Source Code for Module Chem.Lipinski

 1  # $Id: Lipinski.py 746 2008-07-07 13:21:24Z glandrum $ 
 2  # 
 3  # Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  """ Calculation of Lipinski parameters for molecules 
 8   
 9  """ 
10  #from Chem import rdchem 
11  import Chem 
12   
13  #----------------------------------- 
14  # on import build the SMARTS patterns so we only have to do it once 
15  #----------------------------------- 
16   
17  # The Daylight SMARTS expressions for 
18  # recognizing H-bond donors and acceptors in the Lipinski scheme. 
19  # HDonor     '[!#6;!H0;-0]' 
20  # HAcceptor  '[$([!#6;+0]);!$([F,Cl,Br,I]); 
21  #             !$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]' 
22  # Heteroatom '[B,N,O,P,S,F,Cl,Br,I]' 
23   
24   
25  # 2 definitions from Gobbi Paper 
26  #  NOTE: if you want traditional Lipinski numbers, you 
27  #  should use NOCounts (below) instead of HAcceptor 
28  # 
29  HDonorSmarts = Chem.MolFromSmarts('[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]') 
30  HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]') 
31  HeteroatomSmarts = Chem.MolFromSmarts('[!#6;!#1]') 
32  #  NOTE: the Rotatable bond smarts here doesn't treat deuteriums (which are left in the graph 
33  #  and therefore contribute to the degree of a carbon) the same as hydrogens (which are removed 
34  #  from the graph). So the bond in [2H]C([2H])([2H])C([2H])([2H])[2H] *is* considered 
35  #  rotatable. 
36  RotatableBondSmarts = Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]') 
37  NHOHSmarts = Chem.MolFromSmarts('[#8H1,#7H1,#7H2,#7H3]') 
38  NOCountSmarts = Chem.MolFromSmarts('[#7,#8]') 
39   
40  # this little trick saves duplicated code 
41 -def _NumMatches(mol,smarts): 
42    return len(mol.GetSubstructMatches(smarts,uniquify=1)) 
43   
44  NumHDonors = lambda x,y=HDonorSmarts:_NumMatches(x,y) 
45  NumHDonors.__doc__="Number of Hydrogen Bond Donors" 
46  NumHDonors.version="1.0.0" 
47  _HDonors = lambda x,y=HDonorSmarts:x.GetSubstructMatches(y,uniquify=1) 
48  NumHAcceptors = lambda x,y=HAcceptorSmarts:_NumMatches(x,y) 
49  NumHAcceptors.__doc__="Number of Hydrogen Bond Acceptors" 
50  NumHAcceptors.version="1.0.0" 
51  _HAcceptors = lambda x,y=HAcceptorSmarts:x.GetSubstructMatches(y,uniquify=1) 
52  NumHeteroatoms = lambda x,y=HeteroatomSmarts:_NumMatches(x,y) 
53  NumHeteroatoms.__doc__="Number of Heteroatoms" 
54  NumHeteroatoms.version="1.0.0" 
55  _Heteroatoms = lambda x,y=HeteroatomSmarts:x.GetSubstructMatches(y,uniquify=1) 
56  NumRotatableBonds = lambda x,y=RotatableBondSmarts:_NumMatches(x,y) 
57  NumRotatableBonds.__doc__="Number of Rotatable Bonds" 
58  NumRotatableBonds.version="1.0.0" 
59  _RotatableBonds = lambda x,y=RotatableBondSmarts:x.GetSubstructMatches(y,uniquify=1) 
60  NOCount = lambda x,y=NOCountSmarts:_NumMatches(x,y) 
61  NOCount.__doc__="Number of Nitrogens and Oxygens" 
62  NOCount.version="1.0.0" 
63  NHOHCount = lambda x,y=NHOHSmarts:_NumMatches(x,y) 
64  NHOHCount.__doc__="Number of NHs or OHs" 
65  NHOHCount.version="1.0.0" 
66   
67     
68 -def RingCount(mol): 
69    " Number of rings a molecule has." 
70    return mol.GetRingInfo().NumRings() 
71  RingCount.version = "1.0.0" 
72   
73 -def HeavyAtomCount(mol): 
74    " Number of heavy atoms a molecule." 
75    return mol.GetNumAtoms(onlyHeavy=True) 
76  HeavyAtomCount.version = "1.0.0" 
77