Source Code for Module rdkit.Chem.Pharm2D.Gobbi_Pharm2D

 1  # $Id: Gobbi_Pharm2D.py 1022 2009-03-19 04:46:11Z glandrum $ 
 2  # 
 3  #  Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  """ Definitions for 2D Pharmacophores from: 
 8    Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998) 
 9   
10  """ 
11  from rdkit import Chem 
12  from rdkit.Chem.Pharm2D.SigFactory import SigFactory 
13  from rdkit.Chem import ChemicalFeatures 
14   
15  fdef=""" 
16  DefineFeature Hydrophobic [$([C;H2,H1](!=*)[C;H2,H1][C;H2,H1][$([C;H1,H2,H3]);!$(C=*)]),$(C([C;H2,H3])([C;H2,H3])[C;H2,H3])] 
17    Family LH 
18    Weights 1.0 
19  EndFeature 
20  DefineFeature Donor [$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])] 
21    Family HD 
22    Weights 1.0 
23  EndFeature 
24  DefineFeature Acceptor [$([O,S;H1;v2]-[!$(*=[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] 
25    Family HA 
26    Weights 1.0 
27  EndFeature 
28  DefineFeature AromaticAttachment [$([a;D3](@*)(@*)*)] 
29    Family AR 
30    Weights 1.0 
31  EndFeature 
32  DefineFeature AliphaticAttachment [$([A;D3](@*)(@*)*)] 
33    Family RR 
34    Weights 1.0 
35  EndFeature 
36  DefineFeature UnusualAtom [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53] 
37    Family X 
38    Weights 1.0 
39  EndFeature 
40  DefineFeature BasicGroup [$([N;H2&+0][$([C,a]);!$([C,a](=O))]),$([N;H1&+0]([$([C,a]);!$([C,a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0&+0]([C;!$(C(=O))])([C;!$(C(=O))])[C;!$(C(=O))]),$([N,n;X2;+0])] 
41    Family BG 
42    Weights 1.0 
43  EndFeature 
44  DefineFeature AcidicGroup [$([C,S](=[O,S,P])-[O;H1])] 
45    Family AG 
46    Weights 1.0 
47  EndFeature 
48  """ 
49  defaultBins = [(2,3),(3,4),(4,5),(5,6),(6,7),(7,8),(8,100)] 
50   
51 -def _init(): 
52    global labels,patts,factory 
53    featFactory = ChemicalFeatures.BuildFeatureFactoryFromString(fdef) 
54    factory = SigFactory(featFactory,minPointCount=2,maxPointCount=3) 
55    factory.SetBins(defaultBins) 
56    factory.Init() 
57     
58  _init() 
59