OpenFF QCSubmit documentation

openff-qcsubmit

WBOFragmenter

pydantic model openff.qcsubmit.workflow_components.WBOFragmenter

Fragment molecules using the WBO fragmenter class of the fragmenter module. For more information see <https://github.com/openforcefield/fragmenter>.

Show JSON schema

{
   "title": "WBOFragmenter",
   "description": "Fragment molecules using the WBO fragmenter class of the fragmenter module.\nFor more information see <https://github.com/openforcefield/fragmenter>.",
   "type": "object",
   "properties": {
      "type": {
         "title": "Type",
         "default": "WBOFragmenter",
         "enum": [
            "WBOFragmenter"
         ],
         "type": "string"
      },
      "target_torsion_smarts": {
         "title": "Target Torsion Smarts",
         "description": "The list of SMARTS patterns used to identify central target bonds to fragment around. By default this is any single non-termial bond.",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "threshold": {
         "title": "Threshold",
         "description": "The WBO error threshold between the parent and the fragment value, the fragmentation will stop when the difference between the fragment and parent is less than this value.",
         "default": 0.03,
         "type": "number"
      },
      "keep_non_rotor_ring_substituents": {
         "title": "Keep Non Rotor Ring Substituents",
         "description": "If any non rotor ring substituents should be kept during the fragmentation resulting in smaller fragments when `False`.",
         "default": false,
         "type": "boolean"
      },
      "heuristic": {
         "title": "Heuristic",
         "description": "The path fragmenter should take when fragment needs to be grown out. The options are ``['wbo', 'path_length']``.",
         "default": "path_length",
         "enum": [
            "path_length",
            "wbo"
         ],
         "type": "string"
      }
   }
}

Config

• allow_mutation: bool = True

• validate_assignment: bool = True

Fields

• heuristic (Literal['path_length', 'wbo'])

• keep_non_rotor_ring_substituents (bool)

• target_torsion_smarts (Optional[List[str]])

• threshold (float)

• type (Literal['WBOFragmenter'])

Validators

• check_environments » target_torsion_smarts

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

field threshold: float = 0.03

The WBO error threshold between the parent and the fragment value, the fragmentation will stop when the difference between the fragment and parent is less than this value.

field keep_non_rotor_ring_substituents: bool = False

If any non rotor ring substituents should be kept during the fragmentation resulting in smaller fragments when False.

field heuristic: Literal['path_length', 'wbo'] = 'path_length'

The path fragmenter should take when fragment needs to be grown out. The options are ['wbo', 'path_length'].

classmethod description()

Returns a friendly description of the workflow component.

Return type

str

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 fail_reason()

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

Return type

str

classmethod info()

Returns a dictionary of the friendly descriptions of the class.

Return type

Dict[str, str]

classmethod is_available()

Check if fragmenter can be imported.

Return type

bool

classmethod properties()

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

Return type

openff.qcsubmit.common_structures.ComponentProperties

provenance(toolkit_registry)

Collect the toolkit information and add the fragmenter version information.

Parameters

toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) –

Return type

Dict

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

The list of SMARTS patterns used to identify central target bonds to fragment around. By default this is any single non-termial bond.

Validated by

• check_environments