA> R<VAL>A<N> central_sep1 2.82838
+R<VAL>A<CA> R<VAL>A<N> central_sep2 1.40431
+R<VAL>A<CA> R<VAL>A<N> sep1 -2.51854
+R<VAL>A<CA> R<VAL>A<N> sep2 0.465973
+R<VAL>A<CA> R<VAL>A<O> central_sep1 0.84649
+R<VAL>A<CA> R<VAL>A<O> central_sep2 -1.79028
+R<VAL>A<CA> R<VAL>A<O> sep1 -2.206
+R<VAL>A<CA> R<VAL>A<O> sep2 0.0417478
+R<VAL>A<CA> c<solvent> . 1.70247
+R<VAL>A<CB> R<VAL>A<CB> central_sep1 0.104566
+R<VAL>A<CB> R<VAL>A<CB> central_sep2 -1.70839
+R<VAL>A<CB> R<VAL>A<CB> sep1 1.40321
+R<VAL>A<CB> R<VAL>A<CB> sep2 -1.45842
+R<VAL>A<CB> R<VAL>A<CG1> central_sep1 0.244324
+R<VAL>A<CB> R<VAL>A<CG1> central_sep2 -1.40844
+R<VAL>A<CB> R<VAL>A<CG1> sep1 1.32084
+R<VAL>A<CB> R<VAL>A<CG1> sep2 -1.49091
+R<VAL>A<CB> R<VAL>A<CG2> central_sep1 0.339301
+R<VAL>A<CB> R<VAL>A<CG2> central_sep2 -1.60399
+R<VAL>A<CB> R<VAL>A<CG2> sep1 0.745318
+R<VAL>A<CB> R<VAL>A<CG2> sep2 -1.45502
+R<VAL>A<CB> R<VAL>A<N> central_sep1 2.25402
+R<VAL>A<CB> R<VAL>A<N> central_sep2 0.97809
+R<VAL>A<CB> R<VAL>A<N> sep1 -1.31522
+R<VAL>A<CB> R<VAL>A<N> sep2 0.605204
+R<VAL>A<CB> R<VAL>A<O> central_sep1 -1.29606
+R<VAL>A<CB> R<VAL>A<O> central_sep2 -0.596907
+R<VAL>A<CB> R<VAL>A<O> sep1 0.533758
+R<VAL>A<CB> R<VAL>A<O> sep2 -1.36113
+R<VAL>A<CB> c<solvent> . 0.877407
+R<VAL>A<CG1> R<VAL>A<CG1> central_sep1 -0.210061
+R<VAL>A<CG1> R<VAL>A<CG1> central_sep2 -1.8931
+R<VAL>A<CG1> R<VAL>A<CG1> sep1 2.21091
+R<VAL>A<CG1> R<VAL>A<CG1> sep2 -0.728624
+R<VAL>A<CG1> R<VAL>A<CG2> central_sep1 -0.986537
+R<VAL>A<CG1> R<VAL>A<CG2> central_sep2 -1.92735
+R<VAL>A<CG1> R<VAL>A<CG2> sep1 1.8739
+R<VAL>A<CG1> R<VAL>A<CG2> sep2 -0.647755
+R<VAL>A<CG1> R<VAL>A<N> central_sep1 0.339418
+R<VAL>A<CG1> R<VAL>A<N> central_sep2 0.260784
+R<VAL>A<CG1> R<VAL>A<N> sep1 -0.837417
+R<VAL>A<CG1> R<VAL>A<N> sep2 0.0972565
+R<VAL>A<CG1> R<VAL>A<O> central_sep1 -0.232772
+R<VAL>A<CG1> R<VAL>A<O> central_sep2 -0.635732
+R<VAL>A<CG1> R<VAL>A<O> sep1 0.761719
+R<VAL>A<CG1> R<VAL>A<O> sep2 -0.131934
+R<VAL>A<CG1> c<solvent> . 0.631553
+R<VAL>A<CG2> R<VAL>A<CG2> central_sep1 -0.4577
+R<VAL>A<CG2> R<VAL>A<CG2> central_sep2 -1.95541
+R<VAL>A<CG2> R<VAL>A<CG2> sep1 2.58773
+R<VAL>A<CG2> R<VAL>A<CG2> sep2 -0.71938
+R<VAL>A<CG2> R<VAL>A<N> central_sep1 0.813508
+R<VAL>A<CG2> R<VAL>A<N> central_sep2 0.443297
+R<VAL>A<CG2> R<VAL>A<N> sep1 1.19859
+R<VAL>A<CG2> R<VAL>A<N> sep2 0.197303
+R<VAL>A<CG2> R<VAL>A<O> central_sep1 -0.826983
+R<VAL>A<CG2> R<VAL>A<O> central_sep2 -0.35153
+R<VAL>A<CG2> R<VAL>A<O> sep1 0.586664
+R<VAL>A<CG2> R<VAL>A<O> sep2 -0.136113
+R<VAL>A<CG2> c<solvent> . 0.690128
+R<VAL>A<N> R<VAL>A<N> central_sep1 1.77286
+R<VAL>A<N> R<VAL>A<N> central_sep2 1.39866
+R<VAL>A<N> R<VAL>A<N> sep1 -1.6771
+R<VAL>A<N> R<VAL>A<N> sep2 0.51399
+R<VAL>A<N> R<VAL>A<O> central_sep1 -1.68449
+R<VAL>A<N> R<VAL>A<O> central_sep2 -2.19682
+R<VAL>A<N> R<VAL>A<O> sep1 -0.132119
+R<VAL>A<N> R<VAL>A<O> sep2 0.584094
+R<VAL>A<N> c<solvent> . 1.98414
+R<VAL>A<O> R<VAL>A<O> central_sep1 0.910284
+R<VAL>A<O> R<VAL>A<O> central_sep2 -0.402939
+R<VAL>A<O> R<VAL>A<O> sep1 1.09851
+R<VAL>A<O> R<VAL>A<O> sep2 0.374492
+R<VAL>A<O> c<solvent> . 0.829146
+EOF
+fi
+
+if [ "$RESOURCE_NAME" == "energy_means_and_sds" ]
+then
+cat << 'EOF'
+R<ALA>A<C> -0.361355 0.271633
+R<ALA>A<CA> -0.345553 0.267743
+R<ALA>A<CB> -0.3448 0.243304
+R<ALA>A<N> -0.366099 0.260687
+R<ALA>A<O> -0.345946 0.258291
+R<ARG>A<C> -0.314033 0.250329
+R<ARG>A<CA> -0.283062 0.235648
+R<ARG>A<CB> -0.282617 0.196033
+R<ARG>A<CD> -0.300179 0.166284
+R<ARG>A<CG> -0.286845 0.183697
+R<ARG>A<CZ> -0.311343 0.154622
+R<ARG>A<N> -0.326924 0.237998
+R<ARG>A<NE> -0.309583 0.161413
+R<ARG>A<NH1> -0.299401 0.14972
+R<ARG>A<O> -0.306149 0.235503
+R<ASN>A<C> -0.277629 0.234746
+R<ASN>A<CA> -0.239685 0.216018
+R<ASN>A<CB> -0.240536 0.192117
+R<ASN>A<CG> -0.243489 0.177516
+R<ASN>A<N> -0.285685 0.227598
+R<ASN>A<ND2> -0.248695 0.169529
+R<ASN>A<O> -0.275947 0.221397
+R<ASN>A<OD1> -0.240778 0.178939
+R<ASP>A<C> -0.276127 0.230521
+R<ASP>A<CA> -0.227304 0.211296
+R<ASP>A<CB> -0.234205 0.187007
+R<ASP>A<CG> -0.23162 0.164127
+R<ASP>A<N> -0.284671 0.219865
+R<ASP>A<O> -0.275534 0.213786
+R<ASP>A<OD1> -0.240172 0.170026
+R<CYS>A<C> -0.433833 0.263039
+R<CYS>A<CA> -0.452816 0.264808
+R<CYS>A<CB> -0.445575 0.241479
+R<CYS>A<N> -0.452772 0.25979
+R<CYS>A<O> -0.415418 0.249034
+R<CYS>A<SG> -0.453821 0.233319
