rdkit.Chem.Suppliers.DbMolSupplier

Package rdkit :: Package Chem :: Package Suppliers :: Module DbMolSupplier |
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# Source Code for Module rdkit.Chem.Suppliers.DbMolSupplier

      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  """ Supplies a class for working with molecules from databases
     12  #DOC
     13
     14  """
     15  from rdkit import Chem
     16  from rdkit.Chem.Suppliers.MolSupplier import MolSupplier
     17  import sys
     18 -def warning(msg,dest=sys.stderr):
     19    dest.write(msg)
     20
     21 -class DbMolSupplier(MolSupplier):
     22    """
     23      new molecules come back with all additional fields from the
     24      database set in a "_fieldsFromDb" data member
     25
     26    """
     27 -  def __init__(self,dbResults,
     28                 molColumnFormats={'SMILES':'SMI',
     29                                   'SMI':'SMI',
     30                                   'MOLPKL':'PKL'},
     31                 nameCol='',
     32                 transformFunc=None,
     33                 **kwargs):
     34      """
     35
     36        DbResults should be a subclass of Dbase.DbResultSet.DbResultBase
     37
     38      """
     39      self._data = dbResults
     40      self._colNames = [x.upper() for x in self._data.GetColumnNames()]
     41      nameCol = nameCol.upper()
     42      self.molCol = -1
     43      self.transformFunc=transformFunc
     44      try:
     45        self.nameCol = self._colNames.index(nameCol)
     46      except ValueError:
     47        self.nameCol = -1
     48      for name in molColumnFormats.keys():
     49        name = name.upper()
     50        try:
     51          idx = self._colNames.index(name)
     52        except ValueError:
     53          pass
     54        else:
     55          self.molCol = idx
     56          self.molFmt = molColumnFormats[name]
     57          break
     58      if self.molCol < 0:
     59        raise ValueError('DbResultSet has no recognizable molecule column')
     60      del self._colNames[self.molCol]
     61      self._colNames  = tuple(self._colNames)
     62      self._numProcessed=0
     63 -  def GetColumnNames(self):
     64      return self._colNames
     65
     66 -  def _BuildMol(self,data):
     67      data = list(data)
     68      molD = data[self.molCol]
     69      del data[self.molCol]
     70      self._numProcessed+=1;
     71      try:
     72        if self.molFmt =='SMI':
     73          newM = Chem.MolFromSmiles(str(molD))
     74          if not newM:
     75            warning('Problems processing mol %d, smiles: %s\n'%(self._numProcessed,molD))
     76        elif self.molFmt =='PKL':
     77          newM = Chem.Mol(str(molD))
     78      except Exception:
     79        import traceback
     80        traceback.print_exc()
     81        newM = None
     82      else:
     83        if newM and self.transformFunc:
     84          try:
     85            newM = self.transformFunc(newM,data)
     86          except Exception:
     87            import traceback
     88            traceback.print_exc()
     89            newM = None
     90        if newM:
     91          newM._fieldsFromDb = data
     92          nFields = len(data)
     93          for i in range(nFields):
     94            newM.SetProp(self._colNames[i],str(data[i]))
     95          if self.nameCol >=0 :
     96            newM.SetProp('_Name',str(data[self.nameCol]))
     97      return newM
     98
     99 -class ForwardDbMolSupplier(DbMolSupplier):
    100    """ DbMol supplier supporting only forward iteration
    101
    102
    103      new molecules come back with all additional fields from the
    104      database set in a "_fieldsFromDb" data member
    105
    106    """
    107 -  def __init__(self,dbResults,**kwargs):
    108      """
    109
    110        DbResults should be an iterator for Dbase.DbResultSet.DbResultBase
    111
    112      """
    113      DbMolSupplier.__init__(self,dbResults,**kwargs)
    114      self.Reset()
    115
    116 -  def Reset(self):
    117      self._dataIter = iter(self._data)
    118
    119 -  def NextMol(self):
    120      """
    121
    122        NOTE: this has side effects
    123
    124      """
    125      try:
    126        d = self._dataIter.next()
    127      except StopIteration:
    128        d = None
    129      if d is not None:
    130        newM = self._BuildMol(d)
    131      else:
    132        newM = None
    133
    134      return newM
    135
    136 -class RandomAccessDbMolSupplier(DbMolSupplier):
    137 -  def __init__(self,dbResults,**kwargs):
    138      """
    139
    140        DbResults should be a Dbase.DbResultSet.RandomAccessDbResultSet
    141
    142      """
    143      DbMolSupplier.__init__(self,dbResults,**kwargs)
    144      self._pos = -1
    145
    146 -  def __len__(self):
    147      return len(self._data)
    148
    149 -  def __getitem__(self,idx):
    150      newD = self._data[idx]
    151      return self._BuildMol(newD)
    152
    153 -  def Reset(self):
    154      self._pos = -1
    155 -  def NextMol(self):
    156      self._pos += 1
    157      res = None
    158      if self._pos < len(self):
    159        res = self[self._pos]
    160      return res
    161