def choose_action(self, pdb_string):
with self.logger("choose_action") as logger:
with tempfile.TemporaryDirectory() as dirname:
with open("{}/test.pdb".format(dirname), 'w') as f:
f.write(pdb_string)
pdb = oechem.OEMol()
prot = oechem.OEMol()
lig = oechem.OEMol()
wat = oechem.OEGraphMol()
other = oechem.OEGraphMol()
ifs = oechem.oemolistream()
ifs.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_Default
| oechem.OEIFlavor_PDB_DATA
| oechem.OEIFlavor_PDB_ALTLOC) # noqa
if not ifs.open("{}/test.pdb".format(dirname)):
logger.log("crap")
oechem.OEReadMolecule(ifs, pdb)
ifs.close()
if not oechem.OESplitMolComplex(lig, prot, wat, other, pdb):
logger.failure("could not split complex. exiting",
exit_all=True)
else:
logger.log("atom sizes for incoming step",
len(list(lig.GetAtoms())),
len(list(prot.GetAtoms())),
len(list(wat.GetAtoms())),
len(list(other.GetAtoms())))
original_smiles, oeclean_smiles = self.env.action.get_new_action_set(
aligner=lig)
data = self.getscores(
original_smiles,
oeclean_smiles,
prot,
lig,
num_returns=self.num_returns,
return_docked_pose=self.return_docked_pose)
not_worked = True
idxs = list(range(len(data)))
idx = idxs.pop(0)
while not_worked:
try:
new_mol, new_mol2, gs, action = data[idx]
self.env.systemloader.reload_system(
gs, new_mol, "{}/test.pdb".format(dirname))
self.env.openmm_simulation = self.env.config.openmmWrapper.get_obj(
self.env.systemloader, self.env.openmm_simulation)
not_worked = False
except Exception as e:
logger.error("Could not buid system for smiles", gs,
"with exception", e)
traceback.print_tb(e.__traceback__)
if len(idxs) == 0:
logger.failure("No system could build",
exit_all=True)
idx = idxs.pop(0)
self.env.action.apply_action(new_mol2, action)
return new_mol2, action
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 file_to_oemols(filename):
"""Create OEMol from file. If more than one mol in file, return list of OEMols.
Parameters
----------
filename: str
absolute path to oeb file
Returns
-------
mollist: list
list of OEMol for multiple molecules. OEMol if file only has one molecule.
"""
from openeye import oechem
if not os.path.exists(filename):
raise Exception("File {} not found".format(filename))
ifs = oechem.oemolistream(filename)
mollist = []
molecule = oechem.OEMol()
while oechem.OEReadMolecule(ifs, molecule):
molecule_copy = oechem.OEMol(molecule)
oechem.OEPerceiveChiral(molecule_copy)
oechem.OE3DToAtomStereo(molecule_copy)
oechem.OE3DToBondStereo(molecule_copy)
mollist.append(molecule_copy)
ifs.close()
if len(mollist) is 1:
mollist = mollist[0]
return mollist
def enumerate_from_smiles(smiles, oe_options=None):
oe_options = oe_options or OEOptions()
omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Pose)
omegaOpts.SetMaxSearchTime(60)
omega = oeomega.OEOmega(omegaOpts)
if oe_options.use_tautomer:
tautomer_options = oequacpac.OETautomerOptions()
pKa_norm = True
taut_iter = lambda x: oequacpac.OEGetReasonableTautomers(x, tautomer_options, pKa_norm)
else:
taut_iter = lambda x: [x]
if oe_options.use_flipper:
flipper = lambda x: oeomega.OEFlipper(x.GetActive(), oe_options.num_sterocenters, oe_options.force_flipper)
else:
flipper = lambda x: [x]
# get molecule
try:
molecule = mol_from_smiles(smiles)
except ValueError:
return [None]
results = []
for enantiomer in flipper(molecule):
for tautomer in taut_iter(enantiomer):
tautomer = oechem.OEMol(tautomer)
omega.Build(tautomer)
tautomer2 = oechem.OEMol(tautomer)
results.append(tautomer2)
return results
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 genConfs(c_mol, ofsff, ofsTri, index):
# set omega settings
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetIncludeInput(False)