+R<GLN>A<C> -0.288729 0.24214
+R<GLN>A<CA> -0.249327 0.227324
+R<GLN>A<CB> -0.247521 0.200981
+R<GLN>A<CD> -0.268025 0.170638
+R<GLN>A<CG> -0.244308 0.189226
+R<GLN>A<N> -0.294536 0.233243
+R<GLN>A<NE2> -0.263844 0.168541
+R<GLN>A<O> -0.283414 0.229182
+R<GLN>A<OE1> -0.269828 0.173859
+R<GLU>A<C> -0.274567 0.234897
+R<GLU>A<CA> -0.228705 0.219997
+R<GLU>A<CB> -0.228811 0.189035
+R<GLU>A<CD> -0.280044 0.165997
+R<GLU>A<CG> -0.246744 0.177932
+R<GLU>A<N> -0.280941 0.224805
+R<GLU>A<O> -0.271903 0.219933
+R<GLU>A<OE1> -0.289284 0.184738
+R<GLY>A<C> -0.284029 0.238359
+R<GLY>A<CA> -0.255495 0.224329
+R<GLY>A<N> -0.271878 0.243837
+R<GLY>A<O> -0.29364 0.234042
+R<HIS>A<C> -0.333108 0.26356
+R<HIS>A<CA> -0.304916 0.242045
+R<HIS>A<CB> -0.313616 0.232557
+R<HIS>A<CD2> -0.315305 0.202641
+R<HIS>A<CE1> -0.292742 0.17448
+R<HIS>A<CG> -0.321819 0.23152
+R<HIS>A<N> -0.33991 0.253808
+R<HIS>A<ND1> -0.297591 0.198435
+R<HIS>A<NE2> -0.310276 0.183333
+R<HIS>A<O> -0.331277 0.246533
+R<ILE>A<C> -0.450304 0.293395
+R<ILE>A<CA> -0.479819 0.309649
+R<ILE>A<CB> -0.518727 0.337553
+R<ILE>A<CD1> -0.514598 0.274205
+R<ILE>A<CG1> -0.518525 0.291153
+R<ILE>A<CG2> -0.506426 0.274073
+R<ILE>A<N> -0.461542 0.287267
+R<ILE>A<O> -0.449107 0.276286
+R<LEU>A<C> -0.428931 0.282663
+R<LEU>A<CA> -0.433988 0.288229
+R<LEU>A<CB> -0.462253 0.280208
+R<LEU>A<CD1> -0.494805 0.276094
+R<LEU>A<CD2> -0.484707 0.275624
+R<LEU>A<CG> -0.519465 0.308807
+R<LEU>A<N> -0.430719 0.273607
+R<LEU>A<O> -0.412602 0.269545
+R<LYS>A<C> -0.271316 0.243753
+R<LYS>A<CA> -0.231758 0.227465
+R<LYS>A<CB> -0.236498 0.193188
+R<LYS>A<CD> -0.26921 0.162298
+R<LYS>A<CE> -0.293129 0.175876
+R<LYS>A<CG> -0.246717 0.177021
+R<LYS>A<N> -0.288103 0.231916
+R<LYS>A<NZ> -0.334014 0.223843
+R<LYS>A<O> -0.268066 0.229215
+R<MET>A<C> -0.398077 0.27971
+R<MET>A<CA> -0.396421 0.286734
+R<MET>A<CB> -0.411255 0.273216
+R<MET>A<CE> -0.445468 0.264173
+R<MET>A<CG> -0.439682 0.275508
+R<MET>A<N> -0.391078 0.284179
+R<MET>A<O> -0.387303 0.263566
+R<MET>A<SD> -0.458938 0.273885
+R<PHE>A<C> -0.402941 0.27988
+R<PHE>A<CA> -0.4315 0.282044
+R<PHE>A<CB> -0.4593 0.272564
+R<PHE>A<CD1> -0.504217 0.279886
+R<PHE>A<CE1> -0.517273 0.287964
+R<PHE>A<CG> -0.567174 0.402211
+R<PHE>A<CZ> -0.525165 0.297149
+R<PHE>A<N> -0.414952 0.27603
+R<PHE>A<O> -0.410731 0.267482
+R<PRO>A<C> -0.251864 0.227495
+R<PRO>A<CA> -0.235571 0.22395
+R<PRO>A<CB> -0.253491 0.210246
+R<PRO>A<CD> -0.27945 0.208038
+R<PRO>A<CG> -0.285889 0.202525
+R<PRO>A<N> -0.265365 0.239899
+R<PRO>A<O> -0.274112 0.216166
+R<SER>A<C> -0.291562 0.250821
+R<SER>A<CA> -0.265312 0.240888
+R<SER>A<CB> -0.260352 0.203396
+R<SER>A<N> -0.305418 0.242504
+R<SER>A<O> -0.292216 0.235508
+R<SER>A<OG> -0.252789 0.197016
+R<THR>A<C> -0.340493 0.264137
+R<THR>A<CA> -0.30935 0.25289
+R<THR>A<CB> -0.301043 0.220135
+R<THR>A<CG2> -0.318906 0.220701
+R<THR>A<N> -0.336243 0.250223
+R<THR>A<O> -0.335836 0.244642
+R<THR>A<OG1> -0.280829 0.205848
+R<TRP>A<C> -0.390675 0.268288
+R<TRP>A<CA> -0.407684 0.260605
+R<TRP>A<CB> -0.427691 0.260025
+R<TRP>A<CD1> -0.396679 0.216544
+R<TRP>A<CD2> -0.514994 0.27336
+R<TRP>A<CE2> -0.495801 0.273607
+R<TRP>A<CE3> -0.5046 0.26119
+R<TRP>A<CG> -0.490856 0.349568
+R<TRP>A<CH2> -0.479774 0.256487
+R<TRP>A<CZ2> -0.451098 0.231715
+R<TRP>A<CZ3> -0.503666 0.264548
+R<TRP>A<N> -0.388018 0.255962
+R<TRP>A<NE1> -0.418557 0.220445
+R<TRP>A<O> -0.390417 0.252122
+R<TYR>A<C> -0.394996 0.277939
+R<TYR>A<CA> -0.397171 0.266279
+R<TYR>A<CB> -0.424335 0.262804
+R<TYR>A<CD1> -0.418049 0.235199
+R<TYR>A<CE1> -0.406279 0.217514
+R<TYR>A<CG> -0.462158 0.352833
+R<TYR>A<CZ> -0.420874 0.236456
+R<TYR>A<N> -0.395839 0.270795
+R<TYR>A<O> -0.392777 0.260632
+R<TYR>A<OH> -0.382486 0.195056
+R<VAL>A<C> -0.452268 0.294451
+R<VAL>A<CA> -0.47288 0.3119
+R<VAL>A<CB> -0.486325 0.312156
+R<VAL>A<CG1> -0.476699 0.272099
+R<VAL>A<CG2> -0.471999 0.267144
+R<VAL>A<N> -0.446777 0.287806
+R<VAL>A<O> -0.441403 0.275012
+EOF
+fi
diff --git a/voronota-volumes b/voronota-volumes
new file mode 100755
index 0000000..da09d28
--- /dev/null
+++ b/voronota-volumes
@@ -0,0 +1,180 @@
+#!/bin/bash
+
+function print_help_and_exit
+{
+cat >&2 << EOF
+
+'voronota-volumes' script provides a way for calculating and querying atomic volumes
+with just one command (without the need to construct a pipeline from 'voronota' calls).
