mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +08:00
180c15fe0e
* first crude pass * fix a deprecation * change naming scheme, support bools * add standalone function * add a default value for missings * support long lines * stupid typo * make operator[] work * revisit missing value handling * modify missing value handling * switch to an alternate scheme for specifying missing values * clang-format * First pass at property list parser still needs more tests * add test for processMolPropertyLists * get this working as part of the ForwardSDMolSupplier * first pass at python wrappers and tests * clang-format run * add creation of property lists at the mol level * wrap long lines on output * remove PoC implementation * fix python wrappers * remove out-of-date reference to the Python PoC * changes in response to review
113 lines
3.6 KiB
Python
113 lines
3.6 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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from rdkit import RDConfig, rdBase
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from rdkit import Chem
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from io import BytesIO
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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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self.sdf = b"""
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RDKit 2D
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3 3 0 0 0 0 0 0 0 0999 V2000
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0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.4330 0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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-0.4330 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0
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2 3 1 0
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3 1 1 0
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M END
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> <atom.dprop.PartialCharge> (1)
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0.008 -0.314 0.008
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> <atom.iprop.NumHeavyNeighbors> (1)
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2 2 2
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> <atom.prop.AtomLabel> (1)
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C1 N2 C3
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> <atom.bprop.IsCarbon> (1)
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1 0 1
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> <atom.prop.PartiallyMissing> (1)
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one n/a three
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> <atom.iprop.PartiallyMissingInt> (1)
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[?] 2 2 ?
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$$$$"""
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def testForwardSupplier(self):
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sio = BytesIO(self.sdf)
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suppl = Chem.ForwardSDMolSupplier(sio)
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suppl.SetProcessPropertyLists(False)
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m = next(suppl)
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self.assertTrue(m.HasProp("atom.prop.AtomLabel"))
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self.assertFalse(m.GetAtomWithIdx(0).HasProp("AtomLabel"))
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sio = BytesIO(self.sdf)
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suppl = Chem.ForwardSDMolSupplier(sio)
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self.assertTrue(suppl.GetProcessPropertyLists())
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m = next(suppl)
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self.assertTrue(m.HasProp("atom.prop.AtomLabel"))
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self.assertTrue(m.GetAtomWithIdx(0).HasProp("AtomLabel"))
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def testSupplier(self):
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suppl = Chem.SDMolSupplier()
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suppl.SetData(self.sdf)
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suppl.SetProcessPropertyLists(False)
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m = suppl[0]
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self.assertFalse(suppl.GetProcessPropertyLists())
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self.assertTrue(m.HasProp("atom.prop.AtomLabel"))
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self.assertFalse(m.GetAtomWithIdx(0).HasProp("AtomLabel"))
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suppl.SetProcessPropertyLists(True)
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m = suppl[0]
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self.assertTrue(m.HasProp("atom.prop.AtomLabel"))
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self.assertTrue(m.GetAtomWithIdx(0).HasProp("AtomLabel"))
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def testCreateLists(self):
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suppl = Chem.SDMolSupplier()
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suppl.SetData(self.sdf)
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m = suppl[0]
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self.assertTrue(m.GetAtomWithIdx(0).HasProp("NumHeavyNeighbors"))
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m.ClearProp("atom.iprop.NumHeavyNeighbors")
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self.assertFalse(m.HasProp("atom.iprop.NumHeavyNeighbors"))
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Chem.CreateAtomIntPropertyList(m,"NumHeavyNeighbors")
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self.assertTrue(m.HasProp("atom.iprop.NumHeavyNeighbors"))
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self.assertTrue(m.GetAtomWithIdx(0).HasProp("PartialCharge"))
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m.ClearProp("atom.dprop.PartialCharge")
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self.assertFalse(m.HasProp("atom.dprop.PartialCharge"))
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Chem.CreateAtomDoublePropertyList(m,"PartialCharge")
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self.assertTrue(m.HasProp("atom.dprop.PartialCharge"))
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self.assertTrue(m.GetAtomWithIdx(0).HasProp("IsCarbon"))
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m.ClearProp("atom.bprop.IsCarbon")
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self.assertFalse(m.HasProp("atom.bprop.IsCarbon"))
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Chem.CreateAtomBoolPropertyList(m,"IsCarbon")
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self.assertTrue(m.HasProp("atom.bprop.IsCarbon"))
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self.assertTrue(m.GetAtomWithIdx(0).HasProp("PartiallyMissing"))
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m.ClearProp("atom.prop.PartiallyMissing")
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self.assertFalse(m.HasProp("atom.prop.PartiallyMissing"))
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Chem.CreateAtomStringPropertyList(m,"PartiallyMissing")
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self.assertTrue(m.HasProp("atom.prop.PartiallyMissing"))
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self.assertEqual(m.GetProp("atom.prop.PartiallyMissing"),"one n/a three")
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Chem.CreateAtomStringPropertyList(m,"PartiallyMissing",missingValueMarker="?")
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self.assertTrue(m.HasProp("atom.prop.PartiallyMissing"))
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self.assertEqual(m.GetProp("atom.prop.PartiallyMissing"),"[?] one ? three")
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if __name__ == '__main__':
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unittest.main()
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