omega.SetEnergyWindow(15.0)
strict_stereo = True
omega.SetStrictStereo(strict_stereo)
omega.SetSampleHydrogens(True)
omega.SetStrictAtomTypes(True)
mol = oechem.OEMol(c_mol)
status = omega(mol)
if status:
# change title
mol.SetTitle(f'DrugBank_{index}')
# save force field type
mol1 = oechem.OEMol(mol)
oechem.OETriposAtomNames(mol1)
oechem.OEWriteConstMolecule(ofsff, mol1)
# save Tripos atom types
mol2 = oechem.OEMol(mol)
oechem.OETriposAtomTypeNames(mol2)
oechem.OEWriteConstMolecule(ofsTri, mol2)
return status
def test_success(self):
print('Testing cube:', self.cube.name)
# File name
fn_protein = ommutils.get_data_filename('examples',
'data/Bace_solvated.oeb.gz')
fn_ligand = ommutils.get_data_filename('examples',
'data/lig_CAT13a_chg.oeb.gz')
# Read Protein molecule
protein = oechem.OEMol()
with oechem.oemolistream(fn_protein) as ifs:
oechem.OEReadMolecule(ifs, protein)
# Read Ligand molecule
ligand = oechem.OEMol()
with oechem.oemolistream(fn_ligand) as ifs:
oechem.OEReadMolecule(ifs, ligand)
# Process the molecules
self.cube.process(protein, self.cube.intake.name)
# Why do I have to manually set these on?
self.cube.check_system = True
self.cube.system = protein
self.cube.process(ligand, self.cube.system_port)
# Assert that one molecule was emitted on the success port
self.assertEqual(self.runner.outputs['success'].qsize(), 1)
# Assert that zero molecules were emitted on the failure port
self.assertEqual(self.runner.outputs['failure'].qsize(), 0)
complex = self.runner.outputs["success"].get()
self.assertEquals(complex.GetMaxAtomIdx(), 52312)
def delete_shell(core_mol, del_mol, cut_off, in_out='in'):
"""
This function deletes molecules present in the passed argument
del_mol that are far (in_out=out) or close (in_out=in) than the
selected cutoff distance (in A) from the passed molecules core_mol
Parameters:
-----------
core_mol: OEMol molecule
The core molecules
del_mol: OEMol molecule
The molecules to be deleted if their distances from the core_mol
molecules are greater or closer that the selected cutoff distance
cut_off: python float number
The threshold distance in A used to mark atom for deletion
in_out: python string
A flag used to select if delete molecules far or close than
the cutoff distance from the core_mol
Return:
-------
reset_del: copy of del_mol where atoms have been deleted with
reset atom indexes
"""
if in_out not in ['in', 'out']:
raise ValueError(
"The passed in_out parameter is not recognized: {}".format(in_out))
# Copy the passed molecule to delete in
to_del = oechem.OEMol(del_mol)
# Create a OE bit vector mask for each atoms of the
# molecule to delete
bv = oechem.OEBitVector(to_del.GetMaxAtomIdx())
bv.NegateBits()
# Create the Nearest neighbours
nn = oechem.OENearestNbrs(to_del, cut_off)
for nbrs in nn.GetNbrs(core_mol):
# bv.SetBitOff(nbrs.GetBgn().GetIdx())
for atom in oechem.OEGetResidueAtoms(nbrs.GetBgn()):
bv.SetBitOff(atom.GetIdx())
# Invert selection mask
if in_out == 'in':
bv.NegateBits()
pred = oechem.OEAtomIdxSelected(bv)
for atom in to_del.GetAtoms(pred):
to_del.DeleteAtom(atom)
# It is necessary to reset the atom indexes of the molecule with
# delete atoms to avoid possible mismatching
reset_del = oechem.OEMol(to_del)
return reset_del
def strip_water_ions(in_system):
"""
This function remove waters and ions molecules
from the input system
Parameters:
----------
in_system : oechem.OEMol
The bio-molecular system to clean
opt: python dictionary
The system option
Output:
-------
clean_system : oechem.OEMol
The cleaned system
"""
# Copy the input system
system = oechem.OEMol(in_system)