+
+Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --cache-dir string path to cache directory
+ --sum-at-end flag to print sum of areas as the last line in output
+ --help | -h flag to display help message and exit
+
+Advanced options:
+ --atoms-query string atoms query parameters
+ --per-residue flag to output per-residue results
+ --multiple-models flag to handle multiple models in PDB file
+
+Standard output (multiple lines):
+ {name} {volume}
+
+EOF
+exit 1
+}
+
+readonly ZEROARG=$0
+INFILE=""
+INPUT_FILTER_QUERY_PARAMETERS=""
+ATOMS_QUERY_PARAMETERS=""
+CACHE_DIRECTORY=""
+MULTIPLE_MODELS_CHAINS_OPTION=""
+SUM_AT_END=false
+PER_RESIDUE=false
+HELP_MODE=false
+
+while [[ $# > 0 ]]
+do
+ OPTION="$1"
+ OPTARG="$2"
+ shift
+ case $OPTION in
+ -i|--input)
+ INFILE="$OPTARG"
+ shift
+ ;;
+ --input-filter-query)
+ INPUT_FILTER_QUERY_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --atoms-query)
+ ATOMS_QUERY_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --cache-dir)
+ CACHE_DIRECTORY="$OPTARG"
+ shift
+ ;;
+ --multiple-models)
+ MULTIPLE_MODELS_CHAINS_OPTION="--multimodel-chains"
+ ;;
+ --sum-at-end)
+ SUM_AT_END=true
+ ;;
+ --per-residue)
+ PER_RESIDUE=true
+ ;;
+ -h)
+ HELP_MODE=true
+ ;;
+ *)
+ echo >&2 "Error: invalid command line option '$OPTION'"
+ exit 1
+ ;;
+ esac
+done
+
+if [ -z "$INFILE" ] || $HELP_MODE
+then
+ print_help_and_exit
+fi
+
+if [[ $ZEROARG == *"/"* ]]
+then
+ cd $(dirname $ZEROARG)
+ export PATH=$(pwd):$PATH
+ cd - &> /dev/null
+fi
+
+command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; }
+command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; }
+
+if [ ! -s "$INFILE" ]
+then
+ echo >&2 "Error: input file does not exist"
+ exit 1
+fi
+
+readonly TMPLDIR=$(mktemp -d)
+trap "rm -r $TMPLDIR" EXIT
+
+{
+ if [[ "$INFILE" == *".gz" ]]
+ then
+ zcat "$INFILE"
+ else
+ cat "$INFILE"
+ fi
+} \
+| voronota get-balls-from-atoms-file \
+ --annotated $MULTIPLE_MODELS_CHAINS_OPTION \
+ --radii-file <(voronota-resources radii) \
+ --include-heteroatoms \
+| voronota query-balls \
+ --drop-altloc-indicators \
+| voronota query-balls $INPUT_FILTER_QUERY_PARAMETERS \
+> $TMPLDIR/balls
+
+if [ ! -s "$TMPLDIR/balls" ]
+then
+ echo >&2 "Error: no atoms in input file"
+ exit 1
+fi
+
+BALLS_MD5=""
+if [ -n "$CACHE_DIRECTORY" ]
+then
+ BALLS_MD5=$(cat $TMPLDIR/balls | md5sum | awk '{print $1}')
+ if [ -n "$BALLS_MD5" ]
+ then
+ BALLS_MD5="${BALLS_MD5}.voronota.volumes"
+ if [ -s "$CACHE_DIRECTORY/$BALLS_MD5" ]
+ then
+ cp $CACHE_DIRECTORY/$BALLS_MD5 $TMPLDIR/all_volumes
+ fi
+ fi
+fi
+
+if [ ! -s "$TMPLDIR/all_volumes" ]
+then
+ cat $TMPLDIR/balls \
+ | voronota calculate-contacts \
+ --annotated \
+ --volumes-output $TMPLDIR/all_volumes \
+ > /dev/null
+
+ if [ -n "$CACHE_DIRECTORY" ] && [ -n "$BALLS_MD5" ]
+ then
+ mkdir -p $CACHE_DIRECTORY
+ cp $TMPLDIR/all_volumes $CACHE_DIRECTORY/$BALLS_MD5
+ fi
+fi
+
+cat $TMPLDIR/all_volumes \
+| awk '{print $1 " c<volume> " $2 " 1 . ."}' \
+| voronota query-contacts \
+ --match-external-first <(cat $TMPLDIR/balls | voronota query-balls $ATOMS_QUERY_PARAMETERS) \
+| \
+{
+ if $PER_RESIDUE
+ then
+ voronota query-contacts --inter-residue --match-second 'c<volume>'
+ else
+ voronota query-contacts --match-second 'c<volume>'
+ fi
+} \
+> $TMPLDIR/result_as_contacts
+
+{
+cat $TMPLDIR/result_as_contacts
+if $SUM_AT_END
+then
+ cat $TMPLDIR/result_as_contacts \
+ | voronota query-contacts --summarize
+fi
+} \
+| awk '{print $1 " " $3}' \
+| column -t
diff --git a/voronota-voromqa b/voronota-voromqa
new file mode 100755
index 0000000..30c4959
--- /dev/null
+++ b/voronota-voromqa
@@ -0,0 +1,1094 @@
+#!/bin/bash
+
+function print_help_and_exit
+{
+cat >&2 << EOF
+
+'voronota-voromqa' script is an implementation of VoroMQA method using Voronota.
+
+Basic options:
+ --input | -i string * input structure file in PDB format
+ --input-filter-query string input atoms filtering query parameters
+ --output-atom-scores string output text file with atom scores
+ --output-atom-scores-pdb string output PDB file with atom scores as B-factors
+ --output-residue-scores string output text file with residue scores
+ --output-residue-scores-pdb string output PDB file with residue scores as B-factors
+ --output-residue-scores-plot string output PNG image file with residue scores plot, requires R
+ --help | -h flag to display help message and exit
+
+Advanced options:
+ --cache-dir string path to cache directory
+ --smoothing-window number residue scores smoothing window size, default is 5
+ --atoms-query string atoms query parameters to define selection
+ --contacts-query string contacts query parameters to define selection
+ --output-selected-scores string output text file with selected atom scores
+ --reference-sequence string sequence file or string for residue renumbering
+ --output-sequence-alignment string output text file with sequence alignment
+ --multiple-models flag to handle multiple models in PDB file
+
+Standard output (one line):
+ {input file path} {global score} {number of residues} {number of atoms} [ {selection score} {number of selected atoms} ]
+
+EOF
+exit 1
+}
+
+readonly ZEROARG=$0
+INFILE=""
+REFERENCE_SEQUENCE=""
+INPUT_FILTER_QUERY_PARAMETERS=""
+OUTFILE_SEQUENCE_ALIGNMENT=""
+OUTFILE_BALLS=""
+OUTFILE_CONTACTS=""
+OUTFILE_ATOM_SCORES=""
+OUTFILE_ATOM_SCORES_PDB=""
+OUTFILE_RESIDUE_SCORES=""
+OUTFILE_RESIDUE_SCORES_PDB=""
+OUTFILE_ATOM_DEPTHS=""
+OUTFILE_CAMEO_RESIDUE_SCORES=""
+OUTFILE_PLOT=""
+OUTFILE_MAP=""
+OUTFILE_SCREENSHOT=""
+OUTFILE_SCORES_FOR_CASP=""
+OUTFILE_SCORES_FOR_CASP_PDB=""
+OUTFILE_SCORES_FOR_CASP_LOG=""
+OUTFILE_CUTTING_SUGGESTIONS=""
+OUTDIR_SUMMARY_FOR_POTENTIAL=""
+SMOOTHING_WINDOW="5"
+ATOMS_QUERY_PARAMETERS=""
+CONTACTS_QUERY_PARAMETERS=""
+OUTFILE_SELECTED_ATOM_SCORES=""
+CACHE_DIRECTORY=""
+MULTIPLE_MODELS_CHAINS_OPTION=""
+UNTEACHING_DIRECTORY=""
+REBUILD_SIDECHAINS_COMMAND=""
+SCREENSHOT_WIDTH="500"
+SCREENSHOT_HEIGHT="500"
+SCREENSHOT_BACKGROUND="black"
+PLOT_MODE="normal"
+SURFACE_CRAVING_ATOMS_OUTPUT=""
+SURFACE_CRAVING_ATOMS_OUTPUT_PDB=""
