def prefilterIndex(self,
oeQueryMol,
idxP,
matchOpts="relaxed",
skipFeatures=False):
"""Filter the full search index base on minimum chemical formula an feature criteria.
Args:
oeQueryMol (object): search target moleculed (OEMol)
idxP (object): instance ChemCompSearchIndexProvider()
matchOpts (str, optional): search criteria options. Defaults to "default".
skipFeatures (bool, optional): skip feature filters. Defaults to False.
Returns:
(list): list of chemical component identifiers in the filtered search space
"""
startTime = time.time()
oemf = OeMoleculeFactory()
oemf.setOeMol(oeQueryMol, "queryTarget")
typeCountD = oemf.getElementCounts(useSymbol=True)
# ccIdL1 = idxP.filterMinimumMolecularFormula(typeCountD)
#
featureCountD = oemf.getFeatureCounts() if not skipFeatures else {}
# Adjust filter according to search options
if matchOpts in matchOpts in [
"relaxed", "graph-relaxed", "simple",
"sub-struct-graph-relaxed"
]:
for ky in ["rings_ar", "at_ar", "at_ch"]:
featureCountD.pop(ky, None)
elif matchOpts in [
"relaxed-stereo", "graph-relaxed-stereo",
"sub-struct-graph-relaxed-stereo", "graph-relaxed-stereo-sdeq",
"sub-struct-graph-relaxed-stereo-sdeq"
]:
for ky in ["rings_ar", "at_ar"]:
featureCountD.pop(ky, None)
elif matchOpts in [
"default", "strict", "graph-strict", "graph-default",
"sub-struct-graph-strict"
]:
pass
ccIdL = idxP.filterMinimumFormulaAndFeatures(typeCountD, featureCountD)
logger.info(
"Pre-filtering results for formula+feature %d (%.4f seconds)",
len(ccIdL),
time.time() - startTime)
return ccIdL
def write(self, filePath, oeMol, constantMol=False, addSdTags=True):
"""Write an oeMol with format type inferred from the filePath extension (e.g. .mol)
Args:
filePath (str): filepath with a chemical type extension
constantMol (bool, optional): copies molecule before performing format specific perceptions
Returns:
bool: True for success or False otherwise
"""
try:
molId = os.path.splitext(os.path.basename(filePath))[0]
fmt = os.path.splitext(os.path.basename(filePath))[1][1:].lower()
#
if addSdTags:
oemf = OeMoleculeFactory()
oemf.setOeMol(oeMol, molId)
oemf.addSdTags()
oeMol = oemf.getMol()
#
self.__mU.mkdir(os.path.dirname(filePath))
ofs = oechem.oemolostream()
ofs.open(filePath)
logger.debug("Writing (fmt=%s) molId %s path %s title %s", fmt,
molId, filePath, oeMol.GetTitle())
#
if constantMol:
oechem.OEWriteConstMolecule(ofs, oeMol)
else:
oechem.OEWriteMolecule(ofs, oeMol)
#
# If this is a mol2 file, we need to replace the resname
if fmt.startswith("mol2"):
# If this is a mol2/mol2h substitute the default substructure id
with open(filePath, "r", encoding="utf-8") as ifh:
lines = ifh.readlines()
lines = [line.replace("<0>", molId) for line in lines]
with open(filePath, "w", encoding="utf-8") as ofh:
ofh.writelines(lines)
return True
except Exception as e:
logger.exception("Failing for %s with %s", filePath, str(e))
return False
def __getMiscFile(self, filePath, suppressHydrogens=False, importType="2D", title=None, largestPart=False):
"""Fetch a miscellaneous chemical file (ccPath) and build OE molecules
for comparison.
"""
try:
oeioU = OeIoUtils()
oeMolL = oeioU.fileToMols(filePath, use3D=importType == "3D", largestPart=largestPart)
logger.info("Read (%d) from %s ", len(oeMolL), filePath)
oeMol = oeMolL[0]
ccId = title if title else oeMol.GetTitle()
if title:
oeMol.SetTitle(ccId)
#
oemf = OeMoleculeFactory()
if not self.__verbose:
oemf.setQuiet()
oemf.setOeMol(oeMol, ccId)
#
fD = oemf.getOeMoleculeFeatures()
if self.__verbose:
logger.info(" Title = %s", title)
logger.info(" Title OEMF = %s", oemf.getTitle())
logger.info(" SMILES = %s", oemf.getCanSMILES())
logger.info(" SMILES (stereo) = %s", oemf.getIsoSMILES())
logger.info(" Formula (Hill) = %s", oemf.getFormula())
logger.info(" InChI key = %s", oemf.getInChIKey())
logger.info(" InChI = %s", oemf.getInChI())
#
ccId = oemf.getTitle()
if suppressHydrogens:
tMol = oemf.getGraphMolSuppressH()
else:
tMol = oemf.getMol()
molXyzL = []
if importType == "3D":
for atm in tMol.GetAtoms():
xyzL = oechem.OEFloatArray(3)
tMol.GetCoords(atm, xyzL)
molXyzL.append(
ComponentAtomDetails(
atIdx=atm.GetIdx(),
atNo=atm.GetAtomicNum(),
atName=atm.GetName(),
atType=atm.GetType(),
x=xyzL[0],
y=xyzL[1],
z=xyzL[2],
atFormalCharge=atm.GetFormalCharge(),
)
)
fD = {}
fD = {
"Formula": oemf.getFormula(),
"SMILES": oemf.getCanSMILES(),
"SMILES_STEREO": oemf.getIsoSMILES(),
"InChI": oemf.getInChI(),
"InChIKey": oemf.getInChIKey(),
"xyz": molXyzL,
}
for atm in tMol.GetAtoms():
xyzL = oechem.OEFloatArray(3)
tMol.GetCoords(atm, xyzL)
if self.__verbose:
logger.debug("atom %s %s %s %s %r", atm.GetIdx(), atm.GetAtomicNum(), atm.GetName(), atm.GetType(), xyzL)
fD["OEMOL"] = tMol
return (ccId, tMol, fD)
except Exception as e:
logger.exception("Failing with %s", str(e))
return None, None, None