Source Code for Module rdkit.Chem.FeatMaps.FeatMapUtils

  1  ## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c 
  2   
  3  # $Id: FeatMapUtils.py 997 2009-02-25 06:12:43Z glandrum $ 
  4  # 
  5  # Copyright (C) 2006 Greg Landrum 
  6  # 
  7  #   @@ All Rights Reserved  @@ 
  8  # 
  9  from rdkit import Geometry 
 10  import numpy.oldnumeric as Numeric 
 11  from rdkit.Chem.FeatMaps import FeatMaps 
 12  from rdkit.Chem.FeatMaps.FeatMapPoint import FeatMapPoint 
 13  import math,copy 
 14   
 15 -class MergeMethod(object): 
 16    WeightedAverage=0 
 17    """ Put the new point at the weighted average position of the two 
 18     fused points 
 19    """ 
 20   
 21    Average=1 
 22    """ Put the new point at the un-weighted average position of the two 
 23     fused points 
 24    """ 
 25   
 26    UseLarger=2 
 27    """ Put the new point at the position of the larger (by weight) 
 28     of the two points 
 29    """ 
 30   
 31 -class MergeMetric(object): 
 32    NoMerge=0 
 33    """ Do not merge points """ 
 34   
 35    Distance=1 
 36    """ merge two points if they come within a threshold distance """ 
 37   
 38    Overlap=2 
 39    """ merge two points if their percent overlap exceeds a threshold """ 
 40   
 41 -class DirMergeMode(object): 
 42    NoMerge=0 
 43    """ Do not merge directions (i.e. keep all direction vectors) """ 
 44   
 45    Sum=1 
 46    """ Sum direction vectors """ 
 47   
 48 -def __copyAll(res,fm1,fm2): 
 49    """ no user-serviceable parts inside """ 
 50    for feat in fm1.getFeatures(): 
 51      res.addFeatPoint(copy.deepcopy(feat)) 
 52    for feat in fm2.getFeatures(): 
 53      res.addFeatPoint(copy.deepcopy(feat)) 
 54   
 55   
 56 -def GetFeatFeatDistMatrix(fm,mergeMetric,mergeTol,dirMergeMode,compatFunc): 
 57    """ 
 58   
 59      NOTE that mergeTol is a max value for merging when using distance-based 
 60      merging and a min value when using score-based merging. 
 61       
 62    """ 
 63    dists = [[1e8]*fm.GetNumFeatures() for x in range(fm.GetNumFeatures())] 
 64    if mergeMetric==MergeMetric.NoMerge: 
 65      return dists 
 66    elif mergeMetric==MergeMetric.Distance: 
 67      mergeTol2 = mergeTol*mergeTol 
 68      for i in range(fm.GetNumFeatures()): 
 69        ptI = fm.GetFeature(i) 
 70        for j in range(i+1,fm.GetNumFeatures()): 
 71          ptJ = fm.GetFeature(j) 
 72          if compatFunc(ptI,ptJ): 
 73            dist2 = ptI.GetDist2(ptJ) 
 74            if dist2<mergeTol2: 
 75              dists[i][j]=dist2 
 76              dists[j][i]=dist2 
 77    elif mergeMetric==MergeMetric.Overlap: 
 78      for i in range(fm.GetNumFeatures()): 
 79        ptI = fm.GetFeature(i) 
 80        for j in range(i+1,fm.GetNumFeatures()): 
 81          ptJ = fm.GetFeature(j) 
 82          if compatFunc(ptI,ptJ): 
 83            score = fm.GetFeatFeatScore(ptI,ptJ,typeMatch=False) 
 84            score *= -1*ptJ.weight 
 85            if score<mergeTol: 
 86              dists[i][j]=score 
 87              dists[j][i]=score 
 88    else: 
 89      raise ValueError,'unrecognized mergeMetric' 
 90   
 91    return dists 
 92   
 93 -def familiesMatch(f1,f2): 
 94    return f1.GetFamily()==f2.GetFamily() 
 95   
 96 -def feq(v1,v2,tol=1e-4): 
 97    return abs(v1-v2)<tol 
 98   
 99 -def MergeFeatPoints(fm,mergeMetric=MergeMetric.NoMerge,mergeTol=1.5, 
100                      dirMergeMode=DirMergeMode.NoMerge, 
101                      mergeMethod=MergeMethod.WeightedAverage, 
102                      compatFunc=familiesMatch): 
103    """ 
104   
105      NOTE that mergeTol is a max value for merging when using distance-based 
106      merging and a min value when using score-based merging. 
