def mock_force_field(parameters: List[SMIRNOFFParameter]):
"""Mock a ForceBalance forcefield directory."""
# Create the force field directory.
force_field = ForceField("openff-1.2.0.offxml")
parameters_to_fit = defaultdict(lambda: defaultdict(list))
for parameter in parameters:
parameters_to_fit[parameter.handler][parameter.smirks].append(
parameter.attribute)
for handler_name in parameters_to_fit:
handler = force_field.get_parameter_handler(handler_name)
for smirks in parameters_to_fit[handler_name]:
openff_parameter = handler.parameters[smirks]
attributes_string = ", ".join(
parameters_to_fit[handler_name][smirks])
openff_parameter.add_cosmetic_attribute("parameterize",
attributes_string)
os.makedirs("forcefield", exist_ok=True)
force_field.to_file(os.path.join("forcefield", "forcefield.offxml"))
from openforcefield.typing.engines.smirnoff import ForceField
ff = ForceField('param_valence.offxml', allow_cosmetic_attributes=True)
for handler in ff.registered_parameter_handlers:
print(handler)
if len(ff[handler].parameters) == 0:
continue
print(ff[handler].parameters)
for par in ff[handler].parameters:
if hasattr(par, '_parameterize'):
par.delete_cosmetic_attribute('parameterize')
#if hasattr(ff[handler].parameters[0], '_parameterize'):
#ff[handler].parameters[0].delete_cosmetic_attribute('parameterize')
print(ff)
#<Proper smirks="[*:1]~[#6X3:2]-[#7X3:3]-[#6X4,#1:4]" periodicity1="2" phase1="180.0 * degree" k1_bondorder1="1*kilocalories_per_mole" k1_bondorder2="10*kilocalories_per_mole" id="TIG9" idivf1="1.0"></Proper>
torsionhandler = ff['ProperTorsions']
torsionhandler.add_parameter({
'smirks': '[*:1]~[*:2]~[*:3]~[*:4]',
'periodicity1': 2,
'phase1': '180.0 * degree',
'k1_bondorder1': '1 * kilocalories_per_mole',
'k1_bondorder2': '1 * kilocalories_per_mole',
'id': 'TIG0',
'idivf1': 1
})
torsionhandler.parameters[-1].add_cosmetic_attribute(
'parameterize', 'k1_bondorder1,k1_bondorder2')
ff.to_file('test.offxml')
ff = ForceField()
ff._set_aromaticity_model('OEAroModel_MDL')
# Loop over the parameters to convert and their corresponding SMIRNOFF header tags
for smirnoff_tag, param_dicts in { "Bonds": bond_dicts, "Angles": angle_dicts,
"ProperTorsions": proper_dicts,
"AmberImproperTorsions": improper_dicts,
#'LibraryCharges': charge_dicts,
#'vdW': nonbond_dicts
}.items():
# Get the parameter handler for the given tag. The
# "get_parameter_handler" method will initialize an
# empty handler if none exists yet (as is the case here).
handler = ff.get_parameter_handler(smirnoff_tag)
# Loop over the list of parameter dictionaries, using each one as an input to
# handler.add_parameter. This mimics deserializing an OFFXML into a ForceField
# object, and will do any sanitization that we might otherwise miss
from openforcefield.typing.engines.smirnoff.parameters import DuplicateParameterError
for param_dict in param_dicts:
try:
handler.add_parameter(param_dict)
except DuplicateParameterError:
continue
# Add the ElectrostaticsHandler, with the proper 1-4 scaling factors
handler = ff.get_parameter_handler('Electrostatics')
# Write the now-populated forcefield out to OFFXML
ff.to_file('result_backbone.offxml')
from openforcefield.typing.engines.smirnoff import ForceField
from amberimpropertorsionhandler import AmberImproperTorsionHandler
ff = ForceField('result_residues.offxml', 'result_backbone.offxml')
ff.to_file('result_merged.offxml')
from openforcefield.typing.engines.smirnoff import ForceField
ff = ForceField()
ff._set_aromaticity_model('OEAroModel_MDL')
# Loop over the parameters to convert and their corresponding SMIRNOFF header tags
for smirnoff_tag, param_dicts in { "Bonds": bond_dicts, "Angles": angle_dicts,
"ProperTorsions": proper_dicts,
"AmberImproperTorsions": improper_dicts,
'LibraryCharges': charge_dicts,
'vdW': nonbond_dicts}.items():
# Get the parameter handler for the given tag. The
# "get_parameter_handler" method will initialize an
# empty handler if none exists yet (as is the case here).
handler = ff.get_parameter_handler(smirnoff_tag)
# Loop over the list of parameter dictionaries, using each one as an input to
# handler.add_parameter. This mimics deserializing an OFFXML into a ForceField
# object, and will do any sanitization that we might otherwise miss
from openforcefield.typing.engines.smirnoff.parameters import DuplicateParameterError
for param_dict in param_dicts:
try:
handler.add_parameter(param_dict)
except DuplicateParameterError:
continue
# Add the ElectrostaticsHandler, with the proper 1-4 scaling factors
handler = ff.get_parameter_handler('Electrostatics')
# Write the now-populated forcefield out to OFFXML
ff.to_file('result_residues.offxml')
