Variables
BooleanOptionKey const	run ("run")

FileVectorOptionKey const	batches ("run:batches")

BooleanOptionKey const	no_prof_info_in_silentout ("run:no_prof_info_in_silentout")

BooleanOptionKey const	archive ("run:archive")

IntegerOptionKey const	n_replica ("run:n_replica")

BooleanOptionKey const	shuffle ("run:shuffle")

IntegerOptionKey const	n_cycles ("run:n_cycles")

IntegerOptionKey const	repeat ("run:repeat")

IntegerOptionKey const	max_min_iter ("run:max_min_iter")

IntegerOptionKey const	maxruntime ("run:maxruntime")

BooleanOptionKey const	write_failures ("run:write_failures")

BooleanOptionKey const	benchmark ("run:benchmark")

BooleanOptionKey const	test_cycles ("run:test_cycles")

BooleanOptionKey const	memory_test_cycles ("run:memory_test_cycles")

BooleanOptionKey const	dry_run ("run:dry_run")

BooleanOptionKey const	debug ("run:debug")

BooleanOptionKey const	profile ("run:profile")

IntegerOptionKey const	max_retry_job ("run:max_retry_job")

BooleanOptionKey const	version ("run:version")

BooleanOptionKey const	nodelay ("run:nodelay")

IntegerOptionKey const	delay ("run:delay")

IntegerOptionKey const	random_delay ("run:random_delay")

BooleanOptionKey const	timer ("run:timer")

StringOptionKey const	chain ("run:chain")

BooleanOptionKey const	score_only ("run:score_only")

BooleanOptionKey const	decoystats ("run:decoystats")

BooleanOptionKey const	output_hbond_info ("run:output_hbond_info")

RealOptionKey const	wide_nblist_extension ("run:wide_nblist_extension")

BooleanOptionKey const	constant_seed ("run:constant_seed")

IntegerOptionKey const	jran ("run:jran")

BooleanOptionKey const	use_time_as_seed ("run:use_time_as_seed")

StringOptionKey const	rng_seed_device ("run:rng_seed_device")

IntegerOptionKey const	seed_offset ("run:seed_offset")

StringOptionKey const	rng ("run:rng")

BooleanOptionKey const	rebuild_disulf ("run:rebuild_disulf")

BooleanOptionKey const	preserve_header ("run:preserve_header")

BooleanOptionKey const	suppress_checkpoints ("run:suppress_checkpoints")

BooleanOptionKey const	checkpoint ("run:checkpoint")

BooleanOptionKey const	delete_checkpoints ("run:delete_checkpoints")

IntegerOptionKey const	checkpoint_interval ("run:checkpoint_interval")

StringOptionKey const	protocol ("run:protocol")

BooleanOptionKey const	remove_ss_length_screen ("run:remove_ss_length_screen")

StringOptionKey const	min_type ("run:min_type")

RealOptionKey const	min_tolerance ("run:min_tolerance")

BooleanOptionKey const	nblist_autoupdate ("run:nblist_autoupdate")

RealOptionKey const	nblist_autoupdate_narrow ("run:nblist_autoupdate_narrow")

RealOptionKey const	nblist_autoupdate_wide ("run:nblist_autoupdate_wide")

BooleanOptionKey const	skip_set_reasonable_fold_tree ("run:skip_set_reasonable_fold_tree")

BooleanOptionKey const	randomize_missing_coords ("run:randomize_missing_coords")

BooleanOptionKey const	ignore_zero_occupancy ("run:ignore_zero_occupancy")

IntegerOptionKey const	cycles_outer ("run:cycles_outer")

IntegerOptionKey const	cycles_inner ("run:cycles_inner")

IntegerOptionKey const	repack_rate ("run:repack_rate")

BooleanOptionKey const	reinitialize_mover_for_each_job ("run:reinitialize_mover_for_each_job")

BooleanOptionKey const	reinitialize_mover_for_new_input ("run:reinitialize_mover_for_new_input")

BooleanOptionKey const	multiple_processes_writing_to_one_directory ("run:multiple_processes_writing_to_one_directory")

StringOptionKey const	jobdist_miscfile_ext ("run:jobdist_miscfile_ext")

BooleanOptionKey const	no_scorefile ("run:no_scorefile")

BooleanOptionKey const	other_pose_to_scorefile ("run:other_pose_to_scorefile")

FileOptionKey const	other_pose_scorefile ("run:other_pose_scorefile")

BooleanOptionKey const	intermediate_scorefiles ("run:intermediate_scorefiles")

BooleanOptionKey const	intermediate_structures ("run:intermediate_structures")

BooleanOptionKey const	idealize_before_protocol ("run:idealize_before_protocol")

BooleanOptionKey const	interactive ("run:interactive")

BooleanOptionKey const	condor ("run:condor")

IntegerOptionKey const	nproc ("run:nproc")

IntegerOptionKey const	proc_id ("run:proc_id")

BooleanOptionKey const	exit_if_missing_heavy_atoms ("run:exit_if_missing_heavy_atoms")

RealOptionKey const	show_simulation_in_pymol ("run:show_simulation_in_pymol")

BooleanOptionKey const	update_pymol_on_energy_changes_only ("run:update_pymol_on_energy_changes_only")

BooleanOptionKey const	update_pymol_on_conformation_changes_only ("run:update_pymol_on_conformation_changes_only")

BooleanOptionKey const	keep_pymol_simulation_history ("run:keep_pymol_simulation_history")