def testBuildFromFiles(self):
"""Test case - build OE molecule from definition file source data."""
self.__lfh.write("\nStarting OeBuildMolTests testBuildFromFiles\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)
self.assertTrue(ok)
# myReader.write(pdbxFilePath="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())
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def __getOEMol(self, ccPath):
"""Test case - build OE molecule using 3D data in the definition source data"""
self.__lfh.write("\nStarting OeShapeSearchtests __getOEMol\n")
try:
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
myReader = PdbxIoAdapter(self.__verbose, self.__lfh)
ok = myReader.read(pdbxFilePath=ccPath)
self.assertTrue(ok)
#
# myReader.write(pdbxFilePath="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")
if self.__debug:
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())
return oem.getMol()
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testCreateStoreOE(self):
"""Test case - build persistent store of OE molecules using the contents of the persistent store
of chemical component defintions.
"""
startTime = time.time()
self.__lfh.write(
"\nStarting OePersistFullDictTests testCreateStoreOE at %s\n" %
(time.strftime("%Y %m %d %H:%M:%S", time.localtime())))
try:
myPersist = PdbxPersist(self.__verbose, self.__lfh)
indexD = myPersist.getIndex(dbFileName=self.__persistStorePathCC) # noqa: F841 pylint: disable=unused-variable
myPersist.open(dbFileName=self.__persistStorePathCC)
containerNameList = myPersist.getStoreContainerIndex()
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
molList = []
for ccId in containerNameList:
ccAt = myPersist.fetchObject(containerName=ccId,
objectName="chem_comp_atom")
ccBnd = myPersist.fetchObject(containerName=ccId,
objectName="chem_comp_bond")
if ccAt is None or ccBnd is None:
continue
#
oem.set(ccId, dcChemCompAtom=ccAt, dcChemCompBond=ccBnd)
oem.build3D()
if self.__debug:
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())
molD = {}
molD["name"] = ccId
molD["oeb"] = oem.serialize()
molList.append(molD)
myPersist.close()
#
oeP = OePersist(self.__verbose, self.__lfh)
oeP.setMoleculeList(moleculeList=molList)
oeP.store(dbFileName=self.__storePath)
mL = oeP.getIndex(dbFileName=self.__storePath)
#
if self.__debug:
self.__lfh.write(
"OePersistTests(testCreateStore) molecule list %r\n" % mL)
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
endTime = time.time()
self.__lfh.write(
"\nCompleted OePersistFullDictTests testCreateStoreOE at %s (%d seconds)\n"
% (time.strftime("%Y %m %d %H:%M:%S",
time.localtime()), endTime - startTime))
def getFromPathList(self,
pathList,
use3D=True,
coordType="model",
setTitle=True):
""" Return a list of OE mols constructed from the input pathList of chemical definitions.
"""
oemList = []
try:
for pth in pathList:
myReader = PdbxIoAdapter(self.__verbose, self.__lfh)
ok = myReader.read(pdbxFilePath=pth) # noqa: F841 pylint: disable=unused-variable
for container in myReader.getContainerList():
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
oem.setDebug(self.__debug)
oem.set(container.getName(),
dcChemCompAtom=container.getObj("chem_comp_atom"),
dcChemCompBond=container.getObj("chem_comp_bond"))
if use3D:
oem.build3D(coordType=coordType, setTitle=setTitle)
else:
oem.build2D(setTitle=setTitle)
#
oemList.append(oem)
#
if self.__debug:
self.__lfh.write(
"+OeChemCompIoUtils.getOeMols() Title = %s\n"
% oem.getTitle())
self.__lfh.write(
"+OeChemCompIoUtils.getOeMols() SMILES (canonical) = %s\n"
% oem.getCanSMILES())
self.__lfh.write(
"+OeChemCompIoUtils.getOeMols() SMILES (isomeric) = %s\n"
% oem.getIsoSMILES())
except Exception as e:
if self.__verbose:
self.__lfh.write("+OeChemCompIoUtils.getOeMols() Failed %s\n" %
str(e))
traceback.print_exc(file=self.__lfh)
return oemList
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 testCreateStoreOE(self):
"""Test case - build persistent store of serialized OE molecules using the contents of the chemical
dictionary persistent store containing all of chemical component defintions.
***NOTE - This will display diagnostics from OE toolkit for molecules with
problematic features. These issues will not impact the shape search.
"""
startTime = time.time()
self.__lfh.write(
"\nStarting OeShapeSearchtests testCreateCoreOE at %s\n" %
time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
try:
# Get handle for
myPersist = PdbxPersist(self.__verbose, self.__lfh)
indexD = myPersist.getIndex(dbFileName=self.__persistStorePathCC) # noqa: F841 pylint: disable=unused-variable
myPersist.open(dbFileName=self.__persistStorePathCC)
containerNameList = myPersist.getStoreContainerIndex()
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
molList = []
for ccId in containerNameList:
ccAt = myPersist.fetchObject(containerName=ccId,
objectName="chem_comp_atom")
ccBnd = myPersist.fetchObject(containerName=ccId,
objectName="chem_comp_bond")
if ccAt is None or ccBnd is None:
continue
#
oem.set(ccId, dcChemCompAtom=ccAt, dcChemCompBond=ccBnd)
ok = oem.build3D()
if ok:
if self.__debug:
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())
molD = {}
molD["name"] = ccId
molD["oeb"] = oem.serialize()
molList.append(molD)
else:
self.__lfh.write(
"+WARN - failed to build OE molecule for %s\n" % ccId)
myPersist.close()
#
oeP = OePersist(self.__verbose, self.__lfh)
oeP.setMoleculeList(moleculeList=molList)
oeP.store(dbFileName=self.__storePath)
mL = oeP.getIndex(dbFileName=self.__storePath)
#
if self.__debug:
self.__lfh.write(
"OePersistTests(testCreateStore) molecule list %r\n" % mL)
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
endTime = time.time()
self.__lfh.write(
"\nCompleted OeShapeSearchtests testCreateOEStore at %s (%d seconds)\n"
% (time.strftime("%Y %m %d %H:%M:%S",
time.localtime()), endTime - startTime))