debian/0000755000000000000000000000000012200742617007167 5ustar debian/copyright0000644000000000000000000000621612200742410011116 0ustar This package was debianized by Michael Banck on Thu, 29 Jun 2006 17:10:18 +0200. It was downloaded from: http://downloads.sourceforge.net/apbs/. Upstream Author: Nathan A. Baker Copyright Holder: Copyright (C) 2010-2012 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (C) 2002-2010, Washington University in St. Louis. Portions Copyright (C) 2002-2010, Nathan A. Baker. Portions Copyright (C) 1999-2002, The Regents of the University of California. Portions Copyright (C) 1995, Michael Holst. Copyright (C) 2010 Pacific Northwest National Laboratory. Portions Copyright (C) 2002-2010 Washington University in St. Louis. Portions Copyright (C) 2002-2010 Nathan A. Baker. Portions Copyright (C) 2007 Patrice Koehl. Portions Copyright (C) 1999-2002 The Regents of the University of California. Portions Copyright (C) 1995 Michael Holst. License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * 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 Washington University in St. Louis 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 ============================================================================== Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. ============================================================================== The Debian packaging is Coypright (C) 2006-2013 by the debichem team and subject to the GNU General Public License (GPL) version 2, or at your option, any later version, of which a copy is available as `/usr/share/common-licenses/GPL-2'. debian/apbs.10000644000000000000000000000254711230062240010173 0ustar .TH "APBS" "1" "July 2009" "apbs" "User Commands" .SH NAME abps \- Adaptive Poisson Boltzmann Solver .SH SYNOPSIS .B apbs .RB [ options ] .I parameters-file .SH DESCRIPTION The \fBapbs\fR command calculates electrostatic potentials, energies, and forces using both multigrid and finite element methods. .SH OPTIONS At the moment, the following options are supported: .TP .BI \-\-output\-file=< name > Enables output logging to the path listed in <\fIname\fR>. Uses flat-file format if \fB\-\-output\-format\fR is not used. .TP .BI \-\-output\-format=< type > Specifies format for logging. Options for <\fItype\fR> are either "\fIxml\fR" or "\fIflat\fR". .TP .B \-\-help Display this help information. .TP .B \-\-version Display the current \fBapbs\fR version. .SH EXAMPLES .B apbs apbs.in > apbs.out 2> apbs.err .SH CITATION Please cite APBS as follows: .PP .RS 4 Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. .RE .SH "SEE ALSO" For more information read the user guide and/or the tutorial found online at .IR http://apbs.wustl.edu/ . .SH AUTHORS .B apbs was written by Nathan A\. Baker <\&baker@biochem.wustl.edu\&>. .PP This manual page was written by Daniel Leidert <\&daniel.leidert@wgdd.de\&> for the Debian project (but may be used by others). debian/apbs.manpages0000644000000000000000000000001611747327211011632 0ustar debian/apbs.1 debian/source/0000755000000000000000000000000012200742617010467 5ustar debian/source/lintian-overrides0000644000000000000000000000021412200742607014044 0ustar # We don't build contrib/iapbs. Therefor we don't need autotools # and can ignore this warning. apbs source: outdated-autotools-helper-file debian/source/format0000644000000000000000000000001411727120230011667 0ustar 3.0 (quilt) debian/apbs.install0000644000000000000000000000001511747327211011504 0ustar usr/bin/apbs debian/rules0000755000000000000000000000202212200727774010252 0ustar #!