Source Code for Module Chem.Suppliers.DbMolSupplier

  1   
  2  # $Id: DbMolSupplier.py 2 2006-05-06 22:54:39Z glandrum $ 
  3  # 
  4  # Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC 
  5  # 
  6  #   @@ All Rights Reserved  @@ 
  7  # 
  8  """ Supplies a class for working with molecules from databases 
  9  #DOC  
 10   
 11  """ 
 12  import Chem 
 13  from Chem.Suppliers.MolSupplier import MolSupplier 
 14  import sys 
 15 -def warning(msg,dest=sys.stderr): 
 16    dest.write(msg) 
 17     
 18 -class DbMolSupplier(MolSupplier): 
 19    """ 
 20      new molecules come back with all additional fields from the 
 21      database set in a "_fieldsFromDb" data member 
 22     
 23    """ 
 24 -  def __init__(self,dbResults, 
 25                 molColumnFormats={'SMILES':'SMI', 
 26                                   'SMI':'SMI', 
 27                                   'MOLPKL':'PKL'}, 
 28                 nameCol='',**kwargs): 
 29      """ 
 30   
 31        DbResults should be a subclass of Dbase.DbResultSet.DbResultBase 
 32   
 33      """ 
 34      self._data = dbResults 
 35      self._colNames = [x.upper() for x in self._data.GetColumnNames()] 
 36      nameCol = nameCol.upper() 
 37      self.molCol = -1 
 38      try: 
 39        self.nameCol = self._colNames.index(nameCol) 
 40      except ValueError: 
 41        self.nameCol = -1 
 42      for name in molColumnFormats.keys(): 
 43        name = name.upper() 
 44        try: 
 45          idx = self._colNames.index(name) 
 46        except ValueError: 
 47          pass 
 48        else: 
 49          self.molCol = idx 
 50          self.molFmt = molColumnFormats[name] 
 51          break 
 52      if self.molCol < 0: 
 53        raise ValueError,'DbResultSet has no recognizable molecule column' 
 54      del self._colNames[self.molCol] 
 55      self._colNames  = tuple(self._colNames) 
 56      self._numProcessed=0 
 57 -  def GetColumnNames(self): 
 58      return self._colNames 
 59   
 60 -  def _BuildMol(self,data): 
 61      data = list(data) 
 62      molD = data[self.molCol] 
 63      del data[self.molCol] 
 64      self._numProcessed+=1; 
 65      try: 
 66        if self.molFmt =='SMI': 
 67          newM = Chem.MolFromSmiles(molD) 
 68          if not newM: 
 69            warning('Problems processing mol %d, smiles: %s\n'%(self._numProcessed,molD)) 
 70        elif self.molFmt =='PKL': 
 71          newM = Chem.Mol(str(molD)) 
 72      except: 
 73        newM = None 
 74      else: 
 75        if newM: 
 76          newM._fieldsFromDb = data 
 77          nFields = len(data) 
 78          for i in range(nFields): 
 79            newM.SetProp(self._colNames[i],str(data[i])) 
 80          if self.nameCol >=0 : 
 81            newM.SetProp('_Name',str(data[self.nameCol])) 
 82      return newM 
 83     
 84 -class ForwardDbMolSupplier(DbMolSupplier): 
 85    """ DbMol supplier supporting only forward iteration 
 86   
 87   
 88      new molecules come back with all additional fields from the 
 89      database set in a "_fieldsFromDb" data member 
 90     
 91    """ 
 92 -  def __init__(self,dbResults,**kwargs): 
 93      """ 
 94   
 95        DbResults should be an iterator for Dbase.DbResultSet.DbResultBase 
 96   
 97      """ 
 98      DbMolSupplier.__init__(self,dbResults,**kwargs) 
 99      self.Reset() 
100   
101 -  def Reset(self): 
102      self._dataIter = iter(self._data) 
103       
104 -  def NextMol(self): 
105      """  
106   
107        NOTE: this has side effects 
108   
109      """ 
110      try: 
111        d = self._dataIter.next() 
112      except StopIteration: 
113        d = None 
114      if d is not None: 
115        newM = self._BuildMol(d) 
116      else: 
117        newM = None 
118   
119      return newM 
120   
121 -class RandomAccessDbMolSupplier(DbMolSupplier):   
122 -  def __init__(self,dbResults,**kwargs): 
123      """ 
124   
125        DbResults should be a Dbase.DbResultSet.RandomAccessDbResultSet 
126   
127      """ 
128      DbMolSupplier.__init__(self,dbResults,**kwargs) 
129      self._pos = -1 
130       
131 -  def __len__(self): 
132      return len(self._data) 
133     
134 -  def __getitem__(self,idx): 
135      newD = self._data[idx] 
136      return self._BuildMol(newD) 
137   
138 -  def Reset(self): 
139      self._pos = -1 
140 -  def NextMol(self): 
141      self._pos += 1 
142      res = None 
143      if self._pos < len(self): 
144        res = self[self._pos] 
145      return res 
146