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* Fixes #3553 * add another test * Apply suggestions from code review Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com> * add an additional test for that Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
This commit is contained in:
Greg Landrum
GitHub
@@ -5917,11 +5917,14 @@ M END
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self.assertEqual(m_noh.GetNumAtoms(), m.GetNumAtoms() - 2)
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self.assertTrue(m_noh.GetAtomWithIdx(2).HasProp("_isotopicHs"))
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self.assertEqual(tuple(map(int,
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m_noh.GetAtomWithIdx(2).GetProp("_isotopicHs").split())), (2,2))
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m_noh.GetAtomWithIdx(2).GetProp("_isotopicHs").split())), (2, 2))
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m_h = Chem.AddHs(m_noh)
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self.assertFalse(m_h.GetAtomWithIdx(2).HasProp("_isotopicHs"))
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self.assertEqual(sum([1 for nbr in m_h.GetAtomWithIdx(2).GetNeighbors()
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if (nbr.GetAtomicNum() == 1 and nbr.GetIsotope())]), 2)
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self.assertEqual(
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sum([
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1 for nbr in m_h.GetAtomWithIdx(2).GetNeighbors()
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if (nbr.GetAtomicNum() == 1 and nbr.GetIsotope())
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]), 2)
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m = Chem.MolFromSmiles('*[H]', smips)
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ps = Chem.RemoveHsParameters()
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@@ -6166,36 +6169,36 @@ M END
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with open(fileN, 'rb') as inf:
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d = inf.read()
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mol = Chem.MolFromPNGString(d)
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nd = Chem.MolMetadataToPNGString(mol,d)
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vals = {'foo':'1','bar':'2'}
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nd = Chem.MolMetadataToPNGString(mol, d)
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vals = {'foo': '1', 'bar': '2'}
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nd = Chem.AddMetadataToPNGString(vals, nd)
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nvals = Chem.MetadataFromPNGString(nd)
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self.assertTrue('foo' in nvals)
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self.assertEqual(nvals['foo'],b'1')
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self.assertEqual(nvals['foo'], b'1')
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self.assertTrue('bar' in nvals)
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self.assertEqual(nvals['bar'],b'2')
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self.assertEqual(nvals['bar'], b'2')
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nd = Chem.AddMetadataToPNGFile(vals, fileN)
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nvals = Chem.MetadataFromPNGString(nd)
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self.assertTrue('foo' in nvals)
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self.assertEqual(nvals['foo'],b'1')
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self.assertEqual(nvals['foo'], b'1')
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self.assertTrue('bar' in nvals)
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self.assertEqual(nvals['bar'],b'2')
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self.assertEqual(nvals['bar'], b'2')
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vals = {'foo':1,'bar':'2'}
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vals = {'foo': 1, 'bar': '2'}
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with self.assertRaises(TypeError):
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nd = Chem.AddMetadataToPNGString(vals,d)
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nd = Chem.AddMetadataToPNGString(vals, d)
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def test_github3403(self):
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core1 = "[$(C-!@[a])](=O)(Cl)"
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sma = Chem.MolFromSmarts(core1)
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m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
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self.assertFalse(m.HasSubstructMatch(sma, recursionPossible=False))
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m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
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self.assertTrue(m.HasSubstructMatch(sma))
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m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
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self.assertFalse(m.HasSubstructMatch(sma, recursionPossible=False))
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@@ -6208,24 +6211,44 @@ M END
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self.assertEqual(len(mols_list), len(mols_list_compr))
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def test_github3492(self):
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def read_smile(s):
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m = Chem.MolFromSmiles(s)
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rdkit.Chem.rdDepictor.Compute2DCoords(m)
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return m
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m = Chem.MolFromSmiles(s)
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rdkit.Chem.rdDepictor.Compute2DCoords(m)
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return m
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def sq_dist(a, b):
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ab = [a[i] - b[i] for i, _ in enumerate(a)]
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return sum([d * d for d in ab])
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self.assertIsNotNone(Chem.MolFromSmiles("OCCN").GetAtoms()[0].GetOwningMol())
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self.assertEqual([Chem.MolFromSmiles("OCCN").GetAtoms()[i].GetAtomicNum() for i in range(4)], [8, 6, 6, 7])
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self.assertEqual([Chem.MolFromSmiles("OCCN").GetAtoms()[i].GetAtomicNum() for i in range(4)],
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[8, 6, 6, 7])
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self.assertIsNotNone(Chem.MolFromSmiles("O=CCC=N").GetBonds()[0].GetOwningMol())
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self.assertEqual([Chem.MolFromSmiles("O=CCC=N").GetBonds()[i].GetBondType() for i in range(4)],
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[Chem.BondType.DOUBLE, Chem.BondType.SINGLE, Chem.BondType.SINGLE, Chem.BondType.DOUBLE])
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self.assertEqual(
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[Chem.MolFromSmiles("O=CCC=N").GetBonds()[i].GetBondType() for i in range(4)],
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[Chem.BondType.DOUBLE, Chem.BondType.SINGLE, Chem.BondType.SINGLE, Chem.BondType.DOUBLE])
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self.assertIsNotNone(read_smile("CCC").GetConformers()[0].GetOwningMol())
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pos = read_smile("CCC").GetConformers()[0].GetPositions()
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self.assertAlmostEqual(sq_dist(pos[0], pos[1]), sq_dist(pos[1], pos[2]))
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def test_github3553(self):
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from io import StringIO
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fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Wrap', 'test_data',
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'github3553.sdf')
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sdSup = Chem.SDMolSupplier(fileN)
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for mol in sdSup:
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pval = mol.GetProp('boiling.point.predicted')
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sio = StringIO()
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w = Chem.SDWriter(sio)
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w.SetKekulize(True)
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w.SetForceV3000(True)
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w.write(mol)
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w.flush()