/usr/bin/make -f # -*- makefile -*- include /usr/share/mpi-default-dev/debian_defaults export CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS := $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) export CXXFLAGS := $(shell dpkg-buildflags --get CXXFLAGS) $(CPPFLAGS) export LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -Wl,--as-needed %: dh $@ --parallel override_dh_auto_configure: dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=On \ -DBUILD_DOC=Off -DBUILD_TOOLS=Off \ -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_ZLIB=On \ -DENABLE_PYTHON=On -DENABLE_READLINE=Off \ -DFETK_PATH=/usr -DENABLE_FETK=Off override_dh_auto_install: dh_auto_install --destdir=$(CURDIR)/debian/tmp/ override_dh_clean: -(cd $(CURDIR)/build && /bin/bash cleanup.sh) dh_clean override_dh_auto_test: -(cd tests; python apbs_tester.py -c test_cases.cfg) override_dh_install: dh_install --sourcedir=$(CURDIR)/debian/tmp --list-missing override_dh_installchangelogs: dh_installchangelogs ChangeLog debian/watch0000644000000000000000000000014112152373333010215 0ustar # See uscan(1) for format version=3 http://sf.net/apbs/(?i)apbs-([\d\.]+[a-c]?)-source\.tar\.gz debian/patches/0000755000000000000000000000000012200742617010616 5ustar debian/patches/debian_testfiles.patch0000644000000000000000000000413012200735027015136 0ustar Author: Daniel Leidert Description: Don't run very expensive tests. This has been done for a while via debian/patches/03_skip_expensive_tests.patch. . Fix test script to get the dirctories right. --- a/tests/apbs_tester.py +++ b/tests/apbs_tester.py @@ -178,13 +178,15 @@ print "The following sections will be tested: " + ', '.join( test_sections ) print '=' * 80 + current_dir = os.getcwd() + for test_name in test_sections: print "Running tests for " + test_name + " section" if test_name not in config.sections(): print " " + test_name + " section not found in " + options.test_config print " skipping..." continue - test_directory = config.get( test_name, 'input_dir' ) + test_directory = current_dir + "/" + config.get( test_name, 'input_dir' ) config.remove_option( test_name, 'input_dir' ) run_test( binary, config.items( test_name ), test_name, test_directory, logger, options.ocd ) --- a/tests/test_cases.cfg +++ b/tests/test_cases.cfg @@ -6,13 +6,6 @@ apbs-mol-parallel : -2.304918086635E+02 apbs-smol-parallel : -2.293871354771E+02 -[actin-dimer] -input_dir : ../examples/actin-dimer -apbs-mol-auto : 1.048683060915E+02 -apbs-smol-auto : 1.095841074454E+02 -apbs-mol-parallel : 9.817462910199E+01 -apbs-smol-parallel : 1.155422164152E+02 - [alkanes] input_dir : ../examples/alkanes alkanes : 1.439739455792E+01 1.208346456826E+01 1.354016672221E+01 9.363673200142E+00 9.422717598546E+00 1.640068943201E+01 1.323144287435E+01 7.894367190329E+00 1.449633815052E+01 1.447900211546E+01 1.192358496286E+01 @@ -38,13 +31,6 @@ input_dir : ../examples/ion-pmf ion-pmf : -1.125192402906E+03 * -[ion-protein] -input_dir : ../examples/ion-protein -apbs-mol-pdiel2 : 1.559159533685E+01 -apbs-smol-pdiel2 : 2.355542126580E+01 -apbs-mol-pdiel12 : 1.802722643122E+01 -apbs-smol-pdiel12 : 1.928245019838E+01 - [pka-lig] input_dir : ../examples/pka-lig apbs-mol-vdw : 8.083540155785E+00 debian/patches/debian_make.patch0000644000000000000000000000223612200735027014056 0ustar Author: Daniel Leidert Description: Build and use convenience libraries as long as we don't plan to ship libapbs* packages. In such a case we would have to add SOVERSIONs first. . Fix a double inclusion of a directory leading to cmake bailout. --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -32,7 +32,7 @@ message(STATUS "With external header files ${EXTERNAL_HEADERS}") message(STATUS "With internal header files ${INTERNAL_HEADERS}") message(STATUS "With library dependencies ${LIBRARY_DEPENDENCIES}") - add_library(${LIBRARY_NAME} SHARED ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS}) + add_library(${LIBRARY_NAME} STATIC ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS}) target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES}) INSTALL(FILES ${EXTERNAL_HEADERS} DESTINATION ${HEADER_INSTALL_PATH}/${LIBRARY}) INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH}) --- a/tools/CMakeLists.txt +++ b/tools/CMakeLists.txt @@ -1,7 +1,6 @@ set(EXECUTABLE_OUTPUT_PATH ${TOOLS_PATH}/bin) add_subdirectory(mesh) -add_subdirectory(manip) if(ENABLE_PYTHON) add_subdirectory(manip) debian/patches/series0000644000000000000000000000005112200735027012024 0ustar debian_testfiles.patch debian_make.patch debian/upstream0000644000000000000000000000411512200674276010760 0ustar Name: APBS Homepage: http://www.poissonboltzmann.org/apbs Registration: