def test_MDL_aromaticity(verbose=False):
"""Test support for alternate aromaticity models."""
ffxml = StringIO(ffxml_MDL_contents)
ff = ForceField(ffxml)
from openeye import oechem
mol = oechem.OEMol()
oechem.OEParseSmiles(mol, 'c12c(cccc1)occ2')
oechem.OEAddExplicitHydrogens(mol)
labels = ff.labelMolecules([mol], verbose=True)
# The bond 6-7 should get the b16 parameter iff the MDL model is working, otherwise it will pick up just the generic
details = labels[0]['HarmonicBondGenerator']
found = False
for (atom_indices, pid, smirks) in details:
if pid == 'b16' and atom_indices == [6, 7]:
found = True
if not found: raise Exception("Didn't find right param.")
def test_molecule_labeling(verbose = False):
"""Test using labelMolecules to see which parameters applied to an oemol."""
from openeye import oechem
mol = oechem.OEMol()
oechem.OEParseSmiles(mol, 'CCC')
oechem.OEAddExplicitHydrogens(mol)
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
labels = ff.labelMolecules( [mol], verbose = verbose)
# Check that force terms aren't empty
print(labels[0].keys())
if not 'HarmonicBondGenerator' in labels[0].keys():
raise Exception("No force term assigned for harmonic bonds.")
if not 'HarmonicAngleGenerator' in labels[0].keys():
raise Exception("No force term assigned for harmonic angles.")
if not 'PeriodicTorsionGenerator' in labels[0].keys():
raise Exception("No force term assigned for periodic torsions.")
if not 'NonbondedGenerator' in labels[0].keys():
raise Exception("No nonbonded force term assigned.")
def test_molecule_labeling(verbose=False):
"""Test using labelMolecules to see which parameters applied to an oemol."""
from openeye import oechem
mol = oechem.OEMol()
oechem.OEParseSmiles(mol, 'CCC')
oechem.OEAddExplicitHydrogens(mol)
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
labels = ff.labelMolecules([mol], verbose=verbose)
# Check that force terms aren't empty
print(labels[0].keys())
if not 'HarmonicBondGenerator' in labels[0].keys():
raise Exception("No force term assigned for harmonic bonds.")
if not 'HarmonicAngleGenerator' in labels[0].keys():
raise Exception("No force term assigned for harmonic angles.")
if not 'PeriodicTorsionGenerator' in labels[0].keys():
raise Exception("No force term assigned for periodic torsions.")
if not 'NonbondedGenerator' in labels[0].keys():
raise Exception("No nonbonded force term assigned.")
def get_molecule_parameterIDs( oemols, ffxml):
"""Process a list of oemols with a specified SMIRFF ffxml file and determine which parameters are used by which molecules, returning collated results.
Parameters
----------
oemols : list
List of OpenEye OEChem molecules to parse; must have explicit hydrogens.
Returns
-------
parameters_by_molecule : dict
Parameter IDs used in each molecule, keyed by isomeric SMILES
generated from provided OEMols. Each entry in the dict is a list
which does not necessarily have unique entries; i.e. parameter IDs
which are used more than once will occur multiple times.
parameters_by_ID : dict
Molecules in which each parameter ID occur, keyed by parameter ID.
Each entry in the dict is a set of isomeric SMILES for molecules
in which that parameter occurs. No frequency information is stored.
"""
# Create storage
parameters_by_molecule = {}
parameters_by_ID = {}
# Generate isomeric SMILES
isosmiles = list()
for mol in oemols:
smi = oechem.OECreateIsoSmiString(mol)
if not smi in isosmiles:
isosmiles.append(smi)
# If the molecule is already here, raise exception
else:
raise ValueError("Error: get_molecule_parameterIDs has been provided a list of oemols which contains the same molecule, having isomeric smiles %s, more than once." % smi )
# Label molecules
ff = ForceField( ffxml )
labels = ff.labelMolecules( oemols )
# Organize labels into output dictionary by looping over all molecules/smiles
for idx in range(len(isosmiles)):
# Pull smiles, initialize storage
smi = isosmiles[idx]
parameters_by_molecule[smi] = []
# Organize data for this molecule
data = labels[idx]
for force_type in data.keys():
for (atom_indices, pid, smirks) in data[force_type]:
# Store pid to molecule
parameters_by_molecule[smi].append(pid)
# Store which molecule this pid occurred in
if pid not in parameters_by_ID:
parameters_by_ID[pid] = set()
parameters_by_ID[pid].add(smi)
else:
parameters_by_ID[pid].add(smi)
return parameters_by_molecule, parameters_by_ID
def get_molecule_parameterIDs(oemols, ffxml):
"""Process a list of oemols with a specified SMIRFF ffxml file and determine which parameters are used by which molecules, returning collated results.
Parameters
----------
oemols : list
List of OpenEye OEChem molecules to parse; must have explicit hydrogens.
Returns
-------
parameters_by_molecule : dict
Parameter IDs used in each molecule, keyed by isomeric SMILES
generated from provided OEMols. Each entry in the dict is a list
which does not necessarily have unique entries; i.e. parameter IDs
which are used more than once will occur multiple times.
parameters_by_ID : dict
Molecules in which each parameter ID occur, keyed by parameter ID.
Each entry in the dict is a set of isomeric SMILES for molecules
in which that parameter occurs. No frequency information is stored.
"""
# Create storage
parameters_by_molecule = {}
parameters_by_ID = {}
# Generate isomeric SMILES
isosmiles = list()
for mol in oemols:
smi = oechem.OECreateIsoSmiString(mol)
if not smi in isosmiles:
isosmiles.append(smi)
# If the molecule is already here, raise exception
else:
raise ValueError(
"Error: get_molecule_parameterIDs has been provided a list of oemols which contains the same molecule, having isomeric smiles %s, more than once."
% smi)
# Label molecules
ff = ForceField(ffxml)
labels = ff.labelMolecules(oemols)
# Organize labels into output dictionary by looping over all molecules/smiles
for idx in range(len(isosmiles)):
# Pull smiles, initialize storage
smi = isosmiles[idx]
parameters_by_molecule[smi] = []
# Organize data for this molecule
data = labels[idx]
for force_type in data.keys():
for (atom_indices, pid, smirks) in data[force_type]:
# Store pid to molecule
parameters_by_molecule[smi].append(pid)
# Store which molecule this pid occurred in
if pid not in parameters_by_ID:
parameters_by_ID[pid] = set()
parameters_by_ID[pid].add(smi)
else:
parameters_by_ID[pid].add(smi)
return parameters_by_molecule, parameters_by_ID