# Create a bit vector mask
bv = oechem.OEBitVector(system.GetMaxAtomIdx())
bv.NegateBits()
# Create a Hierarchical View of the protein system
hv = oechem.OEHierView(
system,
oechem.OEAssumption_BondedResidue + oechem.OEAssumption_ResPerceived)
# Looping over the system residues
for chain in hv.GetChains():
for frag in chain.GetFragments():
for hres in frag.GetResidues():
res = hres.GetOEResidue()
# Check if a residue is a mono atomic ion
natoms = 0
for at in hres.GetAtoms():
natoms += 1
# Set the atom bit mask off
if oechem.OEGetResidueIndex(
res) == oechem.OEResidueIndex_HOH or natoms == 1:
# Set Bit mask
atms = hres.GetAtoms()
for at in atms:
bv.SetBitOff(at.GetIdx())
# Extract the system without waters or ions
pred = oechem.OEAtomIdxSelected(bv)
clean_system = oechem.OEMol()
oechem.OESubsetMol(clean_system, system, pred)
return clean_system
def dock_molecule(molecule, default_receptor='x0387'):
"""
Dock the specified molecules, writing out to specified file
Parameters
----------
molecule : OEMol
The molecule to dock
default_receptor : str, optional, default='0387'
The default receptor to dock to
Returns
-------
all_docked_molecules : list of OEMol
All docked molecules
"""
import os
import oechem
# Make a copy of the molecule
molecule = oechem.OEMol(molecule)
# Extract list of corresponding receptor(s)
fragments = list()
fragments = oechem.OEGetSDData(molecule, "fragments").split(',')
fragments = [
fragment for fragment in fragments
if os.path.exists(f'../receptors/Mpro-{fragment}-receptor.oeb.gz')
]
if len(fragments) == 0:
fragments = [default_receptor]
# Dock them
all_docked_molecules = list()
for fragment in fragments:
molecule_to_dock = oechem.OEMol(molecule)
import os
receptor_filename = os.path.join(
f'../receptors/Mpro-{fragment}-receptor.oeb.gz')
oechem.OESetSDData(molecule_to_dock, "fragments", fragment)
# Enumerate reasonable protomers/tautomers
from openeye import oequacpac
protomer = oechem.OEMol()
protomers = [
oechem.OEMol(protomer) for protomer in
oequacpac.OEGetReasonableProtomers(molecule_to_dock)
]
docked_molecules = dock_molecules_to_receptor(receptor_filename,
protomers)
all_docked_molecules += docked_molecules
return all_docked_molecules
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData, argv)
# Set up best overlay to the query molecule
qfs = oechem.oemolistream()
if not qfs.open(itf.GetString("-q")):
oechem.OEThrow.Fatal("Unable to open %s" % itf.GetString("-q"))
qmol = oechem.OEMol()
oechem.OEReadMolecule(qfs, qmol)
# Set up overlap to protein exclusion volume
efs = oechem.oemolistream()
if not efs.open(itf.GetString("-e")):
oechem.OEThrow.Fatal("Unable to open %s" % itf.GetString("-e"))
emol = oechem.OEMol()
oechem.OEReadMolecule(efs, emol)
evol = oeshape.OEExactShapeFunc()
evol.SetupRef(emol)
# open database and output streams
ifs = oechem.oemolistream()
if not ifs.open(itf.GetString("-d")):
oechem.OEThrow.Fatal("Unable to open %s" % itf.GetString("-d"))
ofs = oechem.oemolostream()
if not ofs.open(itf.GetString("-o")):
oechem.OEThrow.Fatal("Unable to open %s" % itf.GetString("-o"))
print("Title Combo Rescore")
for mol in ifs.GetOEMols():
res = oeshape.OEROCSResult()
oeshape.OEROCSOverlay(res, qmol, mol)
outmol = res.GetOverlayConf()
# calculate overlap with protein
eres = oeshape.OEOverlapResults()
evol.Overlap(outmol, eres)
frac = eres.GetOverlap() / eres.GetFitSelfOverlap()
rescore = res.GetTanimotoCombo() - frac
# attach data to molecule and write it
oechem.OESetSDData(outmol, "TanimotoCombo", "%-.3f" % res.GetTanimotoCombo())
oechem.OESetSDData(outmol, "Exclusion Volume", "%-.3f" % eres.overlap)
oechem.OESetSDData(outmol, "Fraction Overlap", "%-.3f" % frac)
