def main(argv=[__name__]):
if len(argv) != 5:
oechem.OEThrow.Usage("%s <queryfile> <fitfile> <outfile> <nhits>" %
argv[0])
if oechem.OEGetFileExtension(sys.argv[1]) != "sq":
oechem.OEThrow.Fatal("Requires a shape query .sq input file format")
fitfs = oechem.oemolistream(sys.argv[2])
outfs = oechem.oemolostream(sys.argv[3])
nhits = int(sys.argv[4])
query = oeshape.OEShapeQuery()
oeshape.OEReadShapeQuery(sys.argv[1], query)
# Setup OEROCS with specified number of best hits
options = oeshape.OEROCSOptions()
options.SetNumBestHits(nhits)
rocs = oeshape.OEROCS(options)
rocs.SetDatabase(fitfs)
for res in rocs.Overlay(query):
outmol = res.GetOverlayConf()
oechem.OEWriteMolecule(outfs, outmol)
print("title: %s tanimoto combo = %.2f" %
(outmol.GetTitle(), res.GetTanimotoCombo()))
def run_one_roc(mol):
fitfs = oechem.oemolistream("/Users/austin/Downloads/template_ligands/alls.mol2")
options = oeshape.OEROCSOptions()
options.SetNumBestHits(1)
rocs = oeshape.OEROCS(options)
rocs.SetDatabase(fitfs)
max_score = 0
for res in rocs.Overlay(mol):
max_score = max(res.GetTanimotoCombo(), max_score)
return max_score
def from_oemol(self, from_oemol):
with self.logger("from_oemol") as logger:
tautomer_options = oequacpac.OETautomerOptions()
tautomer_options.SetMaxTautomersGenerated(4096)
tautomer_options.SetMaxTautomersToReturn(16)
tautomer_options.SetCarbonHybridization(True)
tautomer_options.SetMaxZoneSize(50)
tautomer_options.SetApplyWarts(True)
pKa_norm = True
omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Pose)
omegaOpts.SetStrictAtomTypes(False)
omegaOpts.SetSampleHydrogens(True)
omegaOpts.SetMaxSearchTime(30)
omegaOpts.SetFixDeleteH(True)
omega = oeomega.OEOmega(omegaOpts)
options = oeshape.OEROCSOptions()
overlayoptions = oeshape.OEOverlayOptions()
overlayoptions.SetOverlapFunc(
oeshape.OEOverlapFunc(oeshape.OEAnalyticShapeFunc()))
options.SetOverlayOptions(overlayoptions)
# options.SetNumBestHits(10)
options.SetConfsPerHit(200)
# options.SetMaxHits(10000)
rocs = oeshape.OEROCS(options)
for tautomer in oequacpac.OEGetReasonableTautomers(
from_oemol, tautomer_options, pKa_norm):
logger.log("got enantiomer")
for enantiomer in oeomega.OEFlipper(tautomer, 4, False):
logger.log("got tautomer ")
enantiomer_ = oechem.OEMol(enantiomer)
ret_code = omega.Build(enantiomer_)
if ret_code != oeomega.OEOmegaReturnCode_Success:
logger.error("got oemeg_failed",
oeomega.OEGetOmegaError(ret_code))
else:
rocs.AddMolecule(oechem.OEMol(enantiomer_))
for res in rocs.Overlay(self.refmol):
outmol = oechem.OEMol(res.GetOverlayConfs())
good_mol = oechem.OEMol(outmol)
oechem.OEAddExplicitHydrogens(good_mol)
oechem.OEClearSDData(good_mol)
oeshape.OEDeleteCompressedColorAtoms(good_mol)
oeshape.OEClearCachedSelfColor(good_mol)
oeshape.OEClearCachedSelfShape(good_mol)
oeshape.OERemoveColorAtoms(good_mol)
return good_mol
logger.error("Returning None.")
return None
def main(argv=[__name__]):
if len(argv) != 5:
oechem.OEThrow.Usage("%s <reffile> <fitfile> <outfile> <nhits>" %
argv[0])
reffs = oechem.oemolistream(sys.argv[1])
fitfs = oechem.oemolistream(sys.argv[2])
outfs = oechem.oemolostream(sys.argv[3])
nhits = int(sys.argv[4])
refmol = oechem.OEMol()
oechem.OEReadMolecule(reffs, refmol)
# Setup OEROCS with specified number of best hits
options = oeshape.OEROCSOptions()
options.SetNumBestHits(nhits)
rocs = oeshape.OEROCS(options)
rocs.SetDatabase(fitfs)
for res in rocs.Overlay(refmol):
outmol = res.GetOverlayConf()
oechem.OEWriteMolecule(outfs, outmol)
print("title: %s tanimoto combo = %.2f" %
(outmol.GetTitle(), res.GetTanimotoCombo()))