Center

Defines the command-line interface for centering molecular structures.

add_center_subparser(subparsers)

Adds the 'center' subcommand to the provided subparsers.

This function creates a subparser named 'center' under the main Simlify CLI, allowing users to move the center of mass of all frames within a molecular structure to the origin (0.0, 0.0, 0.0). It defines the necessary command-line arguments for specifying the topology, coordinate files, output path, and overwrite behavior.

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

RETURNS	DESCRIPTION
	argparse.ArgumentParser: The newly created 'center' subparser.

The 'center' subparser accepts the following arguments:

positional arguments

topo Path to topology file. output Path to coordinate file to save the centered structure.

optional arguments

--coords Paths to one or more coordinate files. If multiple files are provided, they will be concatenated and treated as frames of the same trajectory. --overwrite Overwrite the output coordinate file if it already exists.

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

cli_center_atoms(args, parser)

Handles the command-line invocation of the structure centering functionality.

This function serves as the entry point when the user executes the 'center' subcommand of the Simlify CLI. It takes the parsed command-line arguments and the argument parser object as input. It performs a basic check to ensure that at least a topology file is provided. If not, it prints the help message for the 'center' subcommand and returns. Otherwise, it extracts the relevant arguments and calls the underlying run_center_structure function to perform the structure centering operation.

PARAMETER	DESCRIPTION
args	An object containing the parsed command-line arguments for the 'center' subcommand. TYPE: Namespace
parser	The argument parser object for the 'center' subcommand, used to display help messages if necessary. TYPE: ArgumentParser

RETURNS	DESCRIPTION
None	None

The function retrieves the following arguments from the args object: - topo: Path to the topology file. - output: Path to the output coordinate file. - coords: A list of paths to coordinate files. - overwrite: A boolean indicating whether to overwrite the output file.

It then calls the run_center_structure function with these arguments to perform the actual centering of the molecular structure(s).