Hi Greg (et al.),
Thanks for the beta! I have been going through some of the recently-added
functionality, and had a couple of questions regarding the PDB reading /
writing.
1. Do I remember correctly that there was a proposal (from Roger) to add
some auto bond-type perception to the PDB parser for ligands (or is that just
wishful thinking!)?
2. If not, I notice that there is an AssignBondOrdersFromTemplate()
method - but the example in the doc-string only shows (I think) the case where
the input PDB is just a single small molecule - so the matching is pretty easy!
I think a more real-World case is when one wants to set the bond orders for
multiple ligands (HETATM residues) based on substructure matches - which will
then return an atom index selection that can be used as a start point. Is
there any way to have the AssignBondOrdersFromTemplate() convenience function
optionally accept a list of atom indexes to specify a substructure?
3. Is there some explanation for what the 'flavor' option does for
reading/writing PDB?
4. Having read in a PDB file I see the correct atoms flagged as HETATM
(from GetIsHeteroAtom()). But when call Chem.MolToPDBBlock() these atoms get
written as ATOM records... Also, a Chem.MolToPDBFile() method would be nice
for completeness / symmetry : )
5. It seems to me that GetResidueNumber() and GetSerialNumber() may have
got mixed-up at some point(?). At least, when I call GetSerialNumber() I see
what appears to be the residue number; and when I call GetResidueNumber() I get
"0"!
6. I also seem to be seeing all of the bonds (for all residues) being
written out in CONECT records - such that they all appear as single bonds in eg
PyMOL - is this expected behaviour at the moment?
Cheers
James
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