def positions_from_oemol(mol):
"""
Extract OpenMM positions from OEMol.
Parameters
----------
mol : oechem.openeye.OEMol
OpenEye molecule from which to extract coordinates.
Returns
-------
positions : simtk.unit.Quantity of dimension (nparticles,3)
"""
from openeye import oechem, oeomega
if mol.GetDimension() != 3:
# Assign coordinates
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetIncludeInput(False)
omega.SetCanonOrder(False)
omega.SetSampleHydrogens(True) # Word to the wise: skipping this step can lead to significantly different charges!
omega(mol) # generate conformation
coordinates = mol.GetCoords()
natoms = len(coordinates)
positions = np.zeros([natoms,3], np.float32)
for index in range(natoms):
(x,y,z) = coordinates[index]
positions[index,0] = x
positions[index,1] = y
positions[index,2] = z
positions = unit.Quantity(positions, unit.angstroms)
return positions
def begin(self):
omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
omega = oeomega.OEOmega()
omega.SetIncludeInput(False)
omega.SetCanonOrder(False)
omega.SetSampleHydrogens(True)
omega.SetStrictStereo(False) # JDC
omega.SetMaxSearchTime(
self.args.max_search_time) # maximum omega search time
omega.SetEnergyWindow(self.args.energy_window)
omega.SetMaxConfs(self.args.max_confs)
omega.SetRMSThreshold(1.0)
self.omega = omega
def create_molecule(iupac_name):
"""
Create an OEMol molecule from an IUPAC name.
Parameters
----------
iupac_name : str
The IUPAC name of the molecule to be created.
Returns
-------
molecule : openeye.oechem.OEMol
A molecule with AM1-BCC charges.
"""
molecule = gaff2xml.openeye.iupac_to_oemol(iupac_name)
# Assign AM1-BCC charges using canonical scheme.
# TODO: Replace wit updated gaff2xml scheme.
molecule = assign_am1bcc_charges(molecule)
# Assign conformations.
from openeye import oeomega
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega(molecule)
return molecule
def test_oemol_nhfcl():
"""Test coordinates for NHFCl read in as OEMol."""
import openeye.oechem as oechem
import openeye.oeomega as oeomega
# coordinates for N, F, H, Cl respectively
# generated after minimization with improper phase of 150 degrees
coordlist = [
0.155, -0.088, -0.496, -1.054, -0.776, -0.340, -0.025, 0.906, -0.516,
1.689, -0.635, -1.263
]
# create OEMol
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, 'FNCl')
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetIncludeInput(False)
omega.SetStrictStereo(False)
status = omega(mol)
oechem.OETriposAtomTypes(mol)
oechem.OETriposAtomNames(mol)
oechem.OEAddExplicitHydrogens(mol)
# set provided coordinates
mol.SetCoords(oechem.OEFloatArray(coordlist))
# calculate and check improper angle
crds, names = find_improper_angles(mol)
ang = calc_improper_angle(crds[0][0], crds[0][1], crds[0][2], crds[0][3])
if abs(ang - 15.0) > 0.1 and abs(ang - 165.0) > 0.1:
raise Exception(
"Error calculating improper of test OEMol. Calculated {} degrees, but should be 15 or 165 degrees."
.format(ang))
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 createOEMolFromSMILES(smiles='CC', title='MOL'):
"""
Generate an oemol with a geometry
"""
from openeye import oechem, oeiupac, oeomega
# Create molecule
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, smiles)
# Set title.
mol.SetTitle(title)
# Assign aromaticity and hydrogens.
oechem.OEAssignAromaticFlags(mol, oechem.OEAroModelOpenEye)
oechem.OEAddExplicitHydrogens(mol)
