[mmdb] 01/03: Imported Upstream version 1.25.5
Frédéric-Emmanuel Picca
picca at moszumanska.debian.org
Fri Jul 25 13:09:13 UTC 2014
This is an automated email from the git hooks/post-receive script.
picca pushed a commit to branch master
in repository mmdb.
commit 54c5247855a4da37b72d54b7c32e21d7a57daea3
Author: Picca Frédéric-Emmanuel <picca at debian.org>
Date: Mon Sep 2 18:48:18 2013 +0200
Imported Upstream version 1.25.5
---
AUTHORS | 0
COPYING | 0
COPYING.LESSER | 0
INSTALL | 0
README | 0
build-aux/config.guess | 405 ++++++++++++++++++++++++++++---------------------
build-aux/config.sub | 279 ++++++++++++++++++++++------------
build-aux/ltmain.sh | 0
config.h.in | 0
configure | 20 +--
configure.ac | 2 +-
m4/libtool.m4 | 0
m4/ltoptions.m4 | 0
m4/ltsugar.m4 | 0
m4/ltversion.m4 | 0
m4/lt~obsolete.m4 | 0
mmdb/bfgs_min.cpp | 0
mmdb/bfgs_min.h | 0
mmdb/file_.cpp | 0
mmdb/file_.h | 0
mmdb/hybrid_36.cpp | 0
mmdb/hybrid_36.h | 0
mmdb/linalg_.cpp | 0
mmdb/linalg_.h | 0
mmdb/machine_.cpp | 0
mmdb/machine_.h | 0
mmdb/math_.cpp | 0
mmdb/math_.h | 0
mmdb/mattype_.cpp | 0
mmdb/mattype_.h | 0
mmdb/mmdb_align.cpp | 0
mmdb/mmdb_align.h | 0
mmdb/mmdb_atom.cpp | 0
mmdb/mmdb_atom.h | 0
mmdb/mmdb_bondmngr.cpp | 0
mmdb/mmdb_bondmngr.h | 0
mmdb/mmdb_chain.cpp | 99 ++++++------
mmdb/mmdb_chain.h | 0
mmdb/mmdb_cifdefs.cpp | 0
mmdb/mmdb_cifdefs.h | 0
mmdb/mmdb_coormngr.cpp | 0
mmdb/mmdb_coormngr.h | 0
mmdb/mmdb_cryst.cpp | 0
mmdb/mmdb_cryst.h | 0
mmdb/mmdb_defs.h | 4 +-
mmdb/mmdb_ficif.cpp | 0
mmdb/mmdb_ficif.h | 0
mmdb/mmdb_file.cpp | 0
mmdb/mmdb_file.h | 0
mmdb/mmdb_graph.cpp | 0
mmdb/mmdb_graph.h | 0
mmdb/mmdb_manager.cpp | 27 ++--
mmdb/mmdb_manager.h | 7 +-
mmdb/mmdb_mask.cpp | 0
mmdb/mmdb_mask.h | 0
mmdb/mmdb_mmcif.cpp | 0
mmdb/mmdb_mmcif.h | 0
mmdb/mmdb_model.cpp | 0
mmdb/mmdb_model.h | 0
mmdb/mmdb_rwbrook.cpp | 0
mmdb/mmdb_rwbrook.h | 0
mmdb/mmdb_sbase.cpp | 0
mmdb/mmdb_sbase.h | 0
mmdb/mmdb_sbase0.cpp | 0
mmdb/mmdb_sbase0.h | 0
mmdb/mmdb_selmngr.cpp | 0
mmdb/mmdb_selmngr.h | 0
mmdb/mmdb_symop.cpp | 0
mmdb/mmdb_symop.h | 0
mmdb/mmdb_tables.cpp | 0
mmdb/mmdb_tables.h | 0
mmdb/mmdb_title.cpp | 6 +-
mmdb/mmdb_title.h | 3 +-
mmdb/mmdb_uddata.cpp | 0
mmdb/mmdb_uddata.h | 0
mmdb/mmdb_utils.cpp | 65 ++++----
mmdb/mmdb_utils.h | 6 +-
mmdb/mmdb_xml.cpp | 0
mmdb/mmdb_xml.h | 0
mmdb/random_n.cpp | 0
mmdb/random_n.h | 0
mmdb/stream_.cpp | 0
mmdb/stream_.h | 0
83 files changed, 545 insertions(+), 378 deletions(-)
diff --git a/AUTHORS b/AUTHORS
old mode 100644
new mode 100755
diff --git a/COPYING b/COPYING
old mode 100644
new mode 100755
diff --git a/COPYING.LESSER b/COPYING.LESSER
old mode 100644
new mode 100755
diff --git a/INSTALL b/INSTALL
old mode 100644
new mode 100755
diff --git a/README b/README
old mode 100644
new mode 100755
diff --git a/build-aux/config.guess b/build-aux/config.guess
index dc84c68..b79252d 100755
--- a/build-aux/config.guess
+++ b/build-aux/config.guess
@@ -1,14 +1,12 @@
#! /bin/sh
# Attempt to guess a canonical system name.
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
-# Free Software Foundation, Inc.
+# Copyright 1992-2013 Free Software Foundation, Inc.
-timestamp='2009-11-20'
+timestamp='2013-06-10'
# This file 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 of the License, or
+# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
@@ -17,26 +15,22 @@ timestamp='2009-11-20'
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# 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 Per Bothner. Please send patches (context
-# diff format) to <config-patches at gnu.org> and include a ChangeLog
-# entry.
+# the same distribution terms that you use for the rest of that
+# program. This Exception is an additional permission under section 7
+# of the GNU General Public License, version 3 ("GPLv3").
#
-# This script attempts to guess a canonical system name similar to
-# config.sub. If it succeeds, it prints the system name on stdout, and
-# exits with 0. Otherwise, it exits with 1.
+# Originally written by Per Bothner.
#
# You can get the latest version of this script from:
# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+#
+# Please send patches with a ChangeLog entry to config-patches at gnu.org.
+
me=`echo "$0" | sed -e 's,.*/,,'`
@@ -56,8 +50,7 @@ version="\
GNU config.guess ($timestamp)
Originally written by Per Bothner.
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
-2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+Copyright 1992-2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -139,12 +132,33 @@ UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+case "${UNAME_SYSTEM}" in
+Linux|GNU|GNU/*)
+ # If the system lacks a compiler, then just pick glibc.
+ # We could probably try harder.
+ LIBC=gnu
+
+ eval $set_cc_for_build
+ cat <<-EOF > $dummy.c
+ #include <features.h>
+ #if defined(__UCLIBC__)
+ LIBC=uclibc
+ #elif defined(__dietlibc__)
+ LIBC=dietlibc
+ #else
+ LIBC=gnu
+ #endif
+ EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
+ ;;
+esac
+
# Note: order is significant - the case branches are not exclusive.
case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
*:NetBSD:*:*)
# NetBSD (nbsd) targets should (where applicable) match one or
- # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*,
# *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
# switched to ELF, *-*-netbsd* would select the old
# object file format. This provides both forward
@@ -180,7 +194,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
fi
;;
*)
- os=netbsd
+ os=netbsd
;;
esac
# The OS release
@@ -201,6 +215,10 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
echo "${machine}-${os}${release}"
exit ;;
+ *:Bitrig:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'`
+ echo ${UNAME_MACHINE_ARCH}-unknown-bitrig${UNAME_RELEASE}
+ exit ;;
*:OpenBSD:*:*)
UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
@@ -223,7 +241,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
;;
*5.*)
- UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
;;
esac
# According to Compaq, /usr/sbin/psrinfo has been available on
@@ -269,7 +287,10 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
# A Xn.n version is an unreleased experimental baselevel.
# 1.2 uses "1.2" for uname -r.
echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
- exit ;;
+ # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
+ exitcode=$?
+ trap '' 0
+ exit $exitcode ;;
Alpha\ *:Windows_NT*:*)
# How do we know it's Interix rather than the generic POSIX subsystem?
# Should we change UNAME_MACHINE based on the output of uname instead
@@ -295,12 +316,12 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
echo s390-ibm-zvmoe
exit ;;
*:OS400:*:*)
- echo powerpc-ibm-os400
+ echo powerpc-ibm-os400
exit ;;
arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
echo arm-acorn-riscix${UNAME_RELEASE}
exit ;;
- arm:riscos:*:*|arm:RISCOS:*:*)
+ arm*:riscos:*:*|arm*:RISCOS:*:*)
echo arm-unknown-riscos
exit ;;
SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
@@ -394,23 +415,23 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
# MiNT. But MiNT is downward compatible to TOS, so this should
# be no problem.
atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
+ echo m68k-atari-mint${UNAME_RELEASE}
exit ;;
atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
echo m68k-atari-mint${UNAME_RELEASE}
- exit ;;
+ exit ;;
*falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
+ echo m68k-atari-mint${UNAME_RELEASE}
exit ;;
milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
- echo m68k-milan-mint${UNAME_RELEASE}
- exit ;;
+ echo m68k-milan-mint${UNAME_RELEASE}
+ exit ;;
hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
- echo m68k-hades-mint${UNAME_RELEASE}
- exit ;;
+ echo m68k-hades-mint${UNAME_RELEASE}
+ exit ;;
*:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
- echo m68k-unknown-mint${UNAME_RELEASE}
- exit ;;
+ echo m68k-unknown-mint${UNAME_RELEASE}
+ exit ;;
m68k:machten:*:*)
echo m68k-apple-machten${UNAME_RELEASE}
exit ;;
@@ -480,8 +501,8 @@ EOF
echo m88k-motorola-sysv3
exit ;;
AViiON:dgux:*:*)
- # DG/UX returns AViiON for all architectures
- UNAME_PROCESSOR=`/usr/bin/uname -p`
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
then
if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
@@ -494,7 +515,7 @@ EOF
else
echo i586-dg-dgux${UNAME_RELEASE}
fi
- exit ;;
+ exit ;;
M88*:DolphinOS:*:*) # DolphinOS (SVR3)
echo m88k-dolphin-sysv3
exit ;;
@@ -551,7 +572,7 @@ EOF
echo rs6000-ibm-aix3.2
fi
exit ;;
- *:AIX:*:[456])
+ *:AIX:*:[4567])
IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
IBM_ARCH=rs6000
@@ -594,52 +615,52 @@ EOF
9000/[678][0-9][0-9])
if [ -x /usr/bin/getconf ]; then
sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
- sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
- case "${sc_cpu_version}" in
- 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
- 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
- 532) # CPU_PA_RISC2_0
- case "${sc_kernel_bits}" in
- 32) HP_ARCH="hppa2.0n" ;;
- 64) HP_ARCH="hppa2.0w" ;;
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case "${sc_cpu_version}" in
+ 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case "${sc_kernel_bits}" in
+ 32) HP_ARCH="hppa2.0n" ;;
+ 64) HP_ARCH="hppa2.0w" ;;
'') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
- esac ;;
- esac
+ esac ;;
+ esac
fi
if [ "${HP_ARCH}" = "" ]; then
eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
+ sed 's/^ //' << EOF >$dummy.c
- #define _HPUX_SOURCE
- #include <stdlib.h>
- #include <unistd.h>
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
- int main ()
- {
- #if defined(_SC_KERNEL_BITS)
- long bits = sysconf(_SC_KERNEL_BITS);
- #endif
- long cpu = sysconf (_SC_CPU_VERSION);
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
- switch (cpu)
- {
- case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
- case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
- case CPU_PA_RISC2_0:
- #if defined(_SC_KERNEL_BITS)
- switch (bits)
- {
- case 64: puts ("hppa2.0w"); break;
- case 32: puts ("hppa2.0n"); break;
- default: puts ("hppa2.0"); break;
- } break;
- #else /* !defined(_SC_KERNEL_BITS) */
- puts ("hppa2.0"); break;
- #endif
- default: puts ("hppa1.0"); break;
- }
- exit (0);
- }
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
EOF
(CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
test -z "$HP_ARCH" && HP_ARCH=hppa
@@ -730,22 +751,22 @@ EOF
exit ;;
C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
echo c1-convex-bsd
- exit ;;
+ exit ;;
C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
if getsysinfo -f scalar_acc
then echo c32-convex-bsd
else echo c2-convex-bsd
fi
- exit ;;
+ exit ;;
C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
echo c34-convex-bsd
- exit ;;
+ exit ;;
C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
echo c38-convex-bsd
- exit ;;
+ exit ;;
C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
echo c4-convex-bsd
- exit ;;
+ exit ;;
CRAY*Y-MP:*:*:*)
echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
exit ;;
@@ -769,14 +790,14 @@ EOF
exit ;;
F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
- echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
- exit ;;
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
5000:UNIX_System_V:4.*:*)
- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
- echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+ echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
exit ;;
i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
@@ -788,30 +809,35 @@ EOF
echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
exit ;;
*:FreeBSD:*:*)
- case ${UNAME_MACHINE} in
- pc98)
- echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ case ${UNAME_PROCESSOR} in
amd64)
echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
*)
- echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
esac
exit ;;
i*:CYGWIN*:*)
echo ${UNAME_MACHINE}-pc-cygwin
exit ;;
+ *:MINGW64*:*)
+ echo ${UNAME_MACHINE}-pc-mingw64
+ exit ;;
*:MINGW*:*)
echo ${UNAME_MACHINE}-pc-mingw32
exit ;;
+ i*:MSYS*:*)
+ echo ${UNAME_MACHINE}-pc-msys
+ exit ;;
i*:windows32*:*)
- # uname -m includes "-pc" on this system.
- echo ${UNAME_MACHINE}-mingw32
+ # uname -m includes "-pc" on this system.
+ echo ${UNAME_MACHINE}-mingw32
exit ;;
i*:PW*:*)
echo ${UNAME_MACHINE}-pc-pw32
exit ;;
*:Interix*:*)
- case ${UNAME_MACHINE} in
+ case ${UNAME_MACHINE} in
x86)
echo i586-pc-interix${UNAME_RELEASE}
exit ;;
@@ -848,15 +874,22 @@ EOF
exit ;;
*:GNU:*:*)
# the GNU system
- echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-${LIBC}`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
exit ;;
*:GNU/*:*:*)
# other systems with GNU libc and userland
- echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC}
exit ;;
i*86:Minix:*:*)
echo ${UNAME_MACHINE}-pc-minix
exit ;;
+ aarch64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ aarch64_be:Linux:*:*)
+ UNAME_MACHINE=aarch64_be
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
alpha:Linux:*:*)
case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
EV5) UNAME_MACHINE=alphaev5 ;;
@@ -866,52 +899,56 @@ EOF
EV6) UNAME_MACHINE=alphaev6 ;;
EV67) UNAME_MACHINE=alphaev67 ;;
EV68*) UNAME_MACHINE=alphaev68 ;;
- esac
+ esac
objdump --private-headers /bin/sh | grep -q ld.so.1
- if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
- echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ if test "$?" = 0 ; then LIBC="gnulibc1" ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ arc:Linux:*:* | arceb:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
arm*:Linux:*:*)
eval $set_cc_for_build
if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ARM_EABI__
then
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
else
- echo ${UNAME_MACHINE}-unknown-linux-gnueabi
+ if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_PCS_VFP
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabi
+ else
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabihf
+ fi
fi
exit ;;
avr32*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
cris:Linux:*:*)
- echo cris-axis-linux-gnu
+ echo ${UNAME_MACHINE}-axis-linux-${LIBC}
exit ;;
crisv32:Linux:*:*)
- echo crisv32-axis-linux-gnu
+ echo ${UNAME_MACHINE}-axis-linux-${LIBC}
exit ;;
frv:Linux:*:*)
- echo frv-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ hexagon:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
i*86:Linux:*:*)
- LIBC=gnu
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #ifdef __dietlibc__
- LIBC=dietlibc
- #endif
-EOF
- eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
- echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+ echo ${UNAME_MACHINE}-pc-linux-${LIBC}
exit ;;
ia64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
m32r*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
m68*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
mips:Linux:*:* | mips64:Linux:*:*)
eval $set_cc_for_build
@@ -930,51 +967,63 @@ EOF
#endif
EOF
eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
- test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-${LIBC}"; exit; }
;;
+ or1k:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
or32:Linux:*:*)
- echo or32-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
padre:Linux:*:*)
- echo sparc-unknown-linux-gnu
+ echo sparc-unknown-linux-${LIBC}
exit ;;
parisc64:Linux:*:* | hppa64:Linux:*:*)
- echo hppa64-unknown-linux-gnu
+ echo hppa64-unknown-linux-${LIBC}
exit ;;
parisc:Linux:*:* | hppa:Linux:*:*)
# Look for CPU level
case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
- PA7*) echo hppa1.1-unknown-linux-gnu ;;
- PA8*) echo hppa2.0-unknown-linux-gnu ;;
- *) echo hppa-unknown-linux-gnu ;;
+ PA7*) echo hppa1.1-unknown-linux-${LIBC} ;;
+ PA8*) echo hppa2.0-unknown-linux-${LIBC} ;;
+ *) echo hppa-unknown-linux-${LIBC} ;;
esac
exit ;;
ppc64:Linux:*:*)
- echo powerpc64-unknown-linux-gnu
+ echo powerpc64-unknown-linux-${LIBC}
exit ;;
ppc:Linux:*:*)
- echo powerpc-unknown-linux-gnu
+ echo powerpc-unknown-linux-${LIBC}
+ exit ;;
+ ppc64le:Linux:*:*)
+ echo powerpc64le-unknown-linux-${LIBC}
+ exit ;;
+ ppcle:Linux:*:*)
+ echo powerpcle-unknown-linux-${LIBC}
exit ;;
s390:Linux:*:* | s390x:Linux:*:*)
- echo ${UNAME_MACHINE}-ibm-linux
+ echo ${UNAME_MACHINE}-ibm-linux-${LIBC}
exit ;;
sh64*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
sh*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
sparc:Linux:*:* | sparc64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ tile*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
vax:Linux:*:*)
- echo ${UNAME_MACHINE}-dec-linux-gnu
+ echo ${UNAME_MACHINE}-dec-linux-${LIBC}
exit ;;
x86_64:Linux:*:*)
- echo x86_64-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
xtensa*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
i*86:DYNIX/ptx:4*:*)
# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
@@ -983,11 +1032,11 @@ EOF
echo i386-sequent-sysv4
exit ;;
i*86:UNIX_SV:4.2MP:2.*)
- # Unixware is an offshoot of SVR4, but it has its own version
- # number series starting with 2...
