def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <input> <output>" % 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])
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
opts = oeszybki.OEFreeFormConfOptions()
ffconf = oeszybki.OEFreeFormConf(opts)
omol = oechem.OEMol(mol)
if not (ffconf.EstimateFreeEnergies(omol) == oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Failed to estimate conformational free energies")
res = oeszybki.OEFreeFormConfResults(omol)
oechem.OEThrow.Info("Number of unique conformations: %d" % res.GetNumUniqueConfs())
oechem.OEThrow.Info("Conf. Delta_G Vibrational_Entropy")
oechem.OEThrow.Info(" [kcal/mol] [J/(mol K)]")
for r in res.GetResultsForConformations():
oechem.OEThrow.Info("%2d %10.2f %14.2f" % (r.GetConfIdx(), r.GetDeltaG(),
r.GetVibrationalEntropy()))
oechem.OEWriteMolecule(ofs, omol)
return 0
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <input> <output>" % 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])
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
opts = oeszybki.OEFreeFormConfOptions()
ffconf = oeszybki.OEFreeFormConf(opts)
# Estimate free energies to ontain the minimum energy conformers
omol = oechem.OEMol(mol)
if not (ffconf.EstimateFreeEnergies(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Failed to estimate conformational free energies")
# Find similar conformers to the ones we started with, from the
# pool of minimum energy conformers
fmol = oechem.OEMol(mol)
for conf in mol.GetConfs():
ffconf.FindSimilarConfs(fmol, omol, conf, oechem.OESimilarByRMSD(0.05))
oechem.OEWriteMolecule(ofs, fmol)
return 0
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <input> <output>" % 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])
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
opts = oeszybki.OEFreeFormConfOptions()
ffconf = oeszybki.OEFreeFormConfAdvanced(opts)
# Make a copy of our MCMol. We will execute the FreeFormConf commands on
# the copied molecule so that our original molecule stays intact.
omol = oechem.OEMol(mol)
# Prepare a comprehensive ensemble of molecule conformers. This will
# generate a comprehensive set of conformers, assign solvent charges on the molecule
# and check that the ensemble is otherwise ready for FreeFormConf calculations.
if not (ffconf.PrepareEnsemble(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error(
"Failed to prepare ensemble for FreeFormConf calculations")
# Perform loose optimization of the ensemble conformers. We will remove
# duplicates based on the loose optimization, to reduce the time needed for
# tighter, more stricter optimization
if not (ffconf.PreOptimizeEnsemble(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Pre-optimization of the ensembles failed")
# Remove duplicates from the pre-optimized ensemble
if not (ffconf.RemoveDuplicates(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Duplicate removal from the ensembles failed")
# Perform the desired optimization. This uses a stricter convergence
# criteria in the default settings.
if not (ffconf.Optimize(omol) == oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Optimization of the ensembles failed")
# Remove duplicates to obtain the set of minimum energy conformers
if not (ffconf.RemoveDuplicates(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Duplicate removal from the ensembles failed")
# Perform FreeFormConf free energy calculations. When all the above steps
# have already been performed on the ensemble, this energy calculation
# step is fast.
if not (ffconf.EstimateEnergies(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Estimation of FreeFormConf energies failed")
# Gather results of calculation into a results object for ease of viewing, etc.
res = oeszybki.OEFreeFormConfResults(omol)
oechem.OEThrow.Info("Number of unique conformations: %d" %
res.GetNumUniqueConfs())
oechem.OEThrow.Info("Conf. Delta_G Vibrational_Entropy")
oechem.OEThrow.Info(" [kcal/mol] [J/(mol K)]")
for r in res.GetResultsForConformations():
oechem.OEThrow.Info(
"%2d %10.2f %14.2f" %
(r.GetConfIdx(), r.GetDeltaG(), r.GetVibrationalEntropy()))
oechem.OEWriteMolecule(ofs, omol)
return 0
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <input> <output>" % 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])
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
opts = oeszybki.OEFreeFormConfOptions()
ffconf = oeszybki.OEFreeFormConfAdvanced(opts)
