[Biopython] Bio.PDB local MMCIF files

[João Rodrigues]

Dear Dave,

I'm not quite sure I understood your question. PDBList is used to download
and maintain a local copy of the PDB, which would not suit you since you
are looking for mmCIF data. It could be tweaked however to download mmCIF
files. Is this what you are looking for?

As for mmCIF parsing and manipulation, currently the parser accepts a path
to the file (relative paths should do) but indeed it does not handle
compression. I think it would be up to the user to inflate the gz file
before parsing..

Best,

João


2013/12/5 Dave Howorth <dhoworth at mrc-lmb.cam.ac.uk>

> I'm just looking at Bio.PDB with a view to switching over to it, so I
> can use it to read MMCIF files in preparation for 4-character chain IDs
> etc. I presently use a homegrown perl module to read PDB files, and I
> have a local PDB mirror. I see from
>
> http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
>
> that there's some sort of facility to use local files, perhaps using
> PDBList() but I don't see from the FAQ or the PDBList class docs exactly
> which directory it wants and whether it is PDB files only or a complete
> archive. The only hints seem to hint at a single directory of PDB files
> or a divided directory hierarchy of PDB files, neither of which will
> contain the MMCIF files. So is it:
>
> /$TOP/data
> /$TOP/data/structures
> /$TOP/data/structures/all
>
> Or is it some other technique entirely to access MMCIF files?
>
> Looking at the code, it seems to want a full path to an MMCIF file, and
> the MMCIF file must be uncompressed. Since all the files in the archive
> are compressed, that would be another thing I'd want to fix.
>
> Oh, I'm currently using the V1.58 that came with the machine I'm testing
> on. I can upgrade if essential.
>
> Thanks and regards,
> Dave
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