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11 """ Definitions for 2D Pharmacophores from:
12 Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998)
13
14 """
15 from rdkit import Chem
16 from rdkit.Chem.Pharm2D.SigFactory import SigFactory
17 from rdkit.Chem import ChemicalFeatures
18
19 fdef="""
20 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])]
21 Family LH
22 Weights 1.0
23 EndFeature
24 DefineFeature Donor [$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]
25 Family HD
26 Weights 1.0
27 EndFeature
28 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]
29 Family HA
30 Weights 1.0
31 EndFeature
32 DefineFeature AromaticAttachment [$([a;D3](@*)(@*)*)]
33 Family AR
34 Weights 1.0
35 EndFeature
36 DefineFeature AliphaticAttachment [$([A;D3](@*)(@*)*)]
37 Family RR
38 Weights 1.0
39 EndFeature
40 DefineFeature UnusualAtom [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53]
41 Family X
42 Weights 1.0
43 EndFeature
44 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))]),$([N,n;X2;+0])]
45 Family BG
46 Weights 1.0
47 EndFeature
48 DefineFeature AcidicGroup [$([C,S](=[O,S,P])-[O;H1])]
49 Family AG
50 Weights 1.0
51 EndFeature
52 """
53 defaultBins = [(2,3),(3,4),(4,5),(5,6),(6,7),(7,8),(8,100)]
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62 _init()
63