def testCreateSGroup(self):
mol = Chem.MolFromMolBlock('''
Mrv1810 10061910532D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 O -14.8632 3.7053 0 0
M V30 2 C -13.3232 3.7053 0 0
M V30 3 O -11.7832 3.7053 0 0
M V30 4 * -10.2453 3.6247 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 END BOND
M V30 END CTAB
M END''')
self.assertTrue(mol is not None)
mcpy = Chem.Mol(mol)
sg = Chem.CreateMolSubstanceGroup(mcpy, "SRU")
self.assertEqual(sg.GetProp("TYPE"), "SRU")
sg = Chem.GetMolSubstanceGroupWithIdx(mcpy, 0)
sg.AddBracket((Geometry.Point3D(-11.1, 4.6,
0), Geometry.Point3D(-11.1, 2.7, 0)))
sg.AddBracket((Geometry.Point3D(-13.9, 2.7,
0), Geometry.Point3D(-13.9, 4.6, 0)))
sg.AddAtomWithIdx(1)
sg.AddAtomWithIdx(2)
sg.AddBondWithIdx(0)
sg.AddBondWithIdx(2)
sg.SetProp("CONNECT", "HT")
sg.SetProp("LABEL", "n")
mb = Chem.MolToMolBlock(mcpy, forceV3000=True)
self.assertNotEqual(mb.find('V30 1 SRU'), -1)
self.assertNotEqual(mb.find('BRKXYZ'), -1)
self.assertNotEqual(mb.find('CONNECT=HT'), -1)
def testAttachPoints(self):
mol = Chem.MolFromMolBlock('''
Mrv2014 09012006262D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 1 0 0
M V30 BEGIN ATOM
M V30 1 C -5.0833 0.0833 0 0
M V30 2 C -3.7497 0.8533 0 0
M V30 3 O -2.416 0.0833 0 0
M V30 4 O -3.7497 2.3933 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 2 2 4
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SUP 0 ATOMS=(3 2 3 4) SAP=(3 2 1 1) XBONDS=(1 1) LABEL=CO2H ESTATE=E
M V30 END SGROUP
M V30 END CTAB
M END''')
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertEqual(len(sgs), 1)
sg0 = sgs[0]
pd = sg0.GetPropsAsDict()
self.assertTrue('TYPE' in pd)
self.assertEqual(pd['TYPE'], 'SUP')
aps = sg0.GetAttachPoints()
self.assertEqual(len(aps), 1)
self.assertEqual(aps[0].aIdx, 1)
self.assertEqual(aps[0].lvIdx, 0)
self.assertEqual(aps[0].id, '1')
mol = Chem.MolFromMolBlock('''
Mrv2014 09012006262D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -5.0833 0.0833 0 0
M V30 2 C -3.7497 0.8533 0 0
M V30 3 O -2.416 0.0833 0 0
M V30 4 O -3.7497 2.3933 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 2 2 4
M V30 END BOND
M V30 END CTAB
M END''')
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertEqual(len(sgs), 0)
sg = Chem.CreateMolSubstanceGroup(mol, "SUP")
sg.AddAtomWithIdx(1)
sg.AddAtomWithIdx(2)
sg.AddAtomWithIdx(3)
sg.AddBondWithIdx(0)
sg.SetProp('LABEL', 'CO2H')
sg.AddAttachPoint(1, 0, '1')
molb = Chem.MolToV3KMolBlock(mol)
self.assertGreater(
molb.find('M V30 1 SUP 0 ATOMS=(3 2 3 4) XBONDS=(1 1) LABEL=CO2H SAP=(3 2 1 1)'), 0)
