[med-svn] r1914 - in trunk/packages/pdb2pqr/trunk: . debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Fri May 23 13:02:22 UTC 2008
Author: smoe-guest
Date: 2008-05-23 13:02:17 +0000 (Fri, 23 May 2008)
New Revision: 1914
Added:
trunk/packages/pdb2pqr/trunk/debian/README.Debian
trunk/packages/pdb2pqr/trunk/debian/README.source
Removed:
trunk/packages/pdb2pqr/trunk/Makefile
trunk/packages/pdb2pqr/trunk/config.log
trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary
trunk/packages/pdb2pqr/trunk/debian/README.Debian.source
trunk/packages/pdb2pqr/trunk/pdb2pka/
trunk/packages/pdb2pqr/trunk/propka/
Modified:
trunk/packages/pdb2pqr/trunk/debian/changelog
trunk/packages/pdb2pqr/trunk/debian/control
trunk/packages/pdb2pqr/trunk/debian/copyright
Log:
Hm. Time for an ITP, so I presume.
Deleted: trunk/packages/pdb2pqr/trunk/Makefile
===================================================================
--- trunk/packages/pdb2pqr/trunk/Makefile 2008-05-23 10:17:55 UTC (rev 1913)
+++ trunk/packages/pdb2pqr/trunk/Makefile 2008-05-23 13:02:17 UTC (rev 1914)
@@ -1,585 +0,0 @@
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-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-recursive
-
-pdf-am:
-
-ps: ps-recursive
-
-ps-am:
-
-uninstall-am: uninstall-info-am
-
-uninstall-info: uninstall-info-recursive
-
-.PHONY: $(RECURSIVE_TARGETS) CTAGS GTAGS all all-am am--refresh check \
- check-am clean clean-generic clean-local clean-recursive ctags \
- ctags-recursive dist dist-all dist-bzip2 dist-gzip dist-shar \
- dist-tarZ dist-zip distcheck distclean distclean-generic \
- distclean-local distclean-recursive distclean-tags \
- distcleancheck distdir distuninstallcheck dvi dvi-am html \
- html-am info info-am install install-am install-data \
- install-data-am install-exec install-exec-am install-info \
- install-info-am install-man install-strip installcheck \
- installcheck-am installdirs installdirs-am maintainer-clean \
- maintainer-clean-generic maintainer-clean-recursive \
- mostlyclean mostlyclean-generic mostlyclean-recursive pdf \
- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \
- uninstall-info-am
-
-distclean-local: clean-local
-clean-local: clean-ac
-clean-ac:
- -rm -rf autom4te.cache
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
Deleted: trunk/packages/pdb2pqr/trunk/config.log
===================================================================
--- trunk/packages/pdb2pqr/trunk/config.log 2008-05-23 10:17:55 UTC (rev 1913)
+++ trunk/packages/pdb2pqr/trunk/config.log 2008-05-23 13:02:17 UTC (rev 1914)
@@ -1,419 +0,0 @@
-This file contains any messages produced by compilers while
-running configure, to aid debugging if configure makes a mistake.
-
-It was created by PDB2PQR configure 1.2.0, which was
-generated by GNU Autoconf 2.59. Invocation command line was
-
- $ ./configure --enable-pdb2pka
-
-## --------- ##
-## Platform. ##
-## --------- ##
-
-hostname = notebook
-uname -m = x86_64
-uname -r = 2.6.23-1-amd64
-uname -s = Linux
-uname -v = #1 SMP Fri Nov 30 12:19:15 UTC 2007
-
-/usr/bin/uname -p = unknown
-/bin/uname -X = unknown
-
-/bin/arch = unknown
-/usr/bin/arch -k = unknown
-/usr/convex/getsysinfo = unknown
-hostinfo = unknown
-/bin/machine = unknown
-/usr/bin/oslevel = unknown
-/bin/universe = unknown
-
-PATH: /home/moeller/bin
-PATH: /usr/local/bin
-PATH: /usr/bin
-PATH: /bin
-PATH: /usr/games
-
-
-## ----------- ##
-## Core tests. ##
-## ----------- ##
-
-configure:1311: checking build system type
-configure:1329: result: x86_64-unknown-linux
-configure:1337: checking host system type
-configure:1351: result: x86_64-unknown-linux
-configure:1359: checking target system type
-configure:1373: result: x86_64-unknown-linux
-configure:1402: checking for a BSD-compatible install
-configure:1457: result: /usr/bin/install -c
-configure:1468: checking whether build environment is sane
-configure:1511: result: yes
-configure:1576: checking for gawk
-configure:1592: found /usr/bin/gawk
-configure:1602: result: gawk
-configure:1612: checking whether make sets $(MAKE)
-configure:1632: result: yes
-configure:1862: checking for g++
-configure:1878: found /usr/bin/g++
-configure:1888: result: g++
-configure:1904: checking for C++ compiler version
-configure:1907: g++ --version </dev/null >&5
-g++ (GCC) 4.2.3 20071123 (prerelease) (Debian 4.2.2-4)
-Copyright (C) 2007 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.
