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.
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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.
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?
Does it support automated homology modelling, given a target sequence?
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.
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.
* 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.
Created attachment 176086 [details] almost-1.0.3.ebuild
Created attachment 176087 [details] gcc-4.3.patch
Created attachment 176089 [details] almost-1.0.3.ebuild
is in the sci-overlay no. All changes can be tracked there.
