rdkit.ML.Descriptors.MoleculeDescriptors

Package rdkit :: Package ML :: Package Descriptors :: Module MoleculeDescriptors |
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# Source Code for Module rdkit.ML.Descriptors.MoleculeDescriptors

      1  # $Id: MoleculeDescriptors.py 1029 2009-03-23 17:00:45Z 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  from rdkit import RDConfig
      9  from rdkit.ML.Descriptors import Descriptors
     10  from rdkit.Chem import AvailDescriptors
     11  AvailDescriptors.Desensitize()
     12  from rdkit.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 = tuple(simpleList)
     36      self.descriptorNames = tuple(self.simpleList)
     37      self.compoundList = None
     38      self._findVersions()
     39
     40 -  def _findVersions(self):
     41      """ returns a tuple of the versions of the descriptor calculators
     42
     43      """
     44      self.descriptorVersions=[]
     45      for nm in self.simpleList:
     46        vers='N/A'
     47        if AvailDescriptors.descDict.has_key(nm):
     48          fn = AvailDescriptors.descDict[nm]
     49          if hasattr(fn,'version'):
     50            vers = fn.version
     51        self.descriptorVersions.append(vers)
     52
     53 -  def SaveState(self,fileName):
     54      """ Writes this calculator off to a file so that it can be easily loaded later
     55
     56       **Arguments**
     57
     58         - fileName: the name of the file to be written
     59
     60      """
     61      import cPickle
     62      try:
     63        f = open(fileName,'wb+')
     64      except:
     65        logger.error('cannot open output file %s for writing'%(fileName))
     66        return
     67      cPickle.dump(self,f)
     68      f.close()
     69
     70 -  def CalcDescriptors(self,mol,*args,**kwargs):
     71      """ calculates all descriptors for a given molecule
     72
     73        **Arguments**
     74
     75          - mol: the molecule to be used
     76
     77        **Returns**
     78          a tuple of all descriptor values
     79
     80      """
     81      res = [-666]*len(self.simpleList)
     82      for i,nm in enumerate(self.simpleList):
     83        fn = AvailDescriptors.descDict.get(nm,lambda x:777)
     84        try:
     85          res[i] = fn(mol)
     86        except:
     87          import traceback
     88          traceback.print_exc()
     89      return tuple(res)
     90
     91 -  def GetDescriptorNames(self):
     92      """ returns a tuple of the names of the descriptors this calculator generates
     93
     94      """
     95      return self.descriptorNames
     96
     97 -  def GetDescriptorSummaries(self):
     98      """ returns a tuple of summaries for the descriptors this calculator generates
     99
    100      """
    101      res = []
    102      for nm in self.simpleList:
    103        fn = AvailDescriptors.descDict.get(nm,lambda x:777)
    104        if hasattr(fn,'__doc__') and fn.__doc__:
    105          doc = fn.__doc__.split('\n\n')[0].strip()
    106          doc = re.sub('\ *\n\ *',' ',doc)
    107        else:
    108          doc = 'N/A'
    109        res.append(doc)
    110      return res
    111
    112 -  def GetDescriptorFuncs(self):
    113      """ returns a tuple of the functions used to generate this calculator's descriptors
    114
    115      """
    116      res = []
    117      for nm in self.simpleList:
    118        fn = AvailDescriptors.descDict.get(nm,lambda x:777)
    119        res.append(fn)
    120      return tuple(res)
    121
    122 -  def GetDescriptorVersions(self):
    123      """ returns a tuple of the versions of the descriptor calculators
    124
    125      """
    126      return tuple(self.descriptorVersions)
    127