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txt = sio.getvalue()
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self.assertTrue(pval in txt)
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if __name__ == '__main__':
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if "RDTESTCASE" in os.environ:
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suite = unittest.TestSuite()
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208
Code/GraphMol/Wrap/test_data/github3553.sdf
Normal file
208
Code/GraphMol/Wrap/test_data/github3553.sdf
Normal file
@@ -0,0 +1,208 @@
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some padding that is just the ri
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RDKit 2D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 12 12 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.08313 -0.7909 0 0
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M V30 2 O -1.08393 -1.7909 0 0
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M V30 3 O -1.94873 -0.2901 0 0
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M V30 4 Cl -1.08153 1.2091 0 0
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M V30 5 Cl 0.648067 -1.7921 0 0
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M V30 6 N 0.651267 2.2079 0 0
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M V30 7 C -0.216733 -0.2915 0 0
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M V30 8 C -0.215933 0.7085 0 0
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M V30 9 C 0.648867 -0.7921 0 0
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M V30 10 C 0.650467 1.2079 0 0
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M V30 11 C 1.51527 -0.2929 0 0
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M V30 12 C 1.51607 0.7071 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 2 1 3
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M V30 3 1 1 7
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M V30 4 1 4 8
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M V30 5 1 5 9
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M V30 6 1 6 10
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M V30 7 2 7 8
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M V30 8 1 7 9
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M V30 9 1 8 10
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M V30 10 2 9 11
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M V30 11 2 10 12
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M V30 12 1 11 12
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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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> <cas.rn> (1)
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paddingpad
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> <cas.index.name> (1)
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paddingpaddingpaddingpaddingpadding
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> <molecular.formula> (1)
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C7H5Cl2NO2
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> <molecular.weight> (1)
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206.03
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> <boiling.point.predicted> (1)
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123.4±56.7 𐍈C paddingpaddingp
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$$$$
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some padding that is just the ri
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RDKit 2D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 12 12 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.08313 -0.7909 0 0
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M V30 2 O -1.08393 -1.7909 0 0
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M V30 3 O -1.94873 -0.2901 0 0
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M V30 4 Cl -1.08153 1.2091 0 0
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M V30 5 Cl 0.648067 -1.7921 0 0
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M V30 6 N 0.651267 2.2079 0 0
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M V30 7 C -0.216733 -0.2915 0 0
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M V30 8 C -0.215933 0.7085 0 0
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M V30 9 C 0.648867 -0.7921 0 0
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M V30 10 C 0.650467 1.2079 0 0
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M V30 11 C 1.51527 -0.2929 0 0
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M V30 12 C 1.51607 0.7071 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 2 1 3
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M V30 3 1 1 7
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M V30 4 1 4 8
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M V30 5 1 5 9
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M V30 6 1 6 10
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M V30 7 2 7 8
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M V30 8 1 7 9
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M V30 9 1 8 10
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M V30 10 2 9 11
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M V30 11 2 10 12
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M V30 12 1 11 12
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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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> <cas.rn> (1)
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paddingpad
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> <cas.index.name> (1)
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paddingpaddingpaddingpaddingpadding
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> <molecular.formula> (1)
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C7H5Cl2NO2
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> <molecular.weight> (1)
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206.03
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> <boiling.point.predicted> (1)
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123.4±56.7 €C paddingpaddingp
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$$$$
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some padding that is just the ri
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RDKit 2D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 12 12 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.08313 -0.7909 0 0
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M V30 2 O -1.08393 -1.7909 0 0
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M V30 3 O -1.94873 -0.2901 0 0
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M V30 4 Cl -1.08153 1.2091 0 0
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M V30 5 Cl 0.648067 -1.7921 0 0
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M V30 6 N 0.651267 2.2079 0 0
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M V30 7 C -0.216733 -0.2915 0 0
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M V30 8 C -0.215933 0.7085 0 0
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M V30 9 C 0.648867 -0.7921 0 0
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M V30 10 C 0.650467 1.2079 0 0
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M V30 11 C 1.51527 -0.2929 0 0
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M V30 12 C 1.51607 0.7071 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 2 1 3
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M V30 3 1 1 7
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M V30 4 1 4 8
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M V30 5 1 5 9
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M V30 6 1 6 10
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M V30 7 2 7 8
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M V30 8 1 7 9
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M V30 9 1 8 10
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M V30 10 2 9 11
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M V30 11 2 10 12
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M V30 12 1 11 12
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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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> <cas.rn> (1)
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paddingpad
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> <cas.index.name> (1)
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paddingpaddingpaddingpaddingpadding
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> <molecular.formula> (1)
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C7H5Cl2NO2
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> <molecular.weight> (1)
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206.03
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> <boiling.point.predicted> (1)
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123.4±56.7 °C paddingpaddingp
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$$$$