https://spreadsheets.google.com/viewform?hl=en&key=0Asy1jmCqCrVxdE03ekdwVHU5N0R2SGZEZGNLc1lIOUE Reference: - Author: Nathan A. Baker and David Sept and Simpson Joseph and Michael J. Holst and J. Andrew McCammon Title: "Electrostatics of nanosystems: application to microtubules and the ribosome" Journal: Proc. Natl. Acad. Sci. Year: 2001 Volume: 98 Number: 18 Pages: 10037-10041 eprint: http://www.pnas.org/content/98/18/10037.full.pdf URL: http://www.pnas.org/content/98/18/10037.full DOI: 10.1073/pnas.181342398 - Author: Michael Holst and Faisal Saied Title: "Multigrid solution of the Poisson-Boltzmann equation" Journal: J. Comput. Chem. Year: 1993 Volume: 14 Number: 1 Pages: 105-113 eprint: http://www.cam.ucsd.edu/~mholst/pubs/dist/HoSa93a.pdf URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.540140114/abstract DOI: 10.1002/jcc.540140114 - Author: Michael Holst and Faisal Saied Title: "Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods" Journal: J. Comput. Chem. Year: 1995 Volume: 16 Number: 3 Pages: 337-364 eprint: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.10.8477&rep=rep1&type=pdf URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.540160308/abstract DOI: 10.1002/jcc.540160308 - Author: Michael Holst Title: "Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics" Journal: Adv. Comp. Math. Year: 2001 Volume: 15 Number: 1-4 Pages: 139-191 eprint: http://arxiv.org/pdf/1001.1367 URL: http://dx.doi.org/10.1023/A:1014246117321 DOI: 10.1023/A:1014246117321 - Author: Randolph E. Bank and Michael Holst Title: "A New Paradigm for Parallel Adaptive Meshing Algorithms" Journal: SIAM Rev. Year: 2003 Volume: 45 Number: 2 Pages: 291-323 eprint: http://www.ccom.ucsd.edu/~mholst/pubs/dist/BaHo02a.pdf URL: http://dx.doi.org/10.1137/S003614450342061 DOI: 10.1137/S003614450342061 debian/changelog0000644000000000000000000002472412200742613011046 0ustar apbs (1.4-1) unstable; urgency=low * New upstream release. [ Daniel Leidert ] * debian/control (Uploaders): Removed myself. (Standards-Version): Bumped to 3.9.4. (Vcs-Browser, Vcs-Svn): Fixed vcs-field-not-canonical. (DM-Upload-Allowed): Dropped. (Build-Depends): Dropped all autotools related build dependencies, libarpack2-dev, libblas-dev and bc. Added cmake, libpython-dev and zlib1g-dev. * debian/copyright: Updated. * debian/rules: Enable hardening. Dropped all autotools related stuff and rewrote it for cmake build system. * debian/watch: Make regex case insensitive. * debian/patches/03_skip_expensive_tests.patch: Dropped. Upstream changed to cmake. * debian/patches/06_quicktest.patch: Ditto. * debian/patches/07_destdir.patch: Ditto. * debian/patches/08_distclean.patch: Ditto. * debian/patches/09_acinclude_fix.patch: Ditto. * debian/patches/debian_make.patch: Added. - Compile internal libraries statically into apbs. * debian/patches/debian_testfiles.patch: Added. - Skip expensive tests (see 03_skip_expensive_tests.patch). * debian/patches/series: Adjusted. [ Andreas Tille ] * debian/upstream: Author field in BibTeX syntax -- Debichem Team Thu, 08 Aug 2013 18:21:30 +0200 apbs (1.3.0-2) unstable; urgency=low * debian/apbs.install: Adjusted. * debian/apbs.manpages: Added to fix binary-without-manpage. * debian/compat: Increased dh level to 7. * debian/control: Used wrap-and-sort. (Standards-Version): Bumped to recent 3.9.3. (Build-Depends): Removed unused cdbs. Added autotools-dev version requirements. Lowered required debhelper version. (Vcs-Browser): Fixed. * debian/copyright: Updated. Removed BSD license file reference to fix copyright-refers-to-deprecated-bsd-license-file. * debian/rules: Run autotools_dev template. Added override target for dh_install. Added target to install upstream changelog file. * debian/upstream: Added. * debian/README.source: Dropped obsolete file. * debian/patches/*.patch: Updated for quilt. * debian/patches/04_remove_install-exec-am_rule.patch: Dropped. Moved patch content to 07_destdir.patch. * debian/patches/series: Adjusted. -- Daniel Leidert (dale) Sun, 29 Apr 2012 23:35:09 +0200 apbs (1.3.0-1) unstable; urgency=low * New upstream release. [ Daniel Leidert (dale) ] * debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Don't