Thanks, I realized the atom types in OpenBabel are not enough for what I want, hence what I did was to ask openbabel for several atom properties and use those properties to assign the atom types I need.
Cheers, Osvaldo On Thu, Jul 30, 2015 at 1:55 PM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > I need to get the atom types from molecules. I am using a Python/PyMOL > script. I have the following code > > Sorry, I realized no one got back to you. Here's code that should work > > http://openbabel.org/api/2.3/classOpenBabel_1_1OBForceField.shtml#aa41fd7cce6a9cf2e56ca603de7fbc507 > > def get_atom_type(selection): > pdb_string = cmd.get_pdbstr(selection) > mol = ob.OBMol() > obconversion = ob.OBConversion() > obconversion.SetInAndOutFormats('pdb', 'pdb') > obconversion.ReadString(mol, pdb_string) > ff = ob.OBForceField.FindForceField('GAFF') > ff.Setup(mol) > ff.GetAtomTypes(mol) > for at in ob.OBMolAtomIter(mol): > type = at.GetData("FFAtomType") # an OBPairData object > print at->GetValue() > > Hope that helps, > -Geoff
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