- # I am not positive that other SVR4 systems won't match this,
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
# I just have to hope. -- rms.
- # Use sysv4.2uw... so that sysv4* matches it.
+ # Use sysv4.2uw... so that sysv4* matches it.
echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
exit ;;
i*86:OS/2:*:*)
@@ -1019,7 +1068,7 @@ EOF
fi
exit ;;
i*86:*:5:[678]*)
- # UnixWare 7.x, OpenUNIX and OpenServer 6.
+ # UnixWare 7.x, OpenUNIX and OpenServer 6.
case `/bin/uname -X | grep "^Machine"` in
*486*) UNAME_MACHINE=i486 ;;
*Pentium) UNAME_MACHINE=i586 ;;
@@ -1047,13 +1096,13 @@ EOF
exit ;;
pc:*:*:*)
# Left here for compatibility:
- # uname -m prints for DJGPP always 'pc', but it prints nothing about
- # the processor, so we play safe by assuming i586.
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i586.
# Note: whatever this is, it MUST be the same as what config.sub
# prints for the "djgpp" host, or else GDB configury will decide that
# this is a cross-build.
echo i586-pc-msdosdjgpp
- exit ;;
+ exit ;;
Intel:Mach:3*:*)
echo i386-pc-mach3
exit ;;
@@ -1088,8 +1137,8 @@ EOF
/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
&& { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
- /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
- && { echo i486-ncr-sysv4; exit; } ;;
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4; exit; } ;;
NCR*:*:4.2:* | MPRAS*:*:4.2:*)
OS_REL='.3'
test -r /etc/.relid \
@@ -1132,10 +1181,10 @@ EOF
echo ns32k-sni-sysv
fi
exit ;;
- PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
- # says <Richard.M.Bartel at ccMail.Census.GOV>
- echo i586-unisys-sysv4
- exit ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel at ccMail.Census.GOV>
+ echo i586-unisys-sysv4
+ exit ;;
*:UNIX_System_V:4*:FTX*)
# From Gerald Hewes <hewes at openmarket.com>.
# How about differentiating between stratus architectures? -djm
@@ -1161,11 +1210,11 @@ EOF
exit ;;
R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
if [ -d /usr/nec ]; then
- echo mips-nec-sysv${UNAME_RELEASE}
+ echo mips-nec-sysv${UNAME_RELEASE}
else
- echo mips-unknown-sysv${UNAME_RELEASE}
+ echo mips-unknown-sysv${UNAME_RELEASE}
fi
- exit ;;
+ exit ;;
BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
echo powerpc-be-beos
exit ;;
@@ -1178,6 +1227,9 @@ EOF
BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
echo i586-pc-haiku
exit ;;
+ x86_64:Haiku:*:*)
+ echo x86_64-unknown-haiku
+ exit ;;
SX-4:SUPER-UX:*:*)
echo sx4-nec-superux${UNAME_RELEASE}
exit ;;
@@ -1204,19 +1256,21 @@ EOF
exit ;;
*:Darwin:*:*)
UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
- case $UNAME_PROCESSOR in
- i386)
- eval $set_cc_for_build
- if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
- if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
- (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
- grep IS_64BIT_ARCH >/dev/null
- then
- UNAME_PROCESSOR="x86_64"
- fi
- fi ;;
- unknown) UNAME_PROCESSOR=powerpc ;;
- esac
+ eval $set_cc_for_build
+ if test "$UNAME_PROCESSOR" = unknown ; then
+ UNAME_PROCESSOR=powerpc
+ fi
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ case $UNAME_PROCESSOR in
+ i386) UNAME_PROCESSOR=x86_64 ;;
+ powerpc) UNAME_PROCESSOR=powerpc64 ;;
+ esac
+ fi
+ fi
echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
exit ;;
*:procnto*:*:* | *:QNX:[0123456789]*:*)
@@ -1230,7 +1284,10 @@ EOF
*:QNX:*:4*)
echo i386-pc-qnx
exit ;;
- NSE-?:NONSTOP_KERNEL:*:*)
+ NEO-?:NONSTOP_KERNEL:*:*)
+ echo neo-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSE-*:NONSTOP_KERNEL:*:*)
echo nse-tandem-nsk${UNAME_RELEASE}
exit ;;
NSR-?:NONSTOP_KERNEL:*:*)
@@ -1275,13 +1332,13 @@ EOF
echo pdp10-unknown-its
exit ;;
SEI:*:*:SEIUX)
- echo mips-sei-seiux${UNAME_RELEASE}
+ echo mips-sei-seiux${UNAME_RELEASE}
exit ;;
*:DragonFly:*:*)
echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
exit ;;
*:*VMS:*:*)
- UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
case "${UNAME_MACHINE}" in
A*) echo alpha-dec-vms ; exit ;;
I*) echo ia64-dec-vms ; exit ;;
@@ -1299,11 +1356,11 @@ EOF
i*86:AROS:*:*)
echo ${UNAME_MACHINE}-pc-aros
exit ;;
+ x86_64:VMkernel:*:*)
+ echo ${UNAME_MACHINE}-unknown-esx
+ exit ;;
esac
-#echo '(No uname command or uname output not recognized.)' 1>&2
-#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
-
eval $set_cc_for_build
cat >$dummy.c <<EOF
#ifdef _SEQUENT_
@@ -1321,11 +1378,11 @@ main ()
#include <sys/param.h>
printf ("m68k-sony-newsos%s\n",
#ifdef NEWSOS4
- "4"
+ "4"
#else
- ""
+ ""
#endif
- ); exit (0);
+ ); exit (0);
#endif
#endif
diff --git a/build-aux/config.sub b/build-aux/config.sub
index 2a55a50..c765b34 100755
--- a/build-aux/config.sub
+++ b/build-aux/config.sub
@@ -1,38 +1,31 @@
#! /bin/sh
# Configuration validation subroutine script.
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
-# Free Software Foundation, Inc.
+# Copyright 1992-2013 Free Software Foundation, Inc.
-timestamp='2009-11-20'
+timestamp='2013-04-24'
-# This file is (in principle) common to ALL GNU software.
-# The presence of a machine in this file suggests that SOME GNU software
-# can handle that machine. It does not imply ALL GNU software can.
-#
-# This file 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 of the License, or
+# This file 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 3 of the License, 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.
+# 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, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# 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.
+# the same distribution terms that you use for the rest of that
+# program. This Exception is an additional permission under section 7
+# of the GNU General Public License, version 3 ("GPLv3").
-# Please send patches to <config-patches at gnu.org>. Submit a context
-# diff and a properly formatted GNU ChangeLog entry.
+# Please send patches with a ChangeLog entry to config-patches at gnu.org.
#
# Configuration subroutine to validate and canonicalize a configuration type.
# Supply the specified configuration type as an argument.
@@ -75,8 +68,7 @@ Report bugs and patches to <config-patches at gnu.org>."
version="\
GNU config.sub ($timestamp)
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
-2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+Copyright 1992-2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -123,13 +115,18 @@ esac
# Here we must recognize all the valid KERNEL-OS combinations.
maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
case $maybe_os in
- nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
- uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+ nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \
+ linux-musl* | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \
+ knetbsd*-gnu* | netbsd*-gnu* | \
kopensolaris*-gnu* | \
storm-chaos* | os2-emx* | rtmk-nova*)
os=-$maybe_os
basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
;;
+ android-linux)
+ os=-linux-android
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
+ ;;
*)
basic_machine=`echo $1 | sed 's/-[^-]*$//'`
if [ $basic_machine != $1 ]
@@ -152,12 +149,12 @@ case $os in
-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
- -apple | -axis | -knuth | -cray | -microblaze)
+ -apple | -axis | -knuth | -cray | -microblaze*)
os=
basic_machine=$1
;;
- -bluegene*)
- os=-cnk
+ -bluegene*)
+ os=-cnk
;;
-sim | -cisco | -oki | -wec | -winbond)
os=
@@ -173,10 +170,10 @@ case $os in
os=-chorusos
basic_machine=$1
;;
- -chorusrdb)
- os=-chorusrdb
+ -chorusrdb)
+ os=-chorusrdb
basic_machine=$1
- ;;
+ ;;
-hiux*)
os=-hiuxwe2
;;
@@ -221,6 +218,12 @@ case $os in
-isc*)
basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
;;
+ -lynx*178)
+ os=-lynxos178
+ ;;
+ -lynx*5)
+ os=-lynxos5
+ ;;
-lynx*)
os=-lynxos
;;
