Bug 292089

Summary:	Please add contactos
Product:	Gentoo Linux	Reporter:	Bjoern Olausson <contactme>
Component:	New packages	Assignee:	Default Assignee for New Packages <maintainer-wanted>
Status:	CONFIRMED ---
Severity:	enhancement	Keywords:	EBUILD, InVCS
Priority:	High
Version:	unspecified
Hardware:	All
OS:	Linux
URL:	http://users.abo.fi/mhuhtala/contactos.html
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	contactos-1.1.ebuild contactos-1.1-r1.ebuild (added MCL useflag for sci-biology/mcl)

Description Bjoern Olausson 2009-11-06 12:17:59 UTC

I found this tool very usefull so i quickly wrote an ebuild for "contactos"

Description from the hompage:
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Contactos is a program for calculating similarities between docked poses of protein ligands. The similarity matrices produced by Contactos can be used to cluster the docking results using an external clustering tool, such as MCL. Contactos itself does not include clustering.

Contactos was conceived and the initial version written by Mikko Huhtala. An efficient grid search algorithm and other optimizations were added by Santeri Puranen.

Contactos has succesfully been used in combination with MCL to cluster docking results from Schrödinger InducedFit and Gold runs.

Features:
The similarity values are based on ligand – protein contacts and are independent of the superposition and conformation of the docked solutions. Contactos can be used for docking results from programs that allow receptor flexibility and for snapshots from dynamics trajectories.

Optionally, similarities for a set of different docked molecules can be calculated in one run. Clustering based on such data will often separate different molecules into their own clusters, but it can also cluster different molecules together and show similarities in their binding modes.

Contactos reads MOL2-format (Sybyl/Tripos) coordinate files.

Contactos writes out a matrix of similarity indices and the same indices in the MCL pair list input format.

Optionally, Contactos can run MCL automatically and symlink the input structure files into directories according to the clustering produced by MCL. This makes visualization somewhat easier.

Requirements:
Contactos is written in Python, so a Python runtime environment is required. Most Linux distributions provide this. Contactos has been developed and tested on Python 2.5 running on Linux, but it may work on other operating systems and versions of Python.

MCL is not required to run Contactos, but it is likely the easiest clustering program to use in conjunction with Contactos. MCL is written by Stijn van Dongen and it is distributed under the GPL license. MCL can be downloaded at micans.org/mcl.
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Cheers
Bjoern Olausson

Reproducible: Always

Comment 1 Bjoern Olausson 2009-11-06 12:18:48 UTC

Created attachment 209415 [details]
contactos-1.1.ebuild

Comment 2 Bjoern Olausson 2009-11-16 14:49:07 UTC

Created attachment 210410 [details]
contactos-1.1-r1.ebuild (added MCL useflag for sci-biology/mcl)

Added MCL useflag for sci-biology/mcl clustering tool.

Cheers
Bjoern