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 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 testDepictSMILES(self):
"""Test case - create depiction from SMILES descriptor."""
self.__lfh.write("\nStarting OeDepictTests testDepictSMILES\n")
try:
imagePath = os.path.join(self.__testoutput, "benzene.svg")
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
ok = oem.importSmiles("c1ccccc1")
self.assertTrue(ok)
oed = OeDepict(verbose=self.__verbose, log=self.__lfh)
oed.setMolTitleList([("benzene", oem, "Title for benzene")])
oed.setDisplayOptions(labelAtomName=False,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
bondDisplayWidth=1.0)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testDepictOneSDF(self):
"""Test case - get, read, build OE molecule from SDF file, and depict the molecule."""
self.__lfh.write("\nStarting OeDepictTests testDepictOneSDF\n")
try:
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
if oem.importFile(self.__sdfFilePath, type="3D"):
self.__lfh.write("Title = %s\n" % oem.getTitle())
#
imagePath = os.path.join(self.__testoutput, "ATP.svg")
oed = OeDepict(verbose=self.__verbose, log=self.__lfh)
oed.setMolTitleList([("ATP", oem, "Title for ATP")])
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
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))
def testBuildMolFromSDF(self):
"""Test case - read a test SDF file and build the corresponding OEGraphMol"""
self.__lfh.write("\nStarting OeBuildMolTests testBuildolFromSDF\n")
try:
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
if oem.importFile(self.__sdfFilePath, type="3D"):
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())
else:
self.__lfh.write("SDF read failed for %s\n" %
self.__sdfFilePath)
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
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 __getMiscFile(self, ccPath, suppressHydrogens=False, importType="2D"):
"""Fetch a miscellaneous chemical file (ccPath) and build OE molecules
for comparison and depiction.
"""
try:
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
if oem.importFile(ccPath, type=importType):
if self.__verbose:
self.__lfh.write("+OEAlignDepilsct.__getMiscFile()\n")
self.__lfh.write(" Title = %s\n" %
oem.getTitle())
self.__lfh.write(" SMILES = %s\n" %
oem.getCanSMILES())
self.__lfh.write(" SMILES (stereo) = %s\n" %
oem.getIsoSMILES())
self.__lfh.write(" Formula (Hill) = %s\n" %
oem.getFormula())
self.__lfh.write(" InChI key = %s\n" %
oem.getInChIKey())
self.__lfh.write(" InChI = %s\n" %
oem.getInChI())
else:
self.__lfh.write(
"+OEAlignDepict.__getMiscFile() Read failed for %s\n" %
ccPath)
return None, None, None
#
# oem.build2D()
ccId = oem.getTitle()
if suppressHydrogens:
tMol = oem.getGraphMolSuppressH()
else:
tMol = oem.getMol()
molXyzL = []
if importType == "3D":
for ii, atm in enumerate(tMol.GetAtoms()):
xyzL = OEFloatArray(3)
tMol.GetCoords(atm, xyzL)
molXyzL.append(
(ii, atm.GetIdx(), atm.GetAtomicNum(), atm.GetName(),
atm.GetType(), "%.3f" % xyzL[0], "%.3f" % xyzL[1],
"%.3f" % xyzL[2]))
fD = {}
fD = {
"Formula": oem.getFormula(),
"SMILES": oem.getCanSMILES(),
"SMILES_STEREO": oem.getIsoSMILES(),
"InChI": oem.getInChI(),
"InChIKey": oem.getInChIKey(),
"xyz": molXyzL,
}
for ii, atm in enumerate(tMol.GetAtoms()):
xyzL = OEFloatArray(3)
tMol.GetCoords(atm, xyzL)
if self.__verbose:
self.__lfh.write(
"OeAlignDepict.__getMiscFile - atom %d %s %s %s %s %r\n"
% (ii, atm.GetIdx(), atm.GetAtomicNum(), atm.GetName(),
atm.GetType(), xyzL))
return (ccId, tMol, fD)
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
# self.fail()
return None, None, None
def __getCCDefFile(self, ccPath, suppressHydrogens=False):
"""Fetch the molecule definition (ccPath) and build OE molecules
for comparison and depiction.
"""
#
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
ccId = oem.setChemCompPath(ccPath)
oem.build2D()
if self.__verbose:
self.__lfh.write("+OEAlignDepilsct.__getCCDefFile() for %s\n" %
ccId)
self.__lfh.write(" Title = %s\n" % oem.getTitle())
self.__lfh.write(" SMILES = %s\n" %
oem.getCanSMILES())
self.__lfh.write(" SMILES (stereo) = %s\n" %
oem.getIsoSMILES())
self.__lfh.write(" Formula (Hill) = %s\n" % oem.getFormula())
self.__lfh.write(" InChI key = %s\n" % oem.getInChIKey())
self.__lfh.write(" InChI = %s\n" % oem.getInChI())
fD = {}
fD = {
"Formula": oem.getFormula(),
"SMILES": oem.getCanSMILES(),
"SMILES_STEREO": oem.getIsoSMILES(),
"InChI": oem.getInChI(),
"InChIKey": oem.getInChIKey()
}
if suppressHydrogens:
return (ccId, oem.getGraphMolSuppressH(), fD)
else:
return (ccId, oem.getMol(), fD)
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 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))