build nor link against shipped copy of zlib. [ Michael Banck ] * Switch packaging to "3.0 (quilt)" format. * debian/rules: Rewritten for dh. * debian/control (Build-Depends): Removed quilt, bumped required debhelper version to 8. * debian/apbs.install: Install apbs executable explicitly. * debian/patches/07_destdir.patch: New patch, fixes DESTDIR in python setup.py installation in a contributed module. * debian/control (Build-Depends): Added dh-autoreconf, autoconf and automake. * debian/rules: Use --with autoreconf. * debian/rules (override_dh_auto_clean): Run make distclean in examples directory and remove all uncleaned Makefiles. * debian/patches/08_distclean.patch: New patch, fixes Makefile.am in various directories to clean all relevant files on make distclean. * debian/patches/09_acinclude_fix.patch: New patches, rewrites some m4 macros so that recent autoconf versions do not produce faulty shell code, taken from Gentoo. * debian/control (Build-Depends): Added python-setuptools. -- Michael Banck Sun, 11 Mar 2012 19:12:24 +0100 apbs (1.2.1b-1) unstable; urgency=low * New upstream (bugfix) release. * debian/control (Standards-Version): Bumped to 3.8.3. (Build-Depends): Replace libmpich1.0-dev with mpi-default-dev. * debian/rules: Added list-missing target. (DEB_CONFIGURE_EXTRA_FLAGS, DEB_CONFIGURE_SCRIPT_ENV): Use the default MPI implementation for the architecture. * debian/watch: Slightly adjusted for upstream version schema. -- Daniel Leidert (dale) Sun, 13 Dec 2009 15:59:00 +0100 apbs (1.1.0-1) unstable; urgency=low * New upstream release. * debian/apbs.1: Added citation section. (SEE ALSO): User guide is not available locally anymore. * debian/apbs.doc-base, debian/apbs.dirs: Dropped useless files. * debian/apbs.install: Removed documentation files, because the user guide is not shipped anymore (closes: #508980). The lintian overrides are considered by dh_lintian. * debian/control (Uploaders): Removed LI as requested. Thanks for your work! (Build-Depends): Re-added arpack, which is back in main. (Standards-Version): Bumped to 3.8.2 (no other changes). (Vcs-Svn): Fixed vcs-field-uses-not-recommended-uri-format. * debian/copyright: Updated and completed. * debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Build with arpack. * debian/README.source: Added to comply to policy. * debian/lintian-overrides/apbs: Dropped. License file is not installed anymore. * debian/patches/01_html_documentation.dpatch: Dropped, as there is no documentation installed anymore. * debian/patches/04_remove_install-exec-am_rule.dpatch: Updated/adjusted. * debian/patches/05_reduce_test_suite.dpatch: Dropped (cannot be applied anymore). * debian/patches/00list: Adjusted. -- Daniel Leidert (dale) Fri, 17 Jul 2009 19:06:05 +0200 apbs (1.0.0-2) unstable; urgency=low * debian/patches/06_quicktest.dpatch: New patch, add a `quicktest' target which only runs a couple of small tests. * debian/rules (DEB_MAKE_CHECK_TARGET): Run quicktest instead of test for now. * debian/control (Build-Depends): Removed libarpack2-dev. (closes: #497722) * debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Removed --with-arpack. -- Michael Banck Thu, 04 Sep 2008 00:00:41 +0200 apbs (1.0.0-1) unstable; urgency=low * New upstream release. + No longer contains a corrupted tarball (closes: #473822). * debian/patches/04_remove_install-exec-am_rule.dpatch: Refreshed. * debian/patches/05_reduce_test_suite.dpatch: New patch, remove most of the coordinates for the ion test to save time (closes: 475064). -- Michael Banck Tue, 10 Jun 2008 14:25:47 +0200 apbs (0.5.1-2) unstable; urgency=low * Acknowledge NMU 0.5.1-1.1 (closes: #462263). Thanks to Colin Tuckley. [ Daniel Leidert ] * debian/apbs.1: Added. * debian/apbs.doc-base (Section): Adjusted accordingly to latest doc-base policy. * debian/apbs.install: Install lintian override. * debian/compat: Raised to level 5. * debian/control: Homepage field transition. Added Vcs fields. Added DM-Upload-Allowed field for DM status. (Maintainer): Set to the debichem team address. Moved Michael to Uploaders. (Uploaders): Added myself and LI