pdb2pqr_2.1.1+dfsg-4build1_amd64.deb


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Description

pdb2pqr - Preparation of protein structures for electrostatics calculations

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename pdb2pqr_2.1.1+dfsg-4build1_amd64.deb
Package name pdb2pqr
Package version 2.1.1+dfsg
Package release 4build1
Package architecture amd64
Package type deb
Category universe/science
Homepage https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 370.61 KB
Installed size 2.78 MB
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.

Alternatives

Package Version Architecture Repository
pdb2pqr_2.1.1+dfsg-4build1_i386.deb 2.1.1+dfsg i386 Ubuntu Universe
pdb2pqr - - -

Requires

Name Value
libc6 >= 2.14
libgcc1 >= 1:3.0
libpython2.7 >= 2.7
libstdc++6 >= 5.2
python-networkx -
python-numpy -
python:any >= 2.6.6-7~

Provides

Name Value
propka -

Replaces

Name Value
propka -

Download

Type URL
Mirror archive.ubuntu.com
Binary Package pdb2pqr_2.1.1+dfsg-4build1_amd64.deb
Source Package pdb2pqr

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install pdb2pqr deb package:
    # sudo apt-get install pdb2pqr

Files

Path
/usr/bin/pdb2pqr
/usr/bin/propka
/usr/bin/psize
/usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so
/usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so
/usr/share/doc/pdb2pqr/AUTHORS
/usr/share/doc/pdb2pqr/NEWS.gz
/usr/share/doc/pdb2pqr/README.Debian
/usr/share/doc/pdb2pqr/README.md
/usr/share/doc/pdb2pqr/changelog.Debian.gz
/usr/share/doc/pdb2pqr/copyright
/usr/share/man/man1/pdb2pqr.1.gz
/usr/share/man/man1/propka.1.gz
/usr/share/man/man1/psize.1.gz
/usr/share/pdb2pqr/main.py
/usr/share/pdb2pqr/main_cgi.py
/usr/share/pdb2pqr/pdb2pqr.py
/usr/share/pdb2pqr/pka.py
/usr/share/pdb2pqr/dat/AA.xml
/usr/share/pdb2pqr/dat/AMBER.DAT
/usr/share/pdb2pqr/dat/AMBER.names
/usr/share/pdb2pqr/dat/CHARMM.DAT
/usr/share/pdb2pqr/dat/CHARMM.names
/usr/share/pdb2pqr/dat/HYDROGENS.xml
/usr/share/pdb2pqr/dat/NA.xml
/usr/share/pdb2pqr/dat/PARSE.DAT
/usr/share/pdb2pqr/dat/PARSE.names
/usr/share/pdb2pqr/dat/PATCHES.xml
/usr/share/pdb2pqr/dat/PEOEPB.DAT
/usr/share/pdb2pqr/dat/PEOEPB.names
/usr/share/pdb2pqr/dat/SWANSON.DAT
/usr/share/pdb2pqr/dat/SWANSON.names
/usr/share/pdb2pqr/dat/TOPOLOGY.xml
/usr/share/pdb2pqr/dat/TYL06.DAT
/usr/share/pdb2pqr/dat/TYL06.names
/usr/share/pdb2pqr/extensions/README
/usr/share/pdb2pqr/extensions/__init__.py
/usr/share/pdb2pqr/extensions/chi.py
/usr/share/pdb2pqr/extensions/contact.py
/usr/share/pdb2pqr/extensions/hbond.py
/usr/share/pdb2pqr/extensions/newresinter.py
/usr/share/pdb2pqr/extensions/rama.py
/usr/share/pdb2pqr/extensions/resinter.py
/usr/share/pdb2pqr/extensions/salt.py
/usr/share/pdb2pqr/extensions/summary.py
/usr/share/pdb2pqr/extensions/template
/usr/share/pdb2pqr/pdb2pka/NEWligand_topology.py
/usr/share/pdb2pqr/pdb2pka/__init__.py
/usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
/usr/share/pdb2pqr/pdb2pka/apbs.py
/usr/share/pdb2pqr/pdb2pka/charge_mon.py
/usr/share/pdb2pqr/pdb2pka/example.py
/usr/share/pdb2pqr/pdb2pka/inputgen_pKa.py
/usr/share/pdb2pqr/pdb2pka/ligand_topology.py
/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
/usr/share/pdb2pqr/pdb2pka/pKa_base.py
/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
/usr/share/pdb2pqr/pdb2pka/pMC_mult.py