+SURFACE_CRAVING_RESIDUES_OUTPUT=""
+SURFACE_CRAVING_RESIDUES_OUTPUT_PDB=""
+SURFACE_CRAVING_ATOMS_ENERGIES_OUTPUT=""
+NEGLECT_SAS=false
+REINTERPRET_SAS=false
+MORE_LOGGING=false
+PRINT_ENERGY_OF_CONTACTS_SELECTION=false
+HELP_MODE=false
+
+while [[ $# > 0 ]]
+do
+ OPTION="$1"
+ OPTARG="$2"
+ shift
+ case $OPTION in
+ -i|--input)
+ INFILE="$OPTARG"
+ shift
+ ;;
+ --reference-sequence)
+ REFERENCE_SEQUENCE="$OPTARG"
+ shift
+ ;;
+ --input-filter-query)
+ INPUT_FILTER_QUERY_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --output-balls)
+ OUTFILE_BALLS="$OPTARG"
+ shift
+ ;;
+ --output-contacts)
+ OUTFILE_CONTACTS="$OPTARG"
+ shift
+ ;;
+ --output-sequence-alignment)
+ OUTFILE_SEQUENCE_ALIGNMENT="$OPTARG"
+ shift
+ ;;
+ --output-atom-scores)
+ OUTFILE_ATOM_SCORES="$OPTARG"
+ shift
+ ;;
+ --output-atom-scores-pdb)
+ OUTFILE_ATOM_SCORES_PDB="$OPTARG"
+ shift
+ ;;
+ --output-residue-scores)
+ OUTFILE_RESIDUE_SCORES="$OPTARG"
+ shift
+ ;;
+ --output-residue-scores-pdb)
+ OUTFILE_RESIDUE_SCORES_PDB="$OPTARG"
+ shift
+ ;;
+ --output-atom-depth-values)
+ OUTFILE_ATOM_DEPTHS="$OPTARG"
+ shift
+ ;;
+ --output-residue-scores-for-CAMEO)
+ OUTFILE_CAMEO_RESIDUE_SCORES="$OPTARG"
+ shift
+ ;;
+ --output-residue-scores-plot)
+ OUTFILE_PLOT="$OPTARG"
+ shift
+ ;;
+ --output-contacts-map-svg)
+ OUTFILE_MAP="$OPTARG"
+ shift
+ ;;
+ --output-screenshot)
+ OUTFILE_SCREENSHOT="$OPTARG"
+ shift
+ ;;
+ --output-scores-for-CASP)
+ OUTFILE_SCORES_FOR_CASP="$OPTARG"
+ shift
+ ;;
+ --output-scores-for-CASP-pdb)
+ OUTFILE_SCORES_FOR_CASP_PDB="$OPTARG"
+ shift
+ ;;
+ --output-scores-for-CASP-log)
+ OUTFILE_SCORES_FOR_CASP_LOG="$OPTARG"
+ shift
+ ;;
+ --output-cutting-suggestions)
+ OUTFILE_CUTTING_SUGGESTIONS="$OPTARG"
+ shift
+ ;;
+ --outdir-summary-for-potential)
+ OUTDIR_SUMMARY_FOR_POTENTIAL="$OPTARG"
+ shift
+ ;;
+ --smoothing-window)
+ SMOOTHING_WINDOW="$OPTARG"
+ shift
+ ;;
+ --atoms-query)
+ ATOMS_QUERY_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --contacts-query)
+ CONTACTS_QUERY_PARAMETERS="$OPTARG"
+ shift
+ ;;
+ --output-selected-scores)
+ OUTFILE_SELECTED_ATOM_SCORES="$OPTARG"
+ shift
+ ;;
+ --cache-dir)
+ CACHE_DIRECTORY="$OPTARG"
+ shift
+ ;;
+ --unteaching-dir)
+ UNTEACHING_DIRECTORY="$OPTARG"
+ shift
+ ;;
+ --rebuild-sidechains)
+ REBUILD_SIDECHAINS_COMMAND="$OPTARG"
+ shift
+ ;;
+ --screenshot-width)
+ SCREENSHOT_WIDTH="$OPTARG"
+ shift
+ ;;
+ --screenshot-height)
+ SCREENSHOT_HEIGHT="$OPTARG"
+ shift
+ ;;
+ --screenshot-background)
+ SCREENSHOT_BACKGROUND="$OPTARG"
+ shift
+ ;;
+ --surface-craving-atoms-output)
+ SURFACE_CRAVING_ATOMS_OUTPUT="$OPTARG"
+ shift
+ ;;
+ --surface-craving-atoms-output-pdb)
+ SURFACE_CRAVING_ATOMS_OUTPUT_PDB="$OPTARG"
+ shift
+ ;;
+ --surface-craving-residues-output)
+ SURFACE_CRAVING_RESIDUES_OUTPUT="$OPTARG"
+ shift
+ ;;
+ --surface-craving-residues-output-pdb)
+ SURFACE_CRAVING_RESIDUES_OUTPUT_PDB="$OPTARG"
+ shift
+ ;;
+ --surface-craving-atoms-energies-output)
+ SURFACE_CRAVING_ATOMS_ENERGIES_OUTPUT="$OPTARG"
+ shift
+ ;;
+ --multiple-models)
+ MULTIPLE_MODELS_CHAINS_OPTION="--multimodel-chains"
+ ;;
+ --small-plot)
+ PLOT_MODE="small"
+ ;;
+ --neglect-SAS)
+ NEGLECT_SAS=true
+ ;;
+ --reinterpret-SAS)
+ REINTERPRET_SAS=true
+ ;;
+ --more-logging)
+ MORE_LOGGING=true
+ ;;
+ --print-energy-of-contacts-selection)
+ PRINT_ENERGY_OF_CONTACTS_SELECTION=true
+ ;;
+ -h|--help)
+ HELP_MODE=true
+ ;;
+ *)
+ echo >&2 "Error: invalid command line option '$OPTION'"
+ exit 1
+ ;;
+ esac
+done
+
+if [ -z "$INFILE" ] || $HELP_MODE
+then
+ print_help_and_exit
+fi
+
+if [ -n "$OUTFILE_CAMEO_RESIDUE_SCORES" ] && [ -n "$MULTIPLE_MODELS_CHAINS_OPTION" ]
+then
+ echo >&2 "Error: '--output-residue-scores-for-CAMEO' and '--multiple-models' cannot be used together"
+ exit 1
+fi
+
+if [ -n "$REBUILD_SIDECHAINS_COMMAND" ] && [ -n "$MULTIPLE_MODELS_CHAINS_OPTION" ]
+then
+ echo >&2 "Error: '--rebuild-side-chains' and '--multiple-models' cannot be used together"
+ exit 1
+fi
+
+if [ -n "$REBUILD_SIDECHAINS_COMMAND" ] && [ -n "$OUTFILE_CAMEO_RESIDUE_SCORES" ]
+then
+ echo >&2 "Error: '--rebuild-sidechains' and '--output-residue-scores-for-CAMEO' cannot be used together"
+ exit 1
+fi
+
+if [ -z "$REFERENCE_SEQUENCE" ] && [ -n "$OUTFILE_SEQUENCE_ALIGNMENT" ]
+then
+ echo >&2 "Error: '--output-sequence-alignment' cannot be used without '--reference-sequence'"
+ exit 1
+fi
+
+if [ -z "$REFERENCE_SEQUENCE" ] && [ -n "$OUTFILE_SCORES_FOR_CASP" ]
+then
+ echo >&2 "Error: '--output-scores-for-CASP' cannot be used without '--reference-sequence'"
+ exit 1
+fi
+
+if [ -z "$OUTFILE_SCORES_FOR_CASP" ] && [ -n "$OUTFILE_SCORES_FOR_CASP_PDB" ]
+then
+ echo >&2 "Error: '--output-scores-for-CASP-pdb' cannot be used without '--output-scores-for-CASP'"
+ exit 1
+fi
+
+if [ -z "$OUTFILE_SCORES_FOR_CASP" ] && [ -n "$OUTFILE_SCORES_FOR_CASP_LOG" ]
+then
+ echo >&2 "Error: '--output-scores-for-CASP-log' cannot be used without '--output-scores-for-CASP'"
+ exit 1
+fi
+
+if [[ "$ZEROARG" == *"/"* ]]
+then
+ cd $(dirname $ZEROARG)
+ export PATH=$(pwd):$PATH
+ cd - &> /dev/null
+fi
+
+command -v voronota &> /dev/null || { echo >&2 "Error: 'voronota' executable not in binaries path"; exit 1; }
+command -v voronota-resources &> /dev/null || { echo >&2 "Error: 'voronota-resources' executable not in binaries path"; exit 1; }
+
+if [ -n "$OUTFILE_PLOT" ]
+then
+ command -v R &> /dev/null || { echo >&2 "Error: 'R' command, needed for plotting, is not available"; exit 1; }
+fi
+
+if [ -n "$OUTFILE_SCREENSHOT" ]
+then
+ command -v pymol &> /dev/null || { echo >&2 "Error: 'pymol' command, needed for making screenshots, is not available"; exit 1; }
+fi
+
+if [ -n "$REBUILD_SIDECHAINS_COMMAND" ]
+then
+ command -v $REBUILD_SIDECHAINS_COMMAND &> /dev/null || { echo >&2 "Error: '$REBUILD_SIDECHAINS_COMMAND' command, requested for rebuilding side-chains, is not available"; exit 1; }
+fi
+
+readonly TMPLDIR=$(mktemp -d)
+trap "rm -r $TMPLDIR" EXIT
+
+if [ -n "$REFERENCE_SEQUENCE" ] && [ ! -s "$REFERENCE_SEQUENCE" ]
+then
+ if [ "$REFERENCE_SEQUENCE" == "$(echo $REFERENCE_SEQUENCE | tr -dc '[:alpha:]')" ]
