Prep

SimPrep()

Bases: ABC

Standardized framework for preparing files for molecular simulation runs.

get_stage_input_lines(simlify_config)

Prepare input file lines for a single stage.

PARAMETER	DESCRIPTION
context	Specifies options and parameters.

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

get_stage_run_command(simlify_config)

Prepare bash command to run a single simulation.

PARAMETER	DESCRIPTION
context	Specifies options and parameters.

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

Notes

prepare_sim_config should be ran before this.

prepare(simlify_config)

Run all steps to prepare simulations.

PARAMETER	DESCRIPTION
simlify_config	Simlify configuration. TYPE: SimlifyConfig

prepare_sim_config(simlify_config)

Preprocessing and validation of a simulation context. This is unique to each simulation package and can be customized based on the context.

PARAMETER	DESCRIPTION
simlify_config	Specifies options and parameters. TYPE: SimlifyConfig

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

prepare_slurm(file_path, simlify_config, write=True)

Prepare slurm submission script lines.

PARAMETER	DESCRIPTION
context	Specifies options and parameters.

prepare_stage(simlify_config, run_commands=None, write=True)

cli_run_sim_slurm_prep()

Command-line interface to prepare files for simulations using slurm.

run_sim_slurm_prep(name_job, dir_work, path_run_write, path_slurm_write, prep_class_string, simlify_config)

Prepare files for simulations using slurm.

PARAMETER	DESCRIPTION
name_job	Unique name for this slurm job. TYPE: str
dir_work	Path to local directory where we will write the simulation files. TYPE: str
path_run_write	Local path to write a run script with respect to dir_write. TYPE: str
path_slurm_write	Local path to write a slurm submission script with respect to dir_write. TYPE: str
prep_class_string	Import string to a simulation preparation class. For example, "simlify.simulation.amber.prep.AmberSimPrep". TYPE: str
simlify_config	Simlify configuration. TYPE: SimlifyConfig