[Biopython] Bio.PDB question - from PQR to an "extended" PDB

[João Rodrigues]

Hello Paul,

Straight from Pymol :)

Bio.PDB cannot read PQR files as is, but since the format is quite similar
to the PDB it should be easy to convert.

The first step is to know if you want to develop a converter too (you will
need the forcefield atomic charges and radius for that) or just a "parser".
Parsing is easy, it's a matter of adapting the current SMCRA objects and
PDBParser. Converting requires much more and is probably superfluous given
the PDB2PQR software.

Some important information on the format:
http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr

I think the best course of action is to add a PQRParser class that has
different residue properties than the regular PDB. For example, occupancy
and bfactor are not used at all..

Let me know what you think,

Cheers,

João