def testRoundTripOps(self):
"""Test IO operation on generated related molecules"""
try:
oeIoU = OeIoUtils()
mU = MarshalUtil()
mU.mkdir(self.__molfileDirPath)
ccMolD = self.__getChemCompDefs()
oemf = OeMoleculeFactory()
for ccId, ccObj in list(ccMolD.items())[:10]:
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
relatedIdxD = oemf.buildRelated(limitPerceptions=False)
logger.info("%s generated %d molecular forms", ccId,
len(relatedIdxD))
for sId, idxD in relatedIdxD.items():
logger.info("sId %r smiles %r", sId, idxD["smiles"])
mol2Path = os.path.join(self.__molfileDirPath,
sId + ".mol2")
oeMol = oeIoU.descriptorToMol(idxD["smiles"],
"oe-iso-smiles",
limitPerceptions=False,
messageTag=None)
oeIoU.write(mol2Path,
oeMol,
constantMol=True,
addSdTags=True)
tMolL = oeIoU.fileToMols(mol2Path)
#
nextMol2Path = os.path.join(self.__molfileDirPath,
sId + "-next.mol2")
oeIoU.write(nextMol2Path,
tMolL[0],
constantMol=True,
addSdTags=True)
sdfPath = os.path.join(self.__molfileDirPath, sId + ".mol")
oeMol = oeIoU.descriptorToMol(idxD["smiles"],
"oe-iso-smiles",
limitPerceptions=False,
messageTag=None)
oeIoU.write(sdfPath,
oeMol,
constantMol=True,
addSdTags=True)
#
tMolL = oeIoU.fileToMols(sdfPath)
nextSdfPath = os.path.join(self.__molfileDirPath,
sId + "-next.sdf")
oeIoU.write(nextSdfPath,
tMolL[0],
constantMol=True,
addSdTags=True)
# ----
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testDepictOneSDF(self):
"""Test case - get, read, build OE molecule from SDF file, and depict the molecule."""
try:
imagePath = os.path.join(self.__workPath, "benzene-from-smi.svg")
sdfPath = os.path.join(self.__dataPath, "ATP.sdf")
oeio = OeIoUtils()
oeMolL = oeio.fileToMols(sdfPath)
#
oed = OeDepict()
oed.setMolTitleList([("ATP", oeMolL[0], "Title for ATP")])
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelBondCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
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
