EnumerateStereoisomers

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

Enumerate the stereo centers and bonds of a molecule using the backend toolkits through the OFFTK, only well defined molecules are returned by this component, this is check via a OFFTK round trip.

Show JSON schema

{
   "title": "EnumerateStereoisomers",
   "description": "Enumerate the stereo centers and bonds of a molecule using the backend toolkits through the OFFTK, only well defined\nmolecules are returned by this component, this is check via a OFFTK round trip.",
   "type": "object",
   "properties": {
      "type": {
         "title": "Type",
         "default": "EnumerateStereoisomers",
         "enum": [
            "EnumerateStereoisomers"
         ],
         "type": "string"
      },
      "undefined_only": {
         "title": "Undefined Only",
         "description": "If we should only enumerate parts of the molecule with undefined stereochemistry or all stereochemistry.",
         "default": false,
         "type": "boolean"
      },
      "max_isomers": {
         "title": "Max Isomers",
         "description": "The maximum number of stereoisomers to be generated.",
         "default": 20,
         "type": "integer"
      },
      "rationalise": {
         "title": "Rationalise",
         "description": "If we should check that the resulting molecules are physically possible by attempting to generate conformers for them.",
         "default": true,
         "type": "boolean"
      }
   }
}

Config

allow_mutation: bool = True
validate_assignment: bool = True

Fields

max_isomers (int)
rationalise (bool)
type (Literal['EnumerateStereoisomers'])
undefined_only (bool)

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

field undefined_only: bool = False: If we should only enumerate parts of the molecule with undefined stereochemistry or all stereochemistry.

field max_isomers: int = 20: The maximum number of stereoisomers to be generated.

field rationalise: bool = True: If we should check that the resulting molecules are physically possible by attempting to generate conformers for them.

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