-
-configure:1910: $? = 0
-configure:1912: g++ -v </dev/null >&5
-Using built-in specs.
-Target: x86_64-linux-gnu
-Configured with: ../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.2 --program-suffix=-4.2 --enable-clocale=gnu --enable-libstdcxx-debug --enable-mpfr --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
-Thread model: posix
-gcc version 4.2.3 20071123 (prerelease) (Debian 4.2.2-4)
-configure:1915: $? = 0
-configure:1917: g++ -V </dev/null >&5
-g++: '-V' option must have argument
-configure:1920: $? = 1
-configure:1943: checking for C++ compiler default output file name
-configure:1946: g++ conftest.cc >&5
-configure:1949: $? = 0
-configure:1995: result: a.out
-configure:2000: checking whether the C++ compiler works
-configure:2006: ./a.out
-configure:2009: $? = 0
-configure:2026: result: yes
-configure:2033: checking whether we are cross compiling
-configure:2035: result: no
-configure:2038: checking for suffix of executables
-configure:2040: g++ -o conftest conftest.cc >&5
-configure:2043: $? = 0
-configure:2068: result:
-configure:2074: checking for suffix of object files
-configure:2095: g++ -c conftest.cc >&5
-configure:2098: $? = 0
-configure:2120: result: o
-configure:2124: checking whether we are using the GNU C++ compiler
-configure:2148: g++ -c conftest.cc >&5
-configure:2154: $? = 0
-configure:2158: test -z
- || test ! -s conftest.err
-configure:2161: $? = 0
-configure:2164: test -s conftest.o
-configure:2167: $? = 0
-configure:2180: result: yes
-configure:2186: checking whether g++ accepts -g
-configure:2207: g++ -c -g conftest.cc >&5
-configure:2213: $? = 0
-configure:2217: test -z
- || test ! -s conftest.err
-configure:2220: $? = 0
-configure:2223: test -s conftest.o
-configure:2226: $? = 0
-configure:2237: result: yes
-configure:2279: g++ -c -g -O2 conftest.cc >&5
-configure:2285: $? = 0
-configure:2289: test -z
- || test ! -s conftest.err
-configure:2292: $? = 0
-configure:2295: test -s conftest.o
-configure:2298: $? = 0
-configure:2324: g++ -c -g -O2 conftest.cc >&5
-conftest.cc: In function 'int main()':
-conftest.cc:15: error: 'exit' was not declared in this scope
-configure:2330: $? = 1
-configure: failed program was:
-| /* confdefs.h. */
-|
-| #define PACKAGE_NAME "PDB2PQR"
-| #define PACKAGE_TARNAME "pdb2pqr"
-| #define PACKAGE_VERSION "1.2.0"
-| #define PACKAGE_STRING "PDB2PQR 1.2.0"
-| #define PACKAGE_BUGREPORT "todd at ccb.wustl.edu"
-| #define PACKAGE "PDB2PQR"
-| #define VERSION "1.2.0"
-| /* end confdefs.h. */
-|
-| int
-| main ()
-| {
-| exit (42);
-| ;
-| return 0;
-| }
-configure:2279: g++ -c -g -O2 conftest.cc >&5
-conftest.cc:11: error: 'void std::exit(int)' should have been declared inside 'std'
-configure:2285: $? = 1
-configure: failed program was:
-| /* confdefs.h. */
-|
-| #define PACKAGE_NAME "PDB2PQR"
-| #define PACKAGE_TARNAME "pdb2pqr"
-| #define PACKAGE_VERSION "1.2.0"
-| #define PACKAGE_STRING "PDB2PQR 1.2.0"
-| #define PACKAGE_BUGREPORT "todd at ccb.wustl.edu"
-| #define PACKAGE "PDB2PQR"
-| #define VERSION "1.2.0"
-| /* end confdefs.h. */
-| extern "C" void std::exit (int) throw (); using std::exit;
-| #include <stdlib.h>
-| int
-| main ()
-| {