/usr/share/pdb2pqr/pdb2pka/pka_help.py
/usr/share/pdb2pqr/pdb2pka/pka_old.py
/usr/share/pdb2pqr/pdb2pka/pka_routines.py
/usr/share/pdb2pqr/pdb2pka/prepare_pKa_ligand.py
/usr/share/pdb2pqr/pdb2pka/graph_cut/__init__.py
/usr/share/pdb2pqr/pdb2pka/graph_cut/create_titration_output.py
/usr/share/pdb2pqr/pdb2pka/graph_cut/graph.py
/usr/share/pdb2pqr/pdb2pka/graph_cut/protein_complex.py
/usr/share/pdb2pqr/pdb2pka/graph_cut/titration_curve.py
/usr/share/pdb2pqr/pdb2pka/graph_cut/uncertainty.py
/usr/share/pdb2pqr/pdb2pka/graph_cut/utils.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/ligff.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/lookuptable.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/peoe_PDB2PQR.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/templates.py
/usr/share/pdb2pqr/pdb2pka/ligandclean/trial_templates.py
/usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
/usr/share/pdb2pqr/pdb2pka/substruct/__init__.py
/usr/share/pdb2pqr/propka30/__init__.py
/usr/share/pdb2pqr/propka30/compare.py
/usr/share/pdb2pqr/propka30/experiment.py
/usr/share/pdb2pqr/propka30/propka.py
/usr/share/pdb2pqr/propka30/propka_det.py
/usr/share/pdb2pqr/propka30/propka_gui.py
/usr/share/pdb2pqr/propka30/propka_mut.py
/usr/share/pdb2pqr/propka30/propka_pdb.py
/usr/share/pdb2pqr/propka30/Source/__init__.py
/usr/share/pdb2pqr/propka30/Source/bonds.py
/usr/share/pdb2pqr/propka30/Source/calculator.py
/usr/share/pdb2pqr/propka30/Source/chain.py
/usr/share/pdb2pqr/propka30/Source/compare.py
/usr/share/pdb2pqr/propka30/Source/corresponding_atoms.py
/usr/share/pdb2pqr/propka30/Source/coupled_residues.py
/usr/share/pdb2pqr/propka30/Source/debug.py
/usr/share/pdb2pqr/propka30/Source/determinant.py
/usr/share/pdb2pqr/propka30/Source/determinants.py
/usr/share/pdb2pqr/propka30/Source/ions.list
/usr/share/pdb2pqr/propka30/Source/iterative.py
/usr/share/pdb2pqr/propka30/Source/lib.py
/usr/share/pdb2pqr/propka30/Source/ligand.py
/usr/share/pdb2pqr/propka30/Source/mutate.py
/usr/share/pdb2pqr/propka30/Source/output.py
/usr/share/pdb2pqr/propka30/Source/parameters.py
/usr/share/pdb2pqr/propka30/Source/parameters_new.py
/usr/share/pdb2pqr/propka30/Source/parameters_std.py
/usr/share/pdb2pqr/propka30/Source/pdb.py
/usr/share/pdb2pqr/propka30/Source/protein.py
/usr/share/pdb2pqr/propka30/Source/protein_bonds.dat
/usr/share/pdb2pqr/propka30/Source/protonate.py
/usr/share/pdb2pqr/propka30/Source/protonator.py
/usr/share/pdb2pqr/propka30/Source/residue.py
/usr/share/pdb2pqr/propka30/Source/rotate.py
/usr/share/pdb2pqr/propka30/Source/vector_algebra.py
/usr/share/pdb2pqr/propka30/Source/version.py
/usr/share/pdb2pqr/src/__init__.py
/usr/share/pdb2pqr/src/aa.py
/usr/share/pdb2pqr/src/aconf.py
/usr/share/pdb2pqr/src/aconf.py.in
/usr/share/pdb2pqr/src/definitions.py
/usr/share/pdb2pqr/src/errors.py
/usr/share/pdb2pqr/src/forcefield.py
/usr/share/pdb2pqr/src/hydrogens.py
/usr/share/pdb2pqr/src/inputgen.py
/usr/share/pdb2pqr/src/na.py
/usr/share/pdb2pqr/src/pdb.py
/usr/share/pdb2pqr/src/protein.py
/usr/share/pdb2pqr/src/psize.py
/usr/share/pdb2pqr/src/quatfit.py
/usr/share/pdb2pqr/src/routines.py
/usr/share/pdb2pqr/src/server.py
/usr/share/pdb2pqr/src/server.py.in
/usr/share/pdb2pqr/src/structures.py
/usr/share/pdb2pqr/src/topology.py
/usr/share/pdb2pqr/src/utilities.py
/usr/share/python/runtime.d/pdb2pqr.rtupdate

