Run

SimulationRunPrep()

Bases: ABC

Standardized framework for preparing molecular simulation runs.

get_stage_input_lines(context) abstractmethod classmethod

Prepare input file lines for a single stage.

PARAMETER	DESCRIPTION
context	Specifies options and parameters. TYPE: dict[str, Any]

RETURNS	DESCRIPTION
Collection[str]	Input file lines for a single simulations. The lines do not end in \n.

get_stage_run_command(context) abstractmethod classmethod

Prepare bash command to run a single simulation.

PARAMETER	DESCRIPTION
context	Specifies options and parameters. TYPE: dict[str, Any]

RETURNS	DESCRIPTION
Collection[str]	Bash commands in a list to run one stage of a simulation.

Notes:

prepare_context should be ran before this.

prepare(simulation_context) classmethod

Run all steps to prepare simulations.

PARAMETER	DESCRIPTION
simulation_context	Context manager for simulations. TYPE: SimulationContextManager

prepare_context(simulation_context) abstractmethod staticmethod

Prepare bash command to run a single simulation. This is unique to each simulation package and can be customized based on the context.

PARAMETER	DESCRIPTION
simulation_context	Specifies options and parameters for preparing run bash command. TYPE: SimulationContextManager

RETURNS	DESCRIPTION
SimulationContextManager	Bash commands in a list to run one stage of a simulation.

Examples:

TODO:

prepare_slurm_lines(context, write=True) classmethod

Prepare slurm submission script lines.

PARAMETER	DESCRIPTION
context	Specifies options and parameters. TYPE: dict[str, Any]

prepare_stage(context, run_commands=None, write=True) classmethod

cli_run_simulation_slurm_prep()

Command-line interface preparing files for running simulations using slurm.

run_simulation_slurm_prep(job_name, write_dir, run_path, slurm_path, prep_class_string, simulation_context)

Run tleap preparation of a system.

PARAMETER	DESCRIPTION
job_name	Unique label for these simulations. TYPE: str
write_dir	Path to local directory where we will write the simulation files. TYPE: str
run_path	Path to write a bash file that runs all simulations prepared here. TYPE: str
slurm_path	Path to write slurm submission script. TYPE: str
prep_class_string	String to a simulation preparation class. For example, "metalflare.simulation.amber.run.AmberRunPrep". TYPE: str
simulation_context	Context manager for simulations. TYPE: SimulationContextManager