+ then
+ echo "$REFERENCE_SEQUENCE" > "$TMPLDIR/reference_sequence_file"
+ REFERENCE_SEQUENCE="$TMPLDIR/reference_sequence_file"
+ else
+ echo >&2 "Error: invalid reference sequence"
+ exit 1
+ fi
+fi
+
+INFILE_CONTENTS=$INFILE
+if [[ "$INFILE" == *"://"* ]]
+then
+ INFILE_CONTENTS=$TMPLDIR/downloaded_input_file
+ curl -s "$INFILE" > $INFILE_CONTENTS
+fi
+
+if [ ! -s "$INFILE_CONTENTS" ]
+then
+ echo >&2 "Error: input file does not exist or is empty"
+ exit 1
+fi
+
+INFILE_CONTENTS_EXTRACTED=$INFILE_CONTENTS
+if [[ "$INFILE" == *".gz" ]]
+then
+ INFILE_CONTENTS_EXTRACTED=$TMPLDIR/extracted_input_file
+ zcat $INFILE_CONTENTS > $INFILE_CONTENTS_EXTRACTED
+ if [ ! -s "$INFILE_CONTENTS_EXTRACTED" ]
+ then
+ echo >&2 "Error: could not extract gzipped file"
+ exit 1
+ fi
+fi
+
+cat $INFILE_CONTENTS_EXTRACTED \
+| voronota get-balls-from-atoms-file \
+ --annotated $MULTIPLE_MODELS_CHAINS_OPTION \
+ --radii-file <(voronota-resources radii) \
+ --include-heteroatoms \
+| voronota query-balls \
+ --match 'R<LEU,ALA,GLY,VAL,GLU,SER,LYS,ILE,ASP,THR,ARG,PRO,ASN,PHE,GLN,TYR,HIS,MET,TRP,CYS,MSE,SEC>' \
+| voronota query-balls \
+ --drop-adjuncts \
+ --drop-altloc-indicators \
+| \
+{
+ if [ -n "$INPUT_FILTER_QUERY_PARAMETERS" ]
+ then
+ voronota query-balls $INPUT_FILTER_QUERY_PARAMETERS
+ else
+ cat
+ fi
+} \
+| \
+{
+ if [ -s "$REFERENCE_SEQUENCE" ]
+ then
+ voronota query-balls \
+ --set-ref-seq-num-adjunct "$REFERENCE_SEQUENCE" \
+ --ref-seq-alignment $TMPLDIR/sequence_alignment \
+ | voronota query-balls \
+ --renumber-from-adjunct refseq \
+ | voronota query-balls \
+ --drop-adjuncts
+ else
+ cat
+ fi
+} \
+| \
+{
+ if [ -n "$REBUILD_SIDECHAINS_COMMAND" ]
+ then
+ voronota query-balls \
+ --match 'A<CA,C,N,O,OXT>' \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output $TMPLDIR/atoms_stripped.pdb \
+ > /dev/null
+
+ $REBUILD_SIDECHAINS_COMMAND -h \
+ -i $TMPLDIR/atoms_stripped.pdb \
+ -o $TMPLDIR/atoms_rebuilt.pdb \
+ > /dev/null
+
+ cat $TMPLDIR/atoms_rebuilt.pdb \
+ | voronota get-balls-from-atoms-file \
+ --annotated \
+ --radii-file <(voronota-resources radii) \
+ | voronota query-balls \
+ --drop-adjuncts
+ else
+ cat
+ fi
+} \
+> $TMPLDIR/balls
+
+if $MORE_LOGGING && [ -f "$TMPLDIR/sequence_alignment" ]
+then
+ cat >&2 "$TMPLDIR/sequence_alignment"
+fi
+
+if [ -n "$OUTFILE_SEQUENCE_ALIGNMENT" ] && [ -f "$TMPLDIR/sequence_alignment" ]
+then
+ cp "$TMPLDIR/sequence_alignment" "$OUTFILE_SEQUENCE_ALIGNMENT"
+fi
+
+if [ ! -s "$TMPLDIR/balls" ]
+then
+ echo >&2 "Error: no atoms in input file"
+ exit 1
+fi
+
+if [ -n "$OUTFILE_BALLS" ]
+then
+ mkdir -p $(dirname $OUTFILE_BALLS)
+ cp "$TMPLDIR/balls" "$OUTFILE_BALLS"
+fi
+
+BALLS_MD5=""
+if [ -n "$CACHE_DIRECTORY" ]
+then
+ BALLS_MD5=$(cat $TMPLDIR/balls | md5sum | awk '{print $1}')
+ if [ -n "$BALLS_MD5" ]
+ then
+ BALLS_MD5="${BALLS_MD5}.voronota.voromqa"
+ if [ -d "$CACHE_DIRECTORY/$BALLS_MD5" ] && [ -s "$CACHE_DIRECTORY/$BALLS_MD5/all_contacts" ] && [ -s "$CACHE_DIRECTORY/$BALLS_MD5/atom_energies" ] && [ -s "$CACHE_DIRECTORY/$BALLS_MD5/depth_values" ]
+ then
+ cp -r $CACHE_DIRECTORY/$BALLS_MD5 $TMPLDIR/foundation
+ fi
+ fi
+fi
+
+if [ ! -d "$TMPLDIR/foundation" ]
+then
+ mkdir -p $TMPLDIR/foundation
+
+ cat $TMPLDIR/balls \
+ | voronota calculate-contacts \
+ --annotated \
+ --tag-centrality \
+ | tee $TMPLDIR/foundation/raw_contacts \
+ | voronota query-contacts \
+ --match-min-seq-sep 1 \
+ | voronota query-contacts \
+ --match-first 'A<C>' \
+ --match-second 'A<N>' \
+ --match-max-seq-sep 1 \
+ --match-max-dist 1.6 \
+ --invert \
+ | voronota query-contacts \
+ --match-min-seq-sep 1 \
+ --match-max-seq-sep 1 \
+ --set-tags 'sep1' \
+ | voronota query-contacts \
+ --match-min-seq-sep 2 \
+ --no-solvent \
+ --set-tags 'sep2' \
+ | tee $TMPLDIR/foundation/all_contacts \
+ | awk '{print $1 " " $2 " " $5 " " $3}' \
+ | tr ';' '_' \
+ | tee $TMPLDIR/contacts \
+ | voronota score-contacts-energy \
+ --potential-file <(voronota-resources energy_potential) \
+ --atom-scores-file $TMPLDIR/foundation/atom_energies \
+ > /dev/null
+
+ cat $TMPLDIR/contacts \
+ | voronota x-query-contacts-depth-values \
+ > $TMPLDIR/foundation/depth_values
+
+ if [ -n "$CACHE_DIRECTORY" ] && [ -n "$BALLS_MD5" ]
+ then
+ mkdir -p $CACHE_DIRECTORY
+ cp -r $TMPLDIR/foundation $CACHE_DIRECTORY/$BALLS_MD5
+ fi
+fi
+
+if [ -n "$OUTFILE_CONTACTS" ]
+then
+ mkdir -p $(dirname $OUTFILE_CONTACTS)
+ cp "$TMPLDIR/foundation/all_contacts" "$OUTFILE_CONTACTS"
+fi
+
+if $NEGLECT_SAS
+then
+ cat $TMPLDIR/foundation/all_contacts \
+ | awk '{print $1 " " $2 " " $5 " " $3}' \
+ | tr ';' '_' \
+ | sed 's|c<solvent>\s\+.\s\+\S\+$|c<solvent> . 0.001|' \
+ | voronota score-contacts-energy \
+ --potential-file <(voronota-resources energy_potential) \
+ --atom-scores-file $TMPLDIR/foundation/atom_energies \
+ > /dev/null
+fi
+
+if $REINTERPRET_SAS
+then
+ cat $TMPLDIR/foundation/all_contacts \
+ | awk '{print $1 " " $2 " " $5 " " $3}' \
+ | tr ';' '_' \
+ | voronota score-contacts-energy \
+ --potential-file <(voronota-resources energy_potential | voronota x-simulate-potential-for-membrane-proteins) \
+ --atom-scores-file $TMPLDIR/foundation/atom_energies \
+ > /dev/null
+fi
+
+if [ -n "$OUTFILE_CUTTING_SUGGESTIONS" ]
+then
+ mkdir -p $(dirname "$OUTFILE_CUTTING_SUGGESTIONS")
+ cat $TMPLDIR/foundation/all_contacts \
+ | awk '{print $1 " " $2 " " $5 " " $3}' \
+ | tr ';' '_' \
+ | voronota x-score-contacts-global-energy-by-cuts \
+ --potential-file <(voronota-resources energy_potential) \
+ --limit-results 10 \
+ | column -t \
+ > "$OUTFILE_CUTTING_SUGGESTIONS"
+fi
+
+if [ -n "$OUTDIR_SUMMARY_FOR_POTENTIAL" ]
+then
+ mkdir -p "$OUTDIR_SUMMARY_FOR_POTENTIAL"
+
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --chains-summary-output $TMPLDIR/chains_counts \
+ > /dev/null
+
+ cat $TMPLDIR/foundation/all_contacts \
+ | voronota query-contacts \
+ --match-min-seq-sep 2 \
+ --match-max-seq-sep 6 \
+ --set-tags 'sep1' \
+ | sed 's/sep1;sep2/sep1/' \
+ | awk '{print $1 " " $2 " " $5 " " $3}' \
+ | tr ';' '_' \
