Comment on TPRReaderDevelopment in mdanalysis

[mdana...@googlecode.com]

Comment by orbeckst:

Jan, looks like a great start for a TPR reader. If you can extract the list
of atoms then you have the basic reader. (Btw, there's a 'return' in the
middle...).

The only difficulty will be keeping up with the constant format changes
during Gromacs development...

All in all: very encouraging!

For more information:
http://code.google.com/p/mdanalysis/wiki/TPRReaderDevelopment

[Andy Somogyi]

In the topology editor / reader / writer I'm finishing up (can do psf, top and tpr), I just use gmxlib's read_tpx which reads a tpr and fills out a gmx_mtop_t structure. top files are a bit more complicated, but do_top essentially reads a .top and fills out a gmx_mtop_t.

IMO, trying to manually parse a tpr is probably not a super great idea because this file format is basically a binary dump of the gmx_mtop_t struct, which changes all the time, read_tpx takes care of all the past gromacs versions.

I'm still working on API cleanup, and build issues. I'm going to see if how feasible it is using setup.py check how gromacs is installed, and set the appropriate preprocessor directives.

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[Jan Domanski]

Hi Andy,

Excellent! If you have the tool ready, then (it's less work for me)
let's stick with what you've written.

Jan

[mdana...@googlecode.com]

Comment by proten...@gmail.com:

Is this still being developed? I've been looking for a unified python-based
tpr reader for a while. I've been looking for the specs

[mdana...@googlecode.com]

Comment by orbeckst:

Not sure if Jan is still working on it. See also Issue 2 and this thread on
[https://groups.google.com/d/topic/mdnalysis-devel/nMwUjAZR-iQ/discussion
Issue 2 in mdanalysis: reading Gromacs tpr files instead of psf] on the
developers mailing list.

I have never found an official API and in fact the TPR format often changes
(that's why you need the format number). You probably need to look at the
Gromacs sources but you can also use gmxdump to get a ASCII version of the
TPR file. The safest approach is probably to wrap the actual Gromacs libgmx
or libmd to access the TPR.

There's also Daniel Seeliger's [http://wwwuser.gwdg.de/~dseelig/pymacs.html
pymacs], which directly uses the Gromacs libs.

For more information:
https://code.google.com/p/mdanalysis/wiki/TPRReaderDevelopment