def matchByDescriptor(self,
descriptor,
descriptorType,
matchOpts="graph-relaxed",
searchId=None):
"""Return graph match (w/ finger print pre-filtering) and finger print search results for the
input desriptor.
Args:
descriptor (str): molecular descriptor (SMILES, InChI)
descriptorType (str): descriptor type (SMILES, InChI
matchOpts (str, optional): graph match criteria (graph-relaxed, graph-relaxed-stereo, graph-strict,
fingerprint-similarity, Defaults to "graph-relaxed")
searchId (str, optional): search identifier for logging. Defaults to None.
Returns:
(statusCode, list, list): status, graph match and finger match lists of type (MatchResults)
-100 descriptor processing error
-200 search execution error
0 search execution success
"""
ssL = fpL = []
retStatus = False
statusCode = -200
try:
fpTypeCuttoffD = self.__configD["oesmpKwargs"][
"fpTypeCuttoffD"] if "fpTypeCuttoffD" in self.__configD[
"oesmpKwargs"] else {}
maxFpResults = self.__configD["oesmpKwargs"][
"maxFpResults"] if "maxFpResults" in self.__configD[
"oesmpKwargs"] else 50
limitPerceptions = self.__configD["oesmpKwargs"][
"limitPerceptions"] if "limitPerceptions" in self.__configD[
"oesmpKwargs"] else False
#
searchId = searchId if searchId else "query"
messageTag = searchId + ":" + descriptorType
oeioU = OeIoUtils()
oeMol = oeioU.descriptorToMol(descriptor,
descriptorType,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
oeMol = oeioU.suppressHydrogens(oeMol)
if not oeMol:
logger.warning("descriptor type %r molecule build fails: %r",
descriptorType, descriptor)
return self.__statusDescriptorError, ssL, fpL
#
retStatus, ssL, fpL = self.__oesU.searchSubStructureAndFingerPrint(
oeMol,
list(fpTypeCuttoffD.items())[:2],
maxFpResults,
matchOpts=matchOpts)
statusCode = 0 if retStatus else self.__searchError
except Exception as e:
logger.exception("Failing with %s", str(e))
#
return statusCode, ssL, fpL
def subStructSearchByDescriptor(self,
descriptor,
descriptorType,
matchOpts="sub-struct-graph-relaxed",
searchId=None):
"""Return graph match (w/ finger print pre-filtering) and finger print search results for the
input desriptor.
Args:
descriptor (str): molecular descriptor (SMILES, InChI)
descriptorType (str): descriptor type (SMILES, InChI)
matchOpts (str, optional): graph match criteria (sub-struct-graph-relaxed, sub-struct-graph-relaxed-stereo,
sub-struct-graph-strict). Defaults to "sub-struct-graph-relaxed".
searchId (str, optional): search identifier for logging. Defaults to None.
Returns:
(statusCode, list, list): status, substructure search results of type (MatchResults), empty list placeholder
-100 descriptor processing error
-200 search execution error
0 search execution success
"""
ssL = []
retStatus = False
statusCode = -200
try:
limitPerceptions = self.__configD["oesmpKwargs"][
"limitPerceptions"] if "limitPerceptions" in self.__configD[
"oesmpKwargs"] else False
numProc = self.__configD["oesmpKwargs"][
"numProc"] if "numProc" in self.__configD["oesmpKwargs"] else 4
#
searchId = searchId if searchId else "query"
messageTag = searchId + ":" + descriptorType
oeioU = OeIoUtils()
oeMol = oeioU.descriptorToMol(descriptor,
descriptorType,
limitPerceptions=limitPerceptions,
messageTag=messageTag)
oeMol = oeioU.suppressHydrogens(oeMol)
if not oeMol:
logger.warning("descriptor type %r molecule build fails: %r",
descriptorType, descriptor)
return self.__statusDescriptorError, ssL, []
#
ccIdL = self.__oesubsU.prefilterIndex(oeMol,
self.__siIdxP,
matchOpts=matchOpts)
retStatus, ssL = self.__oesubsU.searchSubStructure(
oeMol, ccIdList=ccIdL, matchOpts=matchOpts, numProc=numProc)
statusCode = 0 if retStatus else self.__searchError
except Exception as e:
logger.exception("Failing with %s", str(e))
#
return statusCode, ssL, []
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
