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