oechem.OESetSDData(outmol, "Rescore", "%-.3f" % rescore)
oechem.OEWriteMolecule(ofs, outmol)
print("%-20s %.3f %.3f" %
(outmol.GetTitle(), res.GetTanimotoCombo(), rescore))
def draw_frag_pdf(frag_dict, scaffold=None, pdf_filename='fragments.pdf'):
from openeye import oechem, oedepict
import re
itf = oechem.OEInterface()
PageByPage = True
suppress_h = True
rows = 7
cols = 5
ropts = oedepict.OEReportOptions(rows, cols)
ropts.SetHeaderHeight(25)
ropts.SetFooterHeight(25)
ropts.SetCellGap(2)
ropts.SetPageMargins(10)
report = oedepict.OEReport(ropts)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
opts = oedepict.OE2DMolDisplayOptions(cellwidth, cellheight,
oedepict.OEScale_Default * 0.5)
opts.SetAromaticStyle(oedepict.OEAromaticStyle_Circle)
pen = oedepict.OEPen(oechem.OEBlack, oechem.OEBlack, oedepict.OEFill_On,
1.0)
opts.SetDefaultBondPen(pen)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
if scaffold:
oemol = oechem.OEGraphMol()
scaffold_smi = re.sub(r"\(\[R([1-9])+]\)", r"([*])", scaffold.smiles)
oechem.OESmilesToMol(oemol, scaffold_smi)
cell = report.NewCell()
mol = oechem.OEMol(oemol)
mol.SetTitle(f'{scaffold.smiles}')
oedepict.OEPrepareDepiction(mol, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
headerpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey,
oedepict.OEFill_Off, 1.0)
oedepict.OEDrawBorder(cell, headerpen)
for rx, smis in frag_dict.items():
for idx, smi in enumerate(smis):
if smi != None:
# Create oemol
oemol = oechem.OEGraphMol()
oechem.OESmilesToMol(oemol, smi)
# Render molecule
cell = report.NewCell()
mol = oechem.OEMol(oemol)
mol.SetTitle(f'R{rx} #{idx+1}')
oedepict.OEPrepareDepiction(mol, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEWriteReport(pdf_filename, report)
def call_static(data):
original_smiles, oe_smiles, refmol = data
fitfs = oechem.oemolistream()
fitfs.SetFormat(oechem.OEFormat_SMI)
fitfs.openstring(oe_smiles)
mol = oechem.OEMol()
oechem.OEReadMolecule(fitfs, mol)
new_mol = RocsMolAligner.from_oemol_static(mol, refmol)
if new_mol is None:
return None
return new_mol, oechem.OEMol(new_mol), oe_smiles, original_smiles
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 are_equal_microstates(mol1: oechem.OEMol, mol2: oechem.OEMol):
""" Check if two supplied OE(Graph)Mol objects have the same molecular microstate present.
If all atoms and bonds are matched in MCSS returns True. Ignores charges and bond order
to deal with chirality and geometry differences as well as resonance structures
(which we won't consider as different).
Returns
-------
bool
"""
# Copy input
pattern = oechem.OEMol(mol1)
target = oechem.OEMol(mol2)
# Atoms are equal if they have same atomic number (so explicit Hydrogens are needed as well for a match)
atomexpr = oechem.OEExprOpts_AtomicNumber
# single or double bonds are considered identical (resonance,chirality fix)
bondexpr = oechem.OEExprOpts_EqSingleDouble
# create maximum common substructure object
mcss = oechem.OEMCSSearch(pattern, atomexpr, bondexpr,
oechem.OEMCSType_Exhaustive)
# set scoring function
mcss.SetMCSFunc(oechem.OEMCSMaxAtomsCompleteCycles())
# ignore matches smaller than 6 atoms
mcss.SetMinAtoms(6)
unique = True
# loop over matches
count = 0
match = oechem.OEMol()
for i, match in enumerate(mcss.Match(target, unique)):
count = i + 1
logger.debug("Match %d:" % (count))
logger.debug("Num atoms in match %d" % match.NumAtoms())
logger.debug("Num atoms in mol1 %d" % pattern.NumAtoms())
logger.debug("Num atoms in mol2 %d" % target.NumAtoms())
# check if there is only single match
if (count > 1):
logger.warning("Warning! There are multiple matches.")
