Source Code for Module Chem.Pharm2D.Gobbi_Pharm2D

 1  # $Id: Gobbi_Pharm2D.py 2 2006-05-06 22:54:39Z glandrum $ 
 2  # 
 3  #  Copyright (C) 2003-2006 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  import Chem 
12  import RDConfig 
13  import os,sys 
14  from Chem.Pharm2D.SigFactory import SigFactory 
15   
16  patts={ 
17    'LH':('[$([C;H2,H1](!=*)[C;H2,H1][C;H2,H1][$([C;H1,H2,H3]);!$(C=*)]),$(C([C;H2,H3])([C;H2,H3])[C;H2,H3])]', 
18        'Hydrophobic group'), 
19    'HD':('[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]', 
20          'Hydrogen bond donor'), 
21    'HA':('[$([O,S;H1;v2]-[!$(*=[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]', 
22          'Hydrogen bond acceptor'), 
23    'AR':('[$([a;D3](@*)(@*)*)]', 
24          'Aromatic Attachment Point'), 
25    'RR':('[$([A;D3](@*)(@*)*)]', 
26          'Aliphatic Attachment Point'), 
27    'X':('[!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53]', 
28         'Unusual Atom'), 
29    'BG':('[$([N;H2&+0][$([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])]', 
30          'Basic Group'), 
31    'AG':('[C,S](=[O,S,P])-[O;H1]', 
32          'Acidic Group'), 
33    } 
34  defaultBins = [(2,3),(3,4),(4,5),(5,6),(6,7),(7,8),(8,100)] 
35   
36 -def _init(): 
37    global labels,patts,factory 
38   
39    labels = [] 
40    smaPatts = [] 
41    for label in patts.keys(): 
42      sma,desc = patts[label] 
43      p = Chem.MolFromSmarts(sma) 
44      if not p: 
45        sys.stderr.write('feature %s failed to parse'%(label)) 
46      else: 
47        labels.append(label) 
48        patts[label] = p,desc 
49        smaPatts.append(p) 
50    factory = SigFactory()     
51    factory.SetPatterns(smaPatts) 
52    factory.SetLabels(labels) 
53    factory.SetBins(defaultBins) 
54    factory.SetMinCount(2) 
55    factory.SetMaxCount(3) 
56    factory.SetShortestPathsOnly(1) 
57    factory.SetIncludeBondOrder(0) 
58     
59  _init() 
60