[Biopython-dev] [Bug 2943] MMCIFParser only handling a single model.

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2943





------- Comment #12 from biopython-bugzilla at maubp.freeserve.co.uk  2009-12-18 05:24 EST -------
(In reply to comment #11)
> Peter, are you still looking at this bug report?
> Otherwise I could have a look at it.

Thanks Michiel - Please feel free. I didn't feel we had time to get this into
Biopython 1.53, as I think it is going to be a lot of work to assess, but needs
to be done.

I think there are two issues here, poor support for multiple models, and
re-writing the flex parser in pure python. Given time (!) I would want to take
Paul's python parser and use it to replace the flex code (which is currently
not compiled or installed by default, Bug 2619) and verify it is backwards
compatible, and then add in the model support. If we have enough test coverage
already, then doing it in one go might be OK. Up to you.

Other relevant issues include Bug 2626 (files the current parser can't read -
it may turn out that these are also multi-model CIF files).

Also regarding the model support, for PDB files we currently index them
0,1,2,... as found in the file. There are also names given in the PDB file
itself, which need not by continuous etc. See Bug 2950 and Bug 2951 for this.

Thanks,

Peter


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.