-| exit (42);
-| ;
-| return 0;
-| }
-configure:2279: g++ -c -g -O2 conftest.cc >&5
-conftest.cc:11: error: 'void std::exit(int)' should have been declared inside 'std'
-In file included from conftest.cc:12:
-/usr/include/stdlib.h:531: error: declaration of 'void std::exit(int) throw ()' throws different exceptions
-conftest.cc:11: error: from previous declaration 'void std::exit(int)'
-configure:2285: $? = 1
-configure: failed program was:
-| /* confdefs.h. */
-|
-| #define PACKAGE_NAME "PDB2PQR"
-| #define PACKAGE_TARNAME "pdb2pqr"
-| #define PACKAGE_VERSION "1.2.0"
-| #define PACKAGE_STRING "PDB2PQR 1.2.0"
-| #define PACKAGE_BUGREPORT "todd at ccb.wustl.edu"
-| #define PACKAGE "PDB2PQR"
-| #define VERSION "1.2.0"
-| /* end confdefs.h. */
-| extern "C" void std::exit (int); using std::exit;
-| #include <stdlib.h>
-| int
-| main ()
-| {
-| exit (42);
-| ;
-| return 0;
-| }
-configure:2279: g++ -c -g -O2 conftest.cc >&5
-configure:2285: $? = 0
-configure:2289: test -z
- || test ! -s conftest.err
-configure:2292: $? = 0
-configure:2295: test -s conftest.o
-configure:2298: $? = 0
-configure:2324: g++ -c -g -O2 conftest.cc >&5
-configure:2330: $? = 0
-configure:2334: test -z
- || test ! -s conftest.err
-configure:2337: $? = 0
-configure:2340: test -s conftest.o
-configure:2343: $? = 0
-configure:2377: checking for style of include used by make
-configure:2405: result: GNU
-configure:2433: checking dependency style of g++
-configure:2523: result: none
-configure:2544: checking for python
-configure:2562: found /usr/bin/python
-configure:2574: result: /usr/bin/python
-configure:2587: checking for python include directory
-configure:2593: result: -I/usr/include/python2.4
-configure:2637: checking for --disable-propka
-configure:2649: result: no
-configure:2651: result:
-configure:2653: result: ------------- Begin Processing PropKa Configure Options -----------
-configure:2658: result: ------------- End Processing PropKa Configure Options -----------
-configure:2660: result:
-configure:2670: checking for --enable-pdb2pka
-configure:2683: result: yes
-configure:2686: result:
-configure:2688: result: ------------- Begin Processing pdb2pka Configure Options -----------
-configure:2693: checking for Numeric include files
-configure:2697: result: -I/usr/include/python2.4/Numeric
-configure:2762: result: ------------- End Processing pdb2ka Configure Options -----------
-configure:2764: result:
-configure:2780: result: ------------- End Processing PDB2PQR Configure Options -----------
-configure:2782: result:
-configure:2926: creating ./config.status
-
-## ---------------------- ##
-## Running config.status. ##
-## ---------------------- ##
-
-This file was extended by PDB2PQR config.status 1.2.0, which was
-generated by GNU Autoconf 2.59. Invocation command line was
-
- CONFIG_FILES =
- CONFIG_HEADERS =
- CONFIG_LINKS =
- CONFIG_COMMANDS =
- $ ./config.status
-
-on notebook
-
-config.status:701: creating Makefile
-config.status:701: creating pdb2pka/Makefile
-config.status:701: creating pdb2pka/substruct/Makefile
-config.status:884: executing depfiles commands
-configure:3979: result: Please type "make" to complete the installation.
