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 testSerialize2D(self):
"""Test case - build OE molecule using 2D data in the definition source data file
then serialize and deserialize this molecule.
"""
self.__lfh.write("\nStarting OeBuildMolTests testSerialize2D\n")
try:
oem = OeBuildMol(verbose=self.__verbose, log=self.__lfh)
oem.setDebug(True)
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.build2D()
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()