SmartsFilter

pydantic model openff.qcsubmit.workflow_components.SmartsFilter[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 and filtered_substructures are mutually exclusive.

Show JSON schema

{
   "title": "SmartsFilter",
   "description": "Filters molecules based on if they contain certain smarts substructures.\n\nNote:\n    * The smarts tags used for filtering should be numerically tagged in order to work with the toolkit.\n    * The options ``allowed_substructures`` and ``filtered_substructures`` are mutually exclusive.",
   "type": "object",
   "properties": {
      "type": {
         "title": "Type",
         "default": "SmartsFilter",
         "enum": [
            "SmartsFilter"
         ],
         "type": "string"
      },
      "allowed_substructures": {
         "title": "Allowed Substructures",
         "description": "The list of allowed substructures which should be tagged with indices.",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "filtered_substructures": {
         "title": "Filtered Substructures",
         "description": "The list of substructures which should be filtered.",
         "type": "array",
         "items": {
            "type": "string"
         }
      }
   }
}

Config

allow_mutation: bool = True
validate_assignment: bool = True

Fields

allowed_substructures (Optional[List[str]])
filtered_substructures (Optional[List[str]])
type (Literal['SmartsFilter'])

Validators

_validate_mutually_exclusive » all fields
check_environments » allowed_substructures
check_environments » filtered_substructures

field type: Literal['SmartsFilter'] = 'SmartsFilter'

Validated by

_validate_mutually_exclusive

field allowed_substructures: Optional[List[str]] = None

The list of allowed substructures which should be tagged with indices.

Validated by

_validate_mutually_exclusive
check_environments

field filtered_substructures: Optional[List[str]] = None

The list of substructures which should be filtered.

Validated by

_validate_mutually_exclusive
check_environments

classmethod description()[source]

Returns a friendly description of the workflow component.

Return type: str

classmethod fail_reason()[source]

Returns a friendly description of why a molecule would fail to pass the component.

Return type: str

classmethod properties()[source]

Returns the runtime properties of the component such as parallel safe.

Return type: openff.qcsubmit.common_structures.ComponentProperties

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

openff.qcsubmit.workflow_components.utils.ComponentResult

classmethod info()

Returns a dictionary of the friendly descriptions of the class.

Return type: Dict[str, str]

classmethod is_available()

Check if any of the requested backend toolkits can be used.

Return type: bool

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: Dict