Bug 248455

Summary:	[science overlay] sci-chemistry/almost
Product:	Gentoo Linux	Reporter:	Justin Lecher (RETIRED) <jlec>
Component:	New packages	Assignee:	Default Assignee for New Packages <maintainer-wanted>
Status:	CONFIRMED ---
Severity:	enhancement	CC:	sci-chemistry
Priority:	Normal	Keywords:	EBUILD, InOverlay
Version:	unspecified
Hardware:	All
OS:	Linux
URL:	http://www-almost.ch.cam.ac.uk/site/index.html
Whiteboard:	Science overlay
Package list:		Runtime testing required:	---
Attachments:	almost-1.0.3.ebuild files/gcc-4.3.patch almost-1.0.3.ebuild gcc-4.3.patch almost-1.0.3.ebuild

Description Justin Lecher (RETIRED) gentoo-dev

2008-11-23 19:04:08 UTC

about almost

almost - all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.

Written in C++, almost has been specifically designed to be used as an application framework for the rapid development of Computational Biology Software, as Command Line Tool or as a 3D Interactive Modeling Environment.

There is a mpi interface included, but as upstream 	preferential  uses sys-cluster/mpich2 and I don't get any version either from the tree or the overlay to compile and/or to work, I didn't include the mpi support yet. This will be added when my mpich2 is running.

Comment 1 Justin Lecher (RETIRED) gentoo-dev

2008-11-23 19:04:55 UTC

Created attachment 173061 [details]
almost-1.0.3.ebuild

almost-1.0.3.ebuild

Comment 2 Justin Lecher (RETIRED) gentoo-dev

2008-11-23 19:05:15 UTC

Created attachment 173063 [details]
files/gcc-4.3.patch

gcc-4.3.patch

Comment 3 Donnie Berkholz (RETIRED) gentoo-dev

2008-11-26 22:35:39 UTC

I'm curious how this compares to biskit. Have you any experience with that? It's clearly got a wider application than something purely for modeling like mmtk.

Comment 4 Justin Lecher (RETIRED) gentoo-dev

2008-11-27 07:38:15 UTC

Sorry, I can't say anything about it from my own experience. I saw it on a conference, where they show some impressive results. That was the motivation to write an ebuild. I don't have any task for it now, do you?

Comment 5 Donnie Berkholz (RETIRED) gentoo-dev

2008-11-28 05:47:20 UTC

Does it support automated homology modelling, given a target sequence?

Comment 6 Justin Lecher (RETIRED) gentoo-dev

2008-11-28 09:40:04 UTC

Sorry, I can't say anything concrete. I heard Michele Vendruscolo talking about it on a NMR conference last month. This is what his talk was based on: http://www.pnas.org/content/104/23/9615.full. I just thought having this for gentoo would be cool.

Comment 7 Justin Lecher (RETIRED) gentoo-dev

2008-11-28 13:03:46 UTC

Think I will get the whole Chessire/Aqva ebuild ready this weekend. Then we could go for testing.

MPI support will take some time, try to get in touch with upstream solving the problems.

Comment 8 Justin Lecher (RETIRED) gentoo-dev

2008-12-21 20:43:27 UTC

* MPI Support is still broken
* boost-1.3.6 is need. As the portage package is still hardmasked we use the shipped boost. Will fix this when boost-1.3.6 is ~arch.
* Need to mirror it, because upstream changes tarball without bumping version.

Comment 9 Justin Lecher (RETIRED) gentoo-dev

2008-12-21 20:43:56 UTC

Created attachment 176086 [details]
almost-1.0.3.ebuild

Comment 10 Justin Lecher (RETIRED) gentoo-dev

2008-12-21 20:45:01 UTC

Created attachment 176087 [details]
gcc-4.3.patch

Comment 11 Justin Lecher (RETIRED) gentoo-dev

2008-12-21 20:46:42 UTC

Created attachment 176089 [details]
almost-1.0.3.ebuild

Comment 12 Justin Lecher (RETIRED) gentoo-dev

2009-01-26 22:03:25 UTC

is in the sci-overlay no. All changes can be tracked there.