Re: [OpenBabel-Devel] PDB residue assignment problem

2011-12-19 Thread Noel O'Boyle
On 17 December 2011 04:46, Geoff Hutchison ge...@geoffhutchison.net wrote: The weird thing is that IdentifyResidue can identify the first serine without any problems; it just doesn't identify the second one. Also, it will identify them both correctly if the --gen3d is omitted (or more

Re: [OpenBabel-Devel] PDB residue assignment problem

2011-12-16 Thread Geoff Hutchison
The weird thing is that IdentifyResidue can identify the first serine without any problems; it just doesn't identify the second one. Also, it will identify them both correctly if the --gen3d is omitted (or more precisely, if the call to Builder.Build is omitted). This bug report exposed two

Re: [OpenBabel-Devel] PDB residue assignment problem

2011-12-12 Thread Geoffrey Hutchison
I've done a lot of debugging in chains.cpp, but don't have time for a few days. It's sorta like a specialized SMILES/SMARTS parser. result = DetermineHetAtoms(mol) result; result = DetermineConnectedChains(mol)result; result = DeterminePeptideBackbone(mol)result;