# Create atom names.
oechem.OETriposAtomNames(mol)
# Assign geometry
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetIncludeInput(False)
omega.SetStrictStereo(True)
omega(mol)
return mol
def prep_structure(rdmol):
mb = Chem.MolToMolBlock(rdmol)
ims = oechem.oemolistream()
ims.SetFormat(oechem.OEFormat_SDF)
ims.openstring(mb)
for buf_mol in ims.GetOEMols():
oemol = oechem.OEMol(buf_mol)
omega = oeomega.OEOmega()
# omega.SetIncludeInput(True)
omega.SetMaxSearchTime(30)
omega.SetCanonOrder(False)
omega.SetSampleHydrogens(True)
eWindow = 15.0
omega.SetEnergyWindow(eWindow)
# omega.SetMaxConfs(800)
omega.SetMaxConfs(400)
omega.SetRMSThreshold(1.0)
if omega(oemol):
result = oequacpac.OEAssignCharges(oemol,
oequacpac.OEAM1BCCELF10Charges())
if result is False:
return None
else:
charges = []
for index, atom in enumerate(oemol.GetAtoms()):
q = atom.GetPartialCharge() * np.sqrt(ONE_4PI_EPS0)
charges.append(q)
return charges
else:
return None
def FromMol(mol, isomer=True, num_enantiomers=-1):
"""
Generates a set of conformers as an OEMol object
Inputs:
mol is an OEMol
isomers is a boolean controling whether or not the various diasteriomers of a molecule are created
num_enantiomers is the allowable number of enantiomers. For all, set to -1
"""
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetMaxConfs(199)
omega = oeomega.OEOmega(omegaOpts)
out_conf = []
ofs = oechem.oemolostream("test.sdf")
if not isomer:
ret_code = omega.Build(mol)
if ret_code == oeomega.OEOmegaReturnCode_Success:
out_conf.append(mol)
else:
oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))
elif isomer:
for enantiomer in oeomega.OEFlipper(mol.GetActive(), 12, True):
enantiomer = oechem.OEMol(enantiomer)
ret_code = omega.Build(enantiomer)
if ret_code == oeomega.OEOmegaReturnCode_Success:
out_conf.append(enantiomer)
num_enantiomers -= 1
oechem.OEWriteMolecule(ofs, mol)
if num_enantiomers == 0:
break
else:
oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))
return out_conf
def __init__(self, prefix: str, ref_file: str, **kwargs):
"""
Shape alignment on generated molecules to a reference molecule
:param prefix: Name (to help keep track metrics, if using a scoring function class more than once)
:param ref_file: Path to reference file to overlay query to (.pdb)
:param return_best_overlay: Whether to also return best overlay (for use with docking)
:param kwargs: Ignored
"""
self.prefix = prefix.replace(" ", "_")
self.rocs_metrics = [
'GetColorScore', 'GetColorTanimoto', 'GetColorTversky',
'GetComboScore', 'GetFitColorTversky', 'GetFitSelfColor',
'GetFitSelfOverlap', 'GetFitTversky', 'GetFitTverskyCombo',
'GetOverlap', 'GetRefColorTversky', 'GetRefSelfColor',
'GetRefSelfOverlap', 'GetRefTversky', 'GetRefTverskyCombo',
'GetShapeTanimoto', 'GetTanimoto', 'GetTanimotoCombo',
'GetTversky', 'GetTverskyCombo'
]
self.ref_file = ref_file
self.refmol = oechem.OEMol()
ifs = oechem.oemolistream(self.ref_file) # Set up input file stream
oechem.OEReadMolecule(ifs, self.refmol) # Read ifs to empty mol object
self.fitmol = None
self.rocs_results = None
self.best_overlay = None
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetStrictStereo(False)
omegaOpts.SetMaxSearchTime(1.0)
self.omega = oeomega.OEOmega(omegaOpts)
def prep_structure(rdmol):
oemol = convert_to_oe(rdmol)
omega = oeomega.OEOmega()
# omega.SetIncludeInput(True)
omega.SetMaxSearchTime(30)
omega.SetCanonOrder(False)
omega.SetSampleHydrogens(True)
eWindow = 15.0
omega.SetEnergyWindow(eWindow)
# omega.SetMaxConfs(800)
omega.SetMaxConfs(400)
omega.SetRMSThreshold(1.0)
if omega(oemol):
result = oequacpac.OEAssignCharges(oemol,
oequacpac.OEAM1BCCELF10Charges())
if result is False:
return None
else:
charges = []
for index, atom in enumerate(oemol.GetAtoms()):
q = atom.GetPartialCharge() * np.sqrt(ONE_4PI_EPS0)
charges.append(q)
return charges
else:
return None
def configure_omega(library,
rotor_predicate,
rms_cutoff,
energy_window,
num_conformers=MAX_CONFS):
opts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Dense)
opts.SetEnumRing(False)
opts.SetEnumNitrogen(oeomega.OENitrogenEnumeration_Off)
opts.SetSampleHydrogens(True)
opts.SetRotorPredicate(rotor_predicate)
opts.SetIncludeInput(False)
opts.SetEnergyWindow(energy_window)
opts.SetMaxConfs(num_conformers)
opts.SetRMSThreshold(rms_cutoff)
conf_sampler = oeomega.OEOmega(opts)
conf_sampler.SetCanonOrder(False)
torlib = conf_sampler.GetTorLib()
# torlib.ClearTorsionLibrary()
for rule in library:
if not torlib.AddTorsionRule(rule):
oechem.OEThrow.Fatal('Failed to add torsion rule: {}'.format(rule))
conf_sampler.SetTorLib(torlib)
return conf_sampler
def create_molecule(name, filename):
