def reloadSearchDatabase(self):
"""Reload the in-memory search databases from the OE molecule provider.
Resource requirements: ~90sec load time 0.35 GB memory
Returns:
bool: True for success or False otherwise
"""
ok = False
try:
okmp = self.updateSearchMoleculeProvider(useCache=True)
if not okmp:
return ok
fpTypeCuttoffD = self.__configD["oesmpKwargs"][
"fpTypeCuttoffD"] if "fpTypeCuttoffD" in self.__configD[
"oesmpKwargs"] else {}
fpTypeList = [k for k, v in fpTypeCuttoffD.items()]
oesU = OeSearchUtils(self.__oesmP, fpTypeList=fpTypeList)
ok1 = oesU.testCache()
self.__oesU = oesU if ok1 else None
#
oesubsU = OeSubStructSearchUtils(self.__oesmP)
ok2 = oesubsU.testCache()
self.__oesubsU = oesubsU if ok2 else None
except Exception as e:
logger.exception("Failing with %s", str(e))
return ok1 and ok2
class OeSubStructSearchCompareTests(unittest.TestCase):
useFull = False
def setUp(self):
self.__workPath = os.path.join(HERE, "test-output")
self.__dataPath = os.path.join(HERE, "test-data")
self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
self.__ccUrlTarget = os.path.join(self.__dataPath,
"components-abbrev.cif")
self.__birdUrlTarget = os.path.join(self.__dataPath,
"prdcc-abbrev.cif")
self.__doDisplay = True
self.__numProcPrep = 6
self.__numProcSearch = 6
self.__minCount = None
self.__startTime = time.time()
#
if OeSubStructSearchCompareTests.useFull:
self.__myKwargs = {
"cachePath": self.__cachePath,
"useCache": True,
"ccFileNamePrefix": "cc-full",
"oeFileNamePrefix": "oe-full",
"molBuildType": "model-xyz",
"limitPerceptions": False,
"screenTypeList": None,
"numProc": self.__numProcPrep,
"suppressHydrogens": True,
"matchOpts": "sub-struct-graph-relaxed",
"fpTypeCuttoffD": {
"TREE": 0.6,
"MACCS": 0.9
},
"maxFpResults": 50,
}
else:
self.__myKwargs = {
"ccUrlTarget": self.__ccUrlTarget,
"birdUrlTarget": self.__birdUrlTarget,
"cachePath": self.__cachePath,
"useCache": True,
"ccFileNamePrefix": "cc-abbrev",
"oeFileNamePrefix": "oe-abbrev",
"molBuildType": "model-xyz",
"limitPerceptions": False,
"screenTypeList": None,
"numProc": self.__numProcPrep,
"suppressHydrogens": True,
"matchOpts": "sub-struct-graph-relaxed",
"fpTypeCuttoffD": {
"TREE": 0.6,
"MACCS": 0.9
},
"maxFpResults": 50,
}
#
self.__oesmP = OeSearchMoleculeProvider(**self.__myKwargs)
ok = self.__oesmP.testCache()
self.assertTrue(ok)
#
self.__ccmP = ChemCompMoleculeProvider(**self.__myKwargs)
self.__ccmP.testCache()
#
self.__ccsidxP = ChemCompSearchIndexProvider(**self.__myKwargs)
ok = self.__ccsidxP.testCache(minCount=self.__minCount)
self.assertTrue(ok)
self.__oessU = OeSubStructSearchUtils(self.__oesmP)
ok = self.__oessU.testCache()
self.assertTrue(ok)
#
fpTypeCuttoffD = self.__myKwargs.get("fpTypeCuttoffD", {})
fpTypeList = [k for k, v in fpTypeCuttoffD.items()]
self.__oesU = OeSearchUtils(self.__oesmP, fpTypeList=fpTypeList)
ok = self.__oesU.testCache()
self.assertTrue(ok)
#
logger.debug("Running tests on version %s", __version__)
logger.info("Starting %s at %s", self.id(),
time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
def tearDown(self):
endTime = time.time()
logger.info("Completed %s at %s (%.4f seconds)", self.id(),
time.strftime("%Y %m %d %H:%M:%S", time.localtime()),
endTime - self.__startTime)
@unittest.skipIf(not useFull, "Requires full data set")
def testSubStructSearchDescriptor(self):
#
query = "n1ccccc1"
queryId = "query-smiles"
queryType = "oe-iso-smiles"
#
limitPerceptions = self.__myKwargs.get("limitPerceptions", False)
suppressHydrogens = self.__myKwargs.get("suppressHydrogens", True)
numProc = self.__myKwargs.get("numProc", 4)
# for matchOpts in ["sub-struct-graph-relaxed", "sub-struct-graph-relaxed-stereo", "sub-struct-graph-strict"]:
for matchOpts in ["sub-struct-graph-strict"]:
#
oeMol = self.__getMol(query,
queryType,
queryId,
limitPerceptions=limitPerceptions,
suppressHydrogens=suppressHydrogens)
startTime = time.time()
retStatus, mL = self.__search(oeMol, matchOpts, numProc)
logger.info(
"%s status (%r) matchOpts %s result %d in (%.4f seconds)",
queryId, retStatus, matchOpts, len(mL),
time.time() - startTime)
self.assertTrue(retStatus)
