def toMolFile(self,
identifier,
identifierType,
molfilePath=None,
fmt="mol",
**kwargs):
"""Create molfile (fmt) from InChI, SMILES descriptors or PDB identifier."""
try:
molfilePath = molfilePath if molfilePath else self.__makeMolfilePath(
fmt=fmt)
oeio = OeIoUtils()
if identifierType.lower() in ["smiles"]:
oeMol = oeio.smilesToMol(identifier)
oeMol.SetTitle("From SMILES")
elif identifierType.lower() in ["inchi"]:
oeMol = oeio.inchiToMol(identifier)
oeMol.SetTitle("From InChI")
elif identifierType.lower() in ["identifierpdb"]:
ccsw = ChemCompSearchWrapper()
oesmP = ccsw.getSearchMoleculeProvider()
oeMol = oesmP.getMol(identifier)
#
ok = self.__toMolFile(oeMol, molfilePath, **kwargs)
return molfilePath if ok else None
except Exception as e:
logger.exception("Failing with %s", str(e))
return None
def alignMoleculePair(self,
refIdentifier,
refIdentifierType,
fitIdentifier,
fitIdentifierType,
imagePath=None,
**kwargs):
"""Create aligned depiction for a target molecule InChI, SMILES descriptors or PDB identifier."""
try:
imagePath = imagePath if imagePath else self.__makeImagePath()
oeio = OeIoUtils()
ccsw = ChemCompSearchWrapper()
oesmP = ccsw.getSearchMoleculeProvider()
# ---
if refIdentifierType.lower() in ["smiles"]:
oeMolRef = oeio.smilesToMol(refIdentifier)
elif refIdentifierType.lower() in ["inchi"]:
oeMolRef = oeio.inchiToMol(refIdentifier)
elif refIdentifierType.lower() in ["identifierpdb"]:
oeMolRef = oesmP.getMol(refIdentifier)
#
if fitIdentifierType.lower() in ["smiles"]:
oeMolFit = oeio.smilesToMol(fitIdentifier)
elif fitIdentifierType.lower() in ["inchi"]:
oeMolFit = oeio.inchiToMol(fitIdentifier)
elif fitIdentifierType.lower() in ["identifierpdb"]:
oeMolFit = oesmP.getMol(fitIdentifier)
# ---
logger.info("oeMolRef atoms %r", oeMolRef.NumAtoms())
logger.info("oeMolFit atoms %r", oeMolFit.NumAtoms())
displayIdRef = "Ref"
displayIdFit = "Fit"
ok = self.__depictAlignedPair(oeMolRef, displayIdRef, oeMolFit,
displayIdFit, imagePath, **kwargs)
return imagePath if ok else None
except Exception as e:
logger.exception("Failing with %s", str(e))
return None
def depictMolecule(self,
identifier,
identifierType,
imagePath=None,
**kwargs):
"""Create depiction from InChI, SMILES descriptors or PDB identifier."""
try:
imagePath = imagePath if imagePath else self.__makeImagePath()
oeio = OeIoUtils()
if identifierType.lower() in ["smiles"]:
oeMol = oeio.smilesToMol(identifier)
elif identifierType.lower() in ["inchi"]:
oeMol = oeio.inchiToMol(identifier)
elif identifierType.lower() in ["identifierpdb"]:
ccsw = ChemCompSearchWrapper()
oesmP = ccsw.getSearchMoleculeProvider()
oeMol = oesmP.getMol(identifier)
#
ok = self.__depictOne(oeMol, imagePath, **kwargs)
return imagePath if ok else None
except Exception as e:
logger.exception("Failing with %s", str(e))
return None