@@ -245,20 +248,27 @@ case $basic_machine in
# Some are omitted here because they have special meanings below.
1750a | 580 \
| a29k \
+ | aarch64 | aarch64_be \
| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
| am33_2.0 \
- | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
+ | arc | arceb \
+ | arm | arm[bl]e | arme[lb] | armv[2-8] | armv[3-8][lb] | armv7[arm] \
+ | avr | avr32 \
+ | be32 | be64 \
| bfin \
| c4x | clipper \
| d10v | d30v | dlx | dsp16xx \
+ | epiphany \
| fido | fr30 | frv \
| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+ | hexagon \
| i370 | i860 | i960 | ia64 \
| ip2k | iq2000 \
+ | le32 | le64 \
| lm32 \
| m32c | m32r | m32rle | m68000 | m68k | m88k \
- | maxq | mb | microblaze | mcore | mep | metag \
+ | maxq | mb | microblaze | microblazeel | mcore | mep | metag \
| mips | mipsbe | mipseb | mipsel | mipsle \
| mips16 \
| mips64 | mips64el \
@@ -276,34 +286,45 @@ case $basic_machine in
| mipsisa64r2 | mipsisa64r2el \
| mipsisa64sb1 | mipsisa64sb1el \
| mipsisa64sr71k | mipsisa64sr71kel \
+ | mipsr5900 | mipsr5900el \
| mipstx39 | mipstx39el \
| mn10200 | mn10300 \
| moxie \
| mt \
| msp430 \
- | nios | nios2 \
+ | nds32 | nds32le | nds32be \
+ | nios | nios2 | nios2eb | nios2el \
| ns16k | ns32k \
- | or32 \
+ | open8 \
+ | or1k | or32 \
| pdp10 | pdp11 | pj | pjl \
- | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
+ | powerpc | powerpc64 | powerpc64le | powerpcle \
| pyramid \
- | rx \
+ | rl78 | rx \
| score \
| sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
| sh64 | sh64le \
| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
- | spu | strongarm \
- | tahoe | thumb | tic4x | tic80 | tron \
+ | spu \
+ | tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \
| ubicom32 \
- | v850 | v850e \
+ | v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \
| we32k \
- | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
+ | x86 | xc16x | xstormy16 | xtensa \
| z8k | z80)
basic_machine=$basic_machine-unknown
;;
- m6811 | m68hc11 | m6812 | m68hc12 | picochip)
- # Motorola 68HC11/12.
+ c54x)
+ basic_machine=tic54x-unknown
+ ;;
+ c55x)
+ basic_machine=tic55x-unknown
+ ;;
+ c6x)
+ basic_machine=tic6x-unknown
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip)
basic_machine=$basic_machine-unknown
os=-none
;;
@@ -313,6 +334,21 @@ case $basic_machine in
basic_machine=mt-unknown
;;
+ strongarm | thumb | xscale)
+ basic_machine=arm-unknown
+ ;;
+ xgate)
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ xscaleeb)
+ basic_machine=armeb-unknown
+ ;;
+
+ xscaleel)
+ basic_machine=armel-unknown
+ ;;
+
# We use `pc' rather than `unknown'
# because (1) that's what they normally are, and
# (2) the word "unknown" tends to confuse beginning users.
@@ -327,25 +363,30 @@ case $basic_machine in
# Recognize the basic CPU types with company name.
580-* \
| a29k-* \
+ | aarch64-* | aarch64_be-* \
| alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
| alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
- | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* | arceb-* \
| arm-* | armbe-* | armle-* | armeb-* | armv*-* \
| avr-* | avr32-* \
+ | be32-* | be64-* \
| bfin-* | bs2000-* \
- | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
+ | c[123]* | c30-* | [cjt]90-* | c4x-* \
| clipper-* | craynv-* | cydra-* \
| d10v-* | d30v-* | dlx-* \
| elxsi-* \
| f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
| h8300-* | h8500-* \
| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+ | hexagon-* \
| i*86-* | i860-* | i960-* | ia64-* \
| ip2k-* | iq2000-* \
+ | le32-* | le64-* \
| lm32-* \
| m32c-* | m32r-* | m32rle-* \
| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
- | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \
+ | microblaze-* | microblazeel-* \
| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
| mips16-* \
| mips64-* | mips64el-* \
@@ -363,29 +404,34 @@ case $basic_machine in
| mipsisa64r2-* | mipsisa64r2el-* \
| mipsisa64sb1-* | mipsisa64sb1el-* \
| mipsisa64sr71k-* | mipsisa64sr71kel-* \
+ | mipsr5900-* | mipsr5900el-* \
| mipstx39-* | mipstx39el-* \
| mmix-* \
| mt-* \
| msp430-* \
- | nios-* | nios2-* \
+ | nds32-* | nds32le-* | nds32be-* \
+ | nios-* | nios2-* | nios2eb-* | nios2el-* \
| none-* | np1-* | ns16k-* | ns32k-* \
+ | open8-* \
| orion-* \
| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
- | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
+ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
| pyramid-* \
- | romp-* | rs6000-* | rx-* \
+ | rl78-* | romp-* | rs6000-* | rx-* \
| sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
| sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
| sparclite-* \
- | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
- | tahoe-* | thumb-* \
- | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \
+ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \
+ | tahoe-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tile*-* \
| tron-* \
| ubicom32-* \
- | v850-* | v850e-* | vax-* \
+ | v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \
+ | vax-* \
| we32k-* \
- | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
+ | x86-* | x86_64-* | xc16x-* | xps100-* \
| xstormy16-* | xtensa*-* \
| ymp-* \
| z8k-* | z80-*)
@@ -410,7 +456,7 @@ case $basic_machine in
basic_machine=a29k-amd
os=-udi
;;
- abacus)
+ abacus)
basic_machine=abacus-unknown
;;
adobe68k)
@@ -480,11 +526,20 @@ case $basic_machine in
basic_machine=powerpc-ibm
os=-cnk
;;
+ c54x-*)
+ basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c55x-*)
+ basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c6x-*)
+ basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
c90)
basic_machine=c90-cray
os=-unicos
;;
- cegcc)
+ cegcc)
basic_machine=arm-unknown
os=-cegcc
;;
@@ -516,7 +571,7 @@ case $basic_machine in
basic_machine=craynv-cray
os=-unicosmp
;;
- cr16)
+ cr16 | cr16-*)
basic_machine=cr16-unknown
os=-elf
;;
@@ -674,7 +729,6 @@ case $basic_machine in
i370-ibm* | ibm*)
basic_machine=i370-ibm
;;
-# I'm not sure what "Sysv32" means. Should this be sysv3.2?
i*86v32)
basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
os=-sysv32
@@ -732,9 +786,13 @@ case $basic_machine in
basic_machine=ns32k-utek
os=-sysv
;;
- microblaze)
+ microblaze*)
basic_machine=microblaze-xilinx
;;
+ mingw64)
+ basic_machine=x86_64-pc
+ os=-mingw64
+ ;;
mingw32)
basic_machine=i386-pc
os=-mingw32
@@ -771,10 +829,18 @@ case $basic_machine in
ms1-*)
basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
;;
+ msys)
+ basic_machine=i386-pc
+ os=-msys
+ ;;
mvs)
basic_machine=i370-ibm
os=-mvs
;;
+ nacl)
+ basic_machine=le32-unknown
+ os=-nacl
+ ;;
ncr3000)
basic_machine=i486-ncr
os=-sysv4
@@ -839,6 +905,12 @@ case $basic_machine in
np1)
basic_machine=np1-gould
;;
+ neo-tandem)
+ basic_machine=neo-tandem
+ ;;
+ nse-tandem)
+ basic_machine=nse-tandem
+ ;;
nsr-tandem)
basic_machine=nsr-tandem
;;
@@ -921,9 +993,10 @@ case $basic_machine in
;;
power) basic_machine=power-ibm
;;
- ppc) basic_machine=powerpc-unknown
+ ppc | ppcbe) basic_machine=powerpc-unknown
;;
- ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ppc-* | ppcbe-*)
+ basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
;;
ppcle | powerpclittle | ppc-le | powerpc-little)
basic_machine=powerpcle-unknown
@@ -933,7 +1006,7 @@ case $basic_machine in
;;
ppc64) basic_machine=powerpc64-unknown
;;
- ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ppc64-* | ppc64p7-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
;;
ppc64le | powerpc64little | ppc64-le | powerpc64-little)
basic_machine=powerpc64le-unknown
@@ -948,7 +1021,11 @@ case $basic_machine in
basic_machine=i586-unknown
os=-pw32
;;
- rdos)
+ rdos | rdos64)
+ basic_machine=x86_64-pc
+ os=-rdos
+ ;;
+ rdos32)
basic_machine=i386-pc
os=-rdos
;;
@@ -1017,6 +1094,9 @@ case $basic_machine in
basic_machine=i860-stratus
os=-sysv4
;;
+ strongarm-* | thumb-*)
+ basic_machine=arm-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
sun2)
basic_machine=m68000-sun
;;
@@ -1073,20 +1153,8 @@ case $basic_machine in
basic_machine=t90-cray
os=-unicos
;;
- tic54x | c54x*)
- basic_machine=tic54x-unknown
- os=-coff
- ;;
- tic55x | c55x*)
- basic_machine=tic55x-unknown
- os=-coff
- ;;
- tic6x | c6x*)
- basic_machine=tic6x-unknown
- os=-coff
- ;;
tile*)
- basic_machine=tile-unknown
+ basic_machine=$basic_machine-unknown
os=-linux-gnu
;;
tx39)
@@ -1156,6 +1224,9 @@ case $basic_machine in
xps | xps100)
basic_machine=xps100-honeywell
;;
+ xscale-* | xscalee[bl]-*)
+ basic_machine=`echo $basic_machine | sed 's/^xscale/arm/'`
+ ;;
ymp)
basic_machine=ymp-cray
os=-unicos
@@ -1253,11 +1324,11 @@ esac
if [ x"$os" != x"" ]
then
case $os in
- # First match some system type aliases
- # that might get confused with valid system types.
+ # First match some system type aliases
+ # that might get confused with valid system types.