-
-## ---------------- ##
-## Cache variables. ##
-## ---------------- ##
-
-ac_cv_build=x86_64-unknown-linux
-ac_cv_build_alias=x86_64-unknown-linux
-ac_cv_cxx_compiler_gnu=yes
-ac_cv_env_CPPFLAGS_set=
-ac_cv_env_CPPFLAGS_value=
-ac_cv_env_CXXFLAGS_set=
-ac_cv_env_CXXFLAGS_value=
-ac_cv_env_CXX_set=
-ac_cv_env_CXX_value=
-ac_cv_env_LDFLAGS_set=
-ac_cv_env_LDFLAGS_value=
-ac_cv_env_build_alias_set=
-ac_cv_env_build_alias_value=
-ac_cv_env_host_alias_set=
-ac_cv_env_host_alias_value=
-ac_cv_env_target_alias_set=
-ac_cv_env_target_alias_value=
-ac_cv_exeext=
-ac_cv_host=x86_64-unknown-linux
-ac_cv_host_alias=x86_64-unknown-linux
-ac_cv_objext=o
-ac_cv_path_install='/usr/bin/install -c'
-ac_cv_path_py_path=/usr/bin/python
-ac_cv_prog_AWK=gawk
-ac_cv_prog_ac_ct_CXX=g++
-ac_cv_prog_cxx_g=yes
-ac_cv_prog_make_make_set=yes
-ac_cv_target=x86_64-unknown-linux
-ac_cv_target_alias=x86_64-unknown-linux
-am_cv_CXX_dependencies_compiler_type=none
-
-## ----------------- ##
-## Output variables. ##
-## ----------------- ##
-
-ACLOCAL=':'
-AMDEPBACKSLASH='\'
-AMDEP_FALSE='#'
-AMDEP_TRUE=''
-AMTAR='${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/missing --run tar'
-AUTOCONF=':'
-AUTOHEADER=':'
-AUTOMAKE=':'
-AWK='gawk'
-CPPFLAGS=''
-CXX='g++'
-CXXDEPMODE='depmode=none'
-CXXFLAGS='-g -O2'
-CYGPATH_W='echo'
-DEFS='-DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.2.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.2.0\" -DPACKAGE_BUGREPORT=\"todd at ccb.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.2.0\" '
-DEPDIR='.deps'
-ECHO_C=''
-ECHO_N='-n'
-ECHO_T=''
-EXEEXT=''
-INSTALL_DATA='${INSTALL} -m 644'
-INSTALL_PROGRAM='${INSTALL}'
-INSTALL_SCRIPT='${INSTALL}'
-INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
-LDFLAGS=''
-LIBOBJS=''
-LIBS=''
-LTLIBOBJS=''
-MAKEINFO='${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/missing --run makeinfo'
-OBJEXT='o'
-PACKAGE='PDB2PQR'
-PACKAGE_BUGREPORT='todd at ccb.wustl.edu'
-PACKAGE_NAME='PDB2PQR'
-PACKAGE_STRING='PDB2PQR 1.2.0'
-PACKAGE_TARNAME='pdb2pqr'
-PACKAGE_VERSION='1.2.0'
-PATH_SEPARATOR=':'
-PDB2PQR_SUBDIRS='propka pdb2pka'
-PDB2PQR_VERSION='1:2:0'
-PY_CFLAGS='-I/usr/include/python2.4 -I/usr/include/python2.4/Numeric'
-PY_FLAGS='-fPIC'
-PY_HEADER='-I/usr/include/python2.4'
-PY_LDFLAGS=''
-PY_SHARED='-shared'
-SET_MAKE=''
-SHELL='/bin/sh'
-STRIP=''
-VERSION='1.2.0'
-ac_ct_CXX='g++'
-ac_ct_STRIP=''
-am__fastdepCXX_FALSE=''
-am__fastdepCXX_TRUE='#'
-am__include='include'
-am__leading_dot='.'