+ | voronota score-contacts-potential \
+ --multiply-areas $(cat $TMPLDIR/chains_counts | head -1 | awk '{print (24.0/$1*$2)}') \
+ > "$OUTDIR_SUMMARY_FOR_POTENTIAL/$(basename $INFILE .gz)"
+
+ exit 0
+fi
+
+if [ -n "$UNTEACHING_DIRECTORY" ] && [ -s "$UNTEACHING_DIRECTORY/contact_areas" ] && [ -s "$UNTEACHING_DIRECTORY/contact_categories" ]
+then
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --chains-summary-output $TMPLDIR/chains_counts \
+ > /dev/null
+
+ {
+ cat $UNTEACHING_DIRECTORY/contact_areas
+
+ cat $TMPLDIR/foundation/all_contacts \
+ | voronota query-contacts \
+ --match-min-seq-sep 2 \
+ --match-max-seq-sep 6 \
+ --set-tags 'sep1' \
+ | sed 's/sep1;sep2/sep1/' \
+ | awk '{print $1 " " $2 " " $5 " " $3}' \
+ | tr ';' '_' \
+ | voronota score-contacts-potential \
+ --multiply-areas $(cat $TMPLDIR/chains_counts | head -1 | awk '{print (24.0/$1*$2)}') \
+ | awk '{print $1 " " $2 " " $3 " -" $4}'
+ } \
+ | voronota score-contacts-potential \
+ --input-contributions $UNTEACHING_DIRECTORY/contact_categories \
+ --potential-file $TMPLDIR/untaught_potential \
+ > /dev/null
+
+ cat $TMPLDIR/foundation/all_contacts \
+ | awk '{print $1 " " $2 " " $5 " " $3}' \
+ | tr ';' '_' \
+ | voronota score-contacts-energy \
+ --potential-file $TMPLDIR/untaught_potential \
+ --atom-scores-file $TMPLDIR/foundation/atom_energies \
+ > /dev/null
+fi
+
+cat $TMPLDIR/foundation/atom_energies \
+| voronota score-contacts-quality \
+ --default-mean -0.34 \
+ --default-sd 0.19 \
+ --means-and-sds-file <(voronota-resources energy_means_and_sds) \
+ --external-weights-file $TMPLDIR/foundation/depth_values \
+ --smoothing-window $SMOOTHING_WINDOW \
+ --atom-scores-file $TMPLDIR/atom_quality_scores \
+ --residue-scores-file $TMPLDIR/residue_quality_scores \
+> $TMPLDIR/global_quality_score
+
+if [ ! -s "$TMPLDIR/global_quality_score" ] || [ ! -s "$TMPLDIR/atom_quality_scores" ] || [ ! -s "$TMPLDIR/residue_quality_scores" ]
+then
+ echo >&2 "Error: failed to calculate scores"
+ exit 1
+fi
+
+if [ -n "$ATOMS_QUERY_PARAMETERS" ] || [ -n "$CONTACTS_QUERY_PARAMETERS" ]
+then
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --set-external-adjuncts $TMPLDIR/foundation/depth_values \
+ --set-external-adjuncts-name depth \
+ | voronota query-balls $ATOMS_QUERY_PARAMETERS \
+ | awk '{print $1}' \
+ > $TMPLDIR/selection_by_atoms_query
+
+ cat $TMPLDIR/foundation/all_contacts \
+ | voronota query-contacts $CONTACTS_QUERY_PARAMETERS \
+ | awk '{print $1 " " $2}' | tr ' ' '\n' | sort | uniq | grep -v solvent \
+ > $TMPLDIR/selection_by_contacts_query
+
+ join -e EMPTY <(sort -k 1b,1 $TMPLDIR/selection_by_atoms_query) <(sort -k 1b,1 $TMPLDIR/selection_by_contacts_query) \
+ | grep -v EMPTY \
+ > $TMPLDIR/selection_by_queries
+
+ join -e EMPTY <(sort -k 1b,1 $TMPLDIR/foundation/depth_values) <(sort -k 1b,1 $TMPLDIR/selection_by_queries) \
+ | grep -v EMPTY \
+ | awk '{print $1 " " $2}' \
+ > $TMPLDIR/scoring_domain
+
+ join -e EMPTY <(sort -k 1b,1 $TMPLDIR/scoring_domain) <(sort -k 1b,1 $TMPLDIR/atom_quality_scores) \
+ | grep -v EMPTY \
+ > $TMPLDIR/scoring_table
+
+ {
+ if [ -s "$TMPLDIR/scoring_table" ]
+ then
+ cat $TMPLDIR/scoring_table | awk '{sum+=$2;wsum+=($2*$3)} END {print (wsum/sum)}'
+ cat $TMPLDIR/scoring_table | wc -l
+ else
+ echo "0"
+ echo "0"
+ fi
+ } > $TMPLDIR/global_quality_score_of_selection
+fi
+
+if [ -n "$OUTFILE_ATOM_SCORES" ]
+then
+ mkdir -p $(dirname "$OUTFILE_ATOM_SCORES")
+ cp $TMPLDIR/atom_quality_scores "$OUTFILE_ATOM_SCORES"
+fi
+
+if [ -n "$OUTFILE_RESIDUE_SCORES" ]
+then
+ mkdir -p $(dirname "$OUTFILE_RESIDUE_SCORES")
+ cp $TMPLDIR/residue_quality_scores "$OUTFILE_RESIDUE_SCORES"
+fi
+
+if [ -n "$OUTFILE_SELECTED_ATOM_SCORES" ] && [ -f "$TMPLDIR/scoring_table" ]
+then
+ mkdir -p $(dirname "$OUTFILE_SELECTED_ATOM_SCORES")
+ cat $TMPLDIR/scoring_table \
+ | awk '{print $1 " " $3}' \
+ | sort -V \
+ > "$OUTFILE_SELECTED_ATOM_SCORES"
+fi
+
+if [ -n "$OUTFILE_ATOM_SCORES_PDB" ]
+then
+ mkdir -p $(dirname "$OUTFILE_ATOM_SCORES_PDB")
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --drop-altloc-indicators \
+ --set-adjuncts 'oc=1' \
+ --set-external-adjuncts $TMPLDIR/atom_quality_scores \
+ --set-external-adjuncts-name score \
+ | \
+ {
+ if [ -s "$TMPLDIR/selection_by_queries" ]
+ then
+ voronota query-balls \
+ --match-external-annotations $TMPLDIR/selection_by_queries \
+ --set-adjuncts 'oc=2'
+ else
+ cat
+ fi
+ } \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output "$OUTFILE_ATOM_SCORES_PDB" \
+ --pdb-output-b-factor score \
+ > /dev/null
+fi
+
+if [ -n "$OUTFILE_RESIDUE_SCORES_PDB" ]
+then
+ mkdir -p $(dirname "$OUTFILE_RESIDUE_SCORES_PDB")
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --drop-altloc-indicators \
+ --set-adjuncts 'oc=1' \
+ --set-external-adjuncts $TMPLDIR/residue_quality_scores \
+ --set-external-adjuncts-name score \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output "$OUTFILE_RESIDUE_SCORES_PDB" \
+ --pdb-output-b-factor score \
+ > /dev/null
+fi
+
+if [ -n "$OUTFILE_ATOM_DEPTHS" ]
+then
+ mkdir -p $(dirname $OUTFILE_ATOM_DEPTHS)
+ cp $TMPLDIR/foundation/depth_values "$OUTFILE_ATOM_DEPTHS"
+fi
+
+if [ -n "$OUTFILE_CAMEO_RESIDUE_SCORES" ]
+then
+ mkdir -p $(dirname $OUTFILE_CAMEO_RESIDUE_SCORES)
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --set-external-adjuncts <(awk '{print $1 " " (10*(1-$2))}' $TMPLDIR/residue_quality_scores) \
+ --set-external-adjuncts-name rqscore \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output $OUTFILE_CAMEO_RESIDUE_SCORES \
+ --pdb-output-b-factor rqscore \
+ --pdb-output-template $INFILE_CONTENTS_EXTRACTED \
+ > /dev/null
+fi
+
+if [ -n "$OUTFILE_PLOT" ]
+then
+
+mkdir -p $(dirname $OUTFILE_PLOT)
+
+cat $TMPLDIR/foundation/atom_energies \
+| voronota score-contacts-quality \
+ --default-mean -0.34 \
+ --default-sd 0.19 \
+ --means-and-sds-file <(voronota-resources energy_means_and_sds) \
+ --external-weights-file $TMPLDIR/foundation/depth_values \
+ --smoothing-window "$(echo "0,$SMOOTHING_WINDOW" | sed 's|^0,\(.\+,.\+\).*|\1|')" \
