def readMultiMoleculeFile(file, makeZMatrix="true", copyConnectivity="false"): mfr = Utility.getDefaultImplFor(MoleculeFileReaderFactory).newInstance() typ = file[file.index(".")+1:len(file)] rdr = mfr.getReader(typ) br = openFile(file, "r") molList = [] try: i = 0 while 1: mol = rdr.readMolecule(br) if mol.getNumberOfAtoms() == 0: break if ((mol.getTitle()==None) or (mol.getTitle()=="") \ or (mol.getTitle()=="Untitled") \ or (mol.getTitle().index("Molecule")==0)): mol.setTitle(Utility.getFileNamesSansExtension(File(file)) + "-" + repr(i)) molList.append(mol) i += 1 except: print "Warning: Could not read the complete file " + file br.close() buildConnectivity(molList, makeZMatrix, copyConnectivity) return molList