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some padding that is just the ri
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RDKit 2D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 12 12 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.08313 -0.7909 0 0
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M V30 2 O -1.08393 -1.7909 0 0
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M V30 3 O -1.94873 -0.2901 0 0
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M V30 4 Cl -1.08153 1.2091 0 0
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M V30 5 Cl 0.648067 -1.7921 0 0
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M V30 6 N 0.651267 2.2079 0 0
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M V30 7 C -0.216733 -0.2915 0 0
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M V30 8 C -0.215933 0.7085 0 0
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M V30 9 C 0.648867 -0.7921 0 0
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M V30 10 C 0.650467 1.2079 0 0
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M V30 11 C 1.51527 -0.2929 0 0
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M V30 12 C 1.51607 0.7071 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 2 1 3
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M V30 3 1 1 7
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M V30 4 1 4 8
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M V30 5 1 5 9
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M V30 6 1 6 10
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M V30 7 2 7 8
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M V30 8 1 7 9
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M V30 9 1 8 10
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M V30 10 2 9 11
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M V30 11 2 10 12
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M V30 12 1 11 12
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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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> <cas.rn> (1)
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paddingpad
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> <cas.index.name> (1)
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paddingpaddingpaddingpaddingpadding
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> <molecular.formula> (1)
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C7H5Cl2NO2
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> <molecular.weight> (1)
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206.03
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> <boiling.point.predicted> (1)
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123.4±5°°°°°C paddingpaddingp
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$$$$
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@@ -211,17 +211,17 @@ class streambuf : public std::basic_streambuf<char> {
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CHECK_INVARIANT(iobase, "base class not found");
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#endif
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bool isTextMode = PyObject_IsInstance(python_file_obj.ptr(), iobase.ptr());
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df_isTextMode = PyObject_IsInstance(python_file_obj.ptr(), iobase.ptr());
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switch (mode) {
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case 's': /// yeah, is redundant, but it is somehow natural to do "s"
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case 't':
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if (!isTextMode)
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if (!df_isTextMode)
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throw ValueErrorException(
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"Need a text mode file object like StringIO or a file opened "
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"with mode 't'");
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break;
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case 'b':
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if (isTextMode)
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if (df_isTextMode)
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throw ValueErrorException(
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"Need a binary mode file object like BytesIO or a file opened "
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"with mode 'b'");
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@@ -280,17 +280,42 @@ class streambuf : public std::basic_streambuf<char> {
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}
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farthest_pptr = std::max(farthest_pptr, pptr());
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off_type n_written = (off_type)(farthest_pptr - pbase());
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bp::str chunk(pbase(), farthest_pptr);
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off_type orig_n_written = n_written;
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const unsigned int STD_ASCII = 0x7F;
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if (df_isTextMode && c > STD_ASCII) {
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// we're somewhere in the middle of a utf8 block. If we
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// only write part of it we'll end up with an exception,
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// so push everything that could be utf8 into the next block
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while (n_written > 0 &&
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static_cast<unsigned int>(write_buffer[n_written - 1]) > STD_ASCII) {
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--n_written;
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}
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}
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bp::str chunk(pbase(), pbase() + n_written);
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py_write(chunk);
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if (!traits_type::eq_int_type(c, traits_type::eof())) {
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if ((!df_isTextMode || c <= STD_ASCII) &&
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!traits_type::eq_int_type(c, traits_type::eof())) {
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py_write(traits_type::to_char_type(c));
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n_written++;
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}
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setp(pbase(), epptr());
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// ^^^ 27.5.2.4.5 (5)
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farthest_pptr = pptr();
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if (n_written) {
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pos_of_write_buffer_end_in_py_file += n_written;
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setp(pbase(), epptr());
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// ^^^ 27.5.2.4.5 (5)
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farthest_pptr = pptr();
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if (df_isTextMode && c > STD_ASCII &&
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!traits_type::eq_int_type(c, traits_type::eof())) {
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size_t n_to_copy = orig_n_written - n_written;
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for (size_t i = 0; i < n_to_copy; ++i) {
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sputc(write_buffer[n_written + i]);
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++farthest_pptr;
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}
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sputc(c);
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++farthest_pptr;
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}
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}
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return traits_type::eq_int_type(c, traits_type::eof())
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? traits_type::not_eof(c)
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@@ -405,6 +430,7 @@ class streambuf : public std::basic_streambuf<char> {
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de-allocated only at destruction time.
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*/
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char* write_buffer;
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bool df_isTextMode;
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off_type pos_of_read_buffer_end_in_py_file,
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pos_of_write_buffer_end_in_py_file;
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Reference in New Issue
Block a user