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e5620e0c57
* first steps towards StructureGroups being editable in Python * typo fix * Add initial features to allow editing SGroups from Python. * update test * typo
157 lines
5.0 KiB
Python
157 lines
5.0 KiB
Python
#
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# Copyright (C) 2019 Greg Landrum
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# All Rights Reserved
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#
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# This file is part of the RDKit.
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# The contents are covered by the terms of the BSD license
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# which is included in the file license.txt, found at the root
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# of the RDKit source tree.
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#
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from rdkit import Chem
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from rdkit import Geometry
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from rdkit.Chem import RDConfig
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import os
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import sys
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import unittest
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class TestCase(unittest.TestCase):
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def setUp(self):
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mb = """
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ACCLDraw04231812452D
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13 13 0 0 0 0 0 0 0 0999 V2000
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5.0960 -4.3327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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7.4016 -4.3321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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5.0960 -5.6718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.2539 -6.3314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.2510 -2.3329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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7.4056 -1.6662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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5.0963 -1.6662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.2510 -3.6663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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8.5505 -6.3291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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8.5505 -7.6624 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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9.7052 -5.6625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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7.4016 -5.6658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.9416 -2.3329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3 4 2 0 0 0 0
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1 3 1 0 0 0 0
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5 8 1 0 0 0 0
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5 7 2 0 0 0 0
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5 6 1 0 0 0 0
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1 8 2 0 0 0 0
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2 8 1 0 0 0 0
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9 12 1 0 0 0 0
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9 11 2 0 0 0 0
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9 10 1 0 0 0 0
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4 12 1 0 0 0 0
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2 12 2 0 0 0 0
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7 13 1 0 0 0 0
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M STY 2 1 DAT 2 DAT
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M SLB 2 1 1 2 2
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M SAL 1 1 10
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M SDT 1 pH
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M SDD 1 0.0000 0.0000 DR ALL 1 6
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M SED 1 4.6
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M SAL 2 2 5 7
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M SBL 2 1 4
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M SDT 2 Stereo
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M SDD 2 0.0000 0.0000 DR ALL 1 6
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M SED 2 E/Z unknown
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M END"""
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self.m1 = Chem.MolFromMolBlock(mb)
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def testBasics(self):
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self.assertTrue(self.m1 is not None)
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sgs = Chem.GetMolSubstanceGroups(self.m1)
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self.assertEqual(len(sgs), 2)
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self.assertTrue(sgs[0].HasProp("TYPE"))
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self.assertTrue(sgs[1].HasProp("TYPE"))
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self.assertEqual(sgs[0].GetProp("TYPE"), "DAT")
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self.assertEqual(sgs[1].GetProp("TYPE"), "DAT")
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self.assertTrue(sgs[0].HasProp("FIELDNAME"))
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self.assertEqual(sgs[0].GetProp("FIELDNAME"), "pH")
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self.assertEqual(sorted(sgs[0].GetPropNames()), [
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'DATAFIELDS', 'FIELDDISP', 'FIELDINFO', 'FIELDNAME', 'FIELDTYPE', 'ID', 'QUERYOP',
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'QUERYTYPE', 'TYPE'
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])
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dd = sgs[0].GetPropsAsDict()
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self.assertTrue("TYPE" in dd)
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self.assertEqual(dd["TYPE"], "DAT")
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self.assertTrue("FIELDNAME" in dd)
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self.assertEqual(dd["FIELDNAME"], "pH")
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Chem.ClearMolSubstanceGroups(self.m1)
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self.assertEqual(len(Chem.GetMolSubstanceGroups(self.m1)), 0)
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def testLifetime(self):
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self.assertTrue(self.m1 is not None)
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mcpy = Chem.Mol(self.m1)
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smi = Chem.MolToSmiles(mcpy)
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sgs = Chem.GetMolSubstanceGroups(mcpy)
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self.assertEqual(len(sgs), 2)
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mcpy = None
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parent = sgs[0].GetOwningMol()
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self.assertEqual(smi, Chem.MolToSmiles(parent))
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sgl = list(sgs)
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sgs = None
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parent = sgl[0].GetOwningMol()
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self.assertEqual(smi, Chem.MolToSmiles(parent))
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def testSetProp(self):
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self.assertTrue(self.m1 is not None)
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mcpy = Chem.Mol(self.m1)
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sg = Chem.GetMolSubstanceGroupWithIdx(mcpy, 0)
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sg.SetProp("foo", "bar")
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sgs2 = Chem.GetMolSubstanceGroups(mcpy)
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pd = sgs2[0].GetPropsAsDict()
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self.assertTrue('foo' in pd)
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self.assertEqual(pd['foo'], 'bar')
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def testCreateSGroup(self):
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mol = Chem.MolFromMolBlock('''
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Mrv1810 10061910532D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 4 3 0 0 0
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M V30 BEGIN ATOM
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M V30 1 O -14.8632 3.7053 0 0
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M V30 2 C -13.3232 3.7053 0 0
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M V30 3 O -11.7832 3.7053 0 0
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M V30 4 * -10.2453 3.6247 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 3 4
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M V30 END BOND
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M V30 END CTAB
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M END''')
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self.assertTrue(mol is not None)
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mcpy = Chem.Mol(mol)
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sg = Chem.CreateMolSubstanceGroup(mcpy, "SRU")
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self.assertEqual(sg.GetProp("TYPE"), "SRU")
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sg = Chem.GetMolSubstanceGroupWithIdx(mcpy, 0)
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sg.AddBracket((Geometry.Point3D(-11.1, 4.6, 0), Geometry.Point3D(-11.1, 2.7, 0)))
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sg.AddBracket((Geometry.Point3D(-13.9, 2.7, 0), Geometry.Point3D(-13.9, 4.6, 0)))
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sg.AddAtomWithIdx(1)
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sg.AddAtomWithIdx(2)
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sg.AddBondWithIdx(0)
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sg.AddBondWithIdx(2)
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sg.SetProp("CONNECT", "HT")
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sg.SetProp("LABEL", "n")
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mb = Chem.MolToMolBlock(mcpy, forceV3000=True)
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self.assertNotEqual(mb.find('V30 1 SRU'), -1)
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self.assertNotEqual(mb.find('BRKXYZ'), -1)
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self.assertNotEqual(mb.find('CONNECT=HT'), -1)
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if __name__ == '__main__':
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print("Testing SubstanceGroups wrapper")
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unittest.main()
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