def stringToMols(self, txt, sType="mol2", use3D=False):
"""Parse the input string as input format type (sType) returning a list of
molecule objects (OeGraphMol)
Args:
txt (str): string text of molecule data
sType (str, optional): string data format (mol2, sdf, smiles) . Defaults to "mol2".
Returns:
list: list of OeGraphMol() objects
"""
#
mL = []
oemf = OeMoleculeFactory()
try:
if sType not in ["mol2", "sdf", "smiles"]:
logger.error("Unsupported string data format")
return None
fD = {
"mol2": oechem.OEFormat_MOL2,
"sdf": oechem.OEFormat_SDF,
"smiles": oechem.OEFormat_SMI
}
ifs = oechem.oemolistream()
ifs.SetFormat(fD["sType"])
if not ifs.openstring(txt):
logger.error("Unable open string data for molecule reader")
return None
for tMol in ifs.GetOEGraphMols():
oeMol = oechem.OEGraphMol(tMol)
if use3D:
mL.append(
oemf.updateOePerceptions3D(
oeMol, aromaticModel=oechem.OEAroModelOpenEye))
else:
mL.append(
oemf.updateOePerceptions2D(
oeMol, aromaticModel=oechem.OEAroModelOpenEye))
except Exception as e:
logger.exception("Failing with %s", str(e))
return mL
def fileToMols(self, filePath, use3D=False, largestPart=False):
"""Parse the input path returning a list of molecule objects (OeGraphMol).
Args:
filePath (str): file path must have strandard recognized extension ('mol', 'sdf', 'smi', 'oeb').
Returns:
list : list of OeGraphMol() objects
"""
mL = []
oemf = OeMoleculeFactory()
try:
ifs = oechem.oemolistream()
if ifs.open(filePath):
for tMol in ifs.GetOEGraphMols():
oeMol = oechem.OEGraphMol(tMol)
# if oechem.OEReadMolecule(ifs, oeMol):
if largestPart:
molL = oemf.getParts(oeMol)
if len(molL) > 0:
oeMol = molL[0]
logger.info(
"Using largest bonded molecule part (%d/%d)",
len(molL), oeMol.NumAtoms())
if use3D:
mL.append(
oemf.updateOePerceptions3D(
oeMol, aromaticModel=oechem.OEAroModelOpenEye))
else:
mL.append(
oemf.updateOePerceptions2D(
oeMol, aromaticModel=oechem.OEAroModelOpenEye))
except Exception as e:
logger.exception("Failing with %s", str(e))
return mL