rdkit.Chem.Pharm2D.Gobbi_Pharm2D

Package rdkit :: Package Chem :: Package Pharm2D :: Module Gobbi_Pharm2D |
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# Source Code for Module rdkit.Chem.Pharm2D.Gobbi_Pharm2D

     1  #
     2  #  Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
     3  #
     4  #   @@ All Rights Reserved @@
     5  #  This file is part of the RDKit.
     6  #  The contents are covered by the terms of the BSD license
     7  #  which is included in the file license.txt, found at the root
     8  #  of the RDKit source tree.
     9  #
    10  """ Definitions for 2D Pharmacophores from:
    11    Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998)
    12
    13  """
    14  from rdkit.Chem import ChemicalFeatures
    15  from rdkit.Chem.Pharm2D.SigFactory import SigFactory
    16
    17  fdef = """
    18  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])]
    19    Family LH
    20    Weights 1.0
    21  EndFeature
    22  DefineFeature Donor [$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]
    23    Family HD
    24    Weights 1.0
    25  EndFeature
    26  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]
    27    Family HA
    28    Weights 1.0
    29  EndFeature
    30  DefineFeature AromaticAttachment [$([a;D3](@*)(@*)*)]
    31    Family AR
    32    Weights 1.0
    33  EndFeature
    34  DefineFeature AliphaticAttachment [$([A;D3](@*)(@*)*)]
    35    Family RR
    36    Weights 1.0
    37  EndFeature
    38  DefineFeature UnusualAtom [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53]
    39    Family X
    40    Weights 1.0
    41  EndFeature
    42  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))]),$([N,n;X2;+0])]
    43    Family BG
    44    Weights 1.0
    45  EndFeature
    46  DefineFeature AcidicGroup [$([C,S](=[O,S,P])-[O;H1])]
    47    Family AG
    48    Weights 1.0
    49  EndFeature
    50  """
    51  defaultBins = [(2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 100)]
    52
    53
    54 -def _init():
    55    global labels, patts, factory
    56    featFactory = ChemicalFeatures.BuildFeatureFactoryFromString(fdef)
    57    factory = SigFactory(featFactory, minPointCount=2, maxPointCount=3)
    58    factory.SetBins(defaultBins)
    59    factory.Init()
    60
    61
    62  _init()
    63