[Biopython-dev] MMCIF Parser

João Rodrigues anaryin at gmail.com
Fri Mar 9 19:13:26 UTC 2012

Hi Lenna,

First of all, sorry to come so late in the discussion but as I said before,
I was in a conference so I didn't really read my email that frequently..

The PDBe have their own parsers and I am yet to find out what kind of
dependencies and even if it maps to the same SMCRA model we use. I will
keep you informed. I sent them an email today and am waiting for the reply.
I will eventually bring the discussion here so maybe we can take the best
of both parsers. Nevertheless, thanks for the time and effort you are
putting, it will surely be put to good use! :)


João [...] Rodrigues

No dia 9 de Março de 2012 20:00, Lenna Peterson <arklenna at gmail.com>escreveu:

> I am in the process of implementing the formal grammar of CIF in PLY
> (python lex yacc). The result should be a strict, robust, extensible CIF
> parser.
> It's going very smoothly, and I plan on continuing it regardless as a
> learning exercise in lexical analysis.
> Please let me know if PDBe has a robust mmCIF python parser that would
> make mine redundant.
> Lenna
> On Mar 9, 2012, at 10:11, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > On Fri, Mar 9, 2012 at 3:07 PM, João Rodrigues <anaryin at gmail.com>
> wrote:
> >> Hi all,
> >>
> >> I was recently in a conference in Heidelberg and I got to know that the
> >> PDBe is interested in collaborating with us in building a consolidated
> >> Python module for structural bioinformatics. From what I understood they
> >> already used our code sometimes.
> >>
> >> Since there is some movement on the MMCif parser front, maybe it's a
> good
> >> idea to query them and see if they have something implemented already?
> >> Asking first not to step on anyone's toes, but it might save time?
> >>
> >> João [...] Rodrigues
> >> http://nmr.chem.uu.nl/~joao
> >
> > Sounds good - you're one of the experts on the Bio.PDB code now
> > after all, so a good person to talk to them.
> >
> > Peter
> >
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython-dev

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