debian/0000755000000000000000000000000012232157073007170 5ustar debian/psize.1.xml0000644000000000000000000001146711363556231011217 0ustar psize"> ]> PDB2PQR Manual 2008-06-04 psize ManuelPrinz Wrote this manpage for the Debian System.
debian@pinguinkiste.de
 2008Manuel Prinz psize 1 psize Get dimensions and other information from PQR files psize psize DESCRIPTION &psize; derives information from PQR files to preprare the models of proteins and chemicals for electrostatics calculations. The tool calculates dimensions for coarse and fine grids, grid spacings, box size and estimates the memory required to perform an electrostatics calculation. The calculation of this information can be influenced by giving constraints to &psize; as parameters. OPTIONS &psize; accepts the following options: Print a help message and exit. Factor by which to expand the molecule dimensions to get the coarse grid dimensions Amount to add to the molecule dimensions to get the fine grid dimensions. Desired fine mesh resolution. Number of bytes per grid point required for sequential MG calculation. Maximum MB allowed for sequential MG calculation. Adjust this to force the script to perform faster calculations (which require more parallelism). Overlap factor between mesh partitions. Maximum factor by which a domain dimension can be reduced during focusing. SEE ALSO apbs1, pdb2pqr1 debian/control0000644000000000000000000000437612232147005010577 0ustar Source: pdb2pqr Maintainer: Debian Med Uploaders: Steffen Moeller , Manuel Prinz , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), gfortran, swig, xmlto, openbabel, autoconf, automake, libtool, autotools-dev, python-dev, python-numpy Standards-Version: 3.9.4 XS-Python-Version: 2.7 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/pdb2pqr/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/pdb2pqr/trunk/ Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/ Package: pdb2pqr XB-Python-Version: ${python:Versions} Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy Suggests: apbs Enhances: autodocktools Conflicts: propka Provides: propka Replaces: propka 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. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: * Adding a limited number of missing heavy atoms to biomolecular structures * Determining side-chain pKas * Placing missing hydrogens * Optimizing the protein for favorable hydrogen bonding * Assigning charge and radius parameters from a variety of force fields . This package also includes PropKa, a tool to modify the protonation state of protein structures in the Protein Data Bank (PDB) format to match a given pKa value. It can also be used to refine NMR structures, which often yield inaccurate pKa values for some residues. Package: pdb2pqr-doc Architecture: all Section: doc Depends: ${misc:Depends} Recommends: pdb2pqr Description: example files accompanying pdb2pqr Files containing protein structures tend to become large very quickly and most users of this package will refrain from their installation, particularly on larger clusters. debian/pdb2pqr-doc.docs0000644000000000000000000000010311024213155012141 0ustar doc/userguide.html doc/programmerguide.html doc/images/ doc/pydoc/ debian/wrapper.sh0000644000000000000000000000014711017563377011216 0ustar #!/bin/sh app=@SCRIPT@ if [ -x $app ]; then $app $* else echo "No executable at '$app'." exit -1 fi debian/rules0000755000000000000000000000553612232155411010253 0ustar #!/usr/bin/make -f # -*- mode: makefile; coding: utf-8 -*- PACKAGE := $(firstword $(shell dh_listpackages)) VERSION := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }') UPSTREAM := $(shell echo "$(VERSION)" | sed 's/-.