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cli_run_westpa_setup()

Run the WESTPA setup for SubPEx purposes.

This function initializes the WESTPA simulation for SubPEx purposes by parsing command line arguments, loading JSON settings file, and running the WESTPA setup with the provided configurations.

PARAMETER	DESCRIPTION
--write_dir	Directory to write input files. TYPE: str
--yaml_subpex	Paths to YAML files to use for subpex config in decreasing precedence. TYPE: List[str]
--yaml_westpa	Paths to YAML files to use for westpa config in decreasing precedence. TYPE: List[str]
--overwrite	Flag to overwrite files in write_dir. TYPE: bool

RETURNS	DESCRIPTION
	None

create_westpa_dirs(write_dir='', overwrite=False)

Create necessary WESTPA directories.

PARAMETER	DESCRIPTION
write_dir	The directory where the WESTPA directories will be created. Defaults to an empty string. TYPE: str DEFAULT: ''
overwrite	If True, existing directories will be overwritten. Defaults to False. TYPE: bool DEFAULT: False

RETURNS	DESCRIPTION
dict[str, str]	dict[str, str]: A dictionary containing the paths of the created directories.

link_initial_sims(subpex_config, westpa_config, write_dir='', *args, **kwargs)

WESTPA starts from a relaxed molecular simulation using the same MD engine. Instead of copying the preliminary simulation files, we create a soft link to the relevant files.

run_westpa_setup(subpex_config, westpa_config, write_dir='', overwrite=False)

Run the setup process for WESTPA.

PARAMETER	DESCRIPTION
subpex_config	The configuration for the Subpex module. TYPE: SubpexConfig
westpa_config	The configuration for the WESTPA module. TYPE: WestpaConfig
write_dir	The directory to write the setup files to. Defaults to "". TYPE: str DEFAULT: ''
overwrite	Whether to overwrite the existing directory if it exists. Defaults to False. TYPE: bool DEFAULT: False

write_westpa_bash_scripts(subpex_config, westpa_config, write_dir='', *args, **kwargs)

Write WESTPA bash scripts based on the provided configurations.

PARAMETER	DESCRIPTION
subpex_config	The configuration for Subpex. TYPE: SubpexConfig
westpa_config	The configuration for WESTPA. TYPE: WestpaConfig
write_dir	The directory where the scripts will be written. Defaults to "". TYPE: str DEFAULT: ''
*args	Additional positional arguments. TYPE: Any DEFAULT: ()
**kwargs	Additional keyword arguments. TYPE: dict[str, Any] DEFAULT: {}