TorsionIndexer
- class openff.qcsubmit.workflow_components.TorsionIndexer(*, torsions={}, double_torsions={}, impropers={})[source]
A class to keep track of the torsions highlighted for scanning, with methods for combining and deduplication.
- Parameters
- Return type
None
- __init__(**data)
Create a new model by parsing and validating input data from keyword arguments.
Raises ValidationError if the input data cannot be parsed to form a valid model.
- Parameters
data (Any) –
- Return type
None
Methods
__init__
(**data)Create a new model by parsing and validating input data from keyword arguments.
add_double_torsion
(torsion1, torsion2, ...)Add a double torsion to the indexer if this central bond combination has not been tagged and the torsion pair are symmetry unique.
add_improper
(central_atom, improper, ...[, ...])Add an improper torsion to the indexer if its central atom is not already covered and the improper is symmetry unique.
add_torsion
(torsion, symmetry_group[, ...])Add a single torsion to the torsion indexer if this central bond has not already been tagged and the torsion is symmetry unique.
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)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
(torsion_indexer[, reorder_mapping])Update the current torsion indexer with another.
update_forward_refs
(**localns)Try to update ForwardRefs on fields based on this Model, globalns and localns.
validate
(value)Attributes
Return a list of all of the currently covered pairs of torsion symmetry groups.
Return a list of all of the dihedrals tagged making it easy to loop over.
Return a list of all of the currently covered improper torsion symmetry groups.
Return the number of double torsions highlighted.
Return the number of imporpers highlighted.
Return the number of torsions highlighted.
Return a list of all of the currently covered torsion symmetry groups.
torsions
double_torsions
impropers
- property get_dihedrals: List[Union[openff.qcsubmit.workflow_components.utils.SingleTorsion, openff.qcsubmit.workflow_components.utils.DoubleTorsion, openff.qcsubmit.workflow_components.utils.ImproperTorsion]]
Return a list of all of the dihedrals tagged making it easy to loop over.
- property torsion_groups: List[Tuple[int, int]]
Return a list of all of the currently covered torsion symmetry groups. Note this only includes central bond atoms.
- property double_torsion_groups: List[Tuple[Tuple[int, int], Tuple[int, int]]]
Return a list of all of the currently covered pairs of torsion symmetry groups.
- property improper_groups: List[Tuple[int, int, int, int]]
Return a list of all of the currently covered improper torsion symmetry groups.
- add_torsion(torsion, symmetry_group, scan_range=None, scan_increment=[15], overwrite=False)[source]
Add a single torsion to the torsion indexer if this central bond has not already been tagged and the torsion is symmetry unique.
- add_double_torsion(torsion1, torsion2, symmetry_group1, symmetry_group2, scan_range1=None, scan_range2=None, scan_increment=[15, 15], overwrite=False)[source]
Add a double torsion to the indexer if this central bond combination has not been tagged and the torsion pair are symmetry unique.
- Parameters
- Return type
None
- add_improper(central_atom, improper, symmetry_group, scan_range=None, scan_increment=[15], overwrite=False)[source]
Add an improper torsion to the indexer if its central atom is not already covered and the improper is symmetry unique.
- update(torsion_indexer, reorder_mapping=None)[source]
Update the current torsion indexer with another.
- Parameters
torsion_indexer (openff.qcsubmit.workflow_components.utils.TorsionIndexer) – The other torsionindxer that should be used to update the current object.
reorder_mapping (Optional[Dict[int, int]]) – The mapping between the other and current molecule should the order need updating.
- Return type
None
- property n_torsions: int
Return the number of torsions highlighted.
- property n_double_torsions: int
Return the number of double torsions highlighted.
- property n_impropers: int
Return the number of imporpers highlighted.