openff.bespokefit.utilities.smirks.SMIRKSGenerator
- model openff.bespokefit.utilities.smirks.SMIRKSGenerator[source]
Bases:
SMIRKSettings
Generates a set of smirks that describe the requested force groups of the molecule, these can be bespoke or simply extract the current values from the target forcefield.
- Fields
- field initial_force_field: Union[str, ForceFieldEditor] = 'openff_unconstrained-1.3.0.offxml'
The base forcefield the smirks should be generated from.
- field target_smirks: List[SMIRKSType] = [<SMIRKSType.ProperTorsions: 'ProperTorsions'>]
The list of parameters the new smirks patterns should be made for.
- field smirks_layers: Union[Literal['all'], int] = 'all'
The number of layers that should be included into the generated patterns.
- generate_smirks_from_molecule(molecule: Molecule, central_bond: Optional[Tuple[int, int]] = None)[source]
A convenience method for generating SMIRKS patterns that encompass an entire molecules.
- generate_smirks_from_fragment(parent: Molecule, fragment: Molecule, fragment_map_indices: Optional[Tuple[int, int]]) List[ParameterType] [source]
Generates a set of smirks patterns for the fragment corresponding to the types set in the target smirks list.
- Parameters
parent – The parent molecule that was fragmented.
fragment – The fragment of the parent molecule. The map indices in the fragment must match the map indices of the parent.
fragment_map_indices – The map indices of the atoms that the fragment was generated around.
- Returns
A dictionary of new bespoke smirks parameters for the molecule as well as an initial guess of their values.