107   
108      returns whether or not any points were actually merged 
109       
110    """ 
111    res=False 
112    if mergeMetric==MergeMetric.NoMerge: 
113      return res 
114    dists = GetFeatFeatDistMatrix(fm,mergeMetric,mergeTol,dirMergeMode,compatFunc) 
115    distOrders = [None]*len(dists) 
116    for i in range(len(dists)): 
117      distV = dists[i] 
118      distOrders[i] = [] 
119      for j,dist in enumerate(distV): 
120        if dist<mergeTol: 
121          distOrders[i].append((dist,j)) 
122      distOrders[i].sort() 
123   
124    #print 'distOrders:' 
125    #print distOrders 
126   
127    # we now know the "distances" and have rank-ordered list of 
128    # each point's neighbors. Work with that. 
129   
130    # progressively merge nearest neighbors until there 
131    # are no more points left to merge 
132    featsInPlay=range(fm.GetNumFeatures()) 
133    featsToRemove = [] 
134    #print '--------------------------------' 
135    while featsInPlay: 
136      # find two features who are mutual nearest neighbors: 
137      fipCopy=featsInPlay[:] 
138      for fi in fipCopy: 
139        #print '>>>',fi,fipCopy,featsInPlay 
140        #print '\t',distOrders[fi] 
141        mergeThem=False 
142        if not distOrders[fi]: 
143          featsInPlay.remove(fi) 
144          continue 
145        dist,nbr = distOrders[fi][0] 
146        if nbr not in featsInPlay: 
147          continue 
148        if distOrders[nbr][0][1]==fi: 
149          #print 'direct:',fi,nbr 
150          mergeThem=True 
151        else: 
152          # it may be that there are several points at about the same distance, 
153          # check for that now 
154          if(feq(distOrders[nbr][0][0],dist)): 
155            for distJ,nbrJ in distOrders[nbr][1:]: 
156              if feq(dist,distJ): 
157                if nbrJ==fi: 
158                  #print 'indirect: ',fi,nbr 
159                  mergeThem=True 
160                  break 
161              else: 
162                break 
163        #print '    bottom:',mergeThem 
164        if mergeThem: break 
165      if mergeThem: 
166        res=True 
167        featI = fm.GetFeature(fi) 
168        nbrFeat = fm.GetFeature(nbr) 
169         
170        if mergeMethod==MergeMethod.WeightedAverage: 
171          newPos = featI.GetPos()*featI.weight+nbrFeat.GetPos()*nbrFeat.weight 
172          newPos /= (featI.weight+nbrFeat.weight) 
173          newWeight = (featI.weight+nbrFeat.weight)/2 
174        elif mergeMethod==MergeMethod.Average: 
175          newPos = featI.GetPos()+nbrFeat.GetPos() 
176          newPos /= 2 
177          newWeight = (featI.weight+nbrFeat.weight)/2 
178        elif mergeMethod==MergeMethod.UseLarger: 
179          if featI.weight>nbrFeat.weight: 
180            newPos=featI.GetPos() 
181            newWeight = featI.weight 
182          else: 
183            newPos=nbrFeat.GetPos() 
184            newWeight = nbrFeat.weight 
185        else: 
186          raise ValueError,"bad mergeMethod" 
187   
188        featI.SetPos(newPos) 
189        featI.weight = newWeight 
190         
191        # nbr and fi are no longer valid targets: 
192        #print 'nbr done:',nbr,featsToRemove,featsInPlay 
193        featsToRemove.append(nbr) 
194        featsInPlay.remove(fi) 
195        featsInPlay.remove(nbr) 
196        for nbrList in distOrders: 
197          try: 
198            nbrList.remove(fi) 
199          except ValueError: 
200            pass 
201          try: 
202            nbrList.remove(nbr) 
203          except ValueError: 
204            pass 
205      else: 
206        #print ">>>> Nothing found, abort" 
207        break 
208    featsToRemove.sort() 
209    for i,fIdx in enumerate(featsToRemove): 
210      fm.DropFeature(fIdx-i) 
211    return res 
212   
213 -def CombineFeatMaps(fm1,fm2,mergeMetric=MergeMetric.NoMerge,mergeTol=1.5, 
214                      dirMergeMode=DirMergeMode.NoMerge): 
215    """ 
216       the parameters will be taken from fm1 
217    """ 
218    res = FeatMaps.FeatMap(params=fm1.params) 
219   
220    __copyAll(res,fm1,fm2) 
221    if mergeMetric!=MergeMetric.NoMerge: 
222      MergeFeatPoints(res,mergeMetric=mergeMetric,mergeTol=mergeTol) 
223    return res 
224   
225  #------------------------------------ 
226  # 
227  #  doctest boilerplate 
228  # 
229 -def _test(): 
230    import doctest,sys 
231    return doctest.testmod(sys.modules["__main__"]) 
232   
233  if __name__ == '__main__': 
234    import sys 
235    failed,tried = _test() 
236    sys.exit(failed) 
237