Can anyone suggest a reliable parser to extract ligands (coordinates, atom types, et al.) from a PDBML or mmCIF file?
I have tried BioPython (http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ), but it does not support structured formats such as xml or mmCIF.
The plain pdb format file is avoided here. I think it is inferior to the structured formats and more prone to errors.
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GeauxEric •
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mmCIF is the standard format that's used for deposition to PDB, so if I were use I'd use it rather than PDBML.
Have a look at BioPython again. It supports mmCIF files, according to the NEWS files since ver 1.23 (Oct 18, 2003).
Another Python library that can read mmCIF files is cctbx/iotbx - it's used mostly in crystallographic software.
Depending on what exactly you want to do, you may also be interested in Chemical Component Dictionary from wwPDB which contains description of all ligands from PDB entries - already extracted for you and updated weekly.
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I would say it should be easy (but I would be lying, as it wouldn't be easy for me) to write a script to parse the information you want, using any Python XML parser module. If you are able to use BioPython, you probably have the required skills to do this as well.