CoverageFilter

pydantic model openff.qcsubmit.workflow_components.CoverageFilter[source]

Filters molecules based on the requested force field parameter ids.

Note

The options allowed_ids and filtered_ids are mutually exclusive.

Show JSON schema

{
   "title": "CoverageFilter",
   "description": "Filters molecules based on the requested force field parameter ids.\n\nNote:\n    * The options ``allowed_ids`` and ``filtered_ids`` are mutually exclusive.",
   "type": "object",
   "properties": {
      "type": {
         "title": "Type",
         "default": "CoverageFilter",
         "enum": [
            "CoverageFilter"
         ],
         "type": "string"
      },
      "allowed_ids": {
         "title": "Allowed Ids",
         "description": "The SMIRKS parameter ids of the parameters which are allowed to be exercised by the molecules. Molecules should use at least one of these ids to be passed by the component.",
         "type": "array",
         "items": {
            "type": "string"
         },
         "uniqueItems": true
      },
      "filtered_ids": {
         "title": "Filtered Ids",
         "description": "The SMIRKS parameter ids of the parameters which are not allowed to be exercised by the molecules.",
         "type": "array",
         "items": {
            "type": "string"
         },
         "uniqueItems": true
      },
      "forcefield": {
         "title": "Forcefield",
         "description": "The name of the force field which we want to filter against.",
         "default": "openff_unconstrained-1.0.0.offxml",
         "type": "string"
      }
   }
}

Config

allow_mutation: bool = True
validate_assignment: bool = True

Fields

allowed_ids (Optional[Set[str]])
filtered_ids (Optional[Set[str]])
forcefield (str)
type (Literal['CoverageFilter'])

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

Validated by

_validate_mutually_exclusive

field allowed_ids: Optional[Set[str]] = None

The SMIRKS parameter ids of the parameters which are allowed to be exercised by the molecules. Molecules should use at least one of these ids to be passed by the component.

Validated by

_validate_mutually_exclusive

field filtered_ids: Optional[Set[str]] = None

The SMIRKS parameter ids of the parameters which are not allowed to be exercised by the molecules.

Validated by

_validate_mutually_exclusive

field forcefield: str = 'openff_unconstrained-1.0.0.offxml'

The name of the force field which we want to filter against.

Validated by

_validate_mutually_exclusive

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

provenance(toolkit_registry)[source]

Generate version information for all of the software used during the running of this component.

Returns: A dictionary of all of the software used in the component along wither their version numbers.
Parameters: toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) –
Return type: Dict

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