# -solaris* is a basic system type, with this one exception.
- -auroraux)
- os=-auroraux
+ -auroraux)
+ os=-auroraux
;;
-solaris1 | -solaris1.*)
os=`echo $os | sed -e 's|solaris1|sunos4|'`
@@ -1281,20 +1352,21 @@ case $os in
-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
| -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
| -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
- | -sym* | -kopensolaris* \
+ | -sym* | -kopensolaris* | -plan9* \
| -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
| -aos* | -aros* \
| -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
| -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
| -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
- | -openbsd* | -solidbsd* \
+ | -bitrig* | -openbsd* | -solidbsd* \
| -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
| -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
| -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
| -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
| -chorusos* | -chorusrdb* | -cegcc* \
- | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
- | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
+ | -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+ | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
+ | -linux-newlib* | -linux-musl* | -linux-uclibc* \
| -uxpv* | -beos* | -mpeix* | -udk* \
| -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
| -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
@@ -1341,7 +1413,7 @@ case $os in
-opened*)
os=-openedition
;;
- -os400*)
+ -os400*)
os=-os400
;;
-wince*)
@@ -1390,7 +1462,7 @@ case $os in
-sinix*)
os=-sysv4
;;
- -tpf*)
+ -tpf*)
os=-tpf
;;
-triton*)
@@ -1426,15 +1498,14 @@ case $os in
-aros*)
os=-aros
;;
- -kaos*)
- os=-kaos
- ;;
-zvmoe)
os=-zvmoe
;;
-dicos*)
os=-dicos
;;
+ -nacl*)
+ ;;
-none)
;;
*)
@@ -1457,10 +1528,10 @@ else
# system, and we'll never get to this point.
case $basic_machine in
- score-*)
+ score-*)
os=-elf
;;
- spu-*)
+ spu-*)
os=-elf
;;
*-acorn)
@@ -1472,8 +1543,20 @@ case $basic_machine in
arm*-semi)
os=-aout
;;
- c4x-* | tic4x-*)
- os=-coff
+ c4x-* | tic4x-*)
+ os=-coff
+ ;;
+ hexagon-*)
+ os=-elf
+ ;;
+ tic54x-*)
+ os=-coff
+ ;;
+ tic55x-*)
+ os=-coff
+ ;;
+ tic6x-*)
+ os=-coff
;;
# This must come before the *-dec entry.
pdp10-*)
@@ -1493,14 +1576,11 @@ case $basic_machine in
;;
m68000-sun)
os=-sunos3
- # This also exists in the configure program, but was not the
- # default.
- # os=-sunos4
;;
m68*-cisco)
os=-aout
;;
- mep-*)
+ mep-*)
os=-elf
;;
mips*-cisco)
@@ -1509,6 +1589,9 @@ case $basic_machine in
mips*-*)
os=-elf
;;
+ or1k-*)
+ os=-elf
+ ;;
or32-*)
os=-coff
;;
@@ -1527,7 +1610,7 @@ case $basic_machine in
*-ibm)
os=-aix
;;
- *-knuth)
+ *-knuth)
os=-mmixware
;;
*-wec)
diff --git a/build-aux/ltmain.sh b/build-aux/ltmain.sh
old mode 100644
new mode 100755
diff --git a/config.h.in b/config.h.in
old mode 100644
new mode 100755
diff --git a/configure b/configure
index d88fc9e..46aa5d7 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for mmdb 1.25.3.
+# Generated by GNU Autoconf 2.69 for mmdb 1.25.5.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -587,8 +587,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='mmdb'
PACKAGE_TARNAME='mmdb'
-PACKAGE_VERSION='1.25.3'
-PACKAGE_STRING='mmdb 1.25.3'
+PACKAGE_VERSION='1.25.5'
+PACKAGE_STRING='mmdb 1.25.5'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
@@ -1323,7 +1323,7 @@ if test "$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 mmdb 1.25.3 to adapt to many kinds of systems.
+\`configure' configures mmdb 1.25.5 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1393,7 +1393,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of mmdb 1.25.3:";;
+ short | recursive ) echo "Configuration of mmdb 1.25.5:";;
esac
cat <<\_ACEOF
@@ -1504,7 +1504,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-mmdb configure 1.25.3
+mmdb configure 1.25.5
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1903,7 +1903,7 @@ 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 mmdb $as_me 1.25.3, which was
+It was created by mmdb $as_me 1.25.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2771,7 +2771,7 @@ fi
# Define the identity of the package.
PACKAGE='mmdb'
- VERSION='1.25.3'
+ VERSION='1.25.5'
cat >>confdefs.h <<_ACEOF
@@ -16023,7 +16023,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by mmdb $as_me 1.25.3, which was
+This file was extended by mmdb $as_me 1.25.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -16089,7 +16089,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-mmdb config.status 1.25.3
+mmdb config.status 1.25.5
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index 4193561..92ff8d6 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,5 +1,5 @@
-AC_INIT(mmdb, 1.25.3) # keep in sync with mmdb/mmdb_defs.h
+AC_INIT(mmdb, 1.25.5) # keep in sync with mmdb/mmdb_defs.h
AC_CONFIG_AUX_DIR(build-aux)
AC_CONFIG_MACRO_DIR(m4)
diff --git a/m4/libtool.m4 b/m4/libtool.m4
old mode 100644
new mode 100755
diff --git a/m4/ltoptions.m4 b/m4/ltoptions.m4
old mode 100644
new mode 100755
diff --git a/m4/ltsugar.m4 b/m4/ltsugar.m4
old mode 100644
new mode 100755
diff --git a/m4/ltversion.m4 b/m4/ltversion.m4
old mode 100644
new mode 100755
diff --git a/m4/lt~obsolete.m4 b/m4/lt~obsolete.m4
old mode 100644
new mode 100755
diff --git a/mmdb/bfgs_min.cpp b/mmdb/bfgs_min.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/bfgs_min.h b/mmdb/bfgs_min.h
old mode 100644
new mode 100755
diff --git a/mmdb/file_.cpp b/mmdb/file_.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/file_.h b/mmdb/file_.h
old mode 100644
new mode 100755
diff --git a/mmdb/hybrid_36.cpp b/mmdb/hybrid_36.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/hybrid_36.h b/mmdb/hybrid_36.h
old mode 100644
new mode 100755
diff --git a/mmdb/linalg_.cpp b/mmdb/linalg_.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/linalg_.h b/mmdb/linalg_.h
old mode 100644
new mode 100755
diff --git a/mmdb/machine_.cpp b/mmdb/machine_.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/machine_.h b/mmdb/machine_.h
old mode 100644
new mode 100755
diff --git a/mmdb/math_.cpp b/mmdb/math_.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/math_.h b/mmdb/math_.h
old mode 100644
new mode 100755
diff --git a/mmdb/mattype_.cpp b/mmdb/mattype_.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mattype_.h b/mmdb/mattype_.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_align.cpp b/mmdb/mmdb_align.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_align.h b/mmdb/mmdb_align.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_atom.cpp b/mmdb/mmdb_atom.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_atom.h b/mmdb/mmdb_atom.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_bondmngr.cpp b/mmdb/mmdb_bondmngr.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_bondmngr.h b/mmdb/mmdb_bondmngr.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_chain.cpp b/mmdb/mmdb_chain.cpp
old mode 100644
new mode 100755
index e5cf019..137b5ce
--- a/mmdb/mmdb_chain.cpp
+++ b/mmdb/mmdb_chain.cpp
@@ -6,13 +6,13 @@
//
// Copyright (C) Eugene Krissinel 2000-2008.
//
-// This library is free software: you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License version 3, modified in accordance with the provisions
+// This library is free software: you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License version 3, modified in accordance with the provisions
// of the license to address the requirements of UK law.
//
-// You should have received a copy of the modified GNU Lesser
-// General Public License along with this library. If not, copies
+// You should have received a copy of the modified GNU Lesser
+// General Public License along with this library. If not, copies
// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
//
// This program is distributed in the hope that it will be useful,
@@ -22,14 +22,14 @@
//
// =================================================================
//
-// 29.01.10 <-- Date of Last Modification.
