[Biopython-dev] flex, setup.py and Bio.PDB.mmCIF (Bug 2619)

[João Rodrigues]

Hi Michiel,

Speaking without really checking the code.. What we perhaps should have it
the parsers, whatever they are, populating the same type of object in the
end (PDBParser and mmCIFParser). Is this the current status of the mmCIF?

Best,

João


2013/3/15 Michiel de Hoon <mjldehoon at yahoo.com>

> Hi everybody,
>
> I looked at the mmCIF parser again, and it turned out that the Python
> standard library contains a shlex lexical analyzer module that makes mmCIF
> parsing straightforward without relying on flex or PLY. I uploaded a
> modified version of MMCIF2Dict.py to the git repository. This parser does
> the exact same thing as the flex-based parser, but is in pure Python. If
> you're interested, have a look at MMCIF2Dict.py in the git repository;
> comments and suggestions are welcome.
>
> If there are no objections, I think we can remove everything in
> Bio.PDB.mmCIF. Also I'm a bit unhappy with how the information in an mmCIF
> file is represented in Biopython. I think there are more Pythonic ways to
> store the contents of an mmCIF file in a Python object.
>
> Best,
> -Michiel.
>
> --- On Sat, 2/16/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> > From: Peter Cock <p.j.a.cock at googlemail.com>
> > Subject: Re: [Biopython-dev] flex, setup.py and Bio.PDB.mmCIF (Bug 2619)
> > To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> > Cc: "BioPython-Dev Mailing List" <biopython-dev at biopython.org>, "Lenna
> Peterson" <arklenna at gmail.com>
> > Date: Saturday, February 16, 2013, 5:42 AM
> > On Sat, Feb 16, 2013 at 2:46 AM,
> > Michiel de Hoon <mjldehoon at yahoo.com>
> > wrote:
> > > Hi Lenna,
> > >
> > > Maybe we are confusing each other..
> > > I am looking for a solution that (a) doesn't introduce
> > new dependencies,
> >
> > +1
> >
> > > (b) is pure-Python so it can run on Jython,
> >
> > +1 And on PyPy (which to me is more interesting that Jython)
> > etc.
> >
> > > and (c) if that is not possible and we do need to use
> > C, then that C code
> > > should be understandable so that it can be debugged if
> > necessary.
> > >
> > > I was suggesting to clean up lex.yy.c so that we can at
> > least achieve (c).
> >
> > This does mean we essentially give up on ever regenerating
> > the lex.yy.c
> > file every again - could that be a problem if Flex itself
> > changes much?
> >
> > > The alternative is to start from the PLY-based parser
> > and remove the
> > > dependency on PLY.
> > >
> > > Best,
> > > -Michiel.
> >
> > Peter
> >
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