-am__quote=''
-am__tar='${AMTAR} chof - "$$tardir"'
-am__untar='${AMTAR} xf -'
-bindir='${exec_prefix}/bin'
-build='x86_64-unknown-linux'
-build_alias=''
-build_cpu='x86_64'
-build_os='linux'
-build_vendor='unknown'
-datadir='${prefix}/share'
-exec_prefix='${prefix}'
-host='x86_64-unknown-linux'
-host_alias=''
-host_cpu='x86_64'
-host_os='linux'
-host_vendor='unknown'
-includedir='${prefix}/include'
-infodir='${prefix}/info'
-install_sh='/home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/install-sh'
-libdir='${exec_prefix}/lib'
-libexecdir='${exec_prefix}/libexec'
-localstatedir='${prefix}/var'
-mandir='${prefix}/man'
-mkdir_p='mkdir -p --'
-oldincludedir='/usr/include'
-prefix='/home/moeller'
-program_transform_name='s,x,x,'
-py_path='/usr/bin/python'
-sbindir='${exec_prefix}/sbin'
-sharedstatedir='${prefix}/com'
-sysconfdir='${prefix}/etc'
-target='x86_64-unknown-linux'
-target_alias=''
-target_cpu='x86_64'
-target_os='linux'
-target_vendor='unknown'
-
-## ----------- ##
-## confdefs.h. ##
-## ----------- ##
-
-#define PACKAGE "PDB2PQR"
-#define PACKAGE_BUGREPORT "todd at ccb.wustl.edu"
-#define PACKAGE_NAME "PDB2PQR"
-#define PACKAGE_STRING "PDB2PQR 1.2.0"
-#define PACKAGE_TARNAME "pdb2pqr"
-#define PACKAGE_VERSION "1.2.0"
-#define VERSION "1.2.0"
-#endif
-#ifdef __cplusplus
-extern "C" void exit (int) throw ();
-
-configure: exit 0
-
-## ---------------------- ##
-## Running config.status. ##
-## ---------------------- ##
-
-This file was extended by PDB2PQR config.status 1.2.0, which was
-generated by GNU Autoconf 2.59. Invocation command line was
-
- CONFIG_FILES =
- CONFIG_HEADERS =
- CONFIG_LINKS =
- CONFIG_COMMANDS =
- $ ./config.status
-
-on notebook
-
-config.status:701: creating Makefile
-config.status:701: creating pdb2pka/Makefile
-config.status:701: creating pdb2pka/substruct/Makefile
-config.status:884: executing depfiles commands
Copied: trunk/packages/pdb2pqr/trunk/debian/README.Debian (from rev 1836, trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary)
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/README.Debian 2008-05-23 13:02:17 UTC (rev 1914)
@@ -0,0 +1,13 @@
+The packaging of PDB2PQR was stimulated by the AutoDockTools
+and their dependency on it to visualise properties of the
+protein. And yes, if you have interest in this package, please
+help with completing the packaging.
+
+Upstream does not seem to have prepared the installation of
+their work into distinct directories. No time was yet allocated to
+address this.
+
+The code to offer pdb2pqr as a web service was omitted. The extensions
+directory was added as a documentation.
+
+ -- Steffen Moeller Fri, 23 May 2008 14:58:07 +0200
Deleted: trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary 2008-05-23 10:17:55 UTC (rev 1913)
+++ trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary 2008-05-23 13:02:17 UTC (rev 1914)
@@ -1,23 +0,0 @@
-The packaging of PDB2PQR was stimulated by the AutoDockTools
-and their dependency on it to visualise properties of the
-protein. And yes, if you have interest in this package, please
-help with completing the packaging.
-
-At the time this is written it remains unclear if this package
-can be distributed in Debian at all due to the more restrictive
-license of the PROPKA package that is shipped with it. However,
-the python code itself can also be used independent of PROPKA,
-which motivates to ship a stripped-down DFSG-variant. At this
-time, the main interest was in functionality. The whole part seems
-to work just fine.
-
-Upstream does not seem to have prepared the installation of
-their work into distinct directories. No time was yet allocated to
-address this.
