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.

description()

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.

fail_reason()

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.

is_available()

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, ...])

properties()

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

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

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

Dict

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
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