def QuickOpt(Mol):
"""
Fast MM optimization to whittle down number of conformers before QM.
Default Szybki OEOptType type set to steepest descent (SD) based on
preliminary comparisons.
Parameters
----------
Mol: single OEChem molecule (aka single conformer)
Returns
-------
boolean: True if completed successfully, False otherwise.
"""
# set general energy options along with the run type specification
optSzybki = oeszybki.OESzybkiOptions()
optSzybki.SetForceFieldType(oeszybki.OEForceFieldType_MMFF94S)
optSzybki.SetSolventModel(oeszybki.OESolventModel_Sheffield)
optSzybki.SetOptimizerType(oeszybki.OEOptType_SD)
taglabel = 'MM Szybki SD Energy'
# generate szybki MMFF94 engine for minimization
szOpt = oeszybki.OESzybki(optSzybki)
# construct a results object to contain the results of a szybki calculation
szResults = oeszybki.OESzybkiResults()
# work on a copy of the molecule
tmpmol = oechem.OEMol(Mol)
if not szOpt(tmpmol, szResults):
print('szybki run failed for %s' % tmpmol.GetTitle())
return False
Mol.SetCoords(tmpmol.GetCoords())
oechem.OESetSDData(Mol, oechem.OESDDataPair(taglabel, "%.12f" \
% szResults.GetTotalEnergy()))
return True
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 resolve_clashes(mol, clashfile):
"""
Minimize conformers with severe steric interaction.
Parameters
----------
mol : single OEChem molecule (single conformer)
clashfile : string
name of file to write output
Returns
-------
boolean
True if completed successfully, False otherwise.
"""
# set general energy options along with the single-point specification
spSzybki = oeszybki.OESzybkiOptions()
spSzybki.SetForceFieldType(oeszybki.OEForceFieldType_MMFF94S)
spSzybki.SetSolventModel(oeszybki.OESolventModel_Sheffield)
spSzybki.SetRunType(oeszybki.OERunType_SinglePoint)
# generate the szybki MMFF94 engine for single points
szSP = oeszybki.OESzybki(spSzybki)
# construct minimiz options from single-points options to get general optns
optSzybki = oeszybki.OESzybkiOptions(spSzybki)
# now reset the option for minimization
optSzybki.SetRunType(oeszybki.OERunType_CartesiansOpt)
# generate szybki MMFF94 engine for minimization
szOpt = oeszybki.OESzybki(optSzybki)
# add strong harmonic restraints to nonHs
szOpt.SetHarmonicConstraints(10.0)
# construct a results object to contain the results of a szybki calculation
szResults = oeszybki.OESzybkiResults()
# work on a copy of the molecule
tmpmol = oechem.OEMol(mol)
if not szSP(tmpmol, szResults):
print('szybki run failed for %s' % tmpmol.GetTitle())
return False
Etotsp = szResults.GetTotalEnergy()
Evdwsp = szResults.GetEnergyTerm(oeszybki.OEPotentialTerms_MMFFVdW)
if Evdwsp > 35:
if not szOpt(tmpmol, szResults):
print('szybki run failed for %s' % tmpmol.GetTitle())
return False
Etot = szResults.GetTotalEnergy()
Evdw = szResults.GetEnergyTerm(oeszybki.OEPotentialTerms_MMFFVdW)
wfile = open(clashfile, 'a')
wfile.write('%s resolved bad clash: initial vdW: %.4f ; '
'resolved EvdW: %.4f\n' %
(tmpmol.GetTitle(), Evdwsp, Evdw))
wfile.close()
mol.SetCoords(tmpmol.GetCoords())
oechem.OESetSDData(mol, oechem.OESDDataPair('MM Szybki Single Point Energy'\
, "%.12f" % szResults.GetTotalEnergy()))
return True
def DumpSDData(mol):
print("SD data of", mol.GetTitle())
# loop over SD data
for dp in oechem.OEGetSDDataPairs(mol):
print(dp.GetTag(), ':', dp.GetValue())
print()
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1ccccc1")
mol.SetTitle("benzene")
# set some tagged data
oechem.OESetSDData(mol, "color", "brown")
oechem.OESetSDData(mol, oechem.OESDDataPair("size", "small"))
DumpSDData(mol)
# check for existence of data, then delete it
if oechem.OEHasSDData(mol, "size"):
oechem.OEDeleteSDData(mol, "size")
DumpSDData(mol)
# add additional color data
oechem.OEAddSDData(mol, "color", "black")
DumpSDData(mol)
# remove all SD data
oechem.OEClearSDData(mol)
DumpSDData(mol)
# @ </SNIPPET>