Source Code for Module Chem.ChemUtils.SDFToCSV

  1  # $Id: SDFToCSV.py 746 2008-07-07 13:21:24Z glandrum $ 
  2  # 
  3  # Copyright (C) 2004-2006 Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  import RDConfig 
  8  import Chem 
  9  import sys,csv 
 10   
 11 -def Convert(suppl,outFile,keyCol='',stopAfter=-1,includeChirality=0,smilesFrom=''): 
 12    w = csv.writer(outFile) 
 13    mol = suppl[0] 
 14    propNames = list(mol.GetPropNames()) 
 15    if keyCol and keyCol in propNames: 
 16      propNames.remove(keyCol) 
 17   
 18    outL = [] 
 19    if keyCol: 
 20      outL.append(keyCol) 
 21    outL.append('SMILES') 
 22    outL.extend(propNames) 
 23    w.writerow(outL) 
 24    nDone = 0 
 25    for mol in suppl: 
 26      if not mol: 
 27        continue 
 28      if not smilesFrom or not mol.HasProp(smilesFrom): 
 29        smi = Chem.MolToSmiles(mol,includeChirality) 
 30      else: 
 31        smi = mol.GetProp(smilesFrom) 
 32        tMol = Chem.MolFromSmiles(smi) 
 33        smi = Chem.MolToSmiles(tMol,includeChirality) 
 34      outL = [] 
 35      if keyCol: 
 36        outL.append(str(mol.GetProp(keyCol))) 
 37      outL.append(smi) 
 38      for prop in propNames: 
 39        if mol.HasProp(prop): 
 40          outL.append(str(mol.GetProp(prop))) 
 41        else: 
 42          outL.append('') 
 43      w.writerow(outL) 
 44      nDone += 1 
 45      if nDone == stopAfter: 
 46        break 
 47    return 
 48   
 49   
 50  #------------------- 
 51  #  Testing: 
 52  import unittest 
 53 -class TestCase(unittest.TestCase): 
 54 -  def setUp(self): 
 55      pass 
 56 -  def tearDown(self): 
 57      pass 
 58 -  def test1(self): 
 59      import os 
 60      from cStringIO import StringIO 
 61      fName = os.path.join(RDConfig.RDDataDir,'NCI','first_200.props.sdf') 
 62      suppl = Chem.SDMolSupplier(fName) 
 63      io = StringIO() 
 64      try: 
 65        Convert(suppl,io) 
 66      except: 
 67        import traceback 
 68        traceback.print_exc() 
 69        self.fail('conversion failed') 
 70      txt = io.getvalue() 
 71      lines = txt.split('\n') 
 72      if not lines[-1]: 
 73        del lines[-1] 
 74      self.failUnless(len(lines)==201,'bad num lines: %d'%len(lines)) 
 75      line0 = lines[0].split(',') 
 76      self.failUnless(len(line0)==16,'%d'%len(line0)) 
 77      self.failUnless(line0[0]=='SMILES') 
 78 -  def test2(self): 
 79      import os 
 80      from cStringIO import StringIO 
 81      fName = os.path.join(RDConfig.RDDataDir,'NCI','first_200.props.sdf') 
 82      suppl = Chem.SDMolSupplier(fName) 
 83      io = StringIO() 
 84      try: 
 85        Convert(suppl,io,keyCol='AMW',stopAfter=5) 
 86      except: 
 87        import traceback 
 88        traceback.print_exc() 
 89        self.fail('conversion failed') 
 90      txt = io.getvalue() 
 91      lines = txt.split('\n') 
 92      if not lines[-1]: 
 93        del lines[-1] 
 94      self.failUnless(len(lines)==6,'bad num lines: %d'%len(lines)) 
 95      line0 = lines[0].split(',') 
 96      self.failUnless(len(line0)==16,'%d'%len(line0)) 
 97      self.failUnless(line0[0]=='AMW') 
 98      self.failUnless(line0[1]=='SMILES') 
 99       
100       
101       
102     
103   
104   
105   
106  #------------------- 
107  #  CLI STuff: 
108 -def Usage(): 
109    message = """ 
110    Usage: SDFToCSV [-k keyCol] inFile.sdf [outFile.csv] 
111   
112    """ 
113    sys.stderr.write(message) 
114    sys.exit(-1) 
115   
116   
117   
118  if __name__=='__main__': 
119    import getopt 
120   
121    try: 
122      args,extras = getopt.getopt(sys.argv[1:],'hk:', 
123                                  ['test', 
124                                   'chiral', 
125                                   'smilesCol=', 
126                                   ]) 
127    except: 
128      import traceback 
129      traceback.print_exc() 
130      Usage() 
131   
132    keyCol = '' 
133    testIt = 0 
134    useChirality=0 
135    smilesCol='' 
136    for arg,val in args: 
137      if arg=='-k': 
138        keyCol = val 
139      elif arg=='--chiral': 
140        useChirality=1 
141      elif arg=='--smilesCol': 
142        smilesCol=val 
143      elif arg=='--test': 
144        testIt=1 
145      elif arg=='-h': 
146        Usage() 
147   
148    if not testIt and len(extras)<1: 
149      Usage() 
150         
151   
152    if not testIt: 
153      inFilename = extras[0] 
154      if len(extras)>1: 
155        outFilename = extras[1] 
156        outF = open(outFilename,'w+') 
157      else: 
158        outF = sys.stdout 
159   
160      suppl = Chem.SDMolSupplier(inFilename) 
161      Convert(suppl,outF,keyCol=keyCol,includeChirality=useChirality,smilesFrom=smilesCol) 
162    else: 
163      sys.argv = [sys.argv[0]] 
164      unittest.main() 
165