rdkit.Chem.FeatMaps.FeatMaps

Package rdkit :: Package Chem :: Package FeatMaps :: Module FeatMaps |
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# Source Code for Module rdkit.Chem.FeatMaps.FeatMaps

      1  # $Id$
      2  #
      3  # Copyright (C) 2006 Greg Landrum
      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  from rdkit import Geometry
     12  from rdkit import Chem
     13  from rdkit.Chem import ChemicalFeatures
     14  from rdkit.Chem.FeatMaps.FeatMapPoint import FeatMapPoint
     15  import math
     16
     17 -class FeatMapScoreMode(object):
     18    All=0
     19    """ score each feature in the probe against every matching
     20        feature in the FeatMap.
     21    """
     22
     23    Closest=1
     24    """ score each feature in the probe against the closest
     25        matching feature in the FeatMap.
     26    """
     27
     28    Best=2
     29    """ score each feature in the probe against the matching
     30        feature in the FeatMap that leads to the highest score
     31    """
     32
     33 -class FeatDirScoreMode(object):
     34    Ignore=0
     35    """ ignore feature directions
     36    """
     37
     38    DotFullRange=1
     39    """ Use the dot product and allow negative contributions when
     40        directions are anti-parallel.
     41        e.g. score = dot(f1Dir,f2Dir)
     42    """
     43
     44    DotPosRange=2
     45    """ Use the dot product and scale contributions to lie between
     46        zero and one.
     47        e.g. score = ( dot(f1Dir,f2Dir) + 1 ) / 2
     48    """
     49
     50 -class FeatMapParams(object):
     51    """ one of these should be instantiated for each
     52    feature type in the feature map
     53    """
     54    radius=2.5
     55    " cutoff radius "
     56
     57    width=1.0
     58    " width parameter (e.g. the gaussian sigma) "
     59
     60 -  class FeatProfile(object):
     61      " scoring profile of the feature "
     62      Gaussian=0
     63      Triangle=1
     64      Box=2
     65
     66    featProfile=FeatProfile.Gaussian
     67
     68 -class FeatMap(object):
     69    dirScoreMode = FeatDirScoreMode.Ignore
     70    scoreMode=FeatMapScoreMode.All
     71    params = {}
     72 -  def __init__(self,params=None,feats=None,
     73                 weights=None):
     74      if params:
     75        self.params = params
     76      self._initializeFeats(feats,weights)
     77
     78 -  def _initializeFeats(self,feats,weights):
     79      self._feats = []
     80      if feats:
     81        if len(feats)!=len(weights):
     82          raise ValueError('feats and weights lists must be the same length')
     83        for feat,weight in zip(feats,weights):
     84          self.AddFeature(feat,weight)
     85
     86 -  def AddFeature(self,feat,weight=None):
     87      if self.params and not feat.GetFamily() in self.params:
     88        raise ValueError('feature family %s not found in params'%feat.GetFamily())
     89
     90      newFeat = FeatMapPoint()
     91      newFeat.initFromFeat(feat)
     92      newFeat.weight = weight
     93
     94      self.AddFeatPoint(newFeat)
     95
     96 -  def AddFeatPoint(self,featPt):
     97      if not isinstance(featPt,FeatMapPoint):
     98        raise ValueError('addFeatPoint() must be called with a FeatMapPoint instance')
     99      if self.params and not featPt.GetFamily() in self.params:
    100        raise ValueError('feature family %s not found in params'%featPt.GetFamily())
    101      self._feats.append(featPt)
    102
    103
    104 -  def GetFeatures(self):
    105      return self._feats
    106
    107 -  def GetNumFeatures(self):
    108      return len(self._feats)
    109
    110 -  def GetFeature(self, i):
    111      return self._feats[i]
    112
    113 -  def DropFeature(self,i):
    114      del self._feats[i]
    115
    116 -  def _loopOverMatchingFeats(self,oFeat):
    117      for sIdx,sFeat in enumerate(self._feats):
    118        if sFeat.GetFamily()==oFeat.GetFamily():
    119          yield sIdx,sFeat
    120
    121 -  def GetFeatFeatScore(self,feat1,feat2,typeMatch=True):
    122      """ feat1 is one of our feats
    123          feat2 is any Feature
    124
    125
    126      """
    127      if typeMatch and feat1.GetFamily()!=feat2.GetFamily():
    128        return 0.0
    129      d2 = feat1.GetDist2(feat2)
    130      params = self.params[feat1.GetFamily()]
    131      if d2>params.radius*params.radius:
    132        return 0.0
    133
    134      if params.featProfile==FeatMapParams.FeatProfile.Gaussian:
    135        score = math.exp(-d2/params.width)
    136      elif params.featProfile==FeatMapParams.FeatProfile.Triangle:
    137        d = math.sqrt(d2)
    138        if d<params.width:
    139          score = 1.-d/params.width
    140        else:
    141          score=0.0