\+$$//') # Compile with -fPIC on all platforms (fix for #636204, #654240) export DEB_CFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/include/numpy export DEB_CPPFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/include/numpy export DEB_CXXFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/include/numpy export DEB_FFLAGS_MAINT_APPEND = -fPIC %: dh $@ --with python2 --with autotools_dev override_dh_auto_clean: ( cd pdb2pka && \ if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \ if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi ) dh_auto_clean override_dh_auto_configure: dh_auto_configure ( cd pdb2pka && \ cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \ cp -a pMC_mult.py pMC_mult.py.saved && \ swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i ) # Disable tests, as they need an internet connection to download files override_dh_auto_test: override_dh_auto_install: # Install Debian-provided stuff # Install wrappers for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \ sed -e "s,@SCRIPT@,$${app}," debian/wrapper.sh \ >debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \ chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \ done for app in /usr/share/pdb2pqr/propka30/propka.py; do \ sed -e "s,@SCRIPT@,$${app}," debian/wrapper.sh \ >debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \ chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \ done # Install man pages xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/propka.1.xml # dh_auto_install override_dh_fixperms: dh_fixperms chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py chmod 0755 debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py # Remark: The following uscan command requires devscripts > 2.12.4 which is not # yet released at the time of this package release. The code can be obtained # via # git clone git://tille@git.debian.org/git/users/tille/devscripts.git # and then use scripts/uscan.pl get-orig-source: uscan --verbose --force-download --repack-compression xz debian/pdb2pqr.links0000644000000000000000000000037511770626763011626 0ustar usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so #usr/lib/pdb2pqr/propka/_propkalib.so usr/share/pdb2pqr/propka/_propkalib.so debian/watch0000644000000000000000000000014112232152264010212 0ustar version=3 opts=dversionmangle=s/[~+]dfsg[0-9]*// \ http://sf.net/pdb2pqr/pdb2pqr-(.*)\.tar\.gz debian/pdb2pqr.docs0000644000000000000000000000003611521107747011416 0ustar AUTHORS ChangeLog NEWS README debian/pdb2pqr-doc.doc-base0000644000000000000000000000041011521113111012660 0ustar Document: pdb2pqr Title: PDB2PQR User Guide Author: Nathan Baker and others Abstract: This guide explains the use of PDB2PQR Section: Science/Chemistry Format: HTML Index: /usr/share/doc/pdb2pqr-doc/userguide.html Files: /usr/share/doc/pdb2pqr-doc/userguide.html debian/upstream0000644000000000000000000000313111757452051010756 0ustar Name: PDB2PQR Homepage: http://www.poissonboltzmann.org/pdb2pqr Registration: http://spreadsheets.google.com/viewform?hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA.. Reference: - Author: Todd J Dolinsky and Paul Czodrowski and Hui Li and Jens E Nielsen and Jan H Jensen and Gerhard Klebe and Nathan A Baker Title: "PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations" Journal: Nucleic Acids Research Year: 2007 Volume: 35 Pages: W522-5 DOI: 10.1093/nar/gkm276 PMID: 17488841 URL: http://nar.oxfordjournals.org/content/35/suppl_2/W522 eprint: http://nar.oxfordjournals.org/content/35/suppl_2/W522.full.pdf+html - Author: Todd J Dolinsky and Jens E Nielsen and J Andrew McCammon and Nathan A Baker Title: "PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations" Journal: Nucleic Acids Research Year: 2004 Volume: 32 Pages: W665-W667 DOI: 10.1093/nar/gkh381 PMID: 15215472 URL: http://nar.oxfordjournals.org/content/32/suppl_2/W665.abstract eprint: http://nar.oxfordjournals.org/content/32/suppl_2/W665.full.pdf+html - Debian-Package: propka Author: Hui Li and Andrew D Robertson and Jan H Jensen Title: Very fast empirical prediction and rationalization of protein pKa values Journal: Proteins Year: 2005 Volume: 61 Number: 4 Pages: 704-21 DOI: 10.1002/prot.20660 PMID: 