Topo

Command-line interface for preparing simulation topology files.

add_topo_subparser(subparsers)

Adds the 'topo' subcommand to the Simlify CLI for preparing simulation topology files.

This function configures an argparse subparser named 'topo' which allows users to specify the path to a molecular structure file, an import string pointing to a specific topology generation class, and optional YAML configuration files to customize the topology generation process.

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

The 'topo' subcommand accepts the following arguments:

• structure: Path to the molecular structure file (e.g., PDB, GRO) for which the topology will be generated.
• import_string: Import string to a topology generation class. This string should specify the full path to a class that inherits from TopoGen and implements the dry_run and run methods. For example: AmberTopoGen.
• --yaml: One or more paths to YAML configuration files. These files will be loaded in the order provided, with later files overriding settings from earlier ones. This allows users to configure various aspects of the topology generation process.
• --work: Path to the work directory for preparing the topology calculations. This option overrides any work directory specified in the YAML configuration files. If not provided, the work directory will be determined by the configuration.

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

cli_topo(args, parser)

Command-line interface function to prepare simulation topology files.

This function serves as the entry point when the user executes the 'topo' subcommand of the Simlify CLI. It receives the parsed command-line arguments and the argument parser object. It initializes a SimlifyConfig object and loads configuration settings from any YAML files provided via the --yaml argument, with later files taking precedence. It then checks if a work directory was specified using the --work option and overrides the work directory in the SimlifyConfig if it was provided. Finally, it calls run_gen_topo to perform the topology generation.

PARAMETER	DESCRIPTION
args	An argparse.Namespace object containing the parsed command-line arguments for the 'topo' subcommand. TYPE: Namespace
parser	The argument parser object for the 'topo' 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:

• structure: Path to the input structure file.
• import_string: Import string for the topology generation class.
• yaml: A list of paths to YAML configuration files.
• work: Optional path to the work directory.

It initializes a SimlifyConfig, loads YAML configurations, overrides the work directory if provided, and then calls run_gen_topo with the structure path, import string, and the configured SimlifyConfig object.