Resname

Command-line interface for renaming residues within a Protein Data Bank (PDB) file.

add_pdb_resname_subparser(subparsers)

Adds the 'resname' subcommand to the Simlify CLI for renaming residues.

This function configures an argparse subparser named 'resname' which allows users to specify a PDB file, the current residue name to be replaced, the new residue name, and options for specifying an output file and filtering residues based on their indices.

PARAMETER	DESCRIPTION
subparsers	An argparse._SubParsersAction object where the 'resname' 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 'resname' subcommand.

The 'resname' subcommand accepts the following arguments:

• pdb_path: Path to the input PDB file where residue names will be replaced. This argument is optional. If not provided, the program might expect the path through other configuration mechanisms.
• current_resname: The current three-letter code of the residue name that should be replaced (e.g., "ALA").
• new_resname: The new three-letter code to which the residue should be renamed (e.g., "GLY").
• --output: Path to the new PDB file where the modified structure will be saved. If not provided, the output might overwrite the input file or be handled in another way by the underlying function.
• --include: One or more residue indices to only include for renaming. Residues with indices not in this list will not be renamed. Indices should match the residue number in the PDB file.
• --exclude: One or more residue indices to exclude from renaming. All residues except those with indices in this list will be renamed. Indices should match the residue number in the PDB file.

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

cli_replace_resnames(args, parser)

Command-line interface function to rename residues in a PDB file.

This function serves as the entry point when the user executes the 'resname' subcommand of the Simlify CLI. It receives the parsed command-line arguments and the argument parser object. It constructs a dictionary mapping the current residue name to the new residue name. It then determines whether to use a filter function based on the presence of the --include or --exclude arguments. If either of these arguments is provided, the parse_resid function is used as a filter. Finally, it calls the run_replace_resnames function from the simlify.structure.pdb.names module to perform the residue renaming operation.

PARAMETER	DESCRIPTION
args	An argparse.Namespace object containing the parsed command-line arguments for the 'resname' subcommand. TYPE: Namespace
parser	The argument parser object for the 'resname' 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.
• current_resname: The residue name to be replaced.
• new_resname: The new residue name.
• output: Path to the output PDB file.
• include: A list of residue indices to include for renaming.
• exclude: A list of residue indices to exclude from renaming.

It creates a resname_map dictionary with the provided current and new residue names. It also sets the fn_filter to parse_resid if either args.include or args.exclude is provided, otherwise it remains None. Finally, it calls run_replace_resnames with these parameters to perform the residue renaming.