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#
# Copyright (C) 2019 Greg Landrum
# All Rights Reserved
#
import unittest
from io import BytesIO
from rdkit import Chem, RDConfig, rdBase
from rdkit.Chem.rdmolops import _TestSetProps
class TestCase(unittest.TestCase):
def setUp(self):
self.sdf = b"""
RDKit 2D
3 3 0 0 0 0 0 0 0 0999 V2000
0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4330 0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.4330 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 1 1 0
M END
> <atom.dprop.PartialCharge> (1)
0.008 -0.314 0.008
> <atom.iprop.NumHeavyNeighbors> (1)
2 2 2
> <atom.prop.AtomLabel> (1)
C1 N2 C3
> <atom.bprop.IsCarbon> (1)
1 0 1
> <atom.prop.PartiallyMissing> (1)
one n/a three
> <atom.iprop.PartiallyMissingInt> (1)
[?] 2 2 ?
$$$$"""
def testForwardSupplier(self):
sio = BytesIO(self.sdf)
suppl = Chem.ForwardSDMolSupplier(sio)
suppl.SetProcessPropertyLists(False)
m = next(suppl)
self.assertTrue(m.HasProp("atom.prop.AtomLabel"))
self.assertFalse(m.GetAtomWithIdx(0).HasProp("AtomLabel"))
sio = BytesIO(self.sdf)
suppl = Chem.ForwardSDMolSupplier(sio)
self.assertTrue(suppl.GetProcessPropertyLists())
m = next(suppl)
self.assertTrue(m.HasProp("atom.prop.AtomLabel"))
self.assertTrue(m.GetAtomWithIdx(0).HasProp("AtomLabel"))
def testSupplier(self):
suppl = Chem.SDMolSupplier()
suppl.SetData(self.sdf)
suppl.SetProcessPropertyLists(False)
m = suppl[0]
self.assertFalse(suppl.GetProcessPropertyLists())
self.assertTrue(m.HasProp("atom.prop.AtomLabel"))
self.assertFalse(m.GetAtomWithIdx(0).HasProp("AtomLabel"))
suppl.SetProcessPropertyLists(True)
m = suppl[0]
self.assertTrue(m.HasProp("atom.prop.AtomLabel"))
self.assertTrue(m.GetAtomWithIdx(0).HasProp("AtomLabel"))
def testCreateLists(self):
suppl = Chem.SDMolSupplier()
suppl.SetData(self.sdf)
m = suppl[0]
self.assertTrue(m.GetAtomWithIdx(0).HasProp("NumHeavyNeighbors"))
m.ClearProp("atom.iprop.NumHeavyNeighbors")
self.assertFalse(m.HasProp("atom.iprop.NumHeavyNeighbors"))
Chem.CreateAtomIntPropertyList(m, "NumHeavyNeighbors")
self.assertTrue(m.HasProp("atom.iprop.NumHeavyNeighbors"))
self.assertTrue(m.GetAtomWithIdx(0).HasProp("PartialCharge"))
m.ClearProp("atom.dprop.PartialCharge")
self.assertFalse(m.HasProp("atom.dprop.PartialCharge"))
Chem.CreateAtomDoublePropertyList(m, "PartialCharge")
self.assertTrue(m.HasProp("atom.dprop.PartialCharge"))
self.assertTrue(m.GetAtomWithIdx(0).HasProp("IsCarbon"))
m.ClearProp("atom.bprop.IsCarbon")
self.assertFalse(m.HasProp("atom.bprop.IsCarbon"))
Chem.CreateAtomBoolPropertyList(m, "IsCarbon")
self.assertTrue(m.HasProp("atom.bprop.IsCarbon"))
self.assertTrue(m.GetAtomWithIdx(0).HasProp("PartiallyMissing"))
m.ClearProp("atom.prop.PartiallyMissing")
self.assertFalse(m.HasProp("atom.prop.PartiallyMissing"))
Chem.CreateAtomStringPropertyList(m, "PartiallyMissing")
self.assertTrue(m.HasProp("atom.prop.PartiallyMissing"))
self.assertEqual(m.GetProp("atom.prop.PartiallyMissing"), "one n/a three")
Chem.CreateAtomStringPropertyList(m, "PartiallyMissing", missingValueMarker="?")
self.assertTrue(m.HasProp("atom.prop.PartiallyMissing"))
self.assertEqual(m.GetProp("atom.prop.PartiallyMissing"), "[?] one ? three")
def testGithubPR4160(self):
# this shouldn't fail with a bad any cast anymore
from rdkit import Chem
m = Chem.MolFromSmiles("CC")
for a in m.GetAtoms():
a.SetIntProp("foo", 1)
Chem.CreateAtomIntPropertyList(m, "foo")
def testSetProps(self):
from rdkit import Chem
m = Chem.MolFromSmiles("CC")
conf = Chem.Conformer(m.GetNumAtoms())
for i in range(m.GetNumAtoms()):
conf.SetAtomPosition(i, (0., 0., 0.))
m.AddConformer(conf)
_TestSetProps(m)
default_expected = {'bool': True, 'uint': 4294967295, 'double': 3.14159, 'svint': [0, 1, 2, -2], 'svuint': [0, 1, 2, 4294967294], 'svdouble': [0.0, 1.0, 2.0], 'svstring': ['The', 'RDKit']}
def check(ob, prefix):
expected = {prefix + k:v for k,v in default_expected.items()}
d = ob.GetPropsAsDict(False, False)
for k,v in d.items():
if 'sv' in k: d[k] = list(v)
assert d == expected, repr((d, expected))
for k,v in expected.items():
v2 = ob.GetProp(k, True)
if 'sv' in k: v2 = list(v2)
assert v2 == v, repr(k, v2, v)
assert type(ob.GetProp(k)) == str
return len(d) > 0
assert check(m, "mol_")
for atom in m.GetAtoms():
check(atom, f"atom_{atom.GetIdx()}")
for bond in m.GetBonds():
check(bond, f"bond_{bond.GetIdx()}")
for idx, conf in enumerate(m.GetConformers()):
check(conf, f"conf_{idx}")
if __name__ == '__main__':
unittest.main()
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