TorsionDriveEntry
- class openff.qcsubmit.datasets.TorsionDriveEntry(off_molecule=None, *, index, initial_molecules, attributes, extras={}, keywords=TDSettings(grid_spacing=None, dihedral_ranges=None, energy_decrease_thresh=None, energy_upper_limit=None, additional_keywords={}), constraints=Constraints(freeze=[], set=[]), dihedrals)[source]
A Torsiondrive dataset specific class which can check dihedral indices and store torsiondrive specific settings with built in validation.
- Parameters
off_molecule (Optional[openff.toolkit.topology.molecule.Molecule]) –
index (str) –
initial_molecules (List[qcelemental.models.molecule.Molecule]) –
attributes (openff.qcsubmit.common_structures.MoleculeAttributes) –
keywords (Optional[openff.qcsubmit.common_structures.TDSettings]) –
constraints (openff.qcsubmit.constraints.Constraints) –
- Return type
None
- __init__(off_molecule=None, **kwargs)[source]
Here we handle the constraints before calling the super.
- Parameters
off_molecule (Optional[openff.toolkit.topology.molecule.Molecule]) –
Methods
__init__
([off_molecule])Here we handle the constraints before calling the super.
add_constraint
(constraint, constraint_type, ...)Add new constraint of the given type.
construct
([_fields_set])Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data.
copy
(*[, include, exclude, update, deep])Duplicate a model, optionally choose which fields to include, exclude and change.
dict
(*[, include, exclude, by_alias, ...])Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.
from_orm
(obj)get_off_molecule
([include_conformers])Build and openforcefield.topology.Molecule representation of the input molecule.
json
(*[, include, exclude, by_alias, ...])Generate a JSON representation of the model, include and exclude arguments as per dict().
parse_file
(path, *[, content_type, ...])parse_obj
(obj)parse_raw
(b, *[, content_type, encoding, ...])schema
([by_alias, ref_template])schema_json
(*[, by_alias, ref_template])update_forward_refs
(**localns)Try to update ForwardRefs on fields based on this Model, globalns and localns.
validate
(value)Attributes
Format the keywords with constraints.
dihedrals
keywords
- property formatted_keywords: Dict[str, Any]
Format the keywords with constraints.
- add_constraint(constraint, constraint_type, indices, bonded=True, **kwargs)
Add new constraint of the given type.
- Parameters
constraint (Literal['set', 'freeze']) – The major type of constraint, freeze or set
constraint_type (Literal['distance', 'angle', 'dihedral', 'xyz']) – the constraint sub type, angle, distance etc
indices (List[int]) – The atom indices the constraint should be placed on
bonded (bool) – If the constraint is intended to be put a bonded set of atoms
kwargs – Any extra information needed by the constraint, for the set class they need a value value=float
- Return type
None
- get_off_molecule(include_conformers=True)
Build and openforcefield.topology.Molecule representation of the input molecule.
- Parameters
include_conformers (bool) – If True all of the input conformers are included else they are dropped.
- Return type