def __exhaustiveSubStructureSearch(self, numMols, **kwargs):
"""Exhaustive substructure search."""
try:
limitPerceptions = kwargs.get("limitPerceptions", False)
buildTypeList = kwargs.get("buildTypeList", ["oe-iso-smiles"])
oesmP, ccIdxD = self.__getSearchDataProviders(**kwargs)
oesU = OeSearchUtils(oesmP, fpTypeList=[])
oeioU = OeIoUtils()
#
for ccId, ccD in list(ccIdxD.items())[:numMols]:
matchCount = 0
mtS = set()
for buildType in buildTypeList:
if buildType in ccD:
oeMol = oeioU.descriptorToMol(
ccD[buildType],
buildType,
limitPerceptions=limitPerceptions,
messageTag=ccId + ":" + buildType)
if not oeMol:
logger.error(
"%s %s build query molecule build fails (skipping)",
ccId, buildType)
continue
# ----
startTime = time.time()
retStatus, mL = oesU.searchSubStructure(
oeMol, matchOpts="graph-strict")
if not retStatus:
logger.info("%s match fails for build type %s",
ccId, buildType)
elif not self.__resultContains(ccId, mL):
logger.info(
"%s failed match length %d build type %s in (%.4f seconds)",
ccId, len(mL), buildType,
time.time() - startTime)
elif self.__resultContains(ccId, mL):
mtS.update([m.ccId for m in mL])
matchCount += 1
self.assertTrue(retStatus)
self.assertTrue(self.__resultContains(ccId, mL))
if matchCount:
logger.info("%s MATCHES %d: %r", ccId, matchCount, mtS)
else:
logger.info("%s NO MATCHES", ccId)
# ----
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
return False
def testSubStructureSearch(self):
oemp = OeMoleculeProvider(**self.__myKwargs)
ok = oemp.testCache()
ccmP = ChemCompIndexProvider(**self.__myKwargs)
ccIdxD = ccmP.getIndex()
ok = ccmP.testCache(minCount=self.__minCount)
self.assertTrue(ok)
oesU = OeSearchUtils(oemp, fpTypeList=self.__fpTypeList)
numMols = 10
for ccId, _ in list(ccIdxD.items())[:numMols]:
# ----
startTime = time.time()
oeMol = oemp.getMol(ccId)
retStatus, mL = oesU.searchSubStructure(oeMol, matchOpts="relaxed")
logger.info("%s match length %d in (%.4f seconds)", ccId, len(mL),
time.time() - startTime)
self.assertTrue(retStatus)
self.assertTrue(self.__resultContains(ccId, mL))
def __exhaustiveSubStructureSearch(self, numMols, **kwargs):
"""Exhaustive substructure search."""
try:
limitPerceptions = kwargs.get("limitPerceptions", False)
buildTypeList = kwargs.get("buildTypeList", ["oe-iso-smiles"])
oesmP, ccIdxD = self.__getSearchDataProviders(**kwargs)
oesU = OeSearchUtils(oesmP, fpTypeList=[])
oeioU = OeIoUtils()
#
for ccId, ccD in list(ccIdxD.items())[:numMols]:
for buildType in buildTypeList:
if buildType in ccD:
oeMol = oeioU.descriptorToMol(
ccD[buildType],
buildType,
limitPerceptions=limitPerceptions,
messageTag=ccId + ":" + buildType)
if not oeMol:
continue
# ----
startTime = time.time()
retStatus, mL = oesU.searchSubStructure(
oeMol, matchOpts="graph-strict")
if not self.__resultContains(ccId, mL):
logger.info(
"%s match length %d build type %s in (%.4f seconds)",
ccId, len(mL), buildType,
time.time() - startTime)
self.assertTrue(retStatus)
self.assertTrue(self.__resultContains(ccId, mL))
# ----
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
return False