rdkit.Chem.Pharm2D.LazyGenerator

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

      1  # $Id$
      2  #
      3  # Copyright (C) 2003-2006 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  from __future__ import print_function
     12
     13  raise NotImplementedError('not finished yet')
     14  """ lazy generator of 2D pharmacophore signature data
     15
     16  """
     17  import rdkit.Chem
     18  from rdkit.Chem.Pharm2D import SigFactory,Matcher,Utils
     19
     20 -class Generator(object):
     21    """
     22
     23    Important attributes:
     24
     25     - mol: the molecules whose signature is being worked with
     26
     27     - sigFactory : the SigFactory object with signature parameters
     28              NOTE: no preprocessing is carried out for _sigFactory_.
     29                    It *must* be pre-initialized.
     30
     31     **Notes**
     32
     33       -
     34    """
     35 -  def __init__(self,sigFactory,mol,dMat=None,bitCache=True):
     36      """ constructor
     37
     38        **Arguments**
     39
     40         - sigFactory: a signature factory, see class docs
     41
     42         - mol: a molecule, see class docs
     43
     44         - dMat: (optional) a distance matrix for the molecule.  If this
     45           is not provided, one will be calculated
     46
     47         - bitCache: (optional) if nonzero, a local cache of which bits
     48           have been queried will be maintained.  Otherwise things must
     49           be recalculate each time a bit is queried.
     50
     51      """
     52      if not isinstance(sigFactory,SigFactory.SigFactory):
     53        raise ValueError('bad factory')
     54
     55      self.sigFactory = sigFactory
     56      self.mol = mol
     57
     58      if dMat is None:
     59        useBO = sigFactory.includeBondOrder
     60        dMat = Chem.GetDistanceMatrix(mol,useBO)
     61
     62      self.dMat = dMat
     63
     64      if bitCache:
     65        self.bits = {}
     66      else:
     67        self.bits = None
     68
     69      featFamilies=[fam for fam in sigFactory.featFactory.GetFeatureFamilies() if fam not in sigFactory.skipFeats]
     70      nFeats = len(featFamilies)
     71      featMatches={}
     72      for fam in featFamilies:
     73        featMatches[fam] =  []
     74      feats = sigFactory.featFactory.GetFeaturesForMol(mol)
     75      for feat in feats:
     76        if feat.GetFamily() not in sigFactory.skipFeats:
     77          featMatches[feat.GetFamily()].append(feat.GetAtomIds())
     78      featMatches = [None]*nFeats
     79      for i in range(nFeats):
     80        featMatches[i]=sigFactory.featFactory.GetMolFeature()
     81      self.pattMatches = pattMatches
     82
     83 -  def GetBit(self,idx):
     84      """ returns a bool indicating whether or not the bit is set
     85
     86      """
     87      if idx < 0 or idx >= self.sig.GetSize():
     88        raise IndexError('Index %d invalid'%(idx))
     89      if self.bits is not None and self.bits.has_key(idx):
     90        return self.bits[idx]
     91
     92      tmp = Matcher.GetAtomsMatchingBit(self.sig,idx,self.mol,
     93                                        dMat=self.dMat,justOne=1,
     94                                        matchingAtoms=self.pattMatches)
     95      if not tmp or len(tmp)==0: res = 0
     96      else: res = 1
     97
     98      if self.bits is not None:
     99        self.bits[idx] = res
    100      return res
    101
    102 -  def __len__(self):
    103      """ allows class to support len()
    104
    105      """
    106      return self.sig.GetSize()
    107 -  def __getitem__(self,itm):
    108      """ allows class to support random access.
    109        Calls self.GetBit()
    110
    111      """
    112      return self.GetBit(itm)
    113
    114
    115
    116
    117  if __name__ == '__main__':
    118    import time
    119    from rdkit import RDConfig,Chem
    120    from rdkit.Chem.Pharm2D import Gobbi_Pharm2D,Generate
    121    import random
    122
    123    factory = Gobbi_Pharm2D.factory
    124    nToDo=100
    125    inD = open(RDConfig.RDDataDir+"/NCI/first_5K.smi",'r').readlines()[:nToDo]
    126    mols = [None]*len(inD)
    127    for i in range(len(inD)):
    128      smi = inD[i].split('\t')[0]
    129      smi.strip()
    130      mols[i] = Chem.MolFromSmiles(smi)
    131
    132    sig = factory.GetSignature()
    133
    134    nBits = 300
    135    random.seed(23)
    136    bits = [random.randint(0,sig.GetSize()-1) for x in range(nBits)]
    137
    138    print('Using the Lazy Generator')
    139    t1 = time.time()
    140    for i in range(len(mols)):
    141      if not i % 10: print('done mol %d of %d'%(i,len(mols)))
    142      gen = Generator(factory,mols[i])
    143      for bit in bits:
    144        v = gen[bit]
    145    t2 = time.time()
    146    print('\tthat took %4.2f seconds'%(t2-t1))
    147
    148
    149    print('Generating and checking signatures')
    150    t1 = time.time()
    151    for i in range(len(mols)):
    152      if not i % 10: print('done mol %d of %d'%(i,len(mols)))
    153      sig = Generate.Gen2DFingerprint(mols[i],factory)
    154      for bit in bits:
    155        v = sig[bit]
    156    t2 = time.time()
    157    print('\tthat took %4.2f seconds'%(t2-t1))
    158