Source Code for Module rdkit.Chem.Suppliers.DbMolSupplier

  1  # $Id: DbMolSupplier.py 997 2009-02-25 06:12:43Z glandrum $ 
  2  # 
  3  # Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  """ Supplies a class for working with molecules from databases 
  8  #DOC  
  9   
 10  """ 
 11  from rdkit import Chem 
 12  from rdkit.Chem.Suppliers.MolSupplier import MolSupplier 
 13  import sys 
 14 -def warning(msg,dest=sys.stderr): 
 15    dest.write(msg) 
 16     
 17 -class DbMolSupplier(MolSupplier): 
 18    """ 
 19      new molecules come back with all additional fields from the 
 20      database set in a "_fieldsFromDb" data member 
 21     
 22    """ 
 23 -  def __init__(self,dbResults, 
 24                 molColumnFormats={'SMILES':'SMI', 
 25                                   'SMI':'SMI', 
 26                                   'MOLPKL':'PKL'}, 
 27                 nameCol='', 
 28                 transformFunc=None, 
 29                 **kwargs): 
 30      """ 
 31   
 32        DbResults should be a subclass of Dbase.DbResultSet.DbResultBase 
 33   
 34      """ 
 35      self._data = dbResults 
 36      self._colNames = [x.upper() for x in self._data.GetColumnNames()] 
 37      nameCol = nameCol.upper() 
 38      self.molCol = -1 
 39      self.transformFunc=transformFunc 
 40      try: 
 41        self.nameCol = self._colNames.index(nameCol) 
 42      except ValueError: 
 43        self.nameCol = -1 
 44      for name in molColumnFormats.keys(): 
 45        name = name.upper() 
 46        try: 
 47          idx = self._colNames.index(name) 
 48        except ValueError: 
 49          pass 
 50        else: 
 51          self.molCol = idx 
 52          self.molFmt = molColumnFormats[name] 
 53          break 
 54      if self.molCol < 0: 
 55        raise ValueError,'DbResultSet has no recognizable molecule column' 
 56      del self._colNames[self.molCol] 
 57      self._colNames  = tuple(self._colNames) 
 58      self._numProcessed=0 
 59 -  def GetColumnNames(self): 
 60      return self._colNames 
 61   
 62 -  def _BuildMol(self,data): 
 63      data = list(data) 
 64      molD = data[self.molCol] 
 65      del data[self.molCol] 
 66      self._numProcessed+=1; 
 67      try: 
 68        if self.molFmt =='SMI': 
 69          newM = Chem.MolFromSmiles(str(molD)) 
 70          if not newM: 
 71            warning('Problems processing mol %d, smiles: %s\n'%(self._numProcessed,molD)) 
 72        elif self.molFmt =='PKL': 
 73          newM = Chem.Mol(str(molD)) 
 74      except: 
 75        import traceback 
 76        traceback.print_exc() 
 77        newM = None 
 78      else: 
 79        if newM and self.transformFunc: 
 80          try: 
 81            newM = self.transformFunc(newM,data) 
 82          except: 
 83            import traceback 
 84            traceback.print_exc() 
 85            newM = None 
 86        if newM: 
 87          newM._fieldsFromDb = data 
 88          nFields = len(data) 
 89          for i in range(nFields): 
 90            newM.SetProp(self._colNames[i],str(data[i])) 
 91          if self.nameCol >=0 : 
 92            newM.SetProp('_Name',str(data[self.nameCol])) 
 93      return newM 
 94     
 95 -class ForwardDbMolSupplier(DbMolSupplier): 
 96    """ DbMol supplier supporting only forward iteration 
 97   
 98   
 99      new molecules come back with all additional fields from the 
100      database set in a "_fieldsFromDb" data member 
101     
102    """ 
103 -  def __init__(self,dbResults,**kwargs): 
104      """ 
105   
106        DbResults should be an iterator for Dbase.DbResultSet.DbResultBase 
107   
108      """ 
109      DbMolSupplier.__init__(self,dbResults,**kwargs) 
110      self.Reset() 
111   
112 -  def Reset(self): 
113      self._dataIter = iter(self._data) 
114       
115 -  def NextMol(self): 
116      """  
117   
118        NOTE: this has side effects 
119   
120      """ 
121      try: 
122        d = self._dataIter.next() 
123      except StopIteration: 
124        d = None 
125      if d is not None: 
126        newM = self._BuildMol(d) 
127      else: 
128        newM = None 
129   
130      return newM 
131   
132 -class RandomAccessDbMolSupplier(DbMolSupplier):   
133 -  def __init__(self,dbResults,**kwargs): 
134      """ 
135   
136        DbResults should be a Dbase.DbResultSet.RandomAccessDbResultSet 
137   
138      """ 
139      DbMolSupplier.__init__(self,dbResults,**kwargs) 
140      self._pos = -1 
141       
142 -  def __len__(self): 
143      return len(self._data) 
144     
145 -  def __getitem__(self,idx): 
146      newD = self._data[idx] 
147      return self._BuildMol(newD) 
148   
149 -  def Reset(self): 
150      self._pos = -1 
151 -  def NextMol(self): 
152      self._pos += 1 
153      res = None 
154      if self._pos < len(self): 
155        res = self[self._pos] 
156      return res 
157