+// 14.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : MMDB_Chain <implementation>
// ~~~~~~~~~
// **** Project : MacroMolecular Data Base (MMDB)
-// ~~~~~~~~~
+// ~~~~~~~~~
// **** Classes : CChainContainer ( container for in-chain classes )
// ~~~~~~~~~ CContainerChain ( chain containered class template)
// CDBReference ( DBREF records )
@@ -39,7 +39,7 @@
// CHetRec ( HET records )
// CChain ( MMDB chain class )
//
-// Copyright (C) E. Krissinel 2000-2010
+// Copyright (C) E. Krissinel 2000-2013
//
// =================================================================
//
@@ -347,8 +347,8 @@ IDCode idCode;
}
GetIntIns ( seqBeg,insBeg,&(S[14]),4 );
GetIntIns ( seqEnd,insEnd,&(S[20]),4 );
- strcpy_ncs ( database ,&(S[26]),6 );
- strcpy_ncs ( dbAccession ,&(S[33]),8 );
+ strcpy_ncs ( database ,&(S[26]),6 );
+ strcpy_ncs ( dbAccession ,&(S[33]),8 );
strcpy_ncs ( dbIdCode ,&(S[42]),12 );
GetIntIns ( dbseqBeg,dbinsBeg,&(S[55]),5 );
GetIntIns ( dbseqEnd,dbinsEnd,&(S[62]),5 );
@@ -356,9 +356,9 @@ IDCode idCode;
}
void CDBReference::Copy ( PCContainerClass DBRef ) {
-
+
CContainerChain::Copy ( DBRef );
-
+
seqBeg = PCDBReference(DBRef)->seqBeg;
seqEnd = PCDBReference(DBRef)->seqEnd;
dbseqBeg = PCDBReference(DBRef)->dbseqBeg;
@@ -371,8 +371,8 @@ void CDBReference::Copy ( PCContainerClass DBRef ) {
strcpy ( dbinsBeg ,PCDBReference(DBRef)->dbinsBeg );
strcpy ( dbinsEnd ,PCDBReference(DBRef)->dbinsEnd );
-}
-
+}
+
void CDBReference::write ( RCFile f ) {
byte Version=1;
f.WriteByte ( &Version );
@@ -481,10 +481,10 @@ IDCode idCode;
GetString ( idCode,&(S[7]),4 );
Chain->SetEntryID ( idCode );
}
- strcpy_ncs ( resName ,&(S[12]),3 );
+ strcpy_ncs ( resName ,&(S[12]),3 );
GetIntIns ( seqNum,insCode,&(S[18]),4 );
- strcpy_ncs ( database ,&(S[24]),4 );
- strcpy_ncs ( dbAccession ,&(S[29]),9 );
+ strcpy_ncs ( database ,&(S[24]),4 );
+ strcpy_ncs ( dbAccession ,&(S[29]),9 );
strcpy_ncs ( dbRes ,&(S[39]),3 );
GetInteger ( dbSeq,&(S[43]),5 );
CreateCopy ( conflict,&(S[49]) );
@@ -548,6 +548,7 @@ int RC;
// Determine the ChainID first and store it locally. It will
// be used by CModel for generating chains and placing the
// primary structure data BEFORE reading the coordinate section.
+
F = Loop->GetString ( CIFTAG_NDB_PDB_CHAIN_ID,Signal,RC );
if ((!RC) && F) {
strcpy_n0 ( chainID,F,sizeof(ChainID)-1 );
@@ -558,7 +559,8 @@ int RC;
CIFGetString ( resName,Loop,CIFTAG_MON_ID,Signal,sizeof(ResName),
pstr("UNK") );
- if (CIFGetInteger(seqNum,Loop,CIFTAG_SEQ_NUM,Signal)) return;
+ CIFGetIntegerD ( seqNum,Loop,CIFTAG_SEQ_NUM );
+
CIFGetString ( insCode,Loop,CIFTAG_NDB_PDB_INS_CODE,
Signal,sizeof(InsCode),pstr(" ") );
@@ -571,8 +573,9 @@ int RC;
CIFGetString ( dbRes,Loop,CIFTAG_DB_MON_ID,Signal,sizeof(ResName),
pstr(" ") );
- if (CIFGetInteger1(dbSeq,Loop,CIFTAG_NDB_SEQ_DB_SEQ_NUM,Signal))
- dbSeq = MinInt4;
+ CIFGetIntegerD ( dbSeq,Loop,CIFTAG_NDB_SEQ_DB_SEQ_NUM );
+// if (CIFGetInteger1(dbSeq,Loop,CIFTAG_NDB_SEQ_DB_SEQ_NUM,Signal))
+// dbSeq = MinInt4;
F = Loop->GetString ( CIFTAG_DETAILS,Signal,RC );
if ((!RC) && F) {
@@ -599,7 +602,7 @@ void CSeqAdv::Copy ( PCContainerClass SeqAdv ) {
CreateCopy ( conflict,PCSeqAdv(SeqAdv)->conflict );
}
-
+
void CSeqAdv::write ( RCFile f ) {
byte Version=1;
f.WriteByte ( &Version );
@@ -821,7 +824,7 @@ Boolean isMon;
numRes++;
}
}
- }
+ }
if (numRes==0) {
numRes = -1;
@@ -856,7 +859,7 @@ int i;
}
}
-
+
void CSeqRes::write ( RCFile f ) {
int i;
byte Version=1;
@@ -957,7 +960,7 @@ IDCode idCode;
GetString ( idCode,&(S[7]),4 );
Chain->SetEntryID ( idCode );
}
- GetString ( resName ,&(S[12]),3 );
+ GetString ( resName ,&(S[12]),3 );
GetIntIns ( seqNum,insCode,&(S[18]),4 );
GetString ( stdRes ,&(S[24]),3 );
CreateCopy ( comment ,&(S[29]) );
@@ -1075,7 +1078,7 @@ void CModRes::Copy ( PCContainerClass ModRes ) {
strcpy ( stdRes ,PCModRes(ModRes)->stdRes );
CreateCopy ( comment,PCModRes(ModRes)->comment );
}
-
+
void CModRes::write ( RCFile f ) {
byte Version=1;
f.WriteByte ( &Version );
@@ -1156,7 +1159,7 @@ int CHetRec::ConvertPDBASCII ( cpstr S ) {
Chain->chainID[1] = char(0);
} else
Chain->chainID[0] = char(0);
- GetString ( hetID ,&(S[7]) ,3 );
+ GetString ( hetID ,&(S[7]) ,3 );
GetIntIns ( seqNum,insCode,&(S[13]),4 );
GetInteger ( numHetAtoms ,&(S[20]),5 );
CreateCopy ( comment ,&(S[30]) );
@@ -1248,7 +1251,7 @@ void CHetRec::Copy ( PCContainerClass Het ) {
strcpy ( insCode,PCHetRec(Het)->insCode );
CreateCopy ( comment,PCHetRec(Het)->comment );
}
-
+
void CHetRec::write ( RCFile f ) {
byte Version=1;
f.WriteByte ( &Version );
@@ -1369,7 +1372,7 @@ PCContainerChain ContainerChain;
DBReference.AddData ( ContainerChain );
return 0;
}
-
+
int CChain::ConvertSEQADV ( cpstr PDBString ) {
int RC;
PCContainerChain ContainerChain;
@@ -1386,7 +1389,7 @@ PCContainerChain ContainerChain;
int CChain::ConvertSEQRES ( cpstr PDBString ) {
return SeqRes.ConvertPDBASCII ( PDBString );
}
-
+
int CChain::ConvertMODRES ( cpstr PDBString ) {
int RC;
PCContainerChain ContainerChain;
@@ -1399,7 +1402,7 @@ PCContainerChain ContainerChain;
ModRes.AddData ( ContainerChain );
return 0;
}
-
+
int CChain::ConvertHET ( cpstr PDBString ) {
int RC;
PCContainerChain ContainerChain;
@@ -1427,7 +1430,7 @@ void CChain::PDBASCIIDump ( RCFile f ) {
void CChain::PDBASCIIAtomDump ( RCFile f ) {
int i;
for (i=0;i<nResidues;i++)
- if (Residue[i])
+ if (Residue[i])
Residue[i]->PDBASCIIAtomDump ( f );
}
@@ -1482,7 +1485,7 @@ int i;
else if (!Enforce)
return NULL; // duplicate seqNum and insCode!
