openbabel_hbonds

This uses openbabel to detect hydrogen bonds between a receptor and ligand in a PDB file. It attempts to flip or spin hydrogens to make some hydrogen bonds.

Dependencies

This requires having the pybel and openbabel python extensions installed.

It also currently targets python 2.7 , modifications to support python 3 are very welcome.

Usage

openbabel_hbonds_native uses openbabel's native definition of a hydrogen bond acceptor and donor.

openbabel_hbonds_smarts uses smarts to define h-bond donors and acceptors. You may modify it to meet your preferred definition.

Both scipts output a list of h-bonds as Donor (chain, residue id, residue name, atom name) then Acceptor (chain, residue id, residue name, atom name)

A  137 ARG  NH2 A  394 CC3  O27
A  143 LYS  NZ  A  394 CC3  F10
A  213 ALA  N   A  394 CC3  N15
A  394 CC3  N25 A  214 PRO  O  
A  394 CC3  N18 A  213 ALA  O  

Future Work

• H-bonds to aromatic rings
• Tautomers of residues
• Tautomers of ligands
• Flip possibly mis-assigned residues
• Factor out common code between the two scripts