Package rdkit :: Package Chem :: Package Pharm2D :: Module Gobbi_Pharm2D

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# Source Code for Module rdkit.Chem.Pharm2D.Gobbi_Pharm2D

     1  # $Id$
     2  #
     3  #  Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
     4  #
     5  #   @@ All Rights Reserved @@
     6  #  This file is part of the RDKit.
     7  #  The contents are covered by the terms of the BSD license
     8  #  which is included in the file license.txt, found at the root
     9  #  of the RDKit source tree.
    10  #
    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)]
    54
    55 -def _init():
    56    global labels,patts,factory
    57    featFactory = ChemicalFeatures.BuildFeatureFactoryFromString(fdef)
    58    factory = SigFactory(featFactory,minPointCount=2,maxPointCount=3)
    59    factory.SetBins(defaultBins)
    60    factory.Init()
    61
    62  _init()
    63