16231289 URL: http://onlinelibrary.wiley.com/doi/10.1002/prot.20660/abstract eprint: http://onlinelibrary.wiley.com/doi/10.1002/prot.20660/pdf debian/copyright0000644000000000000000000001206612232151601011117 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: pdb2pqr Source: http://sourceforge.net/projects/pdb2pqr/ Files-Excluded: contrib/ jmol/ Files: * Copyright: © 2002-2010 Nathan A. Baker © 2009 Tommy Carstensen © 2004 becker © 2006 Mike Bradley © 1999-2004 Cambridge Crystallographic Data Centre © 2009 Tommy Carstensen © 2002-2010 Paul Czodrowski © 2005-2010 Todd Dolinsky © 2000 EMBL © 1992-2008 Free Software Foundation, Inc. © 1993 Noah Friedman © 2010 Wes Goodman © David J. Heisterberg © 1994-2000 Michael Holst © 2007-2010 Yong Huang © 2004-2005 Hui Li © 2005,2010 Jan H. Jensen © 2000-2010 Gerhard Klebe © 2000-2004 Daniel Kuhn © 2010 Predrag Kukic (kukaq) © 2006 Jan Labanowski © 1991 Massachusetts Institute of Technology © 2007 Julie C. Mitchell © 2002-2010 Jens Erik Nielsen © The Ohio Supercomputer Center, Columbus © 2004 Philipps-University, Marburg © J. Ren © 2000-2004 Stefan Schmitt © 2008 Dave Sept © 2002-2003 UCSD/HHMI © 2003-2008 University College Dublin © 2007-2010 Samir Unni © 2004-2007 Washington University St. Louis © 2004 Nils Weskamp License: BSD3-clause All rights reserved. . 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 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. . 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. Files: propka30/* Copyright: © 2011-2012 Mats H. M. Olsson © 2011-2012 Chresten R. Sondergard License: LGPL2.1+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library 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 Lesser General Public License for more details. . On Debian systems, you can find a copy of the LGPL license in /usr/share/common-licenses/LGPL-2.1. Files: pdb2pka/substruct/clique/* Copyright: © 2010-2011 Andrew Dalke License: GPL2+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This library 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 Library General Public License for more details. . On Debian systems, the complete text of the GNU Library General Public License can be found in /usr/share/common-licenses/GPL-2. Files: debian/* Copyright: © 2007-2010 Steffen Moeller © 2010-2012 Manuel Prinz © 2013 Andreas Tille License: GPL You can find a copy of the GPL text at `/usr/share/common-licenses/GPL'. debian/pdb2pqr.1.xml0000644000000000000000000002146211260414455011430 0ustar pdb2pqr"> ]> PDB2PQR Manual 2008-06-04 pdb2pqr ManuelPrinz Wrote this manpage for the Debian System.
debian@pinguinkiste.de
 2008Manuel Prinz pdb2pqr 1 pdb2pqr Generate PQR files for use in electrostatics calculations pdb2pqr pdb2pqr DESCRIPTION &pdb2pqr; automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a utility for converting protein files in PDB format (path) to PQR format (output-path). These tasks include: Adding a limited number of missing heavy atoms to biomolecular structures Determining side-chain pKas Placing missing hydrogens Optimizing the protein for favorable hydrogen bonding Assigning charge and radius parameters from a variety of force fields OPTIONS &pdb2pqr; accepts the following options: The forcefield to use. Current values are , , and . Print a help message and exit. Do not perform debumping operation. Do not perform hydrogen optimization. Keep the chain ID in the output PQR file. Only assigns charges to add atoms, debump, or optimize. Do no optimization, atom addition, or parameter assignment, just return the original PDB file in alligned format. Instead of using the standard caninical naming scheme for residue and atom names, use the names from the given forcefield. Use propka to calculate pKas and apply them to the molecule given the pH value. Actual PropKa results will be output to output-path.propka. Create an APBS input file based on the generated PQR file. Also create a Python pickle