# Open output file.
ofs = oechem.oemolostream()
ofs.open(filename)
# Create molecule.
mol = oechem.OEMol()
# Speculatively reorder CAS permuted index names
str = oeiupac.OEReorderIndexName(name)
if len(str) == 0:
str = name
done = oeiupac.OEParseIUPACName(mol, str)
# Create conformation.
omega = oeomega.OEOmega()
omega.SetIncludeInput(False) # don't include input
omega.SetMaxConfs(1) # set maximum number of conformations to 1
omega(mol)
# Set molecule name
mol.SetTitle(name)
# Write molecule.
oechem.OEWriteMolecule(ofs, mol)
# Close stream.
ofs.close()
return
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 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 createOEMolFromIUPAC(iupac_name='bosutinib'):
from openeye import oechem, oeiupac, oeomega
# Create molecule.
mol = oechem.OEMol()
oeiupac.OEParseIUPACName(mol, iupac_name)
mol.SetTitle(iupac_name)
# Assign aromaticity and hydrogens.
oechem.OEAssignAromaticFlags(mol, oechem.OEAroModelOpenEye)
oechem.OEAddExplicitHydrogens(mol)
# Create atom names.
oechem.OETriposAtomNames(mol)
# Create bond types
oechem.OETriposBondTypeNames(mol)
# Assign geometry
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetIncludeInput(False)
omega.SetStrictStereo(True)
omega(mol)
return mol
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 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 FromMol(mol, use_flipper=True, num_sterocenters=12, force_flipper=False):
"""
Generates a set of conformers as an OEMol object
Inputs:
mol is an OEMol
isomers is a boolean controling whether or not the various diasteriomers of a molecule are created
num_enantiomers is the allowable number of enantiomers. For all, set to -1
"""
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetMaxConfRange("200,800")
omegaOpts.SetRangeIncrement(8)
omegaOpts.SetMaxSearchTime(30)
omega = oeomega.OEOmega(omegaOpts)
out_conf = []
for enantiomer in oeomega.OEFlipper(mol.GetActive(), num_sterocenters,
force_flipper):
enantiomer = oechem.OEMol(enantiomer)
ret_code = omega.Build(enantiomer)
if ret_code == oeomega.OEOmegaReturnCode_Success:
out_conf.append(enantiomer)
else:
oechem.OEThrow.Warning(
"%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))
return out_conf
def dock_molecules(receptor_filename, molecules, filename):
"""
Dock the specified molecules, writing out to specified file
Parameters
----------
receptor_filename : str
Receptor .oeb.gz filename
molecules : list of openeye.oechem.OEMol
The read molecules to dock
filename : str
The filename to stream docked molecules to
"""
# Read the receptor
print('Loading receptor...')
from openeye import oechem, oedocking
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, 'receptor.oeb.gz'):
oechem.OEThrow.Fatal("Unable to read receptor")
if oedocking.OEReceptorHasBoundLigand(receptor):
print("Receptor has a bound ligand")
else:
print("Receptor does not have bound ligand")
print('Initializing receptor...')
