def testSerialize3D(self):
"""Test case - build OE molecule using 3D data in the definition source data file
then serialize and deserialize this molecule.
"""
self.__lfh.write("\nStarting OeBuildMolTests testSerialize3D\n")
try:
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
for pth in self.__pathList:
myReader = PdbxIoAdapter(self.__verbose, self.__lfh)
ok = myReader.read(pdbxFilePath=pth)
myReader.write(
pdbxFilePath=os.path.join(self.__testoutput, "TMP.cif"))
for container in myReader.getContainerList():
oem.set(container.getName(),
dcChemCompAtom=container.getObj("chem_comp_atom"),
dcChemCompBond=container.getObj("chem_comp_bond"))
oem.build3D(coordType="model")
self.__lfh.write("Title = %s\n" %
oem.getTitle())
self.__lfh.write("SMILES (canonical) = %s\n" %
oem.getCanSMILES())
self.__lfh.write("SMILES (isomeric) = %s\n" %
oem.getIsoSMILES())
oeS = oem.serialize()
#
self.__lfh.write("Serialized string length = %d\n" %
len(oeS))
#
oemD = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
ok = oemD.deserialize(oeS)
self.__lfh.write("Deserialized status = %s\n" % ok)
self.__lfh.write("Deserialized SMILES (canonical) = %s\n" %
oemD.getCanSMILES())
self.__lfh.write("Deserialized SMILES (isomeric) = %s\n" %
oemD.getIsoSMILES())
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testFetchOne(self):
"""Test case - fetch all of the molecules in the persistent store one by one. Each fetch reopens
the store.
"""
startTime = time.time()
self.__lfh.write(
"\nStarting OePersistFullDictTests testFetchOne at %s\n" %
(time.strftime("%Y %m %d %H:%M:%S", time.localtime())))
try:
myPersist = OePersist(self.__verbose, self.__lfh)
moleculeNameList = myPersist.getIndex(dbFileName=self.__storePath)
#
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
for ccId in moleculeNameList:
molD = myPersist.fetchOneMolecule(dbFileName=self.__storePath,
moleculeName=ccId)
# name = molD['name']
ok = oem.deserialize(molD["oeb"])
if not ok:
self.__lfh.write("Deserialized status %s = %s\n" %
(ccId, ok))
continue
if self.__debug:
self.__lfh.write("Deserialized SMILES (canonical) = %s\n" %
oem.getCanSMILES())
self.__lfh.write("Deserialized SMILES (isomeric) = %s\n" %
oem.getIsoSMILES())
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
endTime = time.time()
self.__lfh.write(
"\nCompleted OePersistFullDictTests testFetchOne at %s (%d seconds)\n"
% (time.strftime("%Y %m %d %H:%M:%S",
time.localtime()), endTime - startTime))