def testSubStructureSearchScreened(self):
oeioU = OeIoUtils()
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,
screenType=self.__screenType,
numProc=self.__numProc)
numMols = 20
missL = []
for ccId, ccD in list(ccIdxD.items())[:numMols]:
# ----
startTime = time.time()
if "oe-smiles" not in ccD:
continue
logger.info("Search %s %r", ccId, ccD["oe-smiles"])
oeQMol = oeioU.smartsToQmol(ccD["oe-smiles"])
retStatus, mL = oesU.searchSubStructureScreened(oeQMol,
maxMatches=100)
if retStatus:
logger.info("%s (status=%r) match length %d in (%.4f seconds)",
ccId, retStatus, len(mL),
time.time() - startTime)
if not self.__resultContains(ccId, mL):
missL.append(ccId)
#
# self.assertGreaterEqual(len(mL), 1)
# ----
logger.info("Missed searches (%d) %r", len(missL), missL)
def __subStructureSearchScreened(self, numMols, **kwargs):
#
buildTypeList = kwargs.get("buildTypeList", ["oe-iso-smiles"])
screenTypeList = kwargs.get("screenTypeList", ["SMARTS"])
oesmP, ccIdxD = self.__getSearchDataProviders(**kwargs)
for screenType in screenTypeList:
oesU = OeSearchUtils(oesmP,
screenType=screenType,
numProc=self.__numProc)
oeioU = OeIoUtils()
#
missL = []
numMols = min(len(ccIdxD), numMols) if numMols else len(ccIdxD)
for (
ii,
ccId,
) in enumerate(list(ccIdxD.keys())[:numMols]):
ccD = ccIdxD[ccId]
for buildType in buildTypeList:
if buildType in ccD:
if screenType == "SMARTS":
smiles = oeioU.descriptorToSmiles(ccD[buildType],
buildType,
messageTag=ccId +
":" + buildType)
oeQMol = oeioU.descriptorToMol(smiles,
"SMARTS",
messageTag=ccId +
":" + buildType)
else:
oeQMol = oeioU.descriptorToQMol(ccD[buildType],
"SMARTS",
messageTag=ccId +
":" + buildType)
if not oeQMol:
logger.debug("%s build failed for %s - skipping",
ccId, buildType)
continue
# ----
startTime = time.time()
retStatus, mL = oesU.searchSubStructureScreened(
oeQMol, maxMatches=100)
if retStatus:
logger.debug(
"%s - %s - %s (status=%r) match length %d in (%.4f seconds)",
ccId, buildType, screenType, retStatus,
len(mL),
time.time() - startTime)
if not self.__resultContains(ccId, mL):
missL.append((ccId, buildType, screenType))
# ----
if ii % 100 == 0:
logger.info("Completed %d of %d missed count %d", ii,
numMols, len(missL))
logger.info("Screen %r missed searches (%d) %r", screenType,
len(missL), missL)
return True
def testSubStructureSearchScreenedFiltered(self):
myKwargs = {
"cachePath": self.__cachePath,
"useCache": True,
"fpTypeList": self.__fpTypeList,
"ccFileNamePrefix": "cc-filtered",
"oeFileNamePrefix": "oe-filtered",
"molBuildType": "oe-iso-smiles",
"limitPerceptions": False,
}
oeioU = OeIoUtils()
oemp = OeMoleculeProvider(**myKwargs)
ok = oemp.testCache()
ccmP = ChemCompIndexProvider(**myKwargs)
ccIdxD = ccmP.getIndex()
ok = ccmP.testCache(minCount=self.__minCount)
self.assertTrue(ok)
oesU = OeSearchUtils(oemp,
screenType=self.__screenType,
numProc=self.__numProc)
numMols = 5000
missL = []
for ccId, ccD in list(ccIdxD.items())[:numMols]:
# ----
startTime = time.time()
if "oe-smiles" not in ccD:
continue
logger.info("Search %s %r", ccId, ccD["oe-smiles"])
oeQMol = oeioU.smartsToQmol(ccD["oe-smiles"])
retStatus, mL = oesU.searchSubStructureScreened(oeQMol,
maxMatches=100)
logger.info("%s (status=%r)match length %d in (%.4f seconds)",
ccId, retStatus, len(mL),
time.time() - startTime)
if not self.__resultContains(ccId, mL):
missL.append(ccId)
# self.assertGreaterEqual(len(mL), 1)
# ----
logger.info("Missed searches (%d) %r", len(missL), missL)