Source Code for Module rdkit.Chem.EState.EState_VSA

  1  ## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c 
  2   
  3  # $Id: EState_VSA.py 997 2009-02-25 06:12:43Z glandrum $ 
  4  # 
  5  # Copyright (C)2003-2006 greg Landrum and Rational Discovery LLC 
  6  # 
  7  #   @@ All Rights Reserved  @@ 
  8  # 
  9  """ Hybrid EState-VSA descriptors (like the MOE VSA descriptors) 
 10   
 11  """ 
 12  import numpy.oldnumeric as Numeric 
 13  from rdkit.Chem.EState.EState import EStateIndices as EStateIndices_ 
 14  from rdkit.Chem.MolSurf import _LabuteHelper as VSAContribs_ 
 15  import bisect 
 16   
 17  """ 
 18   
 19  These default VSA bins were chosen using the PP3K solubility data 
 20  set.  An arbitrary number of bins were selected and the 
 21  boundaries were selected to give an approximately equal number of 
 22  atoms per bin 
 23   
 24  """ 
 25  vsaBins=[4.78,5.00,5.410,5.740,6.00,6.07,6.45,7.00,11.0] 
 26 -def VSA_EState_(mol,bins=None,force=1): 
 27    """ *Internal Use Only* 
 28    """ 
 29    if not force and hasattr(mol,'_vsaEState'): 
 30      return mol._vsaEState 
 31   
 32    if bins is None: bins = estateBins 
 33    propContribs = EStateIndices_(mol,force=force) 
 34    volContribs = VSAContribs_(mol) 
 35   
 36    ans = Numeric.zeros(len(bins)+1,Numeric.Float) 
 37    for i,prop in enumerate(propContribs): 
 38      if prop is not None: 
 39        bin = bisect.bisect_right(bins,volContribs[i+1]) 
 40        ans[bin] += prop 
 41    mol._vsaEState=ans 
 42    return ans     
 43   
 44   
 45  """ 
 46   
 47  These default EState bins were chosen using the PP3K solubility data 
 48  set.  An arbitrary number of bins (10) were selected and the 
 49  boundaries were selected to give an approximately equal number of 
 50  atoms per bin 
 51   
 52  """ 
 53  estateBins=[-0.390,0.290,0.717,1.165,1.540,1.807,2.05,4.69,9.17,15.0] 
 54 -def EState_VSA_(mol,bins=None,force=1): 
 55    """ *Internal Use Only* 
 56    """ 
 57    if not force and hasattr(mol,'_eStateVSA'): 
 58      return mol._eStateVSA 
 59   
 60    if bins is None: bins = estateBins 
 61    propContribs = EStateIndices_(mol,force=force) 
 62    volContribs = VSAContribs_(mol) 
 63   
 64    ans = Numeric.zeros(len(bins)+1,Numeric.Float) 
 65    for i,prop in enumerate(propContribs): 
 66      if prop is not None: 
 67        bin = bisect.bisect_right(bins,prop) 
 68        ans[bin] += volContribs[i+1] 
 69    mol._eStateVSA=ans 
 70    return ans     
 71 -def _InstallDescriptors(): 
 72    for i in range(len(vsaBins)): 
 73      fn = lambda x,y=i:VSA_EState_(x,force=0)[y] 
 74      if i > 0: 
 75        fn.__doc__="VSA EState Descriptor %d (% 4.2f <= x < % 4.2f)"%(i+1,vsaBins[i-1],vsaBins[i]) 
 76      else: 
 77        fn.__doc__="VSA EState Descriptor %d (-inf < x < % 4.2f)"%(i+1,vsaBins[i]) 
 78      name="VSA_EState%d"%(i+1) 
 79      fn.version="1.0.0" 
 80      globals()[name]=fn 
 81    i+=1 
 82    fn = lambda x,y=i:VSA_EState_(x,force=0)[y] 
 83    fn.__doc__="VSA EState Descriptor %d (% 4.2f <= x < inf)"%(i+1,vsaBins[i-1]) 
 84    name="VSA_EState%d"%(i+1) 
 85    fn.version="1.0.0" 
 86    globals()[name]=fn 
 87    fn=None 
 88   
 89    for i in range(len(estateBins)): 
 90      fn = lambda x,y=i:EState_VSA_(x,force=0)[y] 
 91      if i > 0: 
 92        fn.__doc__="EState VSA Descriptor %d (% 4.2f <= x < % 4.2f)"%(i+1,estateBins[i-1],estateBins[i]) 
 93      else: 
 94        fn.__doc__="EState VSA Descriptor %d (-inf < x < % 4.2f)"%(i+1,estateBins[i]) 
 95      name="EState_VSA%d"%(i+1) 
 96      fn.version="1.0.1" 
 97      globals()[name]=fn 
 98    i+=1 
 99    fn = lambda x,y=i:EState_VSA_(x,force=0)[y] 
100    fn.__doc__="EState VSA Descriptor %d (% 4.2f <= x < inf)"%(i+1,estateBins[i-1]) 
101    name="EState_VSA%d"%(i+1) 
102    fn.version="1.0.1" 
103    globals()[name]=fn 
104    fn=None 
105  # Change log for EState_VSA descriptors: 
106  #  version 1.0.1: optimizations, values unaffected 
107  _InstallDescriptors() 
108