[Biopython] Numbering MODEL sections in PDBIO?

[Konstantin Okonechnikov]

What about the proposed patch to bug 2950?
There could be another solution - get rid of explicit model id variable, and
use the id as the key in model map, but perhaps this would lead to
compatibility problems.



On Thu, May 13, 2010 at 9:40 AM, Rodrigo Faccioli <
rodrigo_faccioli at uol.com.br> wrote:

>  Hi,
>
> We've spoke with Eric Talevich about our intention to contribute with
> BioPython project. He helped us to participate in GSoC 2010. This project
> can be access in:
>
> https://docs.google.com/fileview?id=0ByNUaKmUm2WoMDVkYWVlMDktZGNlMS00N2UyLThkYTctNDU5MmZlNzhiYjM5&hl=en
>
> Our main contribution is to work with SEQRES section of PDB file.  When we
> was analysing the Bio.PDB module, more specific Select class, we would like
> to develop a new way more flexible and simple for the users.  So, we create
> the FcfrpStructureChains inherited FcfrpStructureSplit. We have the idea to
> develop FcfrpStructureModel inherited FcfrpStructureSplit.
>
> if you want to see the project that we're working, please access:
>
> http://github.com/rodrigofaccioli/ContributeToBioPython
>
> The example file to split chains of PDB is:
>
> http://github.com/rodrigofaccioli/ContributeToBioPython/blob/master/examples/splitPDBChains.py
>
> The execution line is: splitPDBChains.py 4HTC 4HTC.PDB <directory where
> 4HTC.PDB is>
>
> If you want, we can talk in more details.
>
> Our project is still in development version. Apologize for any bugs.
>
> Thanks in advance,
>
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>
> On Wed, May 12, 2010 at 6:54 AM, Peter <biopython at maubp.freeserve.co.uk
> >wrote:
>
> > On Wed, May 12, 2010 at 4:38 AM, João Rodrigues <anaryin at gmail.com>
> wrote:
> > > Hello all,
> > >
> > > I am using Bio.PDB to parse some PDB files and some have multiple MODEL
> > > records. I only want to keep the first one so I created a Select class
> > that
> > > accepts models for model.get_id() == 0. It works :)
> > >
> >
> > This sounds like Bug 2950,
> > http://bugzilla.open-bio.org/show_bug.cgi?id=2950
> >
> > See also:
> > http://bugzilla.open-bio.org/show_bug.cgi?id=2951
> >
> > Peter
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
>
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>



-- 
Best regards,
        Konstantin