Merge

Command-line interface for merging multiple Protein Data Bank (PDB) files into a single file.

add_pdb_merge_subparser(subparsers)

Adds the 'merge' subcommand to the Simlify CLI for combining multiple PDB files.

This function configures an argparse subparser named 'merge' which allows users to specify one or more PDB files to be merged together. It also provides an option to specify the output path for the merged PDB file.

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

The 'merge' subcommand accepts the following arguments:

• pdb_paths: One or more paths to the PDB files that should be merged. These files will be concatenated in the order they are provided.
• --output: Path to the new PDB file where the content of all input PDB files will be written.

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

cli_merge_pdbs(args, parser)

Command-line interface function to merge multiple PDB files into one.

This function serves as the entry point when the user executes the 'merge' subcommand of the Simlify CLI. It receives the parsed command-line arguments and the argument parser object. It first checks if the --output argument was provided, as it is a requirement for this operation. If not, it raises a RuntimeError. Otherwise, it extracts the list of input PDB file paths and the output path and calls the run_merge_pdbs function from the simlify.structure.pdb.utils module to perform the merging operation.

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

RAISES	DESCRIPTION
RuntimeError	If the --output argument is not specified by the user.

The function retrieves the following arguments from the args object:

• pdb_paths: A list of paths to the PDB files to be merged.
• output: The path to the output PDB file.

It then unpacks the pdb_paths list as positional arguments to the run_merge_pdbs function and provides the output path as a keyword argument.