if queryType == "CC":
self.assertTrue(self.__resultContains(queryId, mL))
#
if self.__doDisplay:
self.__display(mL, query, queryId, queryType, matchOpts)
@unittest.skipIf(not useFull, "Requires full data set")
def testSubStructSearchSelected(self):
#
query = queryId = "STI"
queryType = "CC"
#
limitPerceptions = self.__myKwargs.get("limitPerceptions", False)
suppressHydrogens = self.__myKwargs.get("suppressHydrogens", True)
numProc = self.__myKwargs.get("numProc", 4)
for matchOpts in [
"sub-struct-graph-relaxed", "sub-struct-graph-relaxed-stereo",
"sub-struct-graph-strict"
]:
#
oeMol = self.__getMol(query,
queryType,
queryId,
limitPerceptions=limitPerceptions,
suppressHydrogens=suppressHydrogens)
startTime = time.time()
retStatus, mL = self.__search(oeMol, matchOpts, numProc)
logger.info(
"%s status (%r) matchOpts %s result %d in (%.4f seconds)",
queryId, retStatus, matchOpts, len(mL),
time.time() - startTime)
self.assertTrue(retStatus)
if queryType == "CC":
self.assertTrue(self.__resultContains(queryId, mL))
#
if self.__doDisplay:
self.__display(mL, query, queryId, queryType, matchOpts)
@unittest.skipIf(not useFull, "Requires full data set")
def testSubStructSearchAll(self):
#
ccD = self.__ccmP.getMolD()
for ccId in ccD:
query = queryId = ccId
if ccId in ["UNX", "UNL", "UNK", "DUM"]:
continue
queryType = "CC"
#
limitPerceptions = self.__myKwargs.get("limitPerceptions", False)
suppressHydrogens = self.__myKwargs.get("suppressHydrogens", True)
numProc = self.__myKwargs.get("numProc", 5)
for matchOpts in [
"sub-struct-graph-relaxed",
"sub-struct-graph-relaxed-stereo",
"sub-struct-graph-strict"
]:
#
oeMol = self.__getMol(query,
queryType,
queryId,
limitPerceptions=limitPerceptions,
suppressHydrogens=suppressHydrogens)
if oeMol.NumAtoms() < 3:
continue
#
startTime = time.time()
retStatus, mL = self.__search(oeMol, matchOpts, numProc)
logger.info(
"%s status (%r) matchOpts %s result %d in (%.4f seconds)",
queryId, retStatus, matchOpts, len(mL),
time.time() - startTime)
self.assertTrue(retStatus)
if queryType == "CC":
self.assertTrue(self.__resultContains(queryId, mL))
#
if self.__doDisplay:
self.__display(mL, query, queryId, queryType, matchOpts)
@unittest.skipIf(not useFull, "Requires full data set")
def testMatchSearchSelected(self):
#
query = queryId = "STI"
queryType = "CC"
#
limitPerceptions = self.__myKwargs.get("limitPerceptions", False)
suppressHydrogens = self.__myKwargs.get("suppressHydrogens", True)
numProc = self.__myKwargs.get("numProc", 4)
for matchOpts in [
"fingerprint-similarity", "graph-relaxed",
"graph-relaxed-stereo", "graph-strict"
]:
#
oeMol = self.__getMol(query,
queryType,
queryId,
limitPerceptions=limitPerceptions,
suppressHydrogens=suppressHydrogens)
startTime = time.time()
retStatus, mL = self.__search(oeMol, matchOpts, numProc)
logger.info(
"%s status (%r) matchOpts %s result %d in (%.4f seconds)",
queryId, retStatus, matchOpts, len(mL),
time.time() - startTime)
self.assertTrue(retStatus)
if queryType == "CC":
self.assertTrue(self.__resultContains(queryId, mL))
#
if self.__doDisplay:
self.__display(mL, query, queryId, queryType, matchOpts)
def __search(self, oeMol, matchOpts, numProc):
if matchOpts.startswith("sub-struct-"):
retStatus, mL = self.__subStructureSearch(oeMol,
matchOpts=matchOpts,
numProc=numProc)
else:
retStatus, mL, fpL = self.__matchSearch(oeMol, matchOpts=matchOpts)
#
rL = fpL if matchOpts in ["fingerprint-similarity"] else mL
return retStatus, rL
#
def __subStructureSearch(self, oeMol, matchOpts, numProc):
##
ccIdL = self.__oessU.prefilterIndex(oeMol,
self.__ccsidxP,
matchOpts=matchOpts,
skipFeatures=False)
retStatus, mL = self.__oessU.searchSubStructure(oeMol,
ccIdList=ccIdL,
matchOpts=matchOpts,
numProc=numProc)
return retStatus, mL
def __matchSearch(self, oeMol, matchOpts="graph-relaxed"):
ssL = fpL = []
try:
fpTypeCuttoffD = self.__myKwargs.get("fpTypeCuttoffD", {})
maxFpResults = self.__myKwargs.get("maxFpResults", 50)
retStatus, ssL, fpL = self.__oesU.searchSubStructureAndFingerPrint(
oeMol,
list(fpTypeCuttoffD.items())[:2],
maxFpResults,
matchOpts=matchOpts)