elif count == 0:
logger.debug("No match")
m_num = match.NumAtoms()
p_num = pattern.NumAtoms()
t_num = target.NumAtoms()
return m_num == p_num == t_num
def split(mol):
"""
This function splits the passed system in protein, ligand,
water and excipients
Parameters:
----------
mol : oechem.OEMol
The bio-molecular system to split
Output:
-------
protein : oechem.OEMol
The split protein
ligand : oechem.OEMol
The split ligand
wat : oechem.OEMol
The spit water
other : oechem.OEMol
The excipients
"""
# Set empty molecule containers
prot = oechem.OEMol()
lig = oechem.OEMol()
wat = oechem.OEMol()
other = oechem.OEMol()
# Define the Filter options before the splitting
opt = oechem.OESplitMolComplexOptions()
# The protein filter is set to avoid that multiple
# chains are separated during the splitting
pf = oechem.OEMolComplexFilterFactory(oechem.OEMolComplexFilterCategory_Protein)
# The ligand filter is set to recognize just the ligand
lf = oechem.OEMolComplexFilterFactory(oechem.OEMolComplexFilterCategory_Ligand)
# The water filter is set to recognize just water molecules
wf = oechem.OEMolComplexFilterFactory(oechem.OEMolComplexFilterCategory_Water)
opt.SetProteinFilter(pf)
opt.SetLigandFilter(lf)
opt.SetWaterFilter(wf)
# Splitting the system
if not oechem.OESplitMolComplex(lig, prot, wat, other, mol, opt):
oechem.OEThrow.Fatal('Unable to split the complex')
# At this point prot contains the protein, lig contains the ligand,
# wat contains the water and excipients contains the excipients
return prot, lig, wat, other
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <receptor> <conformers>" % argv[0])
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, argv[1])
dock = oedocking.OEDock()
dock.Initialize(receptor)
conformers = oechem.OEMol()
imstr = oechem.oemolistream(argv[2])
for conformers in imstr.GetOEMols():
poses = oechem.OEMol()
dock.DockMultiConformerMolecule(poses, conformers)
TagPoses(dock, poses, dock.GetName())
def gen_conf(mol):
oemols = []
omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_FastROCS)
omega = oeomega.OEOmega(omegaOpts)
for enantiomer in oeomega.OEFlipper(mol.GetActive(), 6, True):
enantiomer = oechem.OEMol(enantiomer)
ret_code = omega.Build(enantiomer)
if ret_code == oeomega.OEOmegaReturnCode_Success:
halfMol = oechem.OEMol(mol, oechem.OEMCMolType_HalfFloatCartesian)
oemols.append(halfMol)
else:
oechem.OEThrow.Warning(
"%s: %s" %
(enantiomer.GetTitle(), oeomega.OEGetOmegaError(ret_code)))
return oemols
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])
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
opts = oeszybki.OESzybkiOptions()
opts.GetOptOptions().SetOptimizerType(oeszybki.OEOptType_NEWTON)
opts.GetSolventOptions().SetSolventModel(oeszybki.OESolventModel_Sheffield)
sz = oeszybki.OESzybki(opts)
res = oeszybki.OESzybkiResults()
if (sz(mol, res)):
oechem.OEWriteMolecule(ofs, mol)
res.Print(oechem.oeout)
return 0
def read_molecules(filename):
"""Read a file into an OpenEye molecule (or list of molecules).
Parameters
----------
filename : str
The name of the file to read (e.g. mol2, sdf)
Returns
-------
molecule : openeye.oechem.OEMol
The OEMol molecule read, or a list of molecules if multiple molecules are read.
If no molecules are read, None is returned.