-
-The code to offer pdb2pqr as a web service was omitted. The extensions
-directory was added as a documentation.
-
-Steffen Moeller
-
-Wed 26. Dez 01:19:54 CET 2007
Deleted: trunk/packages/pdb2pqr/trunk/debian/README.Debian.source
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.Debian.source 2008-05-23 10:17:55 UTC (rev 1913)
+++ trunk/packages/pdb2pqr/trunk/debian/README.Debian.source 2008-05-23 13:02:17 UTC (rev 1914)
@@ -1 +0,0 @@
-The source was stripped from .svn directories.
Copied: trunk/packages/pdb2pqr/trunk/debian/README.source (from rev 1836, trunk/packages/pdb2pqr/trunk/debian/README.Debian.source)
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.source (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/README.source 2008-05-23 13:02:17 UTC (rev 1914)
@@ -0,0 +1 @@
+The source was stripped from .svn directories.
Modified: trunk/packages/pdb2pqr/trunk/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog 2008-05-23 10:17:55 UTC (rev 1913)
+++ trunk/packages/pdb2pqr/trunk/debian/changelog 2008-05-23 13:02:17 UTC (rev 1914)
@@ -1,11 +1,18 @@
pdb2pqr (1.3.0-1) UNRELEASED; urgency=low
+ [ Steffen Moeller ]
+
* New upstream release
+ * Removed artifacts from first upload
+ * Corrected debian/copyright
+
+ [ David Paleino ]
+
* Updated to Standards-Version 3.7.3 (no changes needed)
- -- David Paleino <d.paleino at gmail.com> Wed, 06 Feb 2008 14:26:14 +0100
+ -- Steffen Moeller <moeller at debian.org> Fri, 23 May 2008 14:51:41 +0200
-pdb2pqr (1.2.1-1) unstable; urgency=low
+pdb2pqr (1.2.1-1) UNRELEASED; urgency=low
* Initial release.
Modified: trunk/packages/pdb2pqr/trunk/debian/control
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/control 2008-05-23 10:17:55 UTC (rev 1913)
+++ trunk/packages/pdb2pqr/trunk/debian/control 2008-05-23 13:02:17 UTC (rev 1914)
@@ -1,16 +1,20 @@
Source: pdb2pqr
Section: non-free/science
Priority: optional
-Maintainer: Steffen Moeller <moeller at debian.org>
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>
Build-Depends: debhelper (>= 5.0.38), python-central (>= 0.5.6), cdbs (>= 0.4.49), python-all-dev (>= 2.3.5-11), swig
Standards-Version: 3.7.3
-XS-Python-Version: current
+XS-Python-Version: 2.5
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pdb2pqr/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/pdb2pqr/trunk/
Homepage: http://pdb2pqr.sourceforge.net
Package: pdb2pqr
XB-Python-Version: ${python:Versions}
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-xml, python-zsi, libgfortran3
Description: Preparation of protein structures for electrostatics calculations
PDB2PQR is a Python software package that automates many of the common
tasks of preparing structures for continuum electrostatics calculations,
Modified: trunk/packages/pdb2pqr/trunk/debian/copyright
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/copyright 2008-05-23 10:17:55 UTC (rev 1913)
+++ trunk/packages/pdb2pqr/trunk/debian/copyright 2008-05-23 13:02:17 UTC (rev 1914)
@@ -1,103 +1,88 @@
This package was debianized by Steffen Moeller <moeller at debian.org> on
Thu, 20 Dec 2007 16:27:31 +0100.
-It was downloaded from http://mdltools.scripps.edu
+It was downloaded from http://pdb2pqr.sourceforge.net
Upstream Authors:
- Dr Chandrajit Bajaj,
Copyright:
+ pdb2pqr: Copyright (c) 2002-2007 by
- The University of Texas
+ Jens Erik Nielsen, University College Dublin
+ Nathan A. Baker, Washington University in St. Louis
+ Paul Czodrowski & Gerhard Klebe, University of Marburg
-License:
+ Propka: Copyright (c) 2005 by
+ Jan H. Jensen <Jan-Jensen at uiowa.edu>
+ Hui Li
- TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
- 1. This software is the copyright of THE UNIVERSITY OF TEXAS AT AUSTIN, 2005.
