ElementFilter
- class openff.qcsubmit.workflow_components.ElementFilter(*, type='ElementFilter', allowed_elements=['H', 'C', 'N', 'O', 'F', 'P', 'S', 'Cl', 'Br', 'I'])[source]
Filter the molecules based on a list of allowed elements.
Note
The allowed_elements attribute can take a list of either symbols or atomic numbers and will resolve them to a common internal format as required.
Example
Using atomic symbols or atomic numbers in components.
`python >>> from openff.qcsubmit.workflow_components import ElementFilter >>> efil = ElementFilter() # set the allowed elements to H,C,N,O >>> efil.allowed_elements = ['H', 'C', 'N', 'O'] >>> efil.allowed_elements = [1, 6, 7, 8] `
- Parameters
- Return type
None
- __init__(**data)
Create a new model by parsing and validating input data from keyword arguments.
Raises ValidationError if the input data cannot be parsed to form a valid model.
- Parameters
data (Any) –
- Return type
None
Methods
__init__
(**data)Create a new model by parsing and validating input data from keyword arguments.
apply
(molecules, toolkit_registry[, ...])This is the main feature of the workflow component which should accept a molecule, perform the component action and then return any resulting molecules.
construct
([_fields_set])Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data.
copy
(*[, include, exclude, update, deep])Duplicate a model, optionally choose which fields to include, exclude and change.
Returns a friendly description of the workflow component.
dict
(*[, include, exclude, by_alias, ...])Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.
Returns a friendly description of why a molecule would fail to pass the component.
from_orm
(obj)info
()Returns a dictionary of the friendly descriptions of the class.
Check if any of the requested backend toolkits can be used.
json
(*[, include, exclude, by_alias, ...])Generate a JSON representation of the model, include and exclude arguments as per dict().
parse_file
(path, *[, content_type, ...])parse_obj
(obj)parse_raw
(b, *[, content_type, encoding, ...])Returns the runtime properties of the component such as parallel safe.
provenance
(toolkit_registry)Generate version information for all of the software used during the running of this component.
schema
([by_alias, ref_template])schema_json
(*[, by_alias, ref_template])update_forward_refs
(**localns)Try to update ForwardRefs on fields based on this Model, globalns and localns.
validate
(value)Attributes
type
allowed_elements
- 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.
- provenance(toolkit_registry)[source]
Generate version information for all of the software used during the running of this component.
- Returns
A dictionary of all of the software used in the component along wither their version numbers.
- Parameters
toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) –
- Return type
Note
The element class in OpenMM is used to match the elements so the OpenMM version is given.
- 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