"""
ifs = oechem.oemolistream(filename)
molecules = list()
for mol in ifs.GetOEMols():
mol_copy = oechem.OEMol(mol)
molecules.append(mol_copy)
ifs.close()
if len(molecules) == 0:
return None
elif len(molecules) == 1:
return molecules[0]
else:
return molecules
def read_molecule(filename):
ifs = oechem.oemolistream()
ifs.open(filename)
molecule = oechem.OEMol()
oechem.OEReadMolecule(ifs, molecule)
ifs.close()
return molecule
def test_partial_bondorder(verbose=False):
"""Test setup of a molecule which activates partial bond order code."""
from openeye import oechem
mol = oechem.OEMol()
from openeye import oeiupac
oeiupac.OEParseIUPACName(mol, 'benzene')
positions = positions_from_oemol(mol)
oechem.OETriposAtomNames(mol)
topology = generateTopologyFromOEMol(mol)
# Load forcefield from above
ffxml = StringIO(ffxml_contents_noconstraints)
ff = ForceField(ffxml)
# Set up once using AM1BCC charges
system = ff.createSystem(topology, [mol],
chargeMethod='OECharges_AM1BCCSym',
verbose=verbose)
# Check that energy is what it ought to be -- the partial bond order
# for benzene makes the energy a bit higher than it would be without it
energy = get_energy(system, positions)
if energy < 7.50 or energy > 7.60:
raise Exception(
"Partial bond order code seems to have issues, as energy for benzene is outside of tolerance in tests."
)
# Set up once also without asking for charges
system = ff.createSystem(topology, [mol], verbose=verbose)
energy = get_energy(system, positions)
# Energy is lower with user supplied charges (which in this case are zero)
if energy < 4.00 or energy > 6.0:
raise Exception(
"Partial bond order code seems to have issues when run with user-provided charges, as energy for benzene is out of tolerance in tests."
)
def test_improper(verbose=False):
"""Test implement of impropers on benzene."""
from openeye import oechem
# Load benzene
ifs = oechem.oemolistream(get_data_filename('molecules/benzene.mol2'))
mol = oechem.OEMol()
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
ifs.close()
# Load forcefield
ffxml = get_data_filename('forcefield/benzene_minimal.ffxml')
ff = ForceField(ffxml)
# Load AMBER files and compare
crd = get_data_filename('molecules/benzene.crd')
top = get_data_filename('molecules/benzene.top')
g0, g1, e0, e1 = compare_molecule_energies(top,
crd,
ff,
mol,
skip_assert=True)
# Check that torsional energies the same to 1 in 10^6
rel_error = np.abs((g0['torsion'] - g1['torsion']) / g0['torsion'])
if rel_error > 2e-5: #Note that this will not be tiny because we use six-fold impropers and they use a single improper
raise Exception(
"Improper torsion energy for benzene differs too much (relative error %.4g) between AMBER and SMIRNOFF."
% rel_error)
def test_excipient_successGaff2(self):
print('Testing cube:', self.cube.name)
# File name
fn_complex = ommutils.get_data_filename(
'examples', 'data/pbace_lcat13a_solvated_complex.oeb.gz')
# Read Protein molecule
complex = oechem.OEMol()
with oechem.oemolistream(fn_complex) as ifs:
oechem.OEReadMolecule(ifs, complex)
# Selecting ligand and excipient parametrization
self.cube.args.ligand_forcefield = 'GAFF2'
self.cube.args.other_forcefield = 'GAFF2'
# Process the molecules
self.cube.process(complex, self.cube.intake.name)
# Assert that one molecule was emitted on the success port
self.assertEqual(self.runner.outputs['success'].qsize(), 1)
# Assert that zero molecules were emitted on the failure port
self.assertEqual(self.runner.outputs['failure'].qsize(), 0)
complex = self.runner.outputs["success"].get()
def test_merge_system():
"""Test merging of a system created from AMBER and another created from SMIRNOFF."""