Changelog

2018-07-17 - Matthias Klose <doko@ubuntu.com>
pdb2pqr (2.1.1+dfsg-4build1) cosmic; urgency=medium
* No-change rebuild for libgfortran soname change.
2018-07-14 - Andreas Tille <tille@debian.org>
pdb2pqr (2.1.1+dfsg-4) unstable; urgency=medium
* Adapt test to new location of examples
Closes: #903759
2018-07-13 - Andreas Tille <tille@debian.org>
pdb2pqr (2.1.1+dfsg-3) unstable; urgency=medium
[ Steffen Moeller ]
* debian/upstream/metadata:
- Added references to registries
- yamllint cleanliness
[ Tatiana Malygina ]
* Enhance README.test and README.Debian
[ Andreas Tille ]
* Remove ancient X-Python-Version field
* Fix Homepage
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
* d/rules: do not parse d/changelog
2016-06-13 - Tatiana Malygina <merlettaia@gmail.com>
pdb2pqr (2.1.1+dfsg-2) unstable; urgency=medium
[ Tatiana Malygina ]
* Team upload.
* add README.test, docs, examples and simple testsuite
* enable hardening
* add patch to remove hardening-no-relro warning
* improved tests: add separate tests for use with pdb2pqr-doc installed and
without it
* found parameter set when error raised (described in `pdb2pka-test` 
in testsuite), updated d/docs
* fixed `pdb2pqr-test` - now should work ok (haven't checked with apbs yet)
* add patch to remove debug-file-with-no-debug-symbols warning (turn on debug)
* add networkx to d/control and test dependencies, mention in README.test
* fix order of commands in debian/rules - override_dh_auto_configure:
scons is now called after several files are regenerated with swig.
* updated README.test + README.Debian
[ Andreas Tille ]
* Drop unused lintian overrides
2016-05-07 - Andreas Tille <tille@debian.org>
pdb2pqr (2.1.1+dfsg-1) unstable; urgency=medium
* New upstream version
* Add new options to d/watch
* cme fix dpkg-control
* drop wrapper and use links instead
* fix interpreter lines by dos2unix
2016-01-08 - Andreas Tille <tille@debian.org>
pdb2pqr (2.1.0+dfsg-1) unstable; urgency=medium
* Moved to Git
* New upstream version
* Add lintian overrides for false positives source-is-missing
* Remove unused JS files via Files-Excluded
2015-11-26 - Andreas Tille <tille@debian.org>
pdb2pqr (2.0.0+dfsg-2) unstable; urgency=medium
* Enable building arch independent packages separately
Closes: #806222
* Remove obsolete debian/pycompat
2015-05-18 - Andreas Tille <tille@debian.org>
pdb2pqr (2.0.0+dfsg-1) unstable; urgency=medium
* New upstream version
* cme fix dpkg-control
* Fix bashism
Closes: #772350
* Make the build reproducible by preseting URL and PREFIX (thanks for the
patch to Reiner Herrmann <reiner@reiner-h.de>)
Closes: #785546
2014-04-19 - Andreas Tille <tille@debian.org>
pdb2pqr (1.9.0+dfsg-1) unstable; urgency=medium
* New upstream version
* Adapted watch file
* Move debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* debian/patches/no_privacy_breach_logo.patch: remove potential
privacy breach logo
* drop autotools from Build-Depends since build system was changed
2013-10-24 - Andreas Tille <tille@debian.org>
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

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