def testBasics(self):
self.assertTrue(self.m1 is not None)
sgs = Chem.GetMolSubstanceGroups(self.m1)
self.assertEqual(len(sgs), 2)
self.assertTrue(sgs[0].HasProp("TYPE"))
self.assertTrue(sgs[1].HasProp("TYPE"))
self.assertEqual(sgs[0].GetProp("TYPE"), "DAT")
self.assertEqual(sgs[1].GetProp("TYPE"), "DAT")
self.assertTrue(sgs[0].HasProp("FIELDNAME"))
self.assertEqual(sgs[0].GetProp("FIELDNAME"), "pH")
self.assertEqual(
sorted(sgs[0].GetPropNames()),
['DATAFIELDS', 'FIELDDISP', 'FIELDNAME', 'ID', 'TYPE', 'index'])
dd = sgs[0].GetPropsAsDict()
self.assertTrue("TYPE" in dd)
self.assertEqual(dd["TYPE"], "DAT")
self.assertTrue("FIELDNAME" in dd)
self.assertEqual(dd["FIELDNAME"], "pH")
sgs[0].ClearProp("FIELDNAME")
self.assertFalse(sgs[0].HasProp("FIELDNAME"))
# The property doesn't exist anymore, but this should not fail
sgs[0].ClearProp("FIELDNAME")
self.assertFalse(sgs[0].HasProp("FIELDNAME"))
Chem.ClearMolSubstanceGroups(self.m1)
self.assertEqual(len(Chem.GetMolSubstanceGroups(self.m1)), 0)
def testCopying(self):
mol = Chem.MolFromMolBlock('''
Mrv2014 07312005252D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 7 6 3 0 0
M V30 BEGIN ATOM
M V30 1 * -12.75 11.5 0 0
M V30 2 O -11.4163 12.27 0 0
M V30 3 C -10.0826 11.5 0 0
M V30 4 C -8.749 12.27 0 0
M V30 5 O -10.0826 9.96 0 0
M V30 6 N -7.4153 11.5 0 0
M V30 7 C -6.0816 12.27 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 4 2 3 5
M V30 5 1 4 6
M V30 6 1 6 7
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SRU 0 ATOMS=(3 2 3 5) XBONDS=(2 1 3) BRKXYZ=(9 -9.9955 12.6173 0 -
M V30 -9.0715 11.0169 0 0 0 0) BRKXYZ=(9 -11.5035 11.1527 0 -12.4275 12.7531 -
M V30 0 0 0 0) CONNECT=HT LABEL=n
M V30 2 DAT 0 ATOMS=(1 6) FIELDNAME=foo_data -
M V30 FIELDDISP=" -7.4153 11.5000 DAU ALL 0 0" -
M V30 MRV_FIELDDISP=0 FIELDDATA=bar
M V30 3 DAT 0 ATOMS=(1 7) FIELDNAME=bar_data -
M V30 FIELDDISP=" -6.0816 12.2700 DAU ALL 0 0" -
M V30 MRV_FIELDDISP=0 FIELDDATA=baz
M V30 END SGROUP
M V30 END CTAB
M END''')
self.assertEqual(len(Chem.GetMolSubstanceGroups(mol)), 3)
mol2 = Chem.Mol(mol)
Chem.ClearMolSubstanceGroups(mol2)
self.assertEqual(len(Chem.GetMolSubstanceGroups(mol2)), 0)
sgs = Chem.GetMolSubstanceGroups(mol)
Chem.AddMolSubstanceGroup(mol2, sgs[0])
Chem.AddMolSubstanceGroup(mol2, sgs[2])
self.assertEqual(len(Chem.GetMolSubstanceGroups(mol2)), 2)
molb = Chem.MolToV3KMolBlock(mol2)
self.assertEqual(molb.find("foo_data"), -1)
self.assertGreater(
molb.find("M V30 2 DAT 0 ATOMS=(1 7) FIELDNAME=bar_data"), 0)
# we can also use this to copy SGroups:
sgs2 = Chem.GetMolSubstanceGroups(mol2)
newsg = Chem.AddMolSubstanceGroup(mol2, sgs[1])
newsg.SetProp("FIELDNAME", "blah_data")
molb = Chem.MolToV3KMolBlock(mol2)
print(molb)
self.assertGreater(
molb.find("M V30 3 DAT 0 ATOMS=(1 6) FIELDNAME=blah_data"), 0)
def testBasics3000(self):
self.assertTrue(self.m2 is not None)
sgs = Chem.GetMolSubstanceGroups(self.m2)
self.assertEqual(len(sgs), 2)
self.assertTrue(sgs[0].HasProp("TYPE"))
self.assertTrue(sgs[1].HasProp("TYPE"))
self.assertEqual(sgs[0].GetProp("TYPE"), "DAT")
self.assertEqual(sgs[1].GetProp("TYPE"), "DAT")
self.assertTrue(sgs[0].HasProp("FIELDNAME"))
self.assertEqual(sgs[0].GetProp("FIELDNAME"), "pH")
self.assertEqual(
sorted(sgs[0].GetPropNames()),
['DATAFIELDS', 'FIELDDISP', 'FIELDNAME', 'TYPE', 'index'])
dd = sgs[0].GetPropsAsDict()
self.assertTrue("TYPE" in dd)
self.assertEqual(dd["TYPE"], "DAT")
self.assertTrue("FIELDNAME" in dd)
self.assertEqual(dd["FIELDNAME"], "pH")
Chem.ClearMolSubstanceGroups(self.m2)
self.assertEqual(len(Chem.GetMolSubstanceGroups(self.m2)), 0)
def remove_sgroups_from_mol(m):
""" removes all Sgroups
"""
Chem.ClearMolSubstanceGroups(m)
return m