}
- }
+ }
}
// expand the residue array, if necessary
@@ -1496,7 +1499,7 @@ int i;
Residue[nResidues]->index = nResidues;
nResidues++;
- return Residue[nResidues-1];
+ return Residue[nResidues-1];
}
@@ -1862,7 +1865,7 @@ PCAtom CChain::GetAtom ( int seqNo,
const Element elmnt,
const AltLoc aloc ) {
PCResidue res;
- res = GetResidue ( seqNo,insCode );
+ res = GetResidue ( seqNo,insCode );
if (res) return res->GetAtom ( aname,elmnt,aloc );
return NULL;
}
@@ -1870,7 +1873,7 @@ PCResidue res;
PCAtom CChain::GetAtom ( int seqNo, const InsCode insCode,
int atomNo ) {
PCResidue res;
- res = GetResidue ( seqNo,insCode );
+ res = GetResidue ( seqNo,insCode );
if (res) {
if ((0<=atomNo) && (atomNo<res->nAtoms))
return res->atom[atomNo];
@@ -1892,7 +1895,7 @@ PCAtom CChain::GetAtom ( int resNo,
PCAtom CChain::GetAtom ( int resNo, int atomNo ) {
PCResidue res;
if ((0<=resNo) && (resNo<nResidues)) {
- res = Residue[resNo];
+ res = Residue[resNo];
if (res) {
if ((0<=atomNo) && (atomNo<res->nAtoms))
return res->atom[atomNo];
@@ -1944,7 +1947,7 @@ PCResidue res;
void CChain::GetAtomTable1 ( int resNo, PPCAtom & atomTable,
int & NumberOfAtoms ) {
PCResidue res;
- if ((0<=resNo) && (resNo<nResidues))
+ if ((0<=resNo) && (resNo<nResidues))
res = Residue[resNo];
else res = NULL;
if (res)
@@ -1962,7 +1965,7 @@ int CChain::DeleteAtom ( int seqNo,
const Element elmnt,
const AltLoc aloc ) {
PCResidue res;
- res = GetResidue ( seqNo,insCode );
+ res = GetResidue ( seqNo,insCode );
if (res) return res->DeleteAtom ( aname,elmnt,aloc );
return 0;
}
@@ -1970,7 +1973,7 @@ PCResidue res;
int CChain::DeleteAtom ( int seqNo, const InsCode insCode,
int atomNo ) {
PCResidue res;
- res = GetResidue ( seqNo,insCode );
+ res = GetResidue ( seqNo,insCode );
if (res) return res->DeleteAtom ( atomNo );
return 0;
}
@@ -1997,7 +2000,7 @@ int CChain::DeleteAtom ( int resNo, int atomNo ) {
int CChain::DeleteAllAtoms ( int seqNo, const InsCode insCode ) {
PCResidue res;
- res = GetResidue ( seqNo,insCode );
+ res = GetResidue ( seqNo,insCode );
if (res) return res->DeleteAllAtoms();
return 0;
}
@@ -2040,7 +2043,7 @@ int i,n;
int CChain::AddAtom ( int seqNo, const InsCode insCode,
PCAtom atom ) {
PCResidue res;
- res = GetResidue ( seqNo,insCode );
+ res = GetResidue ( seqNo,insCode );
if (res) return res->AddAtom ( atom );
return 0;
}
@@ -2449,7 +2452,7 @@ byte Version=1;
f.WriteInt ( &nResidues );
for (i=0;i<nResidues;i++)
Residue[i]->write ( f );
-
+
}
void CChain::read ( RCFile f ) {
@@ -2497,7 +2500,7 @@ MakeFactoryFunctions(CChain)
/*
void TestChain() {
-// reads from 'in.chain', writes into
+// reads from 'in.chain', writes into
// 'out.chain' and 'abin.chain'
CFile f;
char S[81];
@@ -2517,7 +2520,7 @@ PCChain Chain;
delete Chain;
return;
}
-
+
f.assign ( "out.chain",True );
if (f.rewrite()) {
Chain->PDBASCIIDump ( f );
@@ -2538,10 +2541,10 @@ PCChain Chain;
delete Chain;
return;
}
-
+
delete Chain;
printf ( " Chain deleted.\n" );
-
+
Chain = newCChain();
if (f.reset()) {
Chain->read ( f );
@@ -2551,12 +2554,12 @@ PCChain Chain;
delete Chain;
return;
}
-
+
f.assign ( "abin.chain",True );
if (f.rewrite()) {
Chain->PDBASCIIDump ( f );
f.shut();
- } else
+ } else
printf ( " Can't open output file 'abin.chain' \n" );
delete Chain;
diff --git a/mmdb/mmdb_chain.h b/mmdb/mmdb_chain.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_cifdefs.cpp b/mmdb/mmdb_cifdefs.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_cifdefs.h b/mmdb/mmdb_cifdefs.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_coormngr.cpp b/mmdb/mmdb_coormngr.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_coormngr.h b/mmdb/mmdb_coormngr.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_cryst.cpp b/mmdb/mmdb_cryst.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_cryst.h b/mmdb/mmdb_cryst.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_defs.h b/mmdb/mmdb_defs.h
old mode 100644
new mode 100755
index 1523669..1d9908f
--- a/mmdb/mmdb_defs.h
+++ b/mmdb/mmdb_defs.h
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 16.05.13 <-- Date of Last Modification.
+// 23.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -47,7 +47,7 @@
#define MMDB_MAJOR_VERSION (1)
#define MMDB_MINOR_VERSION (25)
-#define MMDB_MICRO_VERSION (3)
+#define MMDB_MICRO_VERSION (5)
// ======================= types =================================
diff --git a/mmdb/mmdb_ficif.cpp b/mmdb/mmdb_ficif.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_ficif.h b/mmdb/mmdb_ficif.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_file.cpp b/mmdb/mmdb_file.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_file.h b/mmdb/mmdb_file.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_graph.cpp b/mmdb/mmdb_graph.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_graph.h b/mmdb/mmdb_graph.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_manager.cpp b/mmdb/mmdb_manager.cpp
old mode 100644
new mode 100755
index 5705787..77e46f1
--- a/mmdb/mmdb_manager.cpp
+++ b/mmdb/mmdb_manager.cpp
@@ -6,13 +6,13 @@
//
// Copyright (C) Eugene Krissinel 2000-2008.
//
-// This library is free software: you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License version 3, modified in accordance with the provisions
+// This library is free software: you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License version 3, modified in accordance with the provisions
// of the license to address the requirements of UK law.
//
-// You should have received a copy of the modified GNU Lesser
-// General Public License along with this library. If not, copies
+// You should have received a copy of the modified GNU Lesser
+// General Public License along with this library. If not, copies
// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
//
// This program is distributed in the hope that it will be useful,
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 17.03.09 <-- Date of Last Modification.
+// 23.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -33,7 +33,7 @@
// **** Classes : CMMDBManager ( MMDB file manager class )
// ~~~~~~~~~
//
-// (C) E. Krissinel 2000-2009
+// (C) E. Krissinel 2000-2013
//
// =================================================================
//
@@ -90,7 +90,7 @@ int i,j, nchains;
Atom[i]->SetAtomIndex ( i+1 );
} else
Atom[i] = NULL;
- }
+ }
}
nModels = MMDB->nModels;
@@ -103,7 +103,7 @@ int i,j, nchains;
Model[i]->_copy ( MMDB->Model[i] );
} else
Model[i] = NULL;
- }
+ }
}
crModel = NULL;
@@ -220,7 +220,7 @@ int i,j, nchains;
strncpy ( S,MMDB->S,sizeof(S) );
}
-}
+}
void CMMDBManager::Delete ( word DelMask ) {
PPCModel model;
@@ -282,7 +282,7 @@ int i,j,nm, nchains;
chain[j]->FreeAnnotations();
}
}
-
+
if (DelMask & MMDBFCM_SA) SA.FreeContainer();
if (DelMask & MMDBFCM_SB) SB.FreeContainer();
if (DelMask & MMDBFCM_SC) SC.FreeContainer();
@@ -299,6 +299,11 @@ PCTitleContainer CMMDBManager::GetRemarks() {
return Title.GetRemarks();
}
+
+PCTitleContainer CMMDBManager::GetJournal() {
+ return Title.GetJournal();
+}
+
realtype CMMDBManager::GetResolution() {
return Title.GetResolution();
}
diff --git a/mmdb/mmdb_manager.h b/mmdb/mmdb_manager.h
old mode 100644
new mode 100755
index 13c4026..fd04b58
--- a/mmdb/mmdb_manager.h
+++ b/mmdb/mmdb_manager.h
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 17.03.09 <-- Date of Last Modification.
+// 23.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -33,7 +33,7 @@
// **** Classes : CMMDBManager ( MMDB file manager )
// ~~~~~~~~~
//
-// (C) E. Krissinel 2000-2009
+// (C) E. Krissinel 2000-2013
//
// =================================================================
//
@@ -94,6 +94,7 @@ class CMMDBManager : public CMMDBBondManager {
void Delete ( word DelMask ); // DelMask is the same as CopyMask
PCTitleContainer GetRemarks();
+ PCTitleContainer GetJournal();
realtype GetResolution(); // -1.0 means no resolution record in file
@@ -107,6 +108,8 @@ class CMMDBManager : public CMMDBBondManager {
// returns NULL if bmNo is incorrect
PCMMDBManager MakeBiomolecule ( int bmNo, int modelNo=1 );
+
+
protected :
// --------------- Stream I/O -----------------------------
diff --git a/mmdb/mmdb_mask.cpp b/mmdb/mmdb_mask.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_mask.h b/mmdb/mmdb_mask.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_mmcif.cpp b/mmdb/mmdb_mmcif.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_mmcif.h b/mmdb/mmdb_mmcif.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_model.cpp b/mmdb/mmdb_model.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_model.h b/mmdb/mmdb_model.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_rwbrook.cpp b/mmdb/mmdb_rwbrook.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_rwbrook.h b/mmdb/mmdb_rwbrook.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_sbase.cpp b/mmdb/mmdb_sbase.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_sbase.h b/mmdb/mmdb_sbase.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_sbase0.cpp b/mmdb/mmdb_sbase0.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_sbase0.h b/mmdb/mmdb_sbase0.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_selmngr.cpp b/mmdb/mmdb_selmngr.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_selmngr.h b/mmdb/mmdb_selmngr.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_symop.cpp b/mmdb/mmdb_symop.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_symop.h b/mmdb/mmdb_symop.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_tables.cpp b/mmdb/mmdb_tables.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_tables.h b/mmdb/mmdb_tables.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_title.cpp b/mmdb/mmdb_title.cpp
old mode 100644
new mode 100755
index 05fe320..1d83f80
--- a/mmdb/mmdb_title.cpp
+++ b/mmdb/mmdb_title.cpp
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 16.05.13 <-- Date of Last Modification.
+// 23.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -2023,6 +2023,10 @@ PCTitleContainer CMMDBTitle::GetRemarks() {
return &Remark;
}
+PCTitleContainer CMMDBTitle::GetJournal() {
+ return &Journal;
+}
+
realtype CMMDBTitle::GetResolution() {
// returns -1.0 if there is no resolution record in the file
PCRemark rem;
diff --git a/mmdb/mmdb_title.h b/mmdb/mmdb_title.h
old mode 100644
new mode 100755
index 5d5364e..17a3b78
--- a/mmdb/mmdb_title.h
+++ b/mmdb/mmdb_title.h
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 16.05.13 <-- Date of Last Modification.
