[BioPython] mmCIF parser?

[Cath Lawrence]

On Wednesday, September 24, 2003, at 04:17  PM, Thomas Hamelryck wrote:
> On Wednesday 24 September 2003 03:24 am, Cath Lawrence wrote:
>> So is anyone working on this? I'm just barely beginning to learn what
>> it's all about.
> Bio.PDB only deals with PDB files. However, I do have some code lying
> around that deals with mmCIF files, (lex generated C code + python 
> bindings)
> but I didn't add it to Bio.PDB because (a) I don not use mmCIF and (b) 
> no one
> asked for it - until now that is :-).
> What do you need it for? I might be tempted to add mmCIF support after 
> all.
> OTOH, as Andrew pointed out, PyMMLib indeed comes with mmCIF support, 
> so
> that's an out-of-the-box solution for you.

Well, the PDB data uniformity project is rebuilding PDB with mmCIF 
format files. And a RDBMS but that's in alpha now. We've registered as 
potential beta testers but that won't be until maybe December.

Meanwhile, the mmCIF files in the uniformity project are better 
curated, and the format is less flaky. As you no doubt know, the PDB 
parser breaks on quite a few of the PDB files - for various reasons to 
do with data quality, not poor coding, I hasten to add. And I want all 
the files I can get - my local mathematician wants bulk stats on amino 
acid distances.

I'm looking at PyMMLib now -  thanks to Andrew for the reference. So 
far it builds and the test runs. Now for some larger tests...

cheers
Cath
Cath Lawrence,                       Cath.Lawrence at anu.edu.au
Senior Scientific Programmer,  Centre for Bioinformation Science,
John Curtin School of Medical Research (room 4088)
Australian National University,  Canberra ACT 0200
ph: (02) 61257959   mobile: 0421-902694   fax: (02) 61252595