def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <reffile> <fitfile>" % argv[0])
reffs = oechem.oemolistream(argv[1])
fitfs = oechem.oemolistream(argv[2])
refmol = oechem.OEMol()
oechem.OEReadMolecule(reffs, refmol)
print("Ref. Title:", refmol.GetTitle(), "Num Confs:", refmol.NumConfs())
# Prepare reference molecule for calculation
# With default options this will remove any explicit
# hydrogens present and add color atoms
prep = oeshape.OEOverlapPrep()
prep.Prep(refmol)
overlay = oeshape.OEMultiRefOverlay()
overlay.SetupRef(refmol)
for fitmol in fitfs.GetOEMols():
prep.Prep(fitmol)
score = oeshape.OEBestOverlayScore()
overlay.BestOverlay(score, fitmol, oeshape.OEHighestTanimoto())
print(
"Fit Title: %-4s FitConfIdx: %-4d RefConfIdx: %-4d tanimoto combo: %.2f"
% (fitmol.GetTitle(), score.GetFitConfIdx(), score.GetRefConfIdx(),
score.GetTanimotoCombo()))
def run(self):
for fitmol in self._ifs.GetOEMols():
self._prep.Prep(fitmol)
score = oeshape.OEBestOverlayScore()
self._overlay.BestOverlay(score, fitmol,
oeshape.OEHighestTanimoto())
print(
"Fit Title: %-4s FitConfIdx: %-4d RefConfIdx: %-4d tanimoto combo: %.2f"
% (fitmol.GetTitle(), score.GetFitConfIdx(),
score.GetRefConfIdx(), score.GetTanimotoCombo()))
def overlay_molecules(
reference_molecule: oechem.OEGraphMol,
fit_molecule: oechem.OEMol,
return_overlay: bool = True,
) -> (int, List[oechem.OEGraphMol]):
"""
Overlay two molecules and calculate TanimotoCombo score.
Parameters
----------
reference_molecule: oechem.OEGraphMol
An OpenEye molecule holding the reference molecule for overlay.
fit_molecule: oechem.OEMol
An OpenEye multi-conformer molecule holding the fit molecule for overlay.
return_overlay: bool
If the best scored overlay of molecules should be returned.
Returns
-------
: int or int and list of oechem.OEGraphMol
The TanimotoCombo score of the best overlay and the overlay if score_only is set False.
"""
from openeye import oechem, oeshape
prep = oeshape.OEOverlapPrep()
prep.Prep(reference_molecule)
overlay = oeshape.OEOverlay()
overlay.SetupRef(reference_molecule)
prep.Prep(fit_molecule)
score = oeshape.OEBestOverlayScore()
overlay.BestOverlay(score, fit_molecule, oeshape.OEHighestTanimoto())
if not return_overlay:
return score.GetTanimotoCombo()
else:
overlay = [reference_molecule]
fit_molecule = oechem.OEGraphMol(
fit_molecule.GetConf(oechem.OEHasConfIdx(score.GetFitConfIdx())))
score.Transform(fit_molecule)
overlay.append(fit_molecule)
return score.GetTanimotoCombo(), overlay
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData, argv)
NPolyMax_MAX = itf.GetInt("-NPolyMax_MAX")
ifrefname = itf.GetString("-inputreffile")
iffitname = itf.GetString("-inputfitfile")
ofname = itf.GetString("-outputfile")
ifsref = oechem.oemolistream()
if not ifsref.open(ifrefname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % ifrefname)
ifsfit = oechem.oemolistream()
if not ifsfit.open(iffitname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % iffitname)
refmol = oechem.OEMol()
if not oechem.OEReadMolecule(ifsref, refmol):
oechem.OEThrow.Fatal("Unable to read molecule in %s" % ifrefname)
prep = oeshape.OEOverlapPrep()
prep.SetAssignColor(False)
prep.Prep(refmol)
reftransfm = oechem.OETrans()
oeshape.OEOrientByMomentsOfInertia(refmol, reftransfm)
hermiteoptionsref = oeshape.OEHermiteOptions()
hermiteoptionsref.SetNPolyMax(NPolyMax_MAX)
hermiteoptionsref.SetUseOptimalLambdas(True)
hermiteoptionsfit = oeshape.OEHermiteOptions()
hermiteoptionsfit.SetNPolyMax(NPolyMax_MAX)
hermiteoptionsfit.SetUseOptimalLambdas(True)
hermitefunc = oeshape.OEHermiteShapeFunc(hermiteoptionsref,
hermiteoptionsfit)
options = oeshape.OEOverlayOptions()
options.SetOverlapFunc(hermitefunc)
overlay = oeshape.OEOverlay(options)
overlay.SetupRef(refmol)
ofs = oechem.oemolostream()
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open %s for writing" % ofname)
transfm = oechem.OETrans()
fitmol = oechem.OEMol()
while oechem.OEReadMolecule(ifsfit, fitmol):
prep.Prep(fitmol)
oeshape.OEOrientByMomentsOfInertia(fitmol, transfm)
score = oeshape.OEBestOverlayScore()
overlay.BestOverlay(score, fitmol)
print("Hermite Tanimoto = ", score.GetTanimoto())
oechem.OESetSDData(fitmol, "HermiteTanimoto_" + str(NPolyMax_MAX),
str(score.GetTanimoto()))
score.Transform(fitmol)
# Transform from the inertial frame to the original reference mol frame
reftransfm.Transform(fitmol)
oechem.OEWriteMolecule(ofs, fitmol)