dockMethod = oedocking.OEDockMethod_Hybrid2
dockResolution = oedocking.OESearchResolution_High
dock = oedocking.OEDock(dockMethod, dockResolution)
success = dock.Initialize(receptor)
# Set up Omega
from openeye import oeomega
omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Dense)
#omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
omega.SetStrictStereo(False)
# Dock molecules
with oechem.oemolostream(filename) as ofs:
from tqdm import tqdm
for mol in tqdm(molecules):
dockedMol = oechem.OEGraphMol()
# Expand conformers
omega.Build(mol)
# Dock molecule
retCode = dock.DockMultiConformerMolecule(dockedMol, mol)
if (retCode != oedocking.OEDockingReturnCode_Success):
oechem.OEThrow.Fatal("Docking Failed with error code " + oedocking.OEDockingReturnCodeGetName(retCode))
# Store docking data
sdtag = oedocking.OEDockMethodGetName(dockMethod)
oedocking.OESetSDScore(dockedMol, dock, sdtag)
dock.AnnotatePose(dockedMol)
# Write molecule
oechem.OEWriteMolecule(ofs, dockedMol)
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <infile> <outfile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
ofs = oechem.oemolostream()
if not ofs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[2])
if not oechem.OEIs3DFormat(ofs.GetFormat()):
oechem.OEThrow.Fatal("Invalid output file format for 3D coordinates!")
omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
for mol in ifs.GetOEMols():
oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
for enantiomer in oeomega.OEFlipper(mol.GetActive(), 12, True):
enantiomer = oechem.OEMol(enantiomer)
ret_code = omega.Build(enantiomer)
if ret_code == oeomega.OEOmegaReturnCode_Success:
oechem.OEWriteMolecule(ofs, enantiomer)
else:
oechem.OEThrow.Warning(
"%s: %s" %
(enantiomer.GetTitle(), oeomega.OEGetOmegaError(ret_code)))
return 0
def generate_confs(mol):
"""
Generate conformers of molecule from its SMILES string.
Parameters
----------
mol : OEChem molecule
Returns
-------
molWithConfs : OEChem molecule with omega-generated conformers
"""
molWithConfs = oechem.OEMol(mol)
omega = oeomega.OEOmega()
maxConfs = 0
omega.SetMaxConfs(maxConfs)
omega.SetStrictStereo(False)
omega.SetSampleHydrogens(True)
omega.SetEnumNitrogen(oeomega.OENitrogenEnumeration_All)
if not omega(molWithConfs):
print("omega failed on %s" % mol.GetTitle())
return None
else:
return molWithConfs
def main(argv=[__name__]):
ifs = oechem.oemolistream()
if not ifs.open("lig.smi"): #input: ligand SMILES
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
ofs = oechem.oemolostream()
if not ofs.open("lig.oeb.gz"): #output: OEBinary Format
oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[2])
omegaOpts = oeomega.OEOmegaOptions() #Parameters
omegaOpts.SetMaxConfs(800)
omegaOpts.SetCanonOrder(False)
omegaOpts.SetSampleHydrogens(True)
omegaOpts.SetEnergyWindow(15.0)
omegaOpts.SetRMSThreshold(1.0)
omegaOpts.SetStrictStereo(True)
omegaOpts.SetRangeIncrement(8)
omega = oeomega.OEOmega(omegaOpts)
for mol in ifs.GetOEMols():
oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
if omega(mol):
oechem.OEWriteMolecule(ofs, mol)
return 0
def dock_molecules_to_receptor(receptor_filename):
"""
Dock the specified molecules, writing out to specified file
Parameters
----------
receptor_filename : str
Receptor .oeb.gz filename
fragment : str
The fragment name to dock to
"""
import os
# Read the receptor
from openeye import oechem, oedocking
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, receptor_filename):
oechem.OEThrow.Fatal("Unable to read receptor")
if not oedocking.OEReceptorHasBoundLigand(receptor):
raise Exception("Receptor does not have bound ligand")
#print('Initializing receptor...')
dockMethod = oedocking.OEDockMethod_Hybrid2
dockResolution = oedocking.OESearchResolution_Default
dock = oedocking.OEDock(dockMethod, dockResolution)
success = dock.Initialize(receptor)
# Set up Omega
#print('Expanding conformers...')
from openeye import oeomega
#omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Dense)
omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
omega.SetStrictStereo(False)
# Dock molecules
docked_molecules = list()
for mol in molecules:
dockedMol = oechem.OEGraphMol()
# Expand conformers
omega.Build(mol)
# Dock molecule
#print(f'Docking {mol.NumConfs()} conformers...')
