Source Code for Module Chem.EState.EState_VSA

  1  # $Id: EState_VSA.py 2 2006-05-06 22:54:39Z glandrum $ 
  2  # 
  3  # Copyright (C)2003-2006 greg Landrum and Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  """ Hybrid EState-VSA descriptors (like the MOE VSA descriptors) 
  8   
  9  """ 
 10  import Numeric 
 11  from Chem.EState.EState import EStateIndices as EStateIndices_ 
 12  from Chem.MolSurf import _LabuteHelper as VSAContribs_ 
 13  import bisect 
 14   
 15  """ 
 16   
 17  These default VSA bins were chosen using the PP3K solubility data 
 18  set.  An arbitrary number of bins were selected and the 
 19  boundaries were selected to give an approximately equal number of 
 20  atoms per bin 
 21   
 22  """ 
 23  vsaBins=[4.78,5.00,5.410,5.740,6.00,6.07,6.45,7.00,11.0] 
 24 -def VSA_EState_(mol,bins=None,force=1): 
 25    """ *Internal Use Only* 
 26    """ 
 27    if not force and hasattr(mol,'_vsaEState'): 
 28      return mol._vsaEState 
 29   
 30    if bins is None: bins = estateBins 
 31    propContribs = EStateIndices_(mol,force=force) 
 32    volContribs = VSAContribs_(mol) 
 33   
 34    ans = Numeric.zeros(len(bins)+1,Numeric.Float) 
 35    for i,prop in enumerate(propContribs): 
 36      if prop is not None: 
 37        bin = bisect.bisect_right(bins,volContribs[i+1]) 
 38        ans[bin] += prop 
 39    mol._vsaEState=ans 
 40    return ans     
 41   
 42  for i in range(len(vsaBins)): 
 43    fn = lambda x,y=i:VSA_EState_(x,force=0)[y] 
 44    if i > 0: 
 45      fn.__doc__="VSA EState Descriptor %d (% 4.2f <= x < % 4.2f)"%(i+1,vsaBins[i-1],vsaBins[i]) 
 46    else: 
 47      fn.__doc__="VSA EState Descriptor %d (-inf < x < % 4.2f)"%(i+1,vsaBins[i]) 
 48    name="VSA_EState%d"%(i+1) 
 49    fn.version="1.0.0" 
 50    exec('%s=fn'%(name)) 
 51  i+=1 
 52  fn = lambda x,y=i:VSA_EState_(x,force=0)[y] 
 53  fn.__doc__="VSA EState Descriptor %d (% 4.2f <= x < inf)"%(i+1,vsaBins[i-1]) 
 54  name="VSA_EState%d"%(i+1) 
 55  fn.version="1.0.0" 
 56  exec('%s=fn'%(name)) 
 57  fn=None 
 58   
 59   
 60  """ 
 61   
 62  These default EState bins were chosen using the PP3K solubility data 
 63  set.  An arbitrary number of bins (10) were selected and the 
 64  boundaries were selected to give an approximately equal number of 
 65  atoms per bin 
 66   
 67  """ 
 68  estateBins=[-0.390,0.290,0.717,1.165,1.540,1.807,2.05,4.69,9.17,15.0] 
 69 -def EState_VSA_(mol,bins=None,force=1): 
 70    """ *Internal Use Only* 
 71    """ 
 72    if not force and hasattr(mol,'_eStateVSA'): 
 73      return mol._eStateVSA 
 74   
 75    if bins is None: bins = estateBins 
 76    propContribs = EStateIndices_(mol,force=force) 
 77    volContribs = VSAContribs_(mol) 
 78   
 79    ans = Numeric.zeros(len(bins)+1,Numeric.Float) 
 80    for i,prop in enumerate(propContribs): 
 81      if prop is not None: 
 82        bin = bisect.bisect_right(bins,prop) 
 83        ans[bin] += volContribs[i+1] 
 84    mol._eStateVSA=ans 
 85    return ans     
 86   
 87  for i in range(len(estateBins)): 
 88    fn = lambda x,y=i:EState_VSA_(x,force=0)[y] 
 89    if i > 0: 
 90      fn.__doc__="EState VSA Descriptor %d (% 4.2f <= x < % 4.2f)"%(i+1,estateBins[i-1],estateBins[i]) 
 91    else: 
 92      fn.__doc__="EState VSA Descriptor %d (-inf < x < % 4.2f)"%(i+1,estateBins[i]) 
 93    name="EState_VSA%d"%(i+1) 
 94    fn.version="1.0.1" 
 95    exec('%s=fn'%(name)) 
 96  i+=1 
 97  fn = lambda x,y=i:EState_VSA_(x,force=0)[y] 
 98  fn.__doc__="EState VSA Descriptor %d (% 4.2f <= x < inf)"%(i+1,estateBins[i-1]) 
 99  name="EState_VSA%d"%(i+1) 
100  fn.version="1.0.1" 
101  exec('%s=fn'%(name)) 
102  fn=None 
103  # Change log for EState_VSA descriptors: 
104  #  version 1.0.1: optimizations, values unaffected 
105