rdkit.Chem.Pharm2D.Generate

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

      1  # $Id$
      2  #
      3  # Copyright (C) 2002-2008 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  """ generation of 2D pharmacophores
     12
     13  **Notes**
     14
     15    - The terminology for this gets a bit rocky, so here's a glossary of what
     16      terms used here mean:
     17
     18        1) *N-point pharmacophore* a combination of N features along with
     19           distances betwen them.
     20
     21        2) *N-point proto-pharmacophore*: a combination of N feature
     22           definitions without distances.  Each N-point
     23           proto-pharmacophore defines a manifold of potential N-point
     24           pharmacophores.
     25
     26        3) *N-point scaffold*: a collection of the distances defining
     27           an N-point pharmacophore without feature identities.
     28
     29    See Docs/Chem/Pharm2D.triangles.jpg for an illustration of the way
     30    pharmacophores are broken into triangles and labelled.
     31
     32    See Docs/Chem/Pharm2D.signatures.jpg for an illustration of bit
     33    numbering
     34
     35  """
     36  from __future__ import print_function
     37  from rdkit.Chem.Pharm2D import Utils,SigFactory
     38  from rdkit.RDLogger import logger
     39  logger = logger()
     40
     41  _verbose = 0
     42
     43 -def _ShortestPathsMatch(match,featureSet,sig,dMat,sigFactory):
     44    """  Internal use only
     45
     46    """
     47    if _verbose:
     48      print('match:',match)
     49    nPts = len(match)
     50    distsToCheck =  Utils.nPointDistDict[nPts]
     51    nDists = len(distsToCheck)
     52    dist = [0]*nDists
     53    bins = sigFactory.GetBins()
     54    minD,maxD = bins[0][0],bins[-1][1]
     55
     56    for i in range(nDists):
     57      pt0,pt1 = distsToCheck[i]
     58      minSeen=maxD
     59      for idx1 in match[pt0]:
     60        for idx2 in match[pt1]:
     61          minSeen=min(minSeen, dMat[idx1,idx2])
     62          if minSeen==0 or minSeen<minD: return
     63      # FIX: this won't be an int if we're using the bond order.
     64      d = int(minSeen)
     65      # do a quick distance filter
     66      if d == 0 or d < minD or d >= maxD:
     67        return
     68      dist[i] = d
     69
     70    idx = sigFactory.GetBitIdx(featureSet,dist,sortIndices=False)
     71    if _verbose:
     72      print('\t',dist,minD,maxD,idx)
     73
     74    if sigFactory.useCounts:
     75      sig[idx] = sig[idx]+1
     76    else:
     77      sig.SetBit(idx)
     78    return idx
     79
     80
     81 -def Gen2DFingerprint(mol,sigFactory,perms=None,dMat=None,bitInfo=None):
     82    """ generates a 2D fingerprint for a molecule using the
     83     parameters in _sig_
     84
     85     **Arguments**
     86
     87       - mol: the molecule for which the signature should be generated
     88
     89       - sigFactory : the SigFactory object with signature parameters
     90         NOTE: no preprocessing is carried out for _sigFactory_.
     91               It *must* be pre-initialized.
     92
     93       - perms: (optional) a sequence of permutation indices limiting which
     94         pharmacophore combinations are allowed
     95
     96       - dMat: (optional) the distance matrix to be used
     97
     98       - bitInfo: (optional) used to return the atoms involved in the bits
     99
    100    """
    101    if not isinstance(sigFactory,SigFactory.SigFactory):
    102      raise ValueError('bad factory')
    103    featFamilies=sigFactory.GetFeatFamilies()
    104    if _verbose:
    105      print('* feat famillies:',featFamilies)
    106    nFeats = len(featFamilies)
    107    minCount = sigFactory.minPointCount
    108    maxCount = sigFactory.maxPointCount
    109    if maxCount>3:
    110      logger.warning(' Pharmacophores with more than 3 points are not currently supported.\nSetting maxCount to 3.')
    111      maxCount=3
    112
    113    # generate the molecule's distance matrix, if required
    114    if dMat is None:
    115      from rdkit import Chem
    116      useBO = sigFactory.includeBondOrder
    117      dMat = Chem.GetDistanceMatrix(mol,useBO)
    118
    119    # generate the permutations, if required
    120    if perms is None:
    121      perms = []
    122      for count in range(minCount,maxCount+1):
    123        perms += Utils.GetIndexCombinations(nFeats,count)
    124
    125    # generate the matches:
    126    featMatches = sigFactory.GetMolFeats(mol)
    127    if _verbose:
    128      print('  featMatches:',featMatches)
    129
    130    sig = sigFactory.GetSignature()
    131    for perm in perms:
    132      # the permutation is a combination of feature indices
    133      #   defining the feature set for a proto-pharmacophore
    134      featClasses=[0]
    135      for i in range(1,len(perm)):
    136        if perm[i]==perm[i-1]:
    137          featClasses.append(featClasses[-1])
    138        else:
    139          featClasses.append(featClasses[-1]+1)
    140
    141      # Get a set of matches at each index of
    142      #  the proto-pharmacophore.
    143      matchPerms = [featMatches[x] for x in perm]
    144      if _verbose:
    145        print('\n->Perm: %s'%(str(perm)))
    146        print('    matchPerms: %s'%(str(matchPerms)))
    147
    148      # Get all unique combinations of those possible matches:
    149      matchesToMap=Utils.GetUniqueCombinations(matchPerms,featClasses)
    150      for i,entry in enumerate(matchesToMap):
    151        entry = [x[1] for x in entry]
    152        matchesToMap[i]=entry
    153      if _verbose:
    154        print('    mtM:',matchesToMap)
    155
    156      for match in matchesToMap:
    157        if sigFactory.shortestPathsOnly:
    158          idx=_ShortestPathsMatch(match,perm,sig,dMat,sigFactory)
    159          if idx is not None and bitInfo is not None:
    160            l = bitInfo.get(idx,[])
    161            l.append(match)
    162            bitInfo[idx] = l
    163    return sig
    164