retCode = dock.DockMultiConformerMolecule(dockedMol, mol)
if (retCode != oedocking.OEDockingReturnCode_Success):
print("Docking Failed with error code " + oedocking.OEDockingReturnCodeGetName(retCode))
continue
# Store docking data
sdtag = oedocking.OEDockMethodGetName(dockMethod)
oedocking.OESetSDScore(dockedMol, dock, sdtag)
dock.AnnotatePose(dockedMol)
docked_molecules.append( oechem.OEMol(dockedMol) )
return docked_molecules
def create_molecule_from_smiles(smiles):
"""
Create an ``OEMol`` molecule from a smiles pattern.
.. todo:: Replace with the toolkit function when finished.
Parameters
----------
smiles : str
Smiles pattern
Returns
-------
molecule : OEMol
OEMol with 3D coordinates, but no charges
"""
from openeye import oechem, oeomega
# Check cache
if smiles in _cached_molecules:
return copy.deepcopy(_cached_molecules[smiles])
# Create molecule from smiles.
molecule = oechem.OEMol()
parse_smiles_options = oechem.OEParseSmilesOptions(quiet=True)
if not oechem.OEParseSmiles(molecule, smiles, parse_smiles_options):
logging.warning('Could not parse SMILES: ' + smiles)
return False
# Normalize molecule
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
oechem.OEAddExplicitHydrogens(molecule)
# oechem.OETriposAtomNames(molecule)
# Create configuration
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetIncludeInput(False)
omega.SetCanonOrder(False)
omega.SetSampleHydrogens(True)
omega.SetStrictStereo(True)
omega.SetStrictAtomTypes(False)
status = omega(molecule)
if not status:
logging.warning('Could not generate a conformer for ' + smiles)
return False
_cached_molecules[smiles] = molecule
return molecule
def create_conformers(infile=None, outfile=None, resname=None, folder= None, name = None):
"""
This function takes a mol1 file and runs Openeye's omega to create conformers for the molecules
The conformers are stored in separated files, adding the number of the conformer at the end of the filename
:param infile: Path to input file
:param outfile: Path to output file return
:param folder: Name of the folder for the target. If not specified. {name}-liquid is used.
:param resname: Abbreviation of the Residue. Specified in the mol2
:return: Number of conformers for this molecule
"""
if folder is None and name is None:
log.error('Please specify keyword argument folder or name')
sys.exit(1)
elif folder is None:
folder = name +'-liquid'
infilepath = os.path.join(folder, infile)
outfilepath = os.path.join(folder, outfile)
ifs = oechem.oemolistream()
if not ifs.open(infilepath):
oechem.OEThrow.Fatal("Unable to open %s for reading" % infilepath)
ofs = oechem.oemolostream()
if not ofs.open(outfilepath):
oechem.OEThrow.Fatal("Unable to open %s for writing" % outfilepath)
if not oechem.OEIs2DFormat(ofs.GetFormat()):
oechem.OEThrow.Fatal("Invalid output file format for 2D coordinates!")
omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
omega.SetCommentEnergy(True)
omega.SetEnumNitrogen(True)
omega.SetSampleHydrogens(True)
omega.SetEnergyWindow(9.0)
omega.SetMaxConfs(5)
omega.SetRangeIncrement(2)
omega.SetRMSRange([0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5])
filename = '{}-conformers'.format(resname)
for mol in ifs.GetOEMols():
ret_code = omega.Build(mol)
if ret_code == oeomega.OEOmegaReturnCode_Success:
oechem.OEWriteMolecule(ofs, mol)
for k, conf in enumerate(mol.GetConfs()):
ofs1 = oechem.oemolostream()
if not ofs1.open(os.path.join(folder, filename + '_' + str(k + 1) + '.mol2')):
oechem.OEThrow.Fatal("Unable to open %s for writing" % os.path.join(folder, filename + '_' + str(k + 1) + '.mol2'))
oechem.OEWriteMolecule(ofs1, conf)
nconf = k + 1
log.info('Created conformations for {} and saved them to {}'.format(infilepath, outfilepath))
else:
oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))
return nconf
def __init__(self, receptor: utils.FilePath):
self.receptor_file = receptor
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetStrictStereo(False)
self.omega = oeomega.OEOmega(omegaOpts)
oechem.OEThrow.SetLevel(10000)
oereceptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(oereceptor, self.receptor_file)
self.dock = oedocking.OEDock()
self.dock.Initialize(oereceptor)
def smiles_to_oemol(smiles, title='MOL', max_confs=1):
"""
Generate an oemol from a SMILES string
Parameters
----------
smiles : str
SMILES string of molecule
title : str, default 'MOL'
title of OEMol molecule
max_confs : int, default 1
maximum number of conformers to generate
Returns
-------
molecule : openeye.oechem.OEMol
OEMol object of the molecule
"""
from openeye import oeomega
# Create molecule
molecule = oechem.OEMol()
oechem.OESmilesToMol(molecule, smiles)
# create unique atom names
if len([atom.GetName() for atom in molecule.GetAtoms()]) > len(
set([atom.GetName() for atom in molecule.GetAtoms()])):
# the atom names are not unique
molecule = generate_unique_atom_names(molecule)
else:
pass
# Set title.
molecule.SetTitle(title)
# Assign aromaticity and hydrogens.
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
oechem.OEAssignHybridization(molecule)
oechem.OEAddExplicitHydrogens(molecule)
oechem.OEPerceiveChiral(molecule)
# Create atom names.
oechem.OETriposAtomNames(molecule)
oechem.OETriposBondTypeNames(molecule)
# perceive chirality before attempting omega geometry proposal
assert oechem.OEPerceiveChiral(molecule), f"chirality perception failed"
# Assign geometry
omega = oeomega.OEOmega()
omega.SetMaxConfs(max_confs)
omega.SetIncludeInput(False)
omega.SetStrictStereo(True)
omega(molecule)
return molecule
def fit_smiles_molecule(mol: oechem.OEMol):
"""Modifies the given molecule in-place to give it 3D coordinates"""
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetIncludeInput(True)
omega.SetCanonOrder(True)
omega.SetSampleHydrogens(True)
omega.SetStrictStereo(True)
omega.SetStrictAtomTypes(True)
omega.SetIncludeInput(False)
omega(mol)
def generate_initial_molecule(mol_smiles):
"""
Generate an oemol with a geometry
"""
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, mol_smiles)
oechem.OEAddExplicitHydrogens(mol)
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega(mol)
return mol
def _docking_internal(receptor: oechem.OEGraphMol,
bound_ligand: oechem.OEGraphMol, ligand_string):
"""
Internal method for docking to a receptor given a bound ligand and ligand to dock to
Parameters
----------
receptor: oechem.OEGraphMol, required
An oechem receptor to dock to
bound_ligand: oechem.OEGraphMol, required
The ligand bound to the current receptor pocket
docking_ligand: oechem.OEGraphMol, required
The ligand to dock.
Returns
-------
An oechem molecule with coordinates of its docking
"""
# Create posit config
oedocking.OEReceptorSetBoundLigand(receptor, bound_ligand)
poser = oedocking.OEHybrid(oedocking.OEDockMethod_Hybrid2,
oedocking.OESearchResolution_High)
poser.Initialize(receptor)
# Create multiple conformations
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetMaxConfs(1000)
omega_driver = oeomega.OEOmega(omegaOpts)
conformer_docking = oechem.OEMol() # type: OEMol
oechem.OESmilesToMol(conformer_docking, ligand_string)
oechem.OEAddExplicitHydrogens(conformer_docking)
print(conformer_docking.NumAtoms())
if not omega_driver(conformer_docking):
single_sdf = tempfile.NamedTemporaryFile(suffix=".sdf")
double_sdf = tempfile.NamedTemporaryFile(suffix=".sdf")
smiles = ligand_string
subprocess.run(
"obabel -:'%s' -O %s --gen3d; obabel %s -O %s --confab --conf = 100"
% (smiles, single_sdf.name, single_sdf.name, double_sdf.name),
shell=True)
ins = oechem.oemolistream()
ins.SetConfTest(oechem.OEOmegaConfTest())
ins.open(double_sdf.name)
oechem.OEReadMolecule(ins, conformer_docking)
# Dock and get top conformer
posed_ligand = oechem.OEGraphMol() # type: OEGraphMol
poser.DockMultiConformerMolecule(posed_ligand, conformer_docking)
return posed_ligand