WBOFragmenter
- class openff.qcsubmit.workflow_components.WBOFragmenter(*, type='WBOFragmenter', target_torsion_smarts=None, threshold=0.03, keep_non_rotor_ring_substituents=False, heuristic='path_length')[source]
Fragment molecules using the WBO fragmenter class of the fragmenter module. For more information see <https://github.com/openforcefield/fragmenter>.
- 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.
apply(molecules, toolkit_registry[, ...])This is the main feature of the workflow component which should accept a molecule, perform the component action and then return any resulting molecules.
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.
Returns a friendly description of the workflow component.
dict(*[, include, exclude, by_alias, ...])Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.
Returns a friendly description of why a molecule would fail to pass the component.
from_orm(obj)info()Returns a dictionary of the friendly descriptions of the class.
Check if fragmenter can be imported.
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, ...])Returns the runtime properties of the component such as parallel safe.
provenance(toolkit_registry)Collect the toolkit information and add the fragmenter version information.
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
typethresholdkeep_non_rotor_ring_substituentsheuristic- classmethod description()[source]
Returns a friendly description of the workflow component.
- Return type
- apply(molecules, toolkit_registry, processors=None, verbose=True)
This is the main feature of the workflow component which should accept a molecule, perform the component action and then return any resulting molecules.
- Parameters
molecules (List[openff.toolkit.topology.molecule.Molecule]) – The list of molecules to be processed by this component.
toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) – The openff.toolkit.utils.ToolkitRegistry which declares the available backend toolkits to be used.
processors (Optional[int]) – The number of processor the component can use to run the job in parallel across molecules, None will default to all cores.
verbose (bool) – If true a progress bar should be shown on screen.
- Returns
A component result class which handles collecting together molecules that pass and fail the component
- Return type
- classmethod fail_reason()
Returns a friendly description of why a molecule would fail to pass the component.
- Return type
- provenance(toolkit_registry)
Collect the toolkit information and add the fragmenter version information.
- Parameters
toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) –
- Return type