EnumerateProtomers
- pydantic model openff.qcsubmit.workflow_components.EnumerateProtomers[source]
Enumerate the formal charges of the input molecule using the backend toolkits through the OFFTK.
Important
Only Openeye is supported so far.
Show JSON schema
{ "title": "EnumerateProtomers", "description": "Enumerate the formal charges of the input molecule using the backend toolkits through the OFFTK.\n\nImportant:\n Only Openeye is supported so far.", "type": "object", "properties": { "type": { "title": "Type", "default": "EnumerateProtomers", "enum": [ "EnumerateProtomers" ], "type": "string" }, "max_states": { "title": "Max States", "description": "The maximum number of states that should be generated.", "default": 10, "type": "integer" } } }
- Config
allow_mutation: bool = True
validate_assignment: bool = True
- Fields
max_states (int)
type (Literal['EnumerateProtomers'])
- field max_states: int = 10
The maximum number of states that should be generated.
- classmethod is_available()[source]
Check if any of the requested backend toolkits can be used.
- Return type
- 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