Water

Command-line interface for unifying residue and atom names of water molecules in a PDB file.

add_pdb_water_subparser(subparsers)

Adds the 'unify-wat' subcommand to the Simlify CLI for unifying water labels.

This function configures an argparse subparser named 'unify-wat' which allows users to specify a PDB file and an optional output path. The 'unify-wat' command will standardize the residue and atom names of all water molecules within the PDB file to a consistent format (e.g., residue name to 'HOH' and oxygen atom name to 'O').

PARAMETER	DESCRIPTION
subparsers	An argparse._SubParsersAction object where the 'unify-wat' 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 'unify-wat' subcommand.

The 'unify-wat' subcommand accepts the following arguments:

• pdb_path: Path to the input PDB file containing water molecules whose labels will be unified. 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 water labels have been unified. If not provided, the output might overwrite the input file or be handled in another way by the underlying function.

The function sets the default action for this subparser to be the cli_unify_water_labels function, which will be called when the user invokes the 'unify-wat' subcommand.

cli_unify_water_labels(args, parser)

Command-line interface function to unify water residue and atom names in a PDB file.

This function serves as the entry point when the user executes the 'unify-wat' 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 and then calls the run_unify_water_labels function from the simlify.structure.pdb.names module to perform the unification of water labels.

PARAMETER	DESCRIPTION
args	An argparse.Namespace object containing the parsed command-line arguments for the 'unify-wat' subcommand. TYPE: Namespace
parser	The argument parser object for the 'unify-wat' subcommand. Although passed, it's not directly used in this specific implementation. TYPE: ArgumentParser

RETURNS	DESCRIPTION
None	None

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.

It then calls the run_unify_water_labels function with these paths to perform the standardization of water residue and atom names.