Tolerate hydrogens

[raphtown]

Hello,

Is it possible for this module to work with hydrogens or unknown residue types (i.e., like the --hydrogen and --unknown flags in the underlying module)?

Currently, it fails due to hydrogen atoms on structures such as 4p4h.pdb1 when I run a command such as result, sasa_classes = freesasa.calcBioPDB(bp)

Thank you for your time!

[mittinatten]

Hi, Yes, it's possible, but not very well documented, you can pass an options parameter to the Structure constructor, if you look at the defaultOptions in the source it illustrates the format: https://github.com/freesasa/freesasa-python/blob/master/freesasa.pyx#L421.

I should try to make this more explicit in the docs.

The BioPDB module is experimental, and I haven't had time to do anything about hydrogens there, there is an old open issue on this, which is posted in the wrong repo: https://github.com/mittinatten/freesasa/issues/35.

[raphtown]

Great, thank you!

I got it working pretty simply with:

structure = freesasa.structureFromBioPDB(
     bp, options={'hydrogen': True, 'skip-unknown': True})
result = freesasa.calc(structure)

[raphtown]

Actually, after looking at this more, that didn't actually work. I ended up doing

structure = freesasa.Structure(options={'hydrogen': True, 'skip-unknown': True})

and then doing

structure.addAtom