theseus_1.6.2-2_i386.deb


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Description

theseus - superimpose macromolecules using maximum likelihood

Property Value
Distribution Debian 7 (Wheezy)
Repository Debian Main i386
Package name theseus
Package version 1.6.2
Package release 2
Package architecture i386
Package type deb
Installed size 1.76 KB
Download size 1.11 MB
Official Mirror ftp.br.debian.org
Theseus is a program that simultaneously superimposes multiple
macromolecular structures. Theseus finds the optimal solution to the
superposition problem using the method of maximum likelihood. By
down-weighting variable regions of the superposition and by correcting for
correlations among atoms, the ML superposition method produces very
accurate structural alignments.
When macromolecules with different residue sequences are superimposed,
other programs and algorithms discard residues that are aligned with
gaps. Theseus, however, uses a novel superimposition algorithm that
includes all of the data.

Alternatives

Package Version Architecture Repository
theseus_1.6.2-2_amd64.deb 1.6.2 amd64 Debian Main
theseus - - -

Requires

Name Value
libc6 >= 2.7
libgsl0ldbl >= 1.9
muscle -

Download

Type URL
Binary Package theseus_1.6.2-2_i386.deb
Source Package theseus

Install Howto

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

Files

Path
/usr/bin/theseus
/usr/bin/theseus_align
/usr/share/doc/theseus/README.Debian
/usr/share/doc/theseus/changelog.Debian.gz
/usr/share/doc/theseus/citation.bib
/usr/share/doc/theseus/copyright
/usr/share/doc/theseus/examples/1s40.pdb.gz
/usr/share/doc/theseus/examples/README
/usr/share/doc/theseus/examples/cytc.aln
/usr/share/doc/theseus/examples/cytc.filemap
/usr/share/doc/theseus/examples/d1cih__.pdb.gz
/usr/share/doc/theseus/examples/d1crj__.pdb.gz
/usr/share/doc/theseus/examples/d1csu__.pdb.gz
/usr/share/doc/theseus/examples/d1csx__.pdb.gz
/usr/share/doc/theseus/examples/d1kyow_.pdb.gz
/usr/share/doc/theseus/examples/d1lfma_.pdb.gz
/usr/share/doc/theseus/examples/d1m60a_.pdb.gz
/usr/share/doc/theseus/examples/d1u74d_.pdb.gz
/usr/share/doc/theseus/examples/d1yeb__.pdb.gz
/usr/share/doc/theseus/examples/d2pcbb_.pdb.gz
/usr/share/doc/theseus/examples/getexamples
/usr/share/man/man1/theseus.1.gz
/usr/share/man/man1/theseus_align.1.gz

Changelog

2012-06-08 - Andreas Tille <tille@debian.org>
theseus (1.6.2-2) unstable; urgency=low
* debian/upstream: Added missing space, fixed Name
* debian/patches: Two patches from Simon Ruderich
<simon@ruderich.org> to enable hardening (thanks to Simon)
Closes: #668120
2012-03-24 - Andreas Tille <tille@debian.org>
theseus (1.6.2-1) unstable; urgency=low
* New upstream version (adapted patch)
* debian/control:
- Standards-Version: 3.9.3 (no changes needed)
- Fixed Vcs fields
* debian/{control,rules}: Do not mention quilt explicitly
which is not needed with source version 3.0 (quilt)
* debian/upstream: Use information from debian/citation.bib
for References in upstream yaml format
* debian/upstream: Use information from debian/citation.bib
for References in upstream yaml format
* debian/{control,compat}: debhelper 9 to enable hardening
flags
* debian/patches/20_hardening.patch: Enable building with hardening
options
* debian/patches/20_exclude_apple_options.patch: Prevent trying
to link with Apple specific linker option and enable linking
pthread
* debian/copyright: Rewritten to match DEP5 and verified using
cme fix dpkg-copyright
2011-01-26 - Andreas Tille <tille@debian.org>
theseus (1.6.1-1) unstable; urgency=low
* New upstream version
* debian/patches:
- 99-theseus_align.sh.patch:
Replaced by sed script in debian/rules which works (hopefully)
for future versions as well without manually changing the patch
- use_muscle_instead_of_clustalw.patch:
Removed because clustalw is no in main and we do not need
to actively replace it by muscle
- 00-makefile.patch:
Removed because applied upstream
- 200-make.inc.patch:
Removed
+ One purpose was to replace not working libtool call by ar
which was applied upstream
+ Other purpose was to enable liblapack (patch by Morten
Kjeldgaard) which was discussed with upstream and seems to
cause problems.  So it was deactivated for now and might be
tested later for enabling higher performance if needed.
2010-11-24 - Andreas Tille <tille@debian.org>
theseus (1.5.5-1) unstable; urgency=low
* New upstream version
* Standards-Version: 3.9.1 (no changes needed)
* Adapt debian/patches to new upstream version
* Source format 3.0 (quilt)
* debian/patches/use_muscle_instead_of_clustalw.patch:
The script thesaus_align says it would use muscle as align program
but it actually uses clustalw which is in non-free and thus we can
not recommend it.  The patch makes muscle really the default
* Depends: muscle (instead of Suggests)
* debian/theseus_align.1: Better wording for muscle preference
2009-09-03 - Andreas Tille <tille@debian.org>
theseus (1.4.3-2) unstable; urgency=low
* debian/patches/10_kbsd.patch: Correctly applied patch from
Cyril (sorry for mixing this up)
Closes: #542879

See Also

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thunar-archive-plugin_0.3.0-4_i386.deb Archive plugin for Thunar file manager
thunar-data_1.2.3-4_all.deb Provides thunar documentation, icons and translations
thunar-gtkhash_0.6.0-4_i386.deb thunar extension for computing checksums and more using gtkhash
thunar-media-tags-plugin_0.2.0-1_i386.deb Media tags plugin for Thunar file manager
thunar-vcs-plugin_0.1.4-1_i386.deb VCS plugin for Thunar file manager
thunar-volman_0.6.1-1_i386.deb Thunar extension for volumes management
thunar_1.2.3-4+b1_i386.deb File Manager for Xfce
ticgit_1.0.2.11-2_all.deb ticketing system built on Git
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