+// 23.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -662,6 +662,7 @@ class CMMDBTitle : public CStream {
pstr GetStructureTitle ( pstr & S );
PCTitleContainer GetRemarks();
+ PCTitleContainer GetJournal();
realtype GetResolution(); // -1.0 mean no resolution record in file
diff --git a/mmdb/mmdb_uddata.cpp b/mmdb/mmdb_uddata.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_uddata.h b/mmdb/mmdb_uddata.h
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_utils.cpp b/mmdb/mmdb_utils.cpp
old mode 100644
new mode 100755
index 28880ec..59b6e8d
--- a/mmdb/mmdb_utils.cpp
+++ b/mmdb/mmdb_utils.cpp
@@ -6,13 +6,13 @@
//
// Copyright (C) Eugene Krissinel 2000-2008.
//
-// This library is free software: you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License version 3, modified in accordance with the provisions
+// This library is free software: you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License version 3, modified in accordance with the provisions
// of the license to address the requirements of UK law.
//
-// You should have received a copy of the modified GNU Lesser
-// General Public License along with this library. If not, copies
+// You should have received a copy of the modified GNU Lesser
+// General Public License along with this library. If not, copies
// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
//
// This program is distributed in the hope that it will be useful,
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 29.01.10 <-- Date of Last Modification.
+// 14.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -54,13 +54,13 @@
// CIFGetString (reads and deletes string from CIF)
// CIFGetInteger1 (reads and del-s int from CIF loop)
// CIFGetReal1 (reads and del-s int from CIF loop)
-// Mat4Inverse ( inversion of 4x4 matrices )
+// Mat4Inverse ( inversion of 4x4 matrices )
// GetErrorDescription (ascii line to an Error_XXXXX)
// ParseAtomID ( parses atom ID line )
// ParseResID ( parses residue ID line )
// ParseAtomPath ( parses full atom path )
//
-// (C) E. Krissinel 2000-2010
+// (C) E. Krissinel 2000-2013
//
// =================================================================
//
@@ -306,7 +306,7 @@ char L[50];
if (N==MinInt4)
for (i=0;i<M;i++)
S[i] = ' ';
- else {
+ else {
sprintf ( L,"%*i",M,N );
strncpy ( S,L,M );
}
@@ -324,12 +324,21 @@ char N[50];
if (R==-MaxReal)
for (i=0;i<M;i++)
S[i] = ' ';
- else {
+ else {
sprintf ( N,"%*.*f",M,L,R );
strncpy ( S,N,M );
}
}
+int CIFGetIntegerD ( int & I, PCMMCIFLoop Loop, cpstr Tag,
+ int defValue ) {
+int RC,Signal;
+ Signal = 0;
+ RC = CIFGetInteger ( I,Loop,Tag,Signal );
+ if (RC)
+ I = defValue;
+ return RC;
+}
int CIFGetInteger ( int & I, PCMMCIFLoop Loop, cpstr Tag,
int & Signal ) {
@@ -375,7 +384,7 @@ pstr F;
Loop->GetCategoryName(),Tag,nrow );
return Error_UnrecognizedInteger;
}
- if (RC==CIFRC_WrongIndex)
+ if (RC==CIFRC_WrongIndex)
return Error_NoData;
if (RC) {
F = Loop->GetString ( Tag,nrow,RC );
@@ -593,7 +602,7 @@ int ii,jj,i,i1,j,j1;
// ---- Get inverse matrix
- if (s!=0.0)
+ if (s!=0.0)
for (i=0;i<4;i++)
for (j=0;j<4;j++)
AI[i][j] = c[j][i]/s;
@@ -633,7 +642,7 @@ int ii,jj,i,i1,j,j1;
// Get inverse matrix
- if (s!=0.0)
+ if (s!=0.0)
for (i=0;i<3;i++)
for (j=0;j<3;j++)
AI[i][j] = c[j][i]/s;
@@ -694,7 +703,7 @@ int i,j;
realtype Mat4RotDet ( mat44 & T ) {
// returns determinant of the rotation part
- return T[0][0]*T[1][1]*T[2][2] +
+ return T[0][0]*T[1][1]*T[2][2] +
T[0][1]*T[1][2]*T[2][0] +
T[1][0]*T[2][1]*T[0][2] -
T[0][2]*T[1][1]*T[2][0] -
@@ -862,9 +871,9 @@ static cpstr msWrongSheetOrder = "Incomplete _struct_sheet_order.";
static cpstr msHBondInconsistency =
"Inconsistency in _struct_sheet_hbond.";
-static cpstr msEmptyResidueName =
+static cpstr msEmptyResidueName =
"No residue name on PDB ATOM or TER card.";
-static cpstr msDuplicateSeqNum =
+static cpstr msDuplicateSeqNum =
"Duplicate sequence number and insertion code.";
static cpstr msEmptyFile = "Non-existent or empty file.";
@@ -880,7 +889,7 @@ cpstr GetErrorDescription ( int ErrorCode ) {
case Error_WrongSection : return msWrongSection;
case Error_WrongChainID : return msWrongChainID;
- case Error_WrongEntryID : return msWrongEntryID;
+ case Error_WrongEntryID : return msWrongEntryID;
case Error_SEQRES_serNum : return msSEQRES_serNum;
case Error_SEQRES_numRes : return msSEQRES_numRes;
@@ -1064,9 +1073,9 @@ void CContString::Copy ( PCContainerClass CString ) {
void CContString::write ( RCFile f ) {
byte Version=1;
f.WriteByte ( &Version );
- f.CreateWrite ( Line );
- f.CreateWrite ( CIFCategory );
- f.CreateWrite ( CIFTag );
+ f.CreateWrite ( Line );
+ f.CreateWrite ( CIFCategory );
+ f.CreateWrite ( CIFTag );
}
void CContString::read ( RCFile f ) {
@@ -1107,7 +1116,7 @@ void CClassContainer::FreeContainer() {
int i;
if (Container) {
for (i=0;i<length;i++)
- if (Container[i])
+ if (Container[i])
delete Container[i];
delete[] Container;
}
@@ -1234,7 +1243,7 @@ byte Version;
f.ReadInt ( &ClassID );
if (ClassID>=0) {
Container[i] = MakeContainerClass ( ClassID );
- Container[i]->read ( f );
+ Container[i]->read ( f );
} else
Container[i] = NULL;
}
@@ -1353,7 +1362,7 @@ int i,k;
if (((*p>='0') && (*p<='9')) || (*p=='-') ||
(*p=='(') || (*p=='.')) {
- // sequence number, residue name and insertion code
+ // sequence number, residue name and insertion code
i = 0;
while ((*p) && (*p!='/')) {
if (*p!=' ') N[i++] = *p;
@@ -1369,7 +1378,7 @@ int i,k;
}
if (strchr(p,':') || strchr(p,'[')) {
- // atom name, chemical element and alternative location
+ // atom name, chemical element and alternative location
i = 0;
while (*p) {
if (*p!=' ') N[i++] = *p;
@@ -1466,7 +1475,7 @@ int rm = right+1;
do
rm--;
while ((rm>0) && (Compare(rm,lv)>0));
- do
+ do
lm++;
while ((lm<dlen) && (Compare(lm,lv)<0));
if (lm<rm) {
@@ -1500,7 +1509,7 @@ void takeWord ( pstr & p, pstr wrd, cpstr ter, int l ) {
pstr p1;
int i;
p1 = strpbrk ( p,ter );
- if (!p1)
+ if (!p1)
p1 = p + strlen(p);
i = 0;
while ((p!=p1) && (i<l)) {
@@ -1524,7 +1533,7 @@ pstr p;
strcpy ( elname,"*" );
if (*p) aloc[0] = char(0);
else strcpy ( aloc,"*" );
-
+
takeWord ( p,aname,pstr("[: "),sizeof(AtomName) );
if (*p=='[') {
@@ -1729,7 +1738,7 @@ Boolean wasModel,wasChain,wasRes,haveNeg;
p++;
}
*p1 = char(0);
-
+
p = ID;
iModel = 0;
diff --git a/mmdb/mmdb_utils.h b/mmdb/mmdb_utils.h
old mode 100644
new mode 100755
index 5b6d954..d6083b8
--- a/mmdb/mmdb_utils.h
+++ b/mmdb/mmdb_utils.h
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 29.01.10 <-- Date of Last Modification.
+// 14.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -60,7 +60,7 @@
// ParseResID ( parses residue ID line )
// ParseAtomPath ( parses full atom path )
//
-// (C) E. Krissinel 2000-2010
+// (C) E. Krissinel 2000-2013
//
// =================================================================
//
@@ -170,6 +170,8 @@ extern int CIFGetString ( pstr S, PCMMCIFStruct Struct,
extern int CIFGetInteger ( int & I, PCMMCIFLoop Loop, cpstr Tag,
int & Signal );
+extern int CIFGetIntegerD ( int & I, PCMMCIFLoop Loop, cpstr Tag,
+ int defValue=MinInt4 );
extern int CIFGetInteger1 ( int & I, PCMMCIFLoop Loop, cpstr Tag,
int nrow );
diff --git a/mmdb/mmdb_xml.cpp b/mmdb/mmdb_xml.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/mmdb_xml.h b/mmdb/mmdb_xml.h
old mode 100644
new mode 100755
diff --git a/mmdb/random_n.cpp b/mmdb/random_n.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/random_n.h b/mmdb/random_n.h
old mode 100644
new mode 100755
diff --git a/mmdb/stream_.cpp b/mmdb/stream_.cpp
old mode 100644
new mode 100755
diff --git a/mmdb/stream_.h b/mmdb/stream_.h
old mode 100644
new mode 100755
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/mmdb.git
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