#Create System from AMBER
prefix = os.path.join('systems', 'amber', 'cyclohexane_ethanol_0.4_0.6')
prmtop = get_data_filename(prefix + '.prmtop')
incrd = get_data_filename(prefix + '.inpcrd')
from openforcefield.typing.engines.smirnoff import create_system_from_amber
topology0, system0, positions0 = create_system_from_amber(prmtop, incrd)
from openeye import oechem
# Load simple OEMol
ifs = oechem.oemolistream(
get_data_filename('molecules/AlkEthOH_c100.mol2'))
mol = oechem.OEMol()
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
oechem.OETriposAtomNames(mol)
# Load forcefield file
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEthOH.ffxml'))
topology1, system1, positions1 = create_system_from_molecule(
forcefield, mol)
merge_system(topology0,
topology1,
system0,
system1,
positions0,
positions1,
verbose=True)
def expand_stereochemistry(mols):
"""Expand stereochemistry when uncertain
Parameters
----------
mols : openeye.oechem.OEGraphMol
Molecules to be expanded
Returns
-------
expanded_mols : openeye.oechem.OEMol
Expanded molecules
"""
expanded_mols = list()
from openeye import oechem, oeomega
omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
maxcenters = 12
forceFlip = False
enumNitrogen = True
warts = True # add suffix for stereoisomers
for mol in mols:
for enantiomer in oeomega.OEFlipper(mol, maxcenters, forceFlip, enumNitrogen, warts):
enantiomer = oechem.OEMol(enantiomer)
expanded_mols.append(enantiomer)
return expanded_mols
def get_stage_topology(self, stg_name='last'):
"""
This method returns the MD topology of the selected stage name. If no stage name is passed
the last stage is selected.
Parameters
-----------
stg_name: String
The MD stage name
Returns
-------
topology : OEMol
The topology of the selected MD stage
"""
stage = self.get_stage_by_name(stg_name)
stage_name = stage.get_value(Fields.stage_name)
dir_stage = self.processed[stage_name]
topology_fn = os.path.join(dir_stage, MDFileNames.topology)
topology = oechem.OEMol()
with oechem.oemolistream(topology_fn) as ifs:
oechem.OEReadMolecule(ifs, topology)
return topology
def generate_conformations(molecule: oechem.OEGraphMol,
max_conformations: int = 1000,
dense: bool = False) -> oechem.OEMol:
"""
Generate conformations of a given molecule.
Parameters
----------
molecule: oechem.OEGraphMol
An OpenEye molecule.
max_conformations: int
Maximal number of conformations to generate.
dense: bool
If densely sampled conformers should be generated. Will overwrite max_conformations settings.
Returns
-------
conformations: oechem.OEMol
An OpenEye multi-conformer molecule holding the generated conformations.
"""
from openeye import oechem, oeomega
if dense:
omega_options = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Dense)
else:
omega_options = oeomega.OEOmegaOptions()
omega_options.SetMaxSearchTime(60.0) # time out
omega_options.SetMaxConfs(max_conformations)
omega = oeomega.OEOmega(omega_options)
omega.SetStrictStereo(False)
conformations = oechem.OEMol(molecule)
omega.Build(conformations)
return conformations
def iupac_to_oemol(iupac_name: str) -> oechem.OEMol:
"""
Convert an IUPAC name to an OEMol with openeye
Parameters
----------
iupac_name : str
The name of the molecule
Returns
-------
mol : oechem.OEMol
The OEMol corresponding to the IUPAC name with all hydrogens
"""
mol = oechem.OEMol()
oeiupac.OEParseIUPACName(mol, iupac_name)
oechem.OEAddExplicitHydrogens(mol)
# generate conformers:
omega = oeomega.OEOmega()
omega.SetStrictStereo(False)
omega.SetMaxConfs(1)
omega(mol)
return mol
def convert_mdtraj_to_oemol(traj: md.Trajectory) -> oechem.OEMol:
"""
This method converts an mdtraj Trajectory to an OEMol via saving as a PDBfile
and reading in with OpenEye. Although this seems hacky, it seems less error-prone
than trying to manually construct the OEMol.
Parameters
----------
mdtraj: md.Trajectory
The trajectory to turn into an OEMol
Returns
-------
mol : oechem.OEMol
The trajectory represented as an OEMol
"""
# create a temporary file with a PDB suffix and save with MDTraj
pdb_file = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
traj.save(pdb_file.name)
pdb_file.close()
# Now use the openeye oemolistream to read in this file as an OEMol:
ifs = oechem.oemolistream()
ifs.open(pdb_file.name)
ifs.SetFormat(oechem.OEFormat_PDB)
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
# close the stream and delete the temporary pdb file
ifs.close()
os.unlink(pdb_file.name)
return mol