Wizard

CUR_PATH = os.path.abspath(os.path.dirname(__file__)) module-attribute

PYTHON_EXE = os.path.abspath(sys.executable) module-attribute

STEP_NUM = 1 module-attribute

TEST_MODE = False module-attribute

YAML_LOADER = yaml.SafeLoader module-attribute

check_pocket(westcfg)

Asks user to check the binding pocket.

PARAMETER	DESCRIPTION
westcfg	contents of the west.cfg file as a string. TYPE: str

RETURNS	DESCRIPTION
str	updated west.cfg file as a string. TYPE: str

define_adaptive_bins(adaptivepy, pcoord)

Asks user to define the adaptive bins.

PARAMETER	DESCRIPTION
adaptivepy	contents of the adaptive.py file as a string. TYPE: str
pcoord	progress coordinate to use. TYPE: str

RETURNS	DESCRIPTION
str	updated adaptive.py file as a string. TYPE: str

define_pocket(westcfg)

Asks user to define the binding pocket.

PARAMETER	DESCRIPTION
westcfg	contents of the west.cfg file as a string. TYPE: str

RETURNS	DESCRIPTION
str	updated west.cfg file as a string. TYPE: str

get_prelim_sim_files(engine)

Asks user for preliminary (equilibrated) simulation files.

PARAMETER	DESCRIPTION
engine	MD engine to use. "amber" or "namd" TYPE: str

get_sim_last_frame()

Asks user for the last frame of the preliminary simulation.

get_step_num()

Returns current step number.

RETURNS	DESCRIPTION
str	Current step number. TYPE: str

pick_pcoord(westcfg)

Asks user to pick a progress coordinate.

PARAMETER	DESCRIPTION
westcfg	contents of the west.cfg file as a string. TYPE: str

RETURNS	DESCRIPTION
str	Tuple[str, str]: Tuple containing the updated west.cfg file as a string
str	and the progress coordinate name.

run_init()

Runs the init.sh script to initialize the SubPEx run.

RETURNS	DESCRIPTION
str	contents of the west.cfg file as a string. TYPE: str

run_wizard()

specify_number_iterations(westcfg)

Asks user to specify the number of iterations.

PARAMETER	DESCRIPTION
westcfg	contents of the west.cfg file as a string. TYPE: str

RETURNS	DESCRIPTION
str	updated west.cfg file as a string. TYPE: str

update_envsh(envsh, engine)

Asks user to update the env.sh file.

PARAMETER	DESCRIPTION
envsh	contents of the env.sh file as a string. TYPE: str
engine	engine to use. TYPE: str

RETURNS	DESCRIPTION
str	updated env.sh file as a string. TYPE: str

update_run_time_and_job_name(westcfg)

Asks user to update the run time and job name.

PARAMETER	DESCRIPTION
westcfg	contents of the west.cfg file as a string. TYPE: str

RETURNS	DESCRIPTION
str	updated west.cfg file as a string. TYPE: str

update_westcfg_path_vars(westcfg)

Updates the path variables in the west.cfg file.

PARAMETER	DESCRIPTION
westcfg	contents of the west.cfg file as a string. TYPE: str

RETURNS	DESCRIPTION
str	updated west.cfg file as a string. TYPE: str