def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s input_molecule output_molecule" % args[0])
ifs = oechem.oemolistream()
if not ifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
ofs = oechem.oemolostream()
if not ofs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % args[2])
opts = oeszybki.OESzybkiOptions()
opts.GetOptOptions().SetOptimizerType(oeszybki.OEOptType_NEWTON)
opts.GetGeneralOptions().SetForceFieldType(
oeszybki.OEForceFieldType_MMFF94S)
opts.GetSolventOptions().SetSolventModel(oeszybki.OESolventModel_Sheffield)
opts.GetSolventOptions().SetChargeEngine(oequacpac.OEChargeEngineNoOp())
sz = oeszybki.OESzybki(opts)
res = oeszybki.OESzybkiResults()
for mol in ifs.GetOEMols():
for conf in mol.GetConfs():
if sz(conf, res):
oechem.OESetSDData(
conf,
oechem.OESDDataPair('Total_energy',
"%0.4f" % res.GetTotalEnergy()))
oechem.OEWriteMolecule(ofs, mol)
ifs.close()
ofs.close()
return 0
def min_mmff94x(mol, ofs, mmff94s=False):
"""
Minimize the mol with MMFF94 or MMFF94S force field.
Parameters
----------
mol : OpenEye single-conformer molecule
ofs : OpenEye output filestream
mmff94s : Boolean
True to minimize with MMFF94S
"""
# make copy of the input mol
oe_mol = oechem.OEGraphMol(mol)
# set general energy options along with the run type specification
optSzybki = oeszybki.OESzybkiOptions()
optSzybki.SetSolventModel(oeszybki.OESolventModel_NoSolv)
optSzybki.SetOptimizerType(oeszybki.OEOptType_BFGS)
# minimize with input charges not mmff94(s) charges
# https://docs.eyesopen.com/toolkits/python/szybkitk/examples.html#optimization-of-all-conformers-of-a-ligand
optSzybki.GetSolventOptions().SetChargeEngine(oequacpac.OEChargeEngineNoOp())
# set the particular force field
if mmff94s:
sdlabel = "MMFF94S"
optSzybki.SetForceFieldType(oeszybki.OEForceFieldType_MMFF94S)
else:
sdlabel = "MMFF94"
optSzybki.SetForceFieldType(oeszybki.OEForceFieldType_MMFF94)
# generate minimization engine
szOpt = oeszybki.OESzybki(optSzybki)
# make object to hold szybki results
szResults = oeszybki.OESzybkiResults()
# perform minimization
if not szOpt(oe_mol, szResults):
smilabel = oechem.OEGetSDData(oe_mol, "SMILES QCArchive")
print( ' >>> MMFF94x minimization failed for %s\n' % smilabel )
energy = szResults.GetTotalEnergy()
# save geometry, save energy as tag, write mol to file
oechem.OESetSDData(oe_mol, f"Energy {sdlabel}", str(energy))
oechem.OEWriteConstMolecule(ofs, oe_mol)
def AssignChargesByName(mol, name):
if name == "noop":
return oequacpac.OEAssignCharges(mol, oequacpac.OEChargeEngineNoOp())
elif name == "mmff" or name == "mmff94":
return oequacpac.OEAssignCharges(mol, oequacpac.OEMMFF94Charges())
elif name == "am1bcc":
return oequacpac.OEAssignCharges(mol, oequacpac.OEAM1BCCCharges())
elif name == "am1bccnosymspt":
optimize = True
symmetrize = True
return oequacpac.OEAssignCharges(
mol, oequacpac.OEAM1BCCCharges(not optimize, not symmetrize))
elif name == "amber" or name == "amberff94":
return oequacpac.OEAssignCharges(mol, oequacpac.OEAmberFF94Charges())
elif name == "am1bccelf10":
return oequacpac.OEAssignCharges(mol, oequacpac.OEAM1BCCELF10Charges())
return False
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s input_molecule output_molecule" % args[0])
ifs = oechem.oemolistream()
if not ifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
ofs = oechem.oemolostream()
if not ofs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % args[2])
# input set of conformations in solution
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
opts = oeszybki.OESzybkiOptions()
opts.GetSolventOptions().SetChargeEngine(oequacpac.OEChargeEngineNoOp())
sz = oeszybki.OESzybki(opts)
eres = oeszybki.OESzybkiEnsembleResults()
entropy = sz.GetEntropy(mol, eres, oeszybki.OEEntropyMethod_Analytic,
oeszybki.OEEnvType_SolutionSPT)
oechem.OEThrow.Info(
"Estimated molar solution entropy of the input compound is: %5.1f J/(mol*K)"
% entropy)
oechem.OEThrow.Info(
"Vibrational entropies (in J/(mol*K)) for all conformations:")
for conf, r in zip(mol.GetConfs(), eres.GetResultsForConformations()):
oechem.OEThrow.Info("%2d %5.1f" % (conf.GetIdx(), r.GetVibEntropy()))
# ensemble of unique conformations
oechem.OEWriteMolecule(ofs, mol)
return 0