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11 """ Calculation of Lipinski parameters for molecules
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13 """
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15 from rdkit import Chem
16 from rdkit.Chem import rdMolDescriptors
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34 HDonorSmarts = Chem.MolFromSmarts('[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]')
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37 HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),\
38 $([O,S;H0;v2]),$([O,S;-]),\
39 $([N;v3;!$(N-*=!@[O,N,P,S])]),\
40 $([nH0,o,s;+0])\
41 ]')
42 HeteroatomSmarts = Chem.MolFromSmarts('[!#6;!#1]')
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47 RotatableBondSmarts = Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]')
48 NHOHSmarts = Chem.MolFromSmarts('[#8H1,#7H1,#7H2,#7H3]')
49 NOCountSmarts = Chem.MolFromSmarts('[#7,#8]')
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53 return len(mol.GetSubstructMatches(smarts,uniquify=1))
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55 NumHDonors = lambda x:rdMolDescriptors.CalcNumHBD(x)
56 NumHDonors.__doc__="Number of Hydrogen Bond Donors"
57 NumHDonors.version="1.0.0"
58 _HDonors = lambda x,y=HDonorSmarts:x.GetSubstructMatches(y,uniquify=1)
59 NumHAcceptors = lambda x:rdMolDescriptors.CalcNumHBA(x)
60 NumHAcceptors.__doc__="Number of Hydrogen Bond Acceptors"
61 NumHAcceptors.version="2.0.0"
62 _HAcceptors = lambda x,y=HAcceptorSmarts:x.GetSubstructMatches(y,uniquify=1)
63 NumHeteroatoms = lambda x:rdMolDescriptors.CalcNumHeteroatoms(x)
64 NumHeteroatoms.__doc__="Number of Heteroatoms"
65 NumHeteroatoms.version="1.0.0"
66 _Heteroatoms = lambda x,y=HeteroatomSmarts:x.GetSubstructMatches(y,uniquify=1)
67 NumRotatableBonds = lambda x:rdMolDescriptors.CalcNumRotatableBonds(x)
68 NumRotatableBonds.__doc__="Number of Rotatable Bonds"
69 NumRotatableBonds.version="1.0.0"
70 _RotatableBonds = lambda x,y=RotatableBondSmarts:x.GetSubstructMatches(y,uniquify=1)
71 NOCount = lambda x:rdMolDescriptors.CalcNumLipinskiHBA(x)
72 NOCount.__doc__="Number of Nitrogens and Oxygens"
73 NOCount.version="1.0.0"
74 NHOHCount = lambda x:rdMolDescriptors.CalcNumLipinskiHBD(x)
75 NHOHCount.__doc__="Number of NHs or OHs"
76 NHOHCount.version="2.0.0"
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78 RingCount=lambda x:rdMolDescriptors.CalcNumRings(x)
79 RingCount.version = "1.0.0"
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82 " Number of heavy atoms a molecule."
83 return mol.GetNumHeavyAtoms()
84 HeavyAtomCount.version = "1.0.1"
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86
87 _bulkConvert=("CalcFractionCSP3","CalcNumAromaticRings","CalcNumSaturatedRings","CalcNumAromaticHeterocycles",
88 "CalcNumAromaticCarbocycles","CalcNumSaturatedHeterocycles","CalcNumSaturatedCarbocycles","CalcNumAliphaticRings",
89 "CalcNumAliphaticHeterocycles","CalcNumAliphaticCarbocycles")
90 for txt in _bulkConvert:
91 _cfn = getattr(rdMolDescriptors,txt)
92 _fn = lambda x,y=_cfn:y(x)
93 try:
94 _fn.version=getattr(rdMolDescriptors,"_"+txt+"_version")
95 except AttributeError:
96 pass
97 _fn.__doc__=_cfn.__doc__
98 nm = txt.replace("Calc","")
99 locals()[nm]=_fn
100