def __buildChemCompSearchIndex(self, procName, ccIdList, descrD, limitPerceptions=False, quietFlag=False):
"""Internal method return a dictionary of extracted chemical component descriptors and formula."""
rL = []
fL = []
try:
for ccId in ccIdList:
if ccId not in self.__ccObjD:
logger.error("%s missing chemical definition for %s", procName, ccId)
fL.append(ccId)
continue
dataContainer = self.__ccObjD[ccId]
# ----
oemf = OeMoleculeFactory()
if quietFlag:
oemf.setQuiet()
tId = oemf.setChemCompDef(dataContainer)
if tId != ccId:
logger.error("%s %s chemical component definition import error", procName, ccId)
fL.append(ccId)
continue
# ----
oemf.clearExternalDescriptors()
for smi in descrD[ccId] if ccId in descrD else []:
oemf.addExternalDescriptor("smiles", smi, "chemaxon-smiles")
# ----
relD = oemf.buildRelated(limitPerceptions=limitPerceptions)
logger.debug("%s %s related molecular forms %d", procName, ccId, len(relD))
if relD:
rL.extend([relD[v] for v in relD])
else:
fL.append(ccId)
except Exception as e:
logger.exception("%s failing with %s", procName, str(e))
return rL, fL
def __buildChemCompSearchIndex(self, ccObjD, descrD, limitPerceptions=False, molLimit=None):
"""Internal method return a dictionary of extracted chemical component descriptors and formula."""
rD = {}
try:
for ii, ccId in enumerate(ccObjD, 1):
if molLimit and ii > molLimit:
break
# ----
oemf = OeMoleculeFactory()
oemf.setQuiet()
tId = oemf.setChemCompDef(ccObjD[ccId])
if tId != ccId:
logger.error("%s chemical component definition import error", ccId)
# ----
oemf.clearExternalDescriptors()
for smi in descrD[ccId] if ccId in descrD else []:
oemf.addExternalDescriptor("smiles", smi, "chemaxon-smiles")
# ----
smiD = oemf.buildRelated(limitPerceptions=limitPerceptions)
logger.debug("%s related molecular forms %d", ccId, len(smiD))
rD.update(smiD)
except Exception as e:
logger.exception("Failing with %s", str(e))
return rD
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 testBuildRelated(self):
"""Test build molecules chemical definitions -"""
try:
logger.info("Starting")
ccMolD = self.__getChemCompDefs()
oemf = OeMoleculeFactory(quietMode=True)
relD = {}
for ccId, ccObj in list(ccMolD.items())[:100]:
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
tD = oemf.buildRelated(limitPerceptions=False)
logger.info("%s related molecular forms %d", ccId, len(tD))
relD.update(tD)
logger.info("Total molecular forms (%d)", len(relD))
# ----
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testBuildRelatedExtra(self):
"""Test build molecules chemical definitions including extra chemaxon descriptors"""
try:
caxP = ChemAxonDescriptorProvider(
ccUrlTarget=self.__ccUrlTarget,
birdUrlTarget=self.__birdUrlTarget,
cachePath=self.__cachePath,
useCache=True,
ccFileNamePrefix="cc-abbrev")
ok = caxP.testCache()
self.assertTrue(ok)
descrD = caxP.getDescriptorIndex()
#
ccMolD = self.__getChemCompDefs()
oemf = OeMoleculeFactory(quietMode=True)
relD = {}
for ccId, ccObj in list(ccMolD.items())[:100]:
# ----
tId = oemf.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
#
oemf.clearExternalDescriptors()
for smi in descrD[ccId] if ccId in descrD else []:
oemf.addExternalDescriptor("smiles", smi,
"chemaxon-smiles")
#
tD = oemf.buildRelated(limitPerceptions=False)
logger.info("%s related molecular forms %d", ccId, len(tD))
relD.update(tD)
logger.info("Total molecular forms (%d)", len(relD))
# ----
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()