+License:
- 2. The software is available under multiple licenses.
+ pdb2pqr:
- 3. For non commercial educational and non commercial academic use, the software including source code, interface definitions and compile scripts are freely available. Any distribution of code, library or executables which contains any modules from this software should contain, conspicously and appropriately, on each copy, this copyright and license notice and should be freely distributed.
+ All rights reserved.
- 4. If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible with these, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation.
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
- 5. For any other purpose, including commercial purposes, please contact The University of Texas at Austin for a different license.
+ * Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ * Neither the names of University College Dublin, Washington University in
+ St. Louis, or University of Marburg nor the names of its contributors may
+ be used to endorse or promote products derived from this software without
+ specific prior written permission.
- 6. Credits:
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ OF THE POSSIBILITY OF SUCH DAMAGE.
- This software has been developed at the Computational and Visualization center under
-
- Dr Chandrajit Bajaj,
- Computational Applied Mathematics Chair in Visualization,
- Professor of Computer Sciences,
- Director of Center for Computational Visualization,
- Department of Computer Sciences & The Institute of Computational Engineering and Sciences , Center for Computational Visualization,
- 201 East 24th Street, ACES 2.324A,
- 1 University Station, C0200,
- Austin, TX 78712-0027.
+ Propka:
-We request that you agree to acknowledge the use of the software that results in any published work, including scientific papers, films and videotapes by citing the references listed below
+ PROPKA USER LICENSE AGREEMENT
-For UTblur:
+ PropKa: a program for protein pKa predictions
+ Copyright (c) 2005, Jan H. Jensen and Hui Li
+
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
-C. Bajaj, V. Siddavanahalli
-Fast Feature Adaptive Surfaces and Derivatives Computation for Volumetric Particle Data
-ICES and CS technical reports, The University of Texas at Austin, 2005.
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ * Neither the name of the University of Copenhagen nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-For UTisocontour:
-
-C. Bajaj, V. Pascucci, D. Schikore
-Accelerated IsoContouring of Scalar Fields
-Data Visualization Techniques, edited by C. Bajaj, John Wiley and Sons (1998).
-
-C. Bajaj, V. Pascucci, D. Schikore
-Fast Isocontouring for Improved Interactivity
-Proceedings: ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, (1996), San Francisco, CA. Pages: 39-46 99
-
-
-For UTmesh:
-
-Y. Zhang, C. Bajaj
-Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data
-Computer Methods in Applied Mechanics and Engineering (CMAME), in press, 2005.
-
-Y. Zhang, C. Bajaj, B-S. Sohn
-3D Finite Element Meshing from Imaging Data
-The special issue of Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 194(48-49):5083-5106, 2005.
-
-
-For UTsdf:
-
-C. Bajaj, V. Siddavanahalli
-An Adaptive Grid Based Method for Computing Molecular Surfaces and Properties
-ICES and CS Technical Reports, The University of Texas at Austin, 2005.
-
-
-For UTvolrend:
-
-C. Bajaj, Z. Yu, M. Auer
-Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging.
-Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 132-143
-
-
-For UTmolderivatives:
-
-C. Bajaj, V. Siddavanahalli
-Fast Feature Adaptive Surfaces and Derivatives Computation for Volumetric Particle Data
-ICES and CS Technical Reports, The University of Texas at Austin, 2005.
-
-7. No warranty
-
-7a. Because the library is licensed free of charge, there is no warranty for the library, to the extent permitted by applicable law. except when otherwise stated in writing the copyright holders and/or other parties provide the library "as is" without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. the entire risk as to the quality and performance of the library is with you. should the library prove defective, you assume the cost of all necessary servicing, repair or correction.
-
-7b. In no event unless required by applicable law or agreed to in writing will any copyright holder, or any other party who may modify and/or redistribute the library as permitted above, be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the library (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the library to operate with any other software), even if such holder or other party has been advised of the possibility of such damages.
-
-END OF TERMS AND CONDITIONS
-
The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
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