filter

run_filter(session_dir, /, *, options=None, cache=None, scheduler_address=None, _=None)

Filter structure files based on specified parameters.

Steps:

1. Verify expected uniprot accessions are in structure files and inject uniprot accession if missing. See protein-quest convert structure --uniprots.
2. Convert PDBe structure files to single chain structure files. See protein-quest filter chain.
3. Filters processed PDBe structure files and AlphaFold structure files based on given parameters. See protein-quest filter combined.
4. If secondary structure options are given then filters passed structure files based on secondary structure. See protein-quest filter secondary-structure.

Parameters:

Name	Type	Description	Default
session_dir	Annotated[Path, Parameter(validator=Path(file_okay=False, dir_okay=True, exists=True))]	Directory where the structure files are located.	required
options	FilterOptions | None	The filtering options.	None
cache	CacheParameter | None	Cache options including no_cache, cache_dir, and copy_method.	None
scheduler_address	str | None	Address of the Dask scheduler to connect to. If not provided, will create a local cluster. If set to sequential will run tasks sequentially.	None
_	Common | None	Common CLI options.	None