ComponentResult

class openff.qcsubmit.workflow_components.ComponentResult(component_name, component_description, component_provenance, molecules=None, input_file=None, input_directory=None, skip_unique_check=False, verbose=True)[source]

Class to contain molecules after the execution of a workflow component this automatically applies de-duplication to the molecules. For example if a molecule is already in the molecules list it will not be added but any conformers will be kept and transferred.

If a molecule in the molecules list is then filtered it will be removed from the molecules list.

Parameters

component_name (str) –
component_description (Dict[str, str]) –
component_provenance (Dict[str, str]) –
molecules (Optional[Union[List[openff.toolkit.topology.molecule.Molecule], openff.toolkit.topology.molecule.Molecule]]) –
input_file (Optional[str]) –
input_directory (Optional[str]) –
skip_unique_check (Optional[bool]) –
verbose (bool) –

__init__(component_name, component_description, component_provenance, molecules=None, input_file=None, input_directory=None, skip_unique_check=False, verbose=True)[source]

Parameters

component_name (str) – The name of the component that produced this result.
component_description (Dict[str, str]) – The dictionary representation of the component which details the function and running parameters.
component_provenance (Dict[str, str]) – The dictionary of the modules used and there version number when running the component.
molecules (Optional[Union[List[openff.toolkit.topology.molecule.Molecule], openff.toolkit.topology.molecule.Molecule]]) – The list of molecules that have been possessed by a component and returned as a result.
input_file (Optional[str]) – The name of the input file used to produce the result if not from a component.
input_directory (Optional[str]) – The name of the input directory which contains input molecule files.
verbose (bool) – If the timing information and progress bar should be shown while doing deduplication.
skip_unique_check (Optional[bool]) – Set to True if it is sure that all molecules will be unique in this result

Methods

`__init__`(component_name, ...[, molecules, ...])	Register the list of molecules to process.
`add_molecule`(molecule)	Add a molecule to the molecule list after checking that it is not present already.
`filter_molecule`(molecule)	Filter out a molecule that has not passed this workflow component.

Attributes

`filtered`	Get the list of molecule that have been filtered to iterate over.
`molecules`	Get the list of molecules which can be iterated over.
`n_conformers`	The number of conformers stored in the molecules.
`n_filtered`	The number of filtered molecules.
`n_molecules`	The number of molecules saved in the result.

property molecules: List[openff.toolkit.topology.molecule.Molecule]: Get the list of molecules which can be iterated over.

property filtered: List[openff.toolkit.topology.molecule.Molecule]: Get the list of molecule that have been filtered to iterate over.

property n_molecules: int: The number of molecules saved in the result.

property n_conformers: int: The number of conformers stored in the molecules.

property n_filtered: int: The number of filtered molecules.

add_molecule(molecule)[source]

Add a molecule to the molecule list after checking that it is not present already. If it is de-duplicate the record and condense the conformers and metadata.

Parameters: molecule (openff.toolkit.topology.molecule.Molecule) – The molecule and its conformers which we should try and add to the result.
Returns: True if the molecule is already present and False if not.
Return type: bool

filter_molecule(molecule)[source]

Filter out a molecule that has not passed this workflow component. If the molecule is already in the pass list remove it and ensure it is only in the filtered list.

Parameters: molecule (openff.toolkit.topology.molecule.Molecule) – The molecule which should be filtered.