Daobing. (Standards-Version): Updated to latest 3.7.3 (no other changes). (Build-Depends): Raised debhelper to v5. Added libarpack2-dev. Added libmpich1.0-dev for MPI support. Added python-minimal for some tests. * debian/copyright: Fixed old-fsf-address-in-copyright-file issue. Updated copyright information. Added exception. * debian/rules: Install the newly added apbs.1 manpage. (DEB_CONFIGURE_EXTRA_FLAGS): Enable building with arpack (not useful atm without tools). Set prefix. (DEB_CONFIGURE_EXTRA_FLAGS, DEB_CONFIGURE_SCRIPT_ENV): Enable MPI. (DEB_MAKE_INSTALL_TARGET): Only install from bin/ as long as we don't use the rest. * debian/watch: Updated to fit new source archive naming. * debian/lintian-overrides/apbs: Added. The documentation contains the license in several formats. [ LI Daobing ] * FTBFS if built twice in a row (Closes: #424100) -- Daniel Leidert (dale) Mon, 10 Mar 2008 08:46:53 +0100 apbs (0.5.1-1.1) unstable; urgency=low * Non-maintainer upload * Build depend on libblas-dev instead of refblas3-dev (closes: #462263) * Add gfortran to Build Depends: to fix FTBFS in clean chroot -- Colin Tuckley Mon, 28 Jan 2008 11:05:21 +0000 apbs (0.5.1-1) unstable; urgency=low * New upstream release. [ Daniel Leidert ] * debian/control (Build-Depends): Added dpatch and autotools-dev. (Standards-Version): Changed to latest standards version 3.7.2. (Description): Added Homepage field. * debian/copyright: Fixed download location after apbs has been moved to sourceforge.net. * debian/rules: Changed to use dpatch.mk instead of simple-patchsys.mk. Added buildcore.mk ruleset. Added FFLAGS flags to configure. * debian/watch: Added. * debian/patches/01_html_documentation.dpatch: Added. Replaces debian/patches/01_html_docu.patch. * debian/patches/02_remove_vf2c.dpatch: Added. Replaces debian/patches/02_remove_vf2c.patch. * debian/patches/90_autoreconf.dpatch: Added. Replaces debian/patches/90_autoreconf.patch. Probably closes: #424100. * debian/patches/00list: Added. [ Michael Banck ] * debian/patches/01_html_documentation: Updated. * debian/patches/02_remove_vf2c: Removed; no longer needed. * debian/patches/90_autoreconf: Likewise. * debian/control (Build-Depends): Added bc, needed for the test suite. * debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Added --with-fetk-include=/usr/include --with-fetk-library=/usr/lib --with-blas=-lblas. * debian/rules (DEB_MAKE_CHECK_TARGET): New target, run the test suite. * debian/patches/03_skip_expensive_tests.dpatch: New patch, skip tests which take a lot of memory and CPU. * debian/patches/04_remove_install-exec-am_rule.dpatch: New patch, remove the install-exec-am rule from the top-level Makefile. We can just install that data manually and it does not support DESTDIR anyway. * debian/apbs.install: Updated location of the user's guide and tutorial in the source tree. Install license.html as well. -- Michael Banck Wed, 18 Jul 2007 15:48:58 +0200 apbs (0.4.0-2) unstable; urgency=low * debian/patches: New directory, manage changes to upstream with simple-patchsys.mk. * debian/patches/01_html_docu.patch: New patch, supress link to the programmer's manual we don't ship for now. * debian/patches/02_remove_vf2c.patch: New patch, remove MALOC's own -lvf2c f2c fork from linking. * debian/patches/90_autoreconf.patch: Update libtool; closes: #378211. -- Michael Banck Sun, 10 Sep 2006 19:14:24 +0200 apbs (0.4.0-1) unstable; urgency=low * Initial release. -- Michael Banck Thu, 29 Jun 2006 17:10:18 +0200 debian/control0000644000000000000000000000320212200722036010560 0ustar Source: apbs Section: science Priority: optional Maintainer: Debichem Team Uploaders: Michael Banck Build-Depends: cmake, debhelper (>> 7.0.50~), libmaloc-dev, libpython-dev, mpi-default-dev (>= 0.3), python-minimal (>> 2.6.6-3~), python-setuptools, zlib1g-dev Standards-Version: 3.9.4 Homepage: http://apbs.sourceforge.net Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/unstable/apbs/ Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/apbs/ Package: apbs Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. debian/compat0000644000000000000000000000000211747327211010371 0ustar 7