for using these parameters in other programs. Calculate the parameters for the ligand in MOL2 format at the given path. Pdb2pka must be compiled. Print additional information to screen. EXTENSIONS Extensions add functionality to PDB2PQR and are called by passing a parameter to &pdb2pqr;. They put their results into files located in output-path. The following extensions can be used by &pdb2pqr;: Print the per-residue backbone phi angle to output-path.phi. Print the per-residue backbone psi angle to output-path.phi. Print a list of hygrogen bonds to output-path.hbond. Print the per-residue backbone chi angle to output-path.chi. Print a list of contacts to output-path.con. Print a list of hydrogen bonds to output-path.hbo. Print a list of salt bridges to output-path.salt. Print the per-residue phi and psi angles to outpath-path.rama. CITING PDB2PQR Please acknowledge your use of &pdb2pqr; by citing: Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32, W665-W667 (2004). SEE ALSO psize1 debian/source/0000755000000000000000000000000011770632246010476 5ustar debian/source/format0000644000000000000000000000001411363557767011720 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000075111770626763011251 0ustar PROPKA ====== PDB2PQR can use PROPKA to protonate the structure it converts. PROPKA is packaged along with the PDB2PQR in this package. -- Manuel Prinz Thu, 21 Jun 2012 15:57:01 +0200 Web Service =========== The Debian package of PDB2PQR currently does not provide the parts that are necessary to run PDB2PQR as a web service. If you think that the PDB2PQR web service should be available as a package, please file a wishlist bug. -- Manuel Prinz Sat, 29 Jan 2011 22:53:19 +0100 debian/pdb2pqr-doc.examples0000644000000000000000000000001311023001605013021 0ustar examples/* debian/changelog0000644000000000000000000000335212232156733011047 0ustar pdb2pqr (1.8+dfsg-1) unstable; urgency=low [ Manuel Prinz ] * Fixed build issues on HURD. Thanks to Barry deFreese for the patch! Closes: 674976. * Pass hardening flags to linker. Added fix-hardening.patch, changed debian/rules. [ Andreas Tille ] * Use '+dfsg' appendix to mark repackaged upstream source (adapted debian/watch) * debian/rules: - repackaging is done using enhanced uscan - s/autotools-dev/autotools_dev/ Closes: #727491 * debian/control: - cme fix dpkg-control - canonical Vcs fields * debian/copyright: DEP5 -- Andreas Tille Thu, 24 Oct 2013 09:34:23 +0200 pdb2pqr (1.8-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add publication information [ Manuel Prinz ] * New upstream version. Updated debian/copyright. * Updated Standards-Version to 3.9.3. No changes needed. * Changed Maintainer to Debian Med team. * Pass -fPIC to CXXFLAGS. Thanks to Konstantinos Margaritis for the patch! Closes: 654240. LP: 935357. * Updated PROPKA packaging to new version. (It's written in Python now.) * Added fix-hashbangs.patch. * Merged pdb2pqr and propka packages as they are more interconnected since this upstream version. Updated README.Debian accordingly. -- Manuel Prinz Thu, 21 Jun 2012 16:21:50 +0200 pdb2pqr (1.7-2) unstable; urgency=low * Pass -fPIC to compiler on all architectures. Closes: 636204. LP: 791313. * Bumped Standards-Version to 3.9.2. No changes needed. -- Manuel Prinz Wed, 31 Aug 2011 00:22:15 +0200 pdb2pqr (1.7-1) unstable; urgency=low * New upstream release. Closes: #416269, #420734. -- Manuel Prinz Sun, 30 Jan 2011 11:53:54 +0100 debian/pdb2pqr.install0000644000000000000000000000103011770626763012141 0ustar pdb2pqr.py usr/share/pdb2pqr/ main.py usr/share/pdb2pqr/ main_cgi.py usr/share/pdb2pqr/ dat/* usr/share/pdb2pqr/dat/ extensions/* usr/share/pdb2pqr/extensions/ src/* usr/share/pdb2pqr/src/ pdb2pka/*.py usr/share/pdb2pqr/pdb2pka pdb2pka/ligandclean/*.py usr/share/pdb2pqr/pdb2pka/ligandclean pdb2pka/substruct/*.py usr/share/pdb2pqr/pdb2pka/substruct propka30/* usr/share/pdb2pqr/propka30/ # Binary parts pdb2pka/_pMC_mult.so usr/lib/pdb2pqr/pdb2pka pdb2pka/substruct/Algorithms.so usr/lib/pdb2pqr/pdb2pka/substruct debian/patches/0000755000000000000000000000000012232146060010611 5ustar debian/patches/fix-hashbangs.patch0000644000000000000000000000156411770624213014371 0ustar Subject: Fixes "broken" hashbangs From: Manuel Prinz Last-Update: 2012-06-21 --- pdb2pqr-1.8.repack.orig/pdb2pka/inputgen_pKa.py +++ pdb2pqr-1.8.repack/pdb2pka/inputgen_pKa.py @@ -1,4 +1,4 @@ -#!