ScanFilter

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

A filter to remove/include molecules from the workflow who have scans targeting the specified SMARTS.

Important

Currently only checks against 1D scans.

Show JSON schema

{
   "title": "ScanFilter",
   "description": "A filter to remove/include molecules from the workflow who have scans targeting the specified SMARTS.\n\nImportant:\n    Currently only checks against 1D scans.",
   "type": "object",
   "properties": {
      "type": {
         "title": "Type",
         "default": "ScanFilter",
         "enum": [
            "ScanFilter"
         ],
         "type": "string"
      },
      "scans_to_include": {
         "title": "Scans To Include",
         "description": "Only molecules with SCANs covering these SMARTspatterns should be kept. This option is mutuallyexclusive with ``scans_to_exclude``.",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "scans_to_exclude": {
         "title": "Scans To Exclude",
         "description": "Any molecules with scans covering these SMARTs willbe removed from the dataset. This option is mutallyexclusive with ``scans_to_include``.",
         "type": "array",
         "items": {
            "type": "string"
         }
      }
   }
}

Config

allow_mutation: bool = True
validate_assignment: bool = True

Fields

scans_to_exclude (Optional[List[str]])
scans_to_include (Optional[List[str]])
type (Literal['ScanFilter'])

Validators

_validate_mutally_exclusive » all fields
check_environments » scans_to_exclude
check_environments » scans_to_include

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

Validated by

_validate_mutally_exclusive

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

Only molecules with SCANs covering these SMARTspatterns should be kept. This option is mutuallyexclusive with scans_to_exclude.

Validated by

_validate_mutally_exclusive
check_environments

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

Any molecules with scans covering these SMARTs willbe removed from the dataset. This option is mutallyexclusive with scans_to_include.

Validated by

_validate_mutally_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