def testSelfConsistency(self):
"""Compare constructed molecule with underlying chemical definitions -"""
try:
failL = []
ccMolD = self.__getChemCompDefs()
#
# molBuildTypeL = ["model-xyz", "ideal-xyz", None]
# molBuildTypeL = [None]
#
oemf = OeMoleculeFactory()
macmp = MoleculeAnnotationsCompare()
limitPerceptions = False
# buildTypeRef = "oe-iso-smiles"
buildTypeRef = "model-xyz"
filterHydrogens = False
if buildTypeRef in [
"oe-iso-smiles", "oe-smiles", "cactvs-smiles",
"cactvs-iso-smiles", "acdlabs-smiles", "inchi"
]:
filterHydrogens = True
#
for ccId, ccObj in ccMolD.items():
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
ok = oemf.build(molBuildType=buildTypeRef,
limitPerceptions=limitPerceptions,
normalize=False)
if not ok:
logger.info("Build using %r failed for %s", buildTypeRef,
ccId)
continue
#
doTautomers = False
if doTautomers:
tautomerMolL = oemf.getTautomerMolList()
logger.info("%s number reasonable tautomers %d", ccId,
len(tautomerMolL))
#
refFD = macmp.getChemCompFeatures(
ccObj,
descriptorProgram="OPENEYE",
filterHydrogens=filterHydrogens)
tstFD = oemf.getOeMoleculeFeatures(
filterHydrogens=filterHydrogens)
# logger.info("tstFD %r", tstFD)
ok, retCmp = macmp.compare(refFD,
tstFD,
tstInfo="Openeye ISO SMILES")
if not ok:
logger.info("Comparison failed build type %r and %r",
buildTypeRef, ccId)
logger.debug(
"diff -> atomatic atoms %r stereo atoms %r bond types %r aromatic bonds %r",
retCmp.difAromaticAtoms,
retCmp.difStereoAtoms,
retCmp.difTypeBonds,
retCmp.difAromaticBonds,
)
failL.append(ccId)
#
logger.info("Failures (%d) %r: ", len(failL), failL)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __getMiscFile(self, filePath, suppressHydrogens=False, importType="2D", title=None, largestPart=False):
"""Fetch a miscellaneous chemical file (ccPath) and build OE molecules
for comparison.
"""
try:
oeioU = OeIoUtils()
oeMolL = oeioU.fileToMols(filePath, use3D=importType == "3D", largestPart=largestPart)
logger.info("Read (%d) from %s ", len(oeMolL), filePath)
oeMol = oeMolL[0]
ccId = title if title else oeMol.GetTitle()
if title:
oeMol.SetTitle(ccId)
#
oemf = OeMoleculeFactory()
if not self.__verbose:
oemf.setQuiet()
oemf.setOeMol(oeMol, ccId)
#
fD = oemf.getOeMoleculeFeatures()
if self.__verbose:
logger.info(" Title = %s", title)
logger.info(" Title OEMF = %s", oemf.getTitle())
logger.info(" SMILES = %s", oemf.getCanSMILES())
logger.info(" SMILES (stereo) = %s", oemf.getIsoSMILES())
logger.info(" Formula (Hill) = %s", oemf.getFormula())
logger.info(" InChI key = %s", oemf.getInChIKey())
logger.info(" InChI = %s", oemf.getInChI())
#
ccId = oemf.getTitle()
if suppressHydrogens:
tMol = oemf.getGraphMolSuppressH()
else:
tMol = oemf.getMol()
molXyzL = []
if importType == "3D":
for atm in tMol.GetAtoms():
xyzL = oechem.OEFloatArray(3)
tMol.GetCoords(atm, xyzL)
molXyzL.append(
ComponentAtomDetails(
atIdx=atm.GetIdx(),
atNo=atm.GetAtomicNum(),
atName=atm.GetName(),
atType=atm.GetType(),
x=xyzL[0],
y=xyzL[1],
z=xyzL[2],
atFormalCharge=atm.GetFormalCharge(),
)
)
fD = {}
fD = {
"Formula": oemf.getFormula(),
"SMILES": oemf.getCanSMILES(),
"SMILES_STEREO": oemf.getIsoSMILES(),
"InChI": oemf.getInChI(),
"InChIKey": oemf.getInChIKey(),
"xyz": molXyzL,
}
for atm in tMol.GetAtoms():
xyzL = oechem.OEFloatArray(3)
tMol.GetCoords(atm, xyzL)
if self.__verbose:
logger.debug("atom %s %s %s %s %r", atm.GetIdx(), atm.GetAtomicNum(), atm.GetName(), atm.GetType(), xyzL)
fD["OEMOL"] = tMol
return (ccId, tMol, fD)
except Exception as e:
logger.exception("Failing with %s", str(e))
return None, None, None