    142      elif params.featProfile==FeatMapParams.FeatProfile.Box:
    143        score = 1.0
    144      weight = feat1.weight
    145      score *= weight
    146
    147      if self.dirScoreMode != FeatDirScoreMode.Ignore:
    148        dirScore = feat1.GetDirMatch(feat2)
    149        if self.dirScoreMode==FeatDirScoreMode.DotPosRange:
    150          dirScore = (dirScore + 1.0)/2.0
    151        elif self.dirScoreMode!=FeatDirScoreMode.DotFullRange:
    152          raise NotImplementedError('bad feature dir score mode')
    153        score *= dirScore
    154
    155      return score
    156
    157 -  def ScoreFeats(self,featsToScore,mapScoreVect=[],featsScoreVect=[],
    158                   featsToFeatMapIdx=[]):
    159      nFeats = len(self._feats)
    160      if mapScoreVect and len(mapScoreVect)!=nFeats:
    161        raise ValueError('if provided, len(mapScoreVect) should equal numFeats')
    162      nToScore = len(featsToScore)
    163      if featsScoreVect and len(featsScoreVect)!=nToScore:
    164        raise ValueError('if provided, len(featsScoreVect) should equal len(featsToScore)')
    165      if featsToFeatMapIdx and len(featsToFeatMapIdx)!=nToScore:
    166        raise ValueError('if provided, len(featsToFeatMapIdx) should equal len(featsToScore)')
    167
    168      if mapScoreVect:
    169        for i in range(nFeats): mapScoreVect[i]=0.0
    170      else:
    171        mapScoreVect = [0.0]*nFeats
    172
    173      if self.scoreMode==FeatMapScoreMode.Closest:
    174        defScore=1000.0
    175      else:
    176        defScore=0.0
    177      if featsScoreVect:
    178        for i in range(nToScore): featsScoreVect[i]=defScore
    179      else:
    180        featsScoreVect = [defScore]*nToScore
    181
    182      if not featsToFeatMapIdx:
    183        featsToFeatMapIdx = [None]*nToScore
    184
    185      for i in range(nToScore):
    186        if self.scoreMode != FeatMapScoreMode.All:
    187          featsToFeatMapIdx[i]=[-1]
    188        else:
    189          featsToFeatMapIdx[i]=[]
    190
    191      for oIdx,oFeat in enumerate(featsToScore):
    192        for sIdx,sFeat in self._loopOverMatchingFeats(oFeat):
    193          if self.scoreMode == FeatMapScoreMode.Closest:
    194            d = sFeat.GetDist2(oFeat)
    195            if d<featsScoreVect[oIdx]:
    196              featsScoreVect[oIdx]=d
    197              featsToFeatMapIdx[oIdx][0]=sIdx
    198          else:
    199            lScore = self.GetFeatFeatScore(sFeat,oFeat,typeMatch=False)
    200            if self.scoreMode == FeatMapScoreMode.Best:
    201              if lScore>featsScoreVect[oIdx]:
    202                featsScoreVect[oIdx]=lScore
    203                featsToFeatMapIdx[oIdx][0]=sIdx
    204            elif self.scoreMode == FeatMapScoreMode.All:
    205              featsScoreVect[oIdx] += lScore
    206              mapScoreVect[sIdx] += lScore
    207              featsToFeatMapIdx[oIdx].append(sIdx)
    208            else:
    209              raise ValueError('bad score mode')
    210
    211      totScore = 0.0
    212      if self.scoreMode == FeatMapScoreMode.Closest:
    213        for oIdx,oFeat in enumerate(featsToScore):
    214          sIdx = featsToFeatMapIdx[oIdx][0]
    215          if sIdx>-1:
    216            lScore = self.GetFeatFeatScore(sFeat,oFeat,typeMatch=False)
    217            featsScoreVect[oIdx] = lScore
    218            mapScoreVect[sIdx] = lScore
    219            totScore += lScore
    220          else:
    221            featsScoreVect[oIdx] = 0
    222
    223      else:
    224        totScore = sum(featsScoreVect)
    225        if self.scoreMode == FeatMapScoreMode.Best:
    226          for oIdx,lScore in enumerate(featsScoreVect):
    227            sIdx = featsToFeatMapIdx[oIdx][0]
    228            if sIdx>-1:
    229              mapScoreVect[sIdx]=lScore
    230
    231      # replace placeholders:
    232      if self.scoreMode != FeatMapScoreMode.All:
    233        for elem in featsToFeatMapIdx:
    234          if elem==[-1]:
    235            elem.pop()
    236      return totScore
    237
    238
    239 -  def __str__(self):
    240      res = ''
    241      for i,feat in enumerate(self._feats):
    242        weight = feat.weight
    243        pos = feat.GetPos()
    244        res += '% 3d % 12s % 6.4f % 6.4f % 6.4f % 6.4f\n'%(i+1,
    245                                                           feat.GetFamily(),
    246                                                           pos.x,pos.y,pos.z,weight)
    247      return res
    248
    249
    250  #------------------------------------
    251  #
    252  #  doctest boilerplate
    253  #
    254 -def _test():
    255    import doctest,sys
    256    return doctest.testmod(sys.modules["__main__"])
    257
    258  if __name__ == '__main__':
    259    import sys
    260    failed,tried = _test()
    261    sys.exit(failed)
    262