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
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