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 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 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 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 _createMolecule(self, iupac_name):
"""Create molecule from IUPAC name.
Best practices for creating initial coordinates can be applied here.
Parameters
----------
iupac_name : str
IUPAC name
Returns
-------
molecule : OEMol
OEMol with 3D coordinates, but no charges
"""
# Check cache
if iupac_name in self._cached_molecules:
return copy.deepcopy(self._cached_molecules[iupac_name])
# Create molecule from IUPAC name.
molecule = oechem.OEMol()
if not oeiupac.OEParseIUPACName(molecule, iupac_name):
raise ValueError(
"The supplied IUPAC name '%s' could not be parsed." %
iupac_name)
# Set molecule name
molecule.SetTitle(iupac_name)
# 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:
raise (RuntimeError("omega returned error code %d" % status))
# Cache molecule
self._cached_molecules[iupac_name] = molecule
return molecule
def generate_initial_molecule(iupac_name):
"""
Generate an oemol with a geometry
"""
mol = oechem.OEMol()
oeiupac.OEParseIUPACName(mol, iupac_name)
oechem.OEAddExplicitHydrogens(mol)
oechem.OETriposAtomNames(mol)
oechem.OETriposBondTypeNames(mol)
omega = oeomega.OEOmega()
omega.SetStrictStereo(False)
omega.SetMaxConfs(1)
omega(mol)
return mol
def Nam2Mol(itf):
ifp = sys.stdin
if itf.GetString("-in") != "-":
ifp = open(itf.GetString("-in"))
ofs = oechem.oemolostream()
if not ofs.open(itf.GetString("-out")):
oechem.OEThrow.Fatal("Unable to open output file: %s" %
itf.GetString("-out"))
language = oeiupac.OEGetIUPACLanguage(itf.GetString("-language"))
charset = oeiupac.OEGetIUPACCharSet(itf.GetString("-charset"))
mol = oechem.OEGraphMol()
for name in ifp:
name = name.strip()
mol.Clear()
# Speculatively reorder CAS permuted index names
str = oeiupac.OEReorderIndexName(name)
if len(str) == 0:
str = name
if charset == oeiupac.OECharSet_HTML:
str = oeiupac.OEFromHTML(str)
if charset == oeiupac.OECharSet_UTF8:
str = oeiupac.OEFromUTF8(str)
str = oeiupac.OELowerCaseName(str)
if language != oeiupac.OELanguage_AMERICAN:
str = oeiupac.OEFromLanguage(str, language)
done = oeiupac.OEParseIUPACName(mol, str)
if not done and itf.GetBool("-empty"):
mol.Clear()
done = True
if done:
if itf.HasString("-tag"):
oechem.OESetSDData(mol, itf.GetString("-tag"), name)
mol.SetTitle(name)
oechem.OEWriteMolecule(ofs, mol)
def iupac_to_oemol(iupac, title='MOL', max_confs=1):
"""
Generate an oemol from an IUPAC name
Parameters
----------
iupac : str
iupac name 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 oeiupac, oeomega
# Create molecule
molecule = oechem.OEMol()
oeiupac.OEParseIUPACName(molecule, iupac)
# 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)
# Assign geometry
omega = oeomega.OEOmega()
omega.SetMaxConfs(max_confs)
omega.SetIncludeInput(False)
omega.SetStrictStereo(True)
omega(molecule)
return molecule
molecules = {'BEN': 'benzene', 'TOL': 'toluene'}
from openeye import oechem
from openeye import oeomega
from openeye import oeiupac
from openeye import oequacpac
# Create molecules.
for resname in molecules:
name = molecules[resname]
print name
# Create molecule from IUPAC name.
molecule = oechem.OEMol()
oeiupac.OEParseIUPACName(molecule, name)
molecule.SetTitle(name)
# Normalize molecule.
oechem.OEAddExplicitHydrogens(molecule)
oechem.OETriposAtomNames(molecule)
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
# Create configuration.
omega = oeomega.OEOmega()
omega.SetStrictStereo(True)
omega.SetIncludeInput(False)
omega(molecule)
# Create charges.
oequacpac.OEAssignPartialCharges(molecule, oequacpac.OECharges_AM1BCCSym)
