def buildConnectivity(mol, makeZMatrix="true", copyConnectivity="false"):
mb = Utility.getDefaultImplFor(MoleculeBuilder).newInstance()
if (copyConnectivity == "false"):
try:
if (makeZMatrix == "false"):
for i in range(0, len(mol)):
mb.makeConnectivity(mol[i])
else:
for i in range(0, len(mol)):
mb.makeZMatrix(mol[i])
except:
if (makeZMatrix == "false"):
mb.makeConnectivity(mol)
else:
mb.makeZMatrix(mol)
else:
try:
if (makeZMatrix == "false"):
mb.makeConnectivity(mol[0])
else:
mb.makeZMatrix(mol[0])
for i in range(1, len(mol)):
atms = mol[0].getAtoms();
iatms = mol[i].getAtoms();
while (atms.hasNext() and iatms.hasNext()):
iatms.next().setConnectedList(atms.next().getConnectedList())
except:
if (makeZMatrix == "false"):
mb.makeConnectivity(mol)
else:
mb.makeZMatrix(mol)
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
def buildSimpleConnectivity(mol):
mb = Utility.getDefaultImplFor(MoleculeBuilder).newInstance()
try:
for i in range(0, len(mol)):
mb.makeSimpleConnectivity(mol)
except:
mb.makeSimpleConnectivity(mol)
def molecule(title):
mol = Utility.getDefaultImplFor(Molecule).newInstance()
mol.setTitle(title)
return mol
def getDefaultClass(theClass):
return Utility.getDefaultImplFor(theClass)
def readMoleculeFile(file):
mfr = Utility.getDefaultImplFor(MoleculeFileReaderFactory).newInstance()
typ = file[file.index(".")+1:len(file)]
rdr = mfr.getReader(typ)
return rdr.readMoleculeFile(file)