[Biopython] The PDBParser Permissive setting

[João Rodrigues]

You mean for example, no chain breaks? And no missing atoms in residues?
You can check the first one with a warning catcher (I think I answered
something like this a few time ago here in the mailing list). The second
one is trickier, you'll need a sort of topology to know which atoms belong
to each residue. I have something like that in my GSOC branch but it's very
very very experimental..

Is this what you mean? Which others would you be looking for? I think that
for RMSD alone you need only to make sure that you match equivalent atoms.
That should be easy enough without major modifications or endless
try/excepts :)