+ --residue-scores-file $TMPLDIR/residue_quality_scores_for_plot \
+> /dev/null
+
+cat $TMPLDIR/residue_quality_scores_for_plot \
+| voronota expand-descriptors \
+> $TMPLDIR/table_for_plot
+
+BACK_FILE="none"
+if [ -s "$TMPLDIR/selection_by_queries" ]
+then
+ cat $TMPLDIR/selection_by_queries \
+ | voronota expand-descriptors \
+ | awk '{print $1 " " $2}' | sort | uniq \
+ > $TMPLDIR/back_table_for_plot
+ if [ -s "$TMPLDIR/back_table_for_plot" ]
+ then
+ BACK_FILE="$TMPLDIR/back_table_for_plot"
+ fi
+fi
+
+R --slave --vanilla --args "$TMPLDIR/table_for_plot" "$BACK_FILE" "$OUTFILE_PLOT" "$PLOT_MODE" << 'EOF' &> /dev/null
+ args=commandArgs(TRUE);
+ infile=args[1];
+ back_infile=args[2];
+ outfile=args[3];
+ plot_mode=args[4];
+
+ t=read.table(infile, header=FALSE, stringsAsFactors=FALSE);
+ chains=sort(union(t$V1, t$V1));
+
+ back_t=c();
+ if(back_infile!="none")
+ {
+ back_t=read.table(back_infile, header=FALSE, stringsAsFactors=FALSE);
+ }
+
+ if(plot_mode=="small")
+ {
+ png(filename=outfile, width=8*length(chains), height=2.5, units="in", res=80);
+ par(mfcol=c(1, length(chains)));
+ par(mar=c(2.7,3,1,1));
+ } else
+ {
+ png(filename=outfile, width=10, height=5*length(chains), units="in", res=200);
+ par(mfrow=c(length(chains), 1));
+ }
+
+ for(chain in chains)
+ {
+ title=ifelse(chain==".", "VoroMQA local scores for the unnamed chain", paste("VoroMQA local scores for chain ", chain, sep=""));
+
+ st=t[which(t$V1==chain),];
+ resnums=st$V2;
+ v1=st$V8;
+ v2=st$V9;
+ N=length(v1);
+ mask=rep(0, N);
+ duplicate=identical(v1, v2);
+
+ thick_color=rgb(0.0, 0.0, 0.0);
+ thick_color_back=rgb(1.0, 0.0, 0.0);
+ thin_color=ifelse(duplicate, thick_color, rgb(0.7, 0.7, 0.7));
+ thin_color_back=ifelse(duplicate, thick_color_back, rgb(1.0, 0.7, 0.7));
+
+ if(plot_mode=="small")
+ {
+ plot(c(min(resnums),max(resnums)), c(0, 1), type="n", main="", xlab="", ylab="");
+ } else
+ {
+ plot(c(min(resnums),max(resnums)), c(0, 1), type="n", main=title, xlab="Residue number", ylab="Score");
+ }
+
+ points(c(min(resnums)-50,max(resnums)+50), c(0.5, 0.5), type="l");
+
+ back_resnums=c();
+ if(length(back_t)>0)
+ {
+ back_resnums=back_t$V2[which(back_t$V1==chain)];
+ }
+
+ resnums_col=rep(thin_color, N);
+ resnums_col[which(is.element(resnums, back_resnums))]=thin_color_back;
+ i=1;
+ while(i<N)
+ {
+ if((resnums[i+1]-resnums[i])<2)
+ {
+ points(c(resnums[i], resnums[i+1]), c(v1[i], v1[i+1]), type="l", col=c(resnums_col[i], resnums_col[i+1]), lwd=1);
+ mask[i]=1; mask[i+1]=1;
+ }
+ i=i+1;
+ }
+ sel=which(mask==0);
+ if(length(sel)>0)
+ {
+ points(resnums[sel], v1[sel], col=resnums_col[sel], pch=16, cex=0.5);
+ }
+
+ if(duplicate==FALSE)
+ {
+ resnums_col=rep(thick_color, N);
+ resnums_col[which(is.element(resnums, back_resnums))]=thick_color_back;
+ i=1;
+ while(i<N)
+ {
+ if((resnums[i+1]-resnums[i])<2)
+ {
+ points(c(resnums[i], resnums[i+1]), c(v2[i], v2[i+1]), type="l", col=c(resnums_col[i], resnums_col[i+1]), lwd=3);
+ }
+ i=i+1;
+ }
+ sel=which(mask==0);
+ if(length(sel)>0)
+ {
+ points(resnums[sel], v2[sel], col=resnums_col[sel], pch=16, cex=0.7);
+ }
+ }
+ }
+
+ dev.off();
+EOF
+fi
+
+if [ -n "$OUTFILE_MAP" ]
+then
+ mkdir -p $(dirname $OUTFILE_MAP)
+ cat $TMPLDIR/foundation/all_contacts \
+ | voronota query-contacts \
+ --drop-adjuncts \
+ --set-external-means $TMPLDIR/atom_quality_scores \
+ | voronota query-contacts \
+ --no-solvent \
+ --match-adjuncts em=0:1 \
+ | sed 's|em=||' \
+ | awk '{print $1 " " $2 " " $3 " " $4 " " $5 " em=" ($3*$6)}' \
+ | voronota query-contacts \
+ --inter-residue \
+ | sed 's|em=||' \
+ | awk '{print $1 " " $2 " " $3 " " $4 " " $5 " em=" ($6/$3)}' \
+ | voronota x-plot-contacts \
+ --adjunct-gradient em \
+ --adjunct-gradient-blue 1 \
+ --adjunct-gradient-red 0 \
+ --svg-output $TMPLDIR/map.svg \
+ > /dev/null
+ mv $TMPLDIR/map.svg $OUTFILE_MAP
+fi
+
+if [ -n "$OUTFILE_SCORES_FOR_CASP" ] && [ -s "$TMPLDIR/sequence_alignment" ]
+then
+ mkdir -p $(dirname "$OUTFILE_SCORES_FOR_CASP")
+ voronota x-write-qa-scores-in-casp-format \
+ --name "$(basename $INFILE)" \
+ --global-score "$(cat $TMPLDIR/global_quality_score)" \
+ --sequence-length "$(cat $TMPLDIR/sequence_alignment | head -1 | tr -d '-' | tr -d ' ' | tr -d '\n' | tr -d '\t' | wc -c)" \
+ --local-scores "$TMPLDIR/residue_quality_scores" \
+ --wrap_size 20 \
+ --completeness-threshold 0.85 \
+ --converted-local-scores "$TMPLDIR/residue_quality_scores_for_casp" \
+ > "$OUTFILE_SCORES_FOR_CASP"
+
+ if [ -n "$OUTFILE_SCORES_FOR_CASP_LOG" ]
+ then
+ mkdir -p $(dirname "$OUTFILE_SCORES_FOR_CASP_LOG")
+ paste \
+ "$TMPLDIR/residue_quality_scores" \
+ "$TMPLDIR/residue_quality_scores_for_casp" \
+ | column -t \
+ > "$OUTFILE_SCORES_FOR_CASP_LOG"
+ fi
+
+ if [ -n "$OUTFILE_SCORES_FOR_CASP_PDB" ]
+ then
+ mkdir -p $(dirname "$OUTFILE_SCORES_FOR_CASP_PDB")
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --drop-altloc-indicators \
+ --set-adjuncts 'oc=1' \
+ --set-external-adjuncts "$TMPLDIR/residue_quality_scores_for_casp" \
+ --set-external-adjuncts-name score \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output "$OUTFILE_SCORES_FOR_CASP_PDB" \
+ --pdb-output-b-factor score \
+ > /dev/null
+ fi
+fi
+
+if [ -n "$OUTFILE_SCREENSHOT" ]
+then
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --drop-altloc-indicators \
+ --set-adjuncts 'oc=1' \
+ --set-external-adjuncts "$TMPLDIR/residue_quality_scores" \
+ --set-external-adjuncts-name score \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output "$TMPLDIR/structure_for_screenshot.pdb" \
+ --pdb-output-b-factor score \
+ > /dev/null
+
+ mkdir -p $(dirname "$OUTFILE_SCREENSHOT")
+
+pymol -W "$SCREENSHOT_WIDTH" -H "$SCREENSHOT_HEIGHT" -p -c "$TMPLDIR/structure_for_screenshot.pdb" &> /dev/null << EOF
+ set all_states, on
+ hide all
+ bg_color $SCREENSHOT_BACKGROUND
+ show cartoon
+ spectrum b, red_white_blue, minimum=0, maximum=1
+ orient
+ center
+ zoom complete=1
+ save $OUTFILE_SCREENSHOT
+ quit
+EOF
+
+fi
+
+if $PRINT_ENERGY_OF_CONTACTS_SELECTION
+then
+ cat $TMPLDIR/foundation/all_contacts \
