def testStereoRefsAfterAddingOBMols(self):
"""The stereo ref for an implicit H ref was being set to 0"""
smis = ["C", "[C@@H](Br)(Cl)I"]
mols = [pybel.readstring("smi", smi) for smi in smis]
# FIXME - does not seem to be possible to work out whether
# tetrahedral or not from Python?
stereodata = mols[1].OBMol.GetData(ob.StereoData)
config = ob.toTetrahedralStereo(stereodata).GetConfig()
self.assertEqual(config.from_or_towards, 4294967294)
mols[0].OBMol += mols[1].OBMol
self.assertEqual(mols[0].write("smi").rstrip(), ".".join(smis))
stereodata = mols[0].OBMol.GetData(ob.StereoData)
config = ob.toTetrahedralStereo(stereodata).GetConfig()
self.assertEqual(config.from_or_towards, 4294967294)
def testStereoRefsAfterAddingOBMols(self):
"""The stereo ref for an implicit H ref was being set to 0"""
smis = ["C", "[C@@H](Br)(Cl)I"]
mols = [pybel.readstring("smi", smi) for smi in smis]
# FIXME - does not seem to be possible to work out whether
# tetrahedral or not from Python?
stereodata = mols[1].OBMol.GetData(ob.StereoData)
config = ob.toTetrahedralStereo(stereodata).GetConfig()
self.assertEqual(config.from_or_towards, 4294967294)
mols[0].OBMol += mols[1].OBMol
self.assertEqual(mols[0].write("smi").rstrip(), ".".join(smis))
stereodata = mols[0].OBMol.GetData(ob.StereoData)
config = ob.toTetrahedralStereo(stereodata).GetConfig()
self.assertEqual(config.from_or_towards, 4294967294)
def insert_molproperties(self, obmol):
"""loop over openbabel mols' Properties and insert each"""
for p in obmol.GetData():
if p.GetDataType() == ob.PairData:
if p.GetAttribute() == 'OpenBabel Symmetry Classes': continue
self.db.insert_molproperty(p.GetAttribute(), p.GetValue())
elif p.GetDataType() == ob.StereoData:
ts = ob.toTetrahedralStereo(p)
if ts.IsValid():
cfg = ts.GetConfig()
#print 'stereo',self.stereoCfgToDict(cfg, obmol)
if cfg.specified:
self.db.insert_molproperty('OBTetrahedralStereo', json.dumps(self.stereoCfgToDict(cfg, obmol)))
else:
ct = ob.toCisTransStereo(p)
cfg = ct.GetConfig()
#print 'cistrans',self.cistransCfgToDict(cfg, obmol)
if cfg.specified:
self.db.insert_molproperty('OBCisTransStereo', json.dumps(self.cistransCfgToDict(cfg, obmol)))
def test_stereo(self, mol): """test of successful use of atom and bond stereo configurations""" print 'test stereo',mol.HasChiralityPerceived() #facade = ob.OBStereoFacade(mol); #for atom in ob.OBMolAtomIter(mol): # if facade.HasTetrahedralStereo(atom.GetId()): # stereo = self.get_atom_stereo(facade,mol,atom) # print atom.GetId(), atom.GetIdx(), stereo for p in mol.GetData(): if p.GetDataType() == ob.StereoData: ts = ob.toTetrahedralStereo(p) if ts.IsValid(): cfg = ts.GetConfig() stereo = self.stereoCfgToDict(cfg, mol) print stereo else: ct = ob.toCisTransStereo(p) cfg = ct.GetConfig() cistrans = self.cistransCfgToDict(cfg, mol) print cistrans