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 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
- classmethod fail_reason()[source]
Returns a friendly description of why a molecule would fail to pass the component.
- Return type
- classmethod properties()[source]
Returns the runtime properties of the component such as parallel safe.
- 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
- 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