+ | voronota query-contacts $CONTACTS_QUERY_PARAMETERS \
+ | awk '{print $1 " " $2 " " $5 " " $3}' \
+ | tr ';' '_' \
+ | voronota score-contacts-energy \
+ --potential-file <(voronota-resources energy_potential) \
+ | awk '{print $5 " " $2 " " $3 " " $4 " " ($4/($2+$3))}' \
+ > $TMPLDIR/energy_descriptor_of_contacts_selection
+fi
+
+{
+echo $INFILE
+cat $TMPLDIR/global_quality_score
+cat $TMPLDIR/balls | grep 'A<CA>' | wc -l
+cat $TMPLDIR/balls | wc -l
+if [ -s "$TMPLDIR/global_quality_score_of_selection" ]
+then
+ cat $TMPLDIR/global_quality_score_of_selection
+fi
+if [ -s "$TMPLDIR/energy_descriptor_of_contacts_selection" ]
+then
+ cat $TMPLDIR/energy_descriptor_of_contacts_selection
+fi
+} \
+| tr '\n' ' ' \
+| sed 's/\s$/\n/'
+
+if [ -n "$SURFACE_CRAVING_ATOMS_OUTPUT" ] || [ -n "$SURFACE_CRAVING_ATOMS_OUTPUT_PDB" ] || [ -n "$SURFACE_CRAVING_RESIDUES_OUTPUT" ] || [ -n "$SURFACE_CRAVING_RESIDUES_OUTPUT_PDB" ] || [ -n "$SURFACE_CRAVING_ATOMS_ENERGIES_OUTPUT" ]
+then
+ {
+ echo "c<solvent>"
+ cat $TMPLDIR/foundation/depth_values \
+ | egrep ' 1$' \
+ | awk '{print $1}'
+ } > $TMPLDIR/exposure_ids
+
+ cat $TMPLDIR/foundation/raw_contacts \
+ | voronota query-contacts \
+ --match-external-first $TMPLDIR/exposure_ids \
+ --match-external-second $TMPLDIR/exposure_ids \
+ | awk '{if($2=="c<solvent>") {print $1 " " $2 " " $5 " " $3} else {print $1 " " $2 " " $5 " 0"}}' \
+ | tr ';' '_' \
+ | voronota score-contacts-energy \
+ --potential-file <(voronota-resources energy_potential) \
+ --depth 3 \
+ --atom-scores-file $TMPLDIR/surface_atom_energies \
+ > /dev/null
+
+ cat $TMPLDIR/surface_atom_energies \
+ | voronota score-contacts-quality \
+ --default-mean 0.13 \
+ --default-sd 0.13 \
+ --smoothing-window 0 \
+ --atom-scores-file $TMPLDIR/surface_atom_quality_scores \
+ --residue-scores-file $TMPLDIR/surface_residue_quality_scores \
+ > /dev/null
+
+ cat $TMPLDIR/surface_atom_quality_scores \
+ | awk '{print $1 " " (1-$2)}' \
+ > $TMPLDIR/surface_atom_craving_scores
+
+ cat $TMPLDIR/surface_residue_quality_scores \
+ | awk '{print $1 " " (1-$2)}' \
+ > $TMPLDIR/surface_residue_craving_scores
+
+ if [ -n "$SURFACE_CRAVING_ATOMS_OUTPUT" ]
+ then
+ mkdir -p $(dirname "$SURFACE_CRAVING_ATOMS_OUTPUT")
+ cp $TMPLDIR/surface_atom_craving_scores "$SURFACE_CRAVING_ATOMS_OUTPUT"
+ fi
+
+ if [ -n "$SURFACE_CRAVING_RESIDUES_OUTPUT" ]
+ then
+ mkdir -p $(dirname "$SURFACE_CRAVING_RESIDUES_OUTPUT")
+ cp $TMPLDIR/surface_residue_craving_scores "$SURFACE_CRAVING_RESIDUES_OUTPUT"
+ fi
+
+ if [ -n "$SURFACE_CRAVING_ATOMS_ENERGIES_OUTPUT" ]
+ then
+ mkdir -p $(dirname "$SURFACE_CRAVING_ATOMS_ENERGIES_OUTPUT")
+ cp $TMPLDIR/surface_atom_energies "$SURFACE_CRAVING_ATOMS_ENERGIES_OUTPUT"
+ fi
+
+ if [ -n "$SURFACE_CRAVING_ATOMS_OUTPUT_PDB" ]
+ then
+ mkdir -p $(dirname "$SURFACE_CRAVING_ATOMS_OUTPUT_PDB")
+
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --drop-altloc-indicators \
+ --set-adjuncts 'oc=1' \
+ --set-external-adjuncts $TMPLDIR/surface_atom_craving_scores \
+ --set-external-adjuncts-name score \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output "$SURFACE_CRAVING_ATOMS_OUTPUT_PDB" \
+ --pdb-output-b-factor score \
+ > /dev/null
+ fi
+
+ if [ -n "$SURFACE_CRAVING_RESIDUES_OUTPUT_PDB" ]
+ then
+ mkdir -p $(dirname "$SURFACE_CRAVING_RESIDUES_OUTPUT_PDB")
+
+ cat $TMPLDIR/balls \
+ | voronota query-balls \
+ --drop-altloc-indicators \
+ --set-adjuncts 'oc=1' \
+ --set-external-adjuncts $TMPLDIR/surface_residue_craving_scores \
+ --set-external-adjuncts-name score \
+ | voronota write-balls-to-atoms-file \
+ --pdb-output "$SURFACE_CRAVING_RESIDUES_OUTPUT_PDB" \
+ --pdb-output-b-factor score \
+ > /dev/null
+ fi
+fi
diff --git a/voronota.man b/voronota.man
new file mode 100644
index 0000000..c73bbc6
--- /dev/null
+++ b/voronota.man
@@ -0,0 +1,76 @@
+.TH VORONOTA 1 "May, 2017"
+.SH NAME
+.PP
+Voronota - software for Voronoi tessellation-based analysis of
+macromolecular structures
+.SH SYNOPSIS
+.PP
+voronota \f[I]command\f[] [\f[I]options\f[]]\&...
+.PP
+voronota-voromqa [\f[I]options\f[]]\&...
+.PP
+voronota-cadscore [\f[I]options\f[]]\&...
+.PP
+voronota-contacts [\f[I]options\f[]]\&...
+.PP
+voronota-volumes [\f[I]options\f[]]\&...
+.SH DESCRIPTION
+.PP
+The analysis of macromolecular structures often requires a comprehensive
+definition of atomic neighborhoods.
+Such a definition can be based on the Voronoi diagram of balls, where
+each ball represents an atom of some van der Waals radius.
+Voronota is a software tool for finding all the vertices of the Voronoi
+diagram of balls.
+Such vertices correspond to the centers of the empty tangent spheres
+defined by quadruples of balls.
+Voronota is especially suitable for processing three-dimensional
+structures of biological macromolecules such as proteins and RNA.
+.PP
+Since version 1.2 Voronota also uses the Voronoi vertices to construct
+inter-atom contact surfaces and solvent accessible surfaces.
+Voronota provides tools to query contacts, generate contacts graphics,
+compare contacts and evaluate quality of protein structural models using
+contacts.
+.PP
+The list of all available Voronota commands is displayed when executing
+Voronota without any parameters.
+.PP
+Command help is shown when \f[C]--help\f[] command line option is
+present, for example:
+.IP
+.nf
+\f[C]
+voronota\ calculate-vertices\ --help
+\f[]
+.fi
+.PP
+Using \f[C]--help\f[] option without specific command results in
+printing help for all commands:
+.IP
+.nf
+\f[C]
+voronota\ --help
+\f[]
+.fi
+.PP
+There are several Voronota wrapper scripts, their interfaces can
+displayed similarly:
+.IP
+.nf
+\f[C]
+voronota-voromqa\ --help
+voronota-cadscore\ --help
+voronota-contacts\ --help
+voronota-volumes\ --help
+\f[]
+.fi
+.SH SEE ALSO
+.PP
+The \f[I]README\f[] file distributed with Voronota contains more
+detailed documentation.
+.PP
+The Voronota source code and all the supporting files may be downloaded
+from <https://bitbucket.org/kliment/voronota/downloads>.
+.SH AUTHORS
+Kliment Olechnovic.
--
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