# Make a copy of our MCMol. We will execute the FreeFormConf commands on
# the copied molecule so that our original molecule stays intact.
omol = oechem.OEMol(mol)
# Make further copies of our original molecule. The copied molecule(s) would be used
# as source on which retriction energies would be calculated
rmol = oechem.OEMol(mol)
fmol = oechem.OEMol(mol)
# Prepare a comprehensive ensemble of molecule conformers. For calculation
# of restriction energies we want to make sure that all the corresponding free
# conformers are also part of the comprehensive ensemble. This will also
# assign solvent charges on the molecule and check that the ensemble is
# otherwise ready for FreeFormConf calculations. The resulting `fmol`
# contains the correspondig free conformers.
if not (ffconf.PrepareEnsemble(omol, rmol, fmol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error(
"Failed to prepare ensemble for FreeFormConf calculations")
# Perform loose optimization of the ensemble conformers. We will remove
# duplicates based on the loose optimization, to reduce the time needed for
# tighter, more stricter optimization
if not (ffconf.PreOptimizeEnsemble(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Pre-optimization of the ensembles failed")
# Remove duplicates from the pre-optimized ensemble
if not (ffconf.RemoveDuplicates(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Duplicate removal from the ensembles failed")
# Perform the desired optimization. This uses a stricter convergence
# criteria in the default settings.
if not (ffconf.Optimize(omol) == oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Optimization of the ensembles failed")
# Remove duplicates to obtain the set of minimum energy conformers
if not (ffconf.RemoveDuplicates(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Duplicate removal from the ensembles failed")
# Perform FreeFormConf free energy calculations. When all the above steps
# have already been performed on the ensemble, this energy calculation
# step is fast.
if not (ffconf.EstimateEnergies(omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Estimation of FreeFormConf energies failed")
# Gather results of calculation into a results object for ease of viewing, etc.
res = oeszybki.OEFreeFormConfResults(omol)
oechem.OEThrow.Info("Number of unique conformations: %d" %
res.GetNumUniqueConfs())
oechem.OEThrow.Info("Conf. Delta_G Vibrational_Entropy")
oechem.OEThrow.Info(" [kcal/mol] [J/(mol K)]")
for r in res.GetResultsForConformations():
oechem.OEThrow.Info(
"%2d %10.2f %14.2f" %
(r.GetConfIdx(), r.GetDeltaG(), r.GetVibrationalEntropy()))
# Identify the corresponding conformer(s) to the free minimized conformer(s).
# If identified, the corresponding (Conf)Free energy information is also
# copied to the free conformers
if not (ffconf.IdentifyConformer(fmol, omol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Identification of free conformer(s) failed")
# Estimate restriction energies. Since both restricted and free conformer
# energy components are already available, this operation is fast.
if not (ffconf.EstimateRestrictionEnergy(fmol, rmol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Restriction energy estimation failed")
# Gather restriction energies into a results object for ease of viewing, etc.
rstrRes = oeszybki.OERestrictionEnergyResult(fmol)
oechem.OEThrow.Info("Global strain: %f" % rstrRes.GetGlobalStrain())
oechem.OEThrow.Info("Local strain: %f" % rstrRes.GetLocalStrain())
# Optionally it is desired to perform a restrained optimization of the
# restricted conformer(s) to brush out any energy differences due to
# force field constaints or the sources of coonformer coordinates. Note: The
# high level EstimateFreeEnergy method does not perform this opertion.
if not (ffconf.OptimizeRestraint(rmol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error(
"Restraint optimization of the conformer(s) failed")
# Estimate restriction energies on this optimized conformers.
# Since both restricted and free conformer energy components
# are already available, this operation is fast.
if not (ffconf.EstimateRestrictionEnergy(fmol, rmol)
== oeszybki.OEFreeFormReturnCode_Success):
oechem.OEThrow.Error("Restriction energy estimation failed")
# Gather restriction energies into a results object for ease of viewing, etc.
rstrRes = oeszybki.OERestrictionEnergyResult(fmol)
oechem.OEThrow.Info("Global strain: %f" % rstrRes.GetGlobalStrain())
oechem.OEThrow.Info("Local strain: %f" % rstrRes.GetLocalStrain())
oechem.OEWriteMolecule(ofs, omol)
return 0