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 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 __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