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

[Lenna Peterson]

On Fri, Feb 8, 2013 at 8:42 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> Hi Lenna,
>
>
> --- On *Thu, 2/7/13, Lenna Peterson <arklenna at gmail.com>* wrote:
> > If there are well-defined problems with the PLY parser, I can work on
> > fixing them. I am not currently working with mmCIF so I am not in the
> > best position to evaluate where and how the parser needs to be improved.
>
> I don't know of any problems with the PLY parser, but since it relies on
> PLY, it would add another dependency to Biopython.
>


> On the other hand, a pure-Python solution may be preferable, as it's
> easier to maintain and runs with Jython.
>


As far as I can tell, PLY works with Jython, discussion on this thread:
http://permalink.gmane.org/gmane.comp.python.ply/402

Not sure about pypy. One option would be to deploy the PLY parser for
non-CPython platforms and tell them to manually install PLY if they want to
use mmCIF. Not ideal, but is that preferred to an explicit dependency?


>
> I see three options then:
> 1) Remove the lex stuff from lex.yy.c, and optionally convert the
> remaining C code to Python.
>

As is, the C compiles cross platform with no dependencies. There is nothing
but lex stuff in lex.yy.c - I'm not quite sure what you mean here.


> 2) Remove the PLY dependency from the PLY-based parser.
> 3) Write a new pure-Python parser from scratch.
>
>
I'm not sure whether there is an appreciable difference between options 2
and 3.

Cheers,

Lenna