/bin/env python +#!/usr/bin/python # # $Id: inputgen_pKa.py 974 2011-06-30 14:58:03Z jens_nielsen $ # --- pdb2pqr-1.8.repack.orig/propka30/Source/corresponding_atoms.py +++ pdb2pqr-1.8.repack/propka30/Source/corresponding_atoms.py @@ -1,4 +1,4 @@ -#!/usr/local/bin/python3.0 +#!/usr/bin/python # # * This library is free software; you can redistribute it and/or --- pdb2pqr-1.8.repack.orig/propka30/Source/rotate.py +++ pdb2pqr-1.8.repack/propka30/Source/rotate.py @@ -1,4 +1,4 @@ -#!/usr/local/bin/python3.0 +#!/usr/bin/python # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public debian/patches/fix-hurd.patch0000644000000000000000000000060512214301110013346 0ustar Subject: Fix build issues on HURD From: Barry deFreese Last-Update: 2012-05-29 --- pdb2pqr-1.8.repack.orig/configure +++ pdb2pqr-1.8.repack/configure @@ -3297,6 +3297,8 @@ PY_LDFLAGS="-lF77 -lm -lM77 -lsunmath";; darwin*) PY_LDFLAGS="${LDFLAGS} -Wl,-framework -Wl,Python -bundle";; + gnu*) + PY_SHARED="-shared";; esac case $host_cpu in debian/patches/fix-includes.patch0000644000000000000000000000073611521241022014224 0ustar Subject: Fixes a build issue due to a wrong #include directive From: Manuel Prinz Last-Update: 2011-01-30 --- a/pdb2pka/substruct/Algorithms.cpp +++ b/pdb2pka/substruct/Algorithms.cpp @@ -40,7 +40,7 @@ #include "Python.h" #include "clique/bk.h" #include "clique/util.h" -#include "arrayobject.h" +#include "numpy/arrayobject.h" //#include "smiles.h" /*----------------------------------------------------------------------------*/ using namespace std; debian/patches/series0000644000000000000000000000011212214301110012005 0ustar fix-includes.patch fix-hashbangs.patch fix-hurd.patch fix-hardening.patch debian/patches/fix-hardening.patch0000644000000000000000000000042612214301110014344 0ustar Subject: Pass LDFLAGS to the linker for hardening From: Manuel Prinz Last-Update: 2012-06-22 --- a/configure +++ b/configure @@ -3308,7 +3308,7 @@ PY_SHARED=$PY_SHARED -PY_LDFLAGS=$PY_LDFLAGS +PY_LDFLAGS="$PY_LDFLAGS $LDFLAGS" PY_HEADER=$PY_HEADER debian/compat0000644000000000000000000000000211770626763010403 0ustar 9 debian/propka.1.xml0000644000000000000000000000466511025265612011356 0ustar propka"> ]> PROPKA Manual 2008-06-15 propka ManuelPrinz Wrote this manpage for the Debian System.
debian@pinguinkiste.de
 2008Manuel Prinz propka 1 propka Protonate PDB files based on pKa propka DESCRIPTION &propka; automates the protonation (positioning of hydrogen ions) to a structure in PDB format for any given pKa value. The file to use has to be named PROPKATMP1 in the directory where propka is run. &propka; will generate two output files named PROPKATMP2 and PROPKATMP3. PROPKATMP2 contains the resulting structure in PDB format. PROPKATMP3 contains a summary of the &propka; run. CITING PROPKA Please acknowledge your use of &propka; by citing: Hui Li, Andrew D. Robertson, and Jan H. Jensen: Very Fast Empirical Prediction and Interpretation of Protein pKa Values, Proteins, 2005, 61, 704-721. WEB SERVICE PropKa can be used via a web interface at http://propka.ki.ku.dk/. SEE ALSO pdb2pqr1 debian/pdb2pqr.dirs0000644000000000000000000000041311770626763011440 0ustar /usr/bin /usr/lib/pdb2pqr/pdb2pka/substruct /usr/share/doc/pdb2pqr /usr/share/man/man1 /usr/share/pdb2pqr/dat /usr/share/pdb2pqr/extensions /usr/share/pdb2pqr/pdb2pka/ligandclean /usr/share/pdb2pqr/pdb2pka/substruct /usr/share/pdb2pqr/propka30 /usr/share/pdb2pqr/src debian/pycompat0000644000000000000000000000000210734326726010747 0ustar 2