> Where does OpenBabel store atom names? I realize not all formats have > named atoms, but some (e.g. PDB) do, and I'm not sure where in the > OBAtom/OBMol/other objects I can find this info.
For PDB-related formats, these are stored in the OBResidue: http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBResidue.shtml > Is there a way to tell whether the partial charges came directly from > the input file, or if they have been auto calculated? Yes. Starting in OB 2.2 and later, there should be an OBPairData stored with the molecule (e.g., from a quantum output file): OBPairData *dp = new OBPairData; dp->SetAttribute("PartialCharges"); dp->SetValue("Mulliken"); dp->SetOrigin(fileformatInput); In particular, the SetOrigin method for generic data reflects whether data is perceived (i.e., generated by Open Babel) or from the file format. > I'd like to be able to trust the supplied charges, if any, but would prefer > to use a > different method in preference to OpenBabel's Gasteiger charge calculation. Out of curiosity, what method would you like to use. In the latest development code, there's a new framework for charge models, and we have support for Gasteiger, MMFF94, QEq, and QTPIE. Other methods could certainly be added. Thanks, -Geoff ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
