Source Code for Module rdkit.Chem.Lipinski

 1  # $Id: Lipinski.py 1838 2011-10-01 14:13:43Z glandrum $ 
 2  # 
 3  # Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved @@ 
 6  #  This file is part of the RDKit. 
 7  #  The contents are covered by the terms of the BSD license 
 8  #  which is included in the file license.txt, found at the root 
 9  #  of the RDKit source tree. 
10  # 
11  """ Calculation of Lipinski parameters for molecules 
12   
13  """ 
14  #from Chem import rdchem 
15  from rdkit import Chem 
16  from rdkit.Chem import rdMolDescriptors 
17   
18  #----------------------------------- 
19  # on import build the SMARTS patterns so we only have to do it once 
20  #----------------------------------- 
21   
22  # The Daylight SMARTS expressions for 
23  # recognizing H-bond donors and acceptors in the Lipinski scheme. 
24  # HDonor     '[!#6;!H0;-0]' 
25  # HAcceptor  '[$([!#6;+0]);!$([F,Cl,Br,I]); 
26  #             !$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]' 
27  # Heteroatom '[B,N,O,P,S,F,Cl,Br,I]' 
28   
29   
30  # 2 definitions adapted from those in the Gobbi Paper 
31  #  NOTE: if you want traditional Lipinski numbers, you 
32  #  should use NOCounts (below) instead of HAcceptor 
33  # 
34  HDonorSmarts = Chem.MolFromSmarts('[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]') 
35  # changes log for HAcceptorSmarts: 
36  #  v2, 1-Nov-2008, GL : fix amide-N exclusion; remove Fs from definition 
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  $([nH0,o,s;+0])\ 
41  ]') 
42  HeteroatomSmarts = Chem.MolFromSmarts('[!#6;!#1]') 
43  #  NOTE: the Rotatable bond smarts here doesn't treat deuteriums (which are left in the graph 
44  #  and therefore contribute to the degree of a carbon) the same as hydrogens (which are removed 
45  #  from the graph). So the bond in [2H]C([2H])([2H])C([2H])([2H])[2H] *is* considered 
46  #  rotatable. 
47  RotatableBondSmarts = Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]') 
48  NHOHSmarts = Chem.MolFromSmarts('[#8H1,#7H1,#7H2,#7H3]') 
49  NOCountSmarts = Chem.MolFromSmarts('[#7,#8]') 
50   
51  # this little trick saves duplicated code 
52 -def _NumMatches(mol,smarts): 
53    return len(mol.GetSubstructMatches(smarts,uniquify=1)) 
54   
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" 
77   
78  RingCount=lambda x:rdMolDescriptors.CalcNumRings(x) 
79  RingCount.version = "1.0.0" 
80   
81 -def HeavyAtomCount(mol): 
82    " Number of heavy atoms a molecule." 
83    return mol.GetNumAtoms(onlyHeavy=True) 
84  HeavyAtomCount.version = "1.0.0" 
85