Filter

Command-line interface for filtering specific records within a PDB file.

add_pdb_filter_subparser(subparsers)

Adds the 'filter' subcommand to the Simlify CLI for filtering PDB file lines.

This function configures an argparse subparser named 'filter' which allows users to specify a PDB file, an optional output path, and a list of PDB record types to keep in the output file. Lines with record types not specified will be removed.

PARAMETER	DESCRIPTION
subparsers	An argparse._SubParsersAction object where the 'filter' subparser will be added. This is typically obtained by calling add_subparsers() on an ArgumentParser object.

RETURNS	DESCRIPTION
	The configured argparse parser object for the 'filter' subcommand.

The 'filter' subcommand accepts the following arguments:

• pdb_path: Path to the input PDB file that will be filtered. This argument is optional. If not provided, the program might expect the path through other configuration mechanisms.
• --output: Path to the new PDB file where the filtered content will be saved. If not provided, the output might overwrite the input file or be handled in another way by the underlying function.
• --records: One or more PDB record types (e.g., ATOM, HETATM, TER) to keep in the output file. Only lines starting with these record types will be included in the output. If no records are specified, the behavior will depend on the underlying run_filter_pdb function.

The function sets the default action for this subparser to be the cli_filter_pdb function, which will be called when the user invokes the 'filter' subcommand.

cli_filter_pdb(args, parser)

Command-line interface function to filter lines in a PDB file.

This function serves as the entry point when the user executes the 'filter' subcommand of the Simlify CLI. It receives the parsed command-line arguments and the argument parser object. It extracts the paths to the input PDB file and the desired output PDB file, as well as the list of record types to keep. It then calls the run_filter_pdb function from the simlify.structure.pdb.utils module to perform the filtering operation.

PARAMETER	DESCRIPTION
args	An argparse.Namespace object containing the parsed command-line arguments for the 'filter' subcommand. TYPE: Namespace
parser	The argument parser object for the 'filter' subcommand, used to display help messages if necessary (though not explicitly used in this function). TYPE: ArgumentParser

The function retrieves the following arguments from the args object:

• pdb_path: Path to the input PDB file.
• output: Path to the output PDB file.
• records: A list of PDB record types to keep.

It then directly calls the run_filter_pdb function with these arguments to perform the filtering of the PDB file.