SmartsFilter
- class openff.qcsubmit.workflow_components.SmartsFilter(*, type='SmartsFilter', allowed_substructures=None, filtered_substructures=None)[source]
Filters molecules based on if they contain certain smarts substructures.
Note
The smarts tags used for filtering should be numerically tagged in order to work with the toolkit.
The options
allowed_substructures
andfiltered_substructures
are mutually exclusive.
- 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 any of the requested backend toolkits can be used.
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)This component calls the OFFTK to perform the task and logs information on the backend toolkit used.
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
type
allowed_substructures
filtered_substructures
- classmethod description()[source]
Returns a friendly description of the workflow component.
- Return type
- classmethod fail_reason()[source]
Returns a friendly description of why a molecule would fail to pass the component.
- Return type
- classmethod properties()[source]
Returns the runtime properties of the component such as parallel safe.
- 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
- provenance(toolkit_registry)
This component calls the OFFTK to perform the task and logs information on the backend toolkit used.
- Parameters
toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) – The openff.toolkit.utils.ToolkitRegistry which declares the available toolkits for the component.
- Returns
A dictionary containing the version information about the backend toolkit called to perform the task.
- Return type