Numbering

Command-line interface for unifying numbering within a Protein Data Bank (PDB) file.

add_pdb_unify_numbering_subparser(subparsers)

Adds the unify_numbering subcommand to the Simlify CLI for unifying atom and residue numbering in PDB files.

This function configures an argparse subsparser named unify_numbering which allows users to specify a PDB file and option to control whether the initial residue ID should be reset to 1.

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

Returns: argparse.ArgumentParser: The configured argparse parser object for the unify_numbering subcommand.

The unify_numbering subcommand accepts the following arguments:

positional arguments

pdb_path Path to the input PDB file whose numbering will be processed. This argument is optional. If not provided, the program might expect the path through other configuration mechanisms.

optional arguments

--output Path to the new PDB file where the output will be saved. If not provided, the output might overwrite the input file or be handled in another way by the underlying function. --reset_init_resid reset original first residue ID; do not reset to 1. This Not modify the numbering in the initial amino acid in the chain.

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

cli_unify_numbering(args, parser)

Command-line interface function to for unifying atom and residue numbering in PDB files.

This function serves as the entry point when the user executes the unify_numbering 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_numbering function from the simlify.structure.pdb.numbering.main to renumber resIDs and atom numbers. Args: args: An argparse.Namespace object containing the parsed command-line arguments for the 'unify_numbering' subcommand. parser (argparse.ArgumentParser): The argument parser object for the unify_numbering subcommand, used to display help messages if necessary (though not explicitly used in this function).

RETURNS	DESCRIPTION
None	None

The function retrieves the following arguments from the args object: - pdb_path is the path to the PDB file to be processed. - --reset_init_resid is an optional flag. If present, the initial residue ID will not be reset to 1.

It then directly calls the run_unify_numbering function with these paths to perform the renumbering operation. See Also: run_unify_numbering: The underlying function that performs the PDB numbering unification.