# logger.info("fpL %r", fpL)
except Exception as e:
logger.exception("Failing with %s", str(e))
#
return retStatus, ssL, fpL
def __getMol(self,
query,
queryType,
queryId,
limitPerceptions=False,
suppressHydrogens=True):
oeioU = OeIoUtils()
if queryType == "CC":
oeMol = self.__oesmP.getMol(query)
else:
oeMol = oeioU.descriptorToMol(query,
queryType,
limitPerceptions=limitPerceptions,
messageTag=queryId)
#
if suppressHydrogens:
oeMol = oeioU.suppressHydrogens(oeMol)
oeMol.SetTitle(queryId)
return oeMol
def __resultContains(self, ccId, matchResultList):
for matchResult in matchResultList:
if matchResult.ccId == ccId:
return True
return False
#
# ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------
def __display(self, mL, query, queryId, queryType, matchOpts):
smL = sorted(mL, key=lambda kv: kv.fpScore, reverse=True)
# ----
tD = {}
for sm in smL:
ccId = sm.ccId.split("|")[0]
tD.setdefault(ccId, []).append(sm)
dL = []
for ccId, ttL in tD.items():
if len(ttL) == 1:
dL.append(ttL[0])
else:
parent = False
for tt in ttL:
if tt.ccId == ccId:
dL.append(tt)
parent = True
break
if not parent:
dL.append(ttL[0])
# ----
pdfImagePath = os.path.join(self.__workPath,
queryId + "-" + matchOpts + ".pdf")
self.__displayPaginatedAlignments(pdfImagePath,
query,
queryType,
queryId,
dL,
matchOpts=matchOpts)
def __displayPaginatedAlignments(self,
pdfImagePath,
query,
queryType,
queryId,
matchResultList,
matchOpts="relaxed-stereo",
alignMode="SS"):
refId = queryId
oeMolRef = self.__getMol(query,
queryType,
queryId,
limitPerceptions=False,
suppressHydrogens=True)
pairList = []
for mr in sorted(matchResultList,
key=lambda kv: kv.fpScore,
reverse=True):
fitId = mr.ccId.split("|")[0]
if len(mr.ccId) > 4:
fitId = fitId + " (tautomer/protomer)"
oeMolFit = self.__oesmP.getMol(mr.ccId)
pairList.append((refId, oeMolRef, fitId, oeMolFit))
#
self.__depictFitList(pdfImagePath,
pairList,
matchOpts=matchOpts,
alignMode=alignMode)
def __pairDepictPage(self,
imagePath,
refId,
refTitle,
refMol,
fitId,
fitTitle,
fitMol,
matchOpts="strict"):
"""Depict pairwise alignment of the input reference and fit molecules.
Args:
imagePath (str): path to image (format by path extension)
refId (str): reference molecule identifier
refTitle (str): reference molecule title
refMol (obj): reference OE molecule object
fitId (str): fit molecule identifier
fitTitle (str): fit molecule title
fitMol (obj): fit OE molecule object
matchOpts (str, optional): alignment criteria (relaxed|relaxed-stereo|strict). Defaults to "strict".
Returns:
(list): atom mapping in all aligned figures
[(reference component Id, reference atom name, fit chemical component Id, fit atom name)
"""
aML = []
try:
oed = OeDepictMCSAlignPage()
oed.setSearchType(sType=matchOpts)
oed.setRefMol(refMol, refId, title=refTitle)
oed.setFitMol(fitMol, fitId, title=fitTitle)
oed.setDisplayOptions(
imageSizeX=2000,
imageSizeY=1000,
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
bondDisplayWidth=0.5,
highLightMatchColorRef="green",
highLightNotMatchColorRef="pink",
)
aML = oed.alignPair(imagePath=imagePath)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
except Exception as e:
logger.exception("Failing with %s", str(e))
return aML
def __depictFitList(self,
pdfImagePath,
pairList,
matchOpts="exact",
alignMode="SS"):
"""Depict pairwise alignments with multi-page layout in PDF format.
Args:
pdfImagePath (str): PDF image path
pairList (list): [(refId, refOeMol, fitId, fitOeMol)]
Returns:
(list): atom mapping in all aligned figures
[(reference component Id, reference atom name, fit chemical component Id, fit atom name)
"""
aML = []
try:
if alignMode == "MCSS":
oed = OeDepictMCSAlignMultiPage()
else:
oed = OeDepictSubStructureAlignMultiPage()
oed.setSearchType(sType=matchOpts)
oed.setPairMolList(pairList)
oed.setDisplayOptions(
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
pageOrientation="portrait",
gridRows=4,
bondDisplayWidth=0.5,
highLightMatchColorRef="green",
highLightNotMatchColorRef="pink",
)
aML = oed.alignPairListMulti(imagePath=pdfImagePath)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
return aML