pdb2pqr_2.1.1+dfsg-2_i386.deb


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Description

pdb2pqr - Preparation of protein structures for electrostatics calculations

Property Value
Distribution Ubuntu 17.10 (Artful Aardvark)
Repository Ubuntu Universe i386
Package name pdb2pqr
Package version 2.1.1+dfsg
Package release 2
Package architecture i386
Package type deb
Installed size 2.72 KB
Download size 372.12 KB
Official Mirror archive.ubuntu.com
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-2_amd64.deb 2.1.1+dfsg amd64 Ubuntu Universe
pdb2pqr - - -

Requires

Name Value
libc6 >= 2.4
libgcc1 >= 1:3.0
libpython2.7 >= 2.7
libstdc++6 >= 5.2
python-networkx -
python-numpy -
python2.7:any -
python:any >= 2.6.6-7~

Provides

Name Value
propka -

Replaces

Name Value
propka -

Download

Type URL
Binary Package pdb2pqr_2.1.1+dfsg-2_i386.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

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.
[ 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
2012-06-21 - Manuel Prinz <manuel@debian.org>
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.
2011-08-31 - Manuel Prinz <manuel@debian.org>
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.
2011-01-30 - Manuel Prinz <manuel@debian.org>
pdb2pqr (1.7-1) unstable; urgency=low
* New upstream release. Closes: #416269, #420734.

See Also

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pdfchain_0.4.4.2-1_i386.deb graphical user interface for the PDF Tool Kit
pdfcrack_0.16-1_i386.deb PDF files password cracker
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pdfminer-data_20140328+dfsg-1_all.deb PDF parser and analyser (encoding data)
pdfmod_0.9.1-8_all.deb simple tool for modifying PDF documents
pdfposter_0.6.0-2_all.deb scale and tile PDF images/pages to print on multiple pages
pdfresurrect_0.12-6_i386.deb tool for extracting/scrubbing versioning data from PDF documents
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