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10 """ Calculation of Lipinski parameters for molecules
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12 """
13 from rdkit import Chem
14 from rdkit.Chem import rdMolDescriptors
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29 HDonorSmarts = Chem.MolFromSmarts('[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]')
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32 HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),' +
33 '$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),' +
34 '$([nH0,o,s;+0])]')
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36 HeteroatomSmarts = Chem.MolFromSmarts('[!#6;!#1]')
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41 RotatableBondSmarts = Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]')
42 NHOHSmarts = Chem.MolFromSmarts('[#8H1,#7H1,#7H2,#7H3]')
43 NOCountSmarts = Chem.MolFromSmarts('[#7,#8]')
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49 NumHDonors = lambda x: rdMolDescriptors.CalcNumHBD(x)
50 NumHDonors.__doc__ = "Number of Hydrogen Bond Donors"
51 NumHDonors.version = "1.0.0"
52 _HDonors = lambda x, y=HDonorSmarts: x.GetSubstructMatches(y, uniquify=1)
53 NumHAcceptors = lambda x: rdMolDescriptors.CalcNumHBA(x)
54 NumHAcceptors.__doc__ = "Number of Hydrogen Bond Acceptors"
55 NumHAcceptors.version = "2.0.0"
56 _HAcceptors = lambda x, y=HAcceptorSmarts: x.GetSubstructMatches(y, uniquify=1)
57 NumHeteroatoms = lambda x: rdMolDescriptors.CalcNumHeteroatoms(x)
58 NumHeteroatoms.__doc__ = "Number of Heteroatoms"
59 NumHeteroatoms.version = "1.0.0"
60 _Heteroatoms = lambda x, y=HeteroatomSmarts: x.GetSubstructMatches(y, uniquify=1)
61 NumRotatableBonds = lambda x: rdMolDescriptors.CalcNumRotatableBonds(x)
62 NumRotatableBonds.__doc__ = "Number of Rotatable Bonds"
63 NumRotatableBonds.version = "1.0.0"
64 _RotatableBonds = lambda x, y=RotatableBondSmarts: x.GetSubstructMatches(y, uniquify=1)
65 NOCount = lambda x: rdMolDescriptors.CalcNumLipinskiHBA(x)
66 NOCount.__doc__ = "Number of Nitrogens and Oxygens"
67 NOCount.version = "1.0.0"
68 NHOHCount = lambda x: rdMolDescriptors.CalcNumLipinskiHBD(x)
69 NHOHCount.__doc__ = "Number of NHs or OHs"
70 NHOHCount.version = "2.0.0"
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72 RingCount = lambda x: rdMolDescriptors.CalcNumRings(x)
73 RingCount.version = "1.0.0"
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77 " Number of heavy atoms a molecule."
78 return mol.GetNumHeavyAtoms()
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81 HeavyAtomCount.version = "1.0.1"
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83 _bulkConvert = ("CalcFractionCSP3", "CalcNumAromaticRings", "CalcNumSaturatedRings",
84 "CalcNumAromaticHeterocycles", "CalcNumAromaticCarbocycles",
85 "CalcNumSaturatedHeterocycles", "CalcNumSaturatedCarbocycles",
86 "CalcNumAliphaticRings", "CalcNumAliphaticHeterocycles",
87 "CalcNumAliphaticCarbocycles")
88 for txt in _bulkConvert:
89 _cfn = getattr(rdMolDescriptors, txt)
90 _fn = lambda x, y=_cfn: y(x)
91 try:
92 _fn.version = getattr(rdMolDescriptors, "_" + txt + "_version")
93 except AttributeError:
94 pass
95 _fn.__doc__ = _cfn.__doc__
96 nm = txt.replace("Calc", "")
97 locals()[nm] = _fn
98