def parse_gamout(self, gamout, mol):
result = gparse(gamout)
if not result.success:
raise GamessError(result.error_message)
nmol = Chem.Mol(mol)
conf = nmol.GetConformer(0)
nmol.SetDoubleProp("total_energy", result.total_energy)
nmol.SetDoubleProp("H**O", result.H**O)
nmol.SetDoubleProp("LUMO", result.LUMO)
nmol.SetDoubleProp("nHOMO", result.nHOMO)
nmol.SetDoubleProp("nLUMO", result.nLUMO)
nmol.SetDoubleProp("dipole_moment", result.dipole_moment[3])
nmol.SetDoubleProp("dx", result.dipole_moment[0])
nmol.SetDoubleProp("dy", result.dipole_moment[1])
nmol.SetDoubleProp("dz", result.dipole_moment[2])
nmol.SetProp("orbital_energies",
" ".join([str(v) for v in result.orbital_energies]))
nmol.SetProp("program", "GAMESS")
nmol.SetProp("basis", str(self._options['basis']))
nmol.SetProp("method", str(self._options['contrl']))
for i, cds in enumerate(result.coordinates):
conf.SetAtomPosition(i, cds)
for i, c in enumerate(
zip(result.mulliken_charges, result.lowdin_charges)):
atom = nmol.GetAtomWithIdx(i)
atom.SetDoubleProp("mulliken_charge", c[0])
atom.SetDoubleProp("lowdin_charge", c[1])
Chem.CreateAtomDoublePropertyList(nmol, "mulliken_charge")
Chem.CreateAtomDoublePropertyList(nmol, "lowdin_charge")
result.mol = nmol
return result
def testCreateLists(self):
suppl = Chem.SDMolSupplier()
suppl.SetData(self.sdf)
m = suppl[0]
self.assertTrue(m.GetAtomWithIdx(0).HasProp("NumHeavyNeighbors"))
m.ClearProp("atom.iprop.NumHeavyNeighbors")
self.assertFalse(m.HasProp("atom.iprop.NumHeavyNeighbors"))
Chem.CreateAtomIntPropertyList(m, "NumHeavyNeighbors")
self.assertTrue(m.HasProp("atom.iprop.NumHeavyNeighbors"))
self.assertTrue(m.GetAtomWithIdx(0).HasProp("PartialCharge"))
m.ClearProp("atom.dprop.PartialCharge")
self.assertFalse(m.HasProp("atom.dprop.PartialCharge"))
Chem.CreateAtomDoublePropertyList(m, "PartialCharge")
self.assertTrue(m.HasProp("atom.dprop.PartialCharge"))
self.assertTrue(m.GetAtomWithIdx(0).HasProp("IsCarbon"))
m.ClearProp("atom.bprop.IsCarbon")
self.assertFalse(m.HasProp("atom.bprop.IsCarbon"))
Chem.CreateAtomBoolPropertyList(m, "IsCarbon")
self.assertTrue(m.HasProp("atom.bprop.IsCarbon"))
self.assertTrue(m.GetAtomWithIdx(0).HasProp("PartiallyMissing"))
m.ClearProp("atom.prop.PartiallyMissing")
self.assertFalse(m.HasProp("atom.prop.PartiallyMissing"))
Chem.CreateAtomStringPropertyList(m, "PartiallyMissing")
self.assertTrue(m.HasProp("atom.prop.PartiallyMissing"))
self.assertEqual(m.GetProp("atom.prop.PartiallyMissing"),
"one n/a three")
Chem.CreateAtomStringPropertyList(m,
"PartiallyMissing",
missingValueMarker="?")
self.assertTrue(m.HasProp("atom.prop.PartiallyMissing"))
self.assertEqual(m.GetProp("atom.prop.PartiallyMissing"),
"[?] one ? three")
def molecule_to_rdkit(molecule):
if molecule._rdmol is None:
rdmol = rdmol_from_qcelemental(molecule.qcmol, guess_connectivity=True)
else:
rdmol = Chem.Mol(molecule._rdmol)
for conformer in molecule.conformers:
add_conformer_from_coordinates(rdmol, conformer.coordinates)
charges = molecule.charges
if charges is not None:
for charge, atom in zip(charges, rdmol.GetAtoms()):
atom.SetDoubleProp("PartialCharge", charge)
Chem.CreateAtomDoublePropertyList(rdmol, "PartialCharge")
rdmol.UpdatePropertyCache(strict=False)
return Chem.Mol(rdmol)
