Source Code for Module ML.Descriptors.MoleculeDescriptors

  1  # $Id: MoleculeDescriptors.py 746 2008-07-07 13:21:24Z glandrum $ 
  2  # 
  3  #  Copyright (C) 2002-2008  greg Landrum and Rational Discovery LLC 
  4  # 
  5  """ Various bits and pieces for calculating Molecular descriptors 
  6   
  7  """ 
  8  import RDConfig 
  9  from ML.Descriptors import Descriptors 
 10  from Chem import AvailDescriptors 
 11  AvailDescriptors.Desensitize() 
 12  from RDLogger import logger 
 13  logger = logger() 
 14  import re 
 15   
 16 -class MolecularDescriptorCalculator(Descriptors.DescriptorCalculator): 
 17    """ used for calculating descriptors for molecules 
 18   
 19    """ 
 20 -  def __init__(self,simpleList,*args,**kwargs): 
 21      """ Constructor 
 22   
 23        **Arguments** 
 24   
 25          - simpleList: list of simple descriptors to be calculated 
 26                (see below for format)  
 27   
 28        **Note** 
 29   
 30          - format of simpleList: 
 31   
 32             a list of strings which are keys into _AvailDescriptors.descDict_ 
 33   
 34      """ 
 35      self.simpleList = simpleList[:] 
 36      self.descriptorNames = self.simpleList[:] 
 37      self.compoundList = None 
 38     
 39 -  def SaveState(self,fileName): 
 40      """ Writes this calculator off to a file so that it can be easily loaded later 
 41   
 42       **Arguments** 
 43   
 44         - fileName: the name of the file to be written 
 45          
 46      """ 
 47      import cPickle 
 48      try: 
 49        f = open(fileName,'wb+') 
 50      except: 
 51        logger.error('cannot open output file %s for writing'%(fileName)) 
 52        return 
 53      cPickle.dump(self,f) 
 54      f.close() 
 55   
 56 -  def CalcDescriptors(self,mol,*args,**kwargs): 
 57      """ calculates all descriptors for a given molecule 
 58   
 59        **Arguments** 
 60   
 61          - mol: the molecule to be used 
 62   
 63        **Returns**   
 64          a tuple of all descriptor values 
 65   
 66      """ 
 67      res = [-666]*len(self.simpleList) 
 68      for i,nm in enumerate(self.simpleList): 
 69        fn = AvailDescriptors.descDict.get(nm,lambda x:777) 
 70        try: 
 71          res[i] = fn(mol) 
 72        except: 
 73          import traceback 
 74          traceback.print_exc() 
 75      return tuple(res) 
 76   
 77 -  def GetDescriptorNames(self): 
 78      """ returns a tuple of the names of the descriptors this calculator generates 
 79   
 80      """ 
 81      return tuple(self.descriptorNames) 
 82   
 83 -  def GetDescriptorSummaries(self): 
 84      """ returns a tuple of summaries for the descriptors this calculator generates 
 85   
 86      """ 
 87      res = [] 
 88      for nm in self.simpleList: 
 89        fn = AvailDescriptors.descDict.get(nm,lambda x:777) 
 90        if hasattr(fn,'__doc__') and fn.__doc__: 
 91          doc = fn.__doc__.split('\n\n')[0].strip() 
 92          doc = re.sub('\ *\n\ *',' ',doc) 
 93        else: 
 94          doc = 'N/A' 
 95        res.append(doc) 
 96      return res 
 97   
 98 -  def GetDescriptorFuncs(self): 
 99      """ returns a tuple of the functions used to generate this calculator's descriptors 
100   
101      """ 
102      res = [] 
103      for nm in self.simpleList: 
104        fn = AvailDescriptors.descDict.get(nm,lambda x:777) 
105        res.append(fn) 
106      return tuple(res)   
107       
108 -  def GetDescriptorVersions(self): 
109      """ returns a tuple of the versions of the descriptor calculators 
110   
111      """ 
112      res = [] 
113      for nm in self.simpleList: 
114        fn = AvailDescriptors.descDict.get(nm,lambda x:777) 
115        if hasattr(fn,'version'): 
116          vers = fn.version 
117        else: 
118          vers="N/A" 
119        res.append(vers) 
120      return tuple(res) 
121