def testSubStructureSearchBase(self):
matchOpts = self.__myKwargs.get("matchOpts", "sub-struct-graph-relaxed")
numProc = self.__numProcSearch
oemp = OeMoleculeProvider(**self.__myKwargs)
ok = oemp.testCache()
self.assertTrue(ok)
oesU = OeSubStructSearchUtils(oemp)
#
ccIdxP = ChemCompIndexProvider(**self.__myKwargs)
ok = ccIdxP.testCache(minCount=self.__minCount)
self.assertTrue(ok)
ccIdxD = ccIdxP.getIndex()
#
ky = next(iter(ccIdxD))
oeMol = oemp.getMol(ky)
#
numMols = 10
for ccId, _ in list(ccIdxD.items())[:numMols]:
# ----
startTime = time.time()
oeMol = oemp.getMol(ccId)
ccIdL = oesU.prefilterIndex(oeMol, ccIdxP, matchOpts=matchOpts)
logger.info("%s search length %d in (%.4f seconds)", ccId, len(ccIdL), time.time() - startTime)
#
retStatus, mL = oesU.searchSubStructure(oeMol, ccIdList=ccIdL, matchOpts=matchOpts, numProc=numProc)
logger.info("%s result length %d in (%.4f seconds)", ccId, len(mL), time.time() - startTime)
self.assertTrue(retStatus)
self.assertTrue(self.__resultContains(ccId, mL))
def testFingerPrintSearch(self):
oemp = OeMoleculeProvider(**self.__myKwargs)
# This will reload the oe binary cache.
oeMol = oemp.getMol("004")
self.assertGreaterEqual(len(list(oeMol.GetAtoms())), 12)
#
ok = oemp.testCache()
ccmP = ChemCompIndexProvider(**self.__myKwargs)
ccIdxD = ccmP.getIndex()
ok = ccmP.testCache(minCount=self.__minCount)
self.assertTrue(ok)
minScore = 0.50
maxResults = 50
numMols = 50
oesU = OeSearchUtils(oemp, fpTypeList=self.__fpTypeList)
# ----
startTime = time.time()
for ccId, _ in list(ccIdxD.items())[:numMols]:
for fpType in self.__fpTypeList:
oeMol = oemp.getMol(ccId)
retStatus, mL = oesU.searchFingerPrints(
oeMol,
fpType=fpType,
minFpScore=minScore,
maxFpResults=maxResults)
self.assertTrue(retStatus)
self.assertTrue(self.__resultContains(ccId, mL))
# self.assertGreaterEqual(len(mL), 1)
logger.info("%s fingerprints search on %d in (%.4f seconds)",
len(self.__fpTypeList), numMols,
time.time() - startTime)
def testSubStructureSearchWithFingerPrint(self):
oemp = OeMoleculeProvider(**self.__myKwargs)
#
ok = oemp.testCache()
ccmP = ChemCompIndexProvider(**self.__myKwargs)
ccIdxD = ccmP.getIndex()
ok = ccmP.testCache(minCount=self.__minCount)
self.assertTrue(ok)
minFpScore = 0.40
maxFpResults = 50
numMols = 20
matchOpts = "graph-relaxed"
oesU = OeSearchUtils(oemp, fpTypeList=self.__fpTypeList)
# ----
startTime = time.time()
for ccId, _ in list(ccIdxD.items())[:numMols]:
for fpType in self.__fpTypeList:
oeMol = oemp.getMol(ccId)
retStatus, mL = oesU.searchSubStructureWithFingerPrint(
oeMol,
fpType,
minFpScore,
maxFpResults,
matchOpts=matchOpts)
self.assertTrue(retStatus)
self.assertTrue(self.__resultContains(ccId, mL))
logger.info("%s fingerprints search on %d in (%.4f seconds)",
len(self.__fpTypeList), numMols,
time.time() - startTime)
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 __testBuildMoleculeCacheFiles(self, **kwargs):
"""Test build OE cache files from full component dictionary"""
ccUrlTarget = kwargs.get("ccUrlTarget", None)
birdUrlTarget = kwargs.get("birdUrlTarget", None)
molLimit = kwargs.get("molLimit", 0)
quietFlag = kwargs.get("quietFlag", True)
molBuildType = kwargs.get("molBuildType", "ideal-xyz")
fpTypeList = kwargs.get("fpTypeList", ["TREE"])
screenTypeList = kwargs.get("screenTypeList", [])
ccFileNamePrefix = kwargs.get("ccFileNamePrefix", "cc")
oeFileNamePrefix = kwargs.get("oeFileNamePrefix", "oe")
#
startTime = time.time()
oemp = OeMoleculeProvider(
ccUrlTarget=ccUrlTarget,
birdUrlTarget=birdUrlTarget,
cachePath=self.__cachePath,
ccFileNamePrefix=ccFileNamePrefix,
oeFileNamePrefix=oeFileNamePrefix,
molBuildType=molBuildType,
useCache=False,
quietFlag=quietFlag,
fpTypeList=fpTypeList,
screenTypeList=screenTypeList,
)
ok = oemp.testCache()
self.assertTrue(ok)
oemp = OeMoleculeProvider(
ccUrlTarget=ccUrlTarget,
birdUrlTarget=birdUrlTarget,
cachePath=self.__cachePath,
ccFileNamePrefix=ccFileNamePrefix,
oeFileNamePrefix=oeFileNamePrefix,
molBuildType=molBuildType,
useCache=True,
)
endTime = time.time()
logger.info(">> Completed load molBuildType %r molLimit %r (%.4f seconds)", molBuildType, molLimit, endTime - startTime)
#
# ---
deltaMol = 2
minMol = minNumFp = molLimit - deltaMol if molLimit else 30000
for fpType in fpTypeList:
fpDb = oemp.getFingerPrintDb(fpType="TREE")
logger.debug("fpType %r length %d", fpType, fpDb.NumFingerPrints())
self.assertGreaterEqual(fpDb.NumFingerPrints(), minNumFp)
#
ccId = "004"
oeMol = oemp.getMol(ccId)
logger.debug("%s atom count %d", ccId, len(list(oeMol.GetAtoms())))
#
if molBuildType in ["oe-iso-smiles"]:
self.assertGreaterEqual(len(list(oeMol.GetAtoms())), 12)
else:
self.assertGreaterEqual(len(list(oeMol.GetAtoms())), 20)
#
oeDb, oeDbIdx = oemp.getOeMolDatabase()
logger.debug("Type db %r length %d type idx %r length %d", type(oeDb), oeDb.NumMols(), type(oeDbIdx), len(oeDbIdx))
self.assertGreaterEqual(oeDb.NumMols(), minMol)
self.assertGreaterEqual(len(oeDbIdx), minMol)
#
if molBuildType in ["oe-iso-smiles"] and screenTypeList:
ssDb = oemp.getSubSearchDb()
self.assertGreaterEqual(ssDb.NumMolecules(), minMol)
return True