run Namespace Reference

Namespaces
	PyMOLMover

Functions
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")
RealOptionKey const	maxruntime_bufferfactor ("run:maxruntime_bufferfactor")
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	nosignal ("run:nosignal")
BooleanOptionKey const	crash_to_console ("run:crash_to_console")
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")

Function Documentation

archive()

BooleanOptionKey const run::archive

(

"run:archive"

)

batches()

FileVectorOptionKey const run::batches

(

"run:batches"

)

benchmark()

BooleanOptionKey const run::benchmark

(

"run:benchmark"

)

chain()

StringOptionKey const run::chain

(

"run:chain"

)

Referenced by HDmakerMover::HDmakerMover().

checkpoint()

BooleanOptionKey const run::checkpoint

(

"run:checkpoint"

)

Referenced by main().

checkpoint_interval()

IntegerOptionKey const run::checkpoint_interval

(

"run:checkpoint_interval"

)

Referenced by main().

condor()

BooleanOptionKey const run::condor

(

"run:condor"

)

constant_seed()

BooleanOptionKey const run::constant_seed

(

"run:constant_seed"

)

Referenced by basic::random::RandomGeneratorSettings::initialize_from_options(), basic::random::RandomGeneratorSettings::list_options_read(), and basic::options::pre_tracer_process().

crash_to_console()

BooleanOptionKey const run::crash_to_console

(

"run:crash_to_console"

)

cycles_inner()

IntegerOptionKey const run::cycles_inner

(

"run:cycles_inner"

)

cycles_outer()

IntegerOptionKey const run::cycles_outer

(

"run:cycles_outer"

)

debug()

BooleanOptionKey const run::debug

(

"run:debug"

)

Referenced by main(), SuperDeviationMover::print_stats(), and SpartaSuperDeviationMover::print_stats().

decoystats()

BooleanOptionKey const run::decoystats

(

"run:decoystats"

)

delay()

IntegerOptionKey const run::delay

(

"run:delay"

)

delete_checkpoints()

BooleanOptionKey const run::delete_checkpoints

(

"run:delete_checkpoints"

)

dry_run()

BooleanOptionKey const run::dry_run

(

"run:dry_run"

)

exit_if_missing_heavy_atoms()

BooleanOptionKey const run::exit_if_missing_heavy_atoms

(

"run:exit_if_missing_heavy_atoms"

)

idealize_before_protocol()

BooleanOptionKey const run::idealize_before_protocol

(

"run:idealize_before_protocol"

)

Referenced by main().

ignore_zero_occupancy()

BooleanOptionKey const run::ignore_zero_occupancy

(

"run:ignore_zero_occupancy"

)

Referenced by main().

interactive()

BooleanOptionKey const run::interactive

(

"run:interactive"

)

intermediate_scorefiles()

BooleanOptionKey const run::intermediate_scorefiles

(

"run:intermediate_scorefiles"

)

intermediate_structures()

BooleanOptionKey const run::intermediate_structures

(

"run:intermediate_structures"

)

jobdist_miscfile_ext()

StringOptionKey const run::jobdist_miscfile_ext

(

"run:jobdist_miscfile_ext"

)

jran()

IntegerOptionKey const run::jran

(

"run:jran"

)

Referenced by basic::random::RandomGeneratorSettings::initialize_from_options(), and basic::random::RandomGeneratorSettings::list_options_read().

keep_pymol_simulation_history()

BooleanOptionKey const run::keep_pymol_simulation_history

(

"run:keep_pymol_simulation_history"

)

max_min_iter()

IntegerOptionKey const run::max_min_iter

(

"run:max_min_iter"

)

Referenced by MinCenrotMover::apply(), CenRotRelaxMover::apply(), RepackMinCenrotMover::apply(), and CenRotRBRelaxMover::apply().

max_retry_job()

IntegerOptionKey const run::max_retry_job

(

"run:max_retry_job"

)

maxruntime()

IntegerOptionKey const run::maxruntime

(

"run:maxruntime"

)

maxruntime_bufferfactor()

RealOptionKey const run::maxruntime_bufferfactor

(

"run:maxruntime_bufferfactor"

)

memory_test_cycles()

BooleanOptionKey const run::memory_test_cycles

(

"run:memory_test_cycles"

)

min_tolerance()

RealOptionKey const run::min_tolerance

(

"run:min_tolerance"

)

min_type()

StringOptionKey const run::min_type

(

"run:min_type"

)

Referenced by main(), and simple_opte_test().

multiple_processes_writing_to_one_directory()

BooleanOptionKey const run::multiple_processes_writing_to_one_directory

(

"run:multiple_processes_writing_to_one_directory"

)

n_cycles()

IntegerOptionKey const run::n_cycles

(

"run:n_cycles"

)

Referenced by main().

n_replica()

IntegerOptionKey const run::n_replica

(

"run:n_replica"

)

nblist_autoupdate()

BooleanOptionKey const run::nblist_autoupdate

(

"run:nblist_autoupdate"

)

nblist_autoupdate_narrow()

RealOptionKey const run::nblist_autoupdate_narrow

(

"run:nblist_autoupdate_narrow"

)

nblist_autoupdate_wide()

RealOptionKey const run::nblist_autoupdate_wide

(

"run:nblist_autoupdate_wide"

)

no_prof_info_in_silentout()

BooleanOptionKey const run::no_prof_info_in_silentout

(

"run:no_prof_info_in_silentout"

)

Referenced by basic::options::pre_tracer_process().

no_scorefile()

BooleanOptionKey const run::no_scorefile

(

"run:no_scorefile"

)

nodelay()

BooleanOptionKey const run::nodelay

(

"run:nodelay"

)

Referenced by basic::options::pre_tracer_process().

nosignal()

BooleanOptionKey const run::nosignal

(

"run:nosignal"

)

nproc()

IntegerOptionKey const run::nproc

(

"run:nproc"

)

other_pose_scorefile()

FileOptionKey const run::other_pose_scorefile

(

"run:other_pose_scorefile"

)

other_pose_to_scorefile()

BooleanOptionKey const run::other_pose_to_scorefile

(

"run:other_pose_to_scorefile"

)

output_hbond_info()

BooleanOptionKey const run::output_hbond_info

(

"run:output_hbond_info"

)

preserve_header()

BooleanOptionKey const run::preserve_header

(

"run:preserve_header"

)

proc_id()

IntegerOptionKey const run::proc_id

(

"run:proc_id"

)

profile()

BooleanOptionKey const run::profile

(

"run:profile"

)

protocol()

StringOptionKey const run::protocol

(

"run:protocol"

)

random_delay()

IntegerOptionKey const run::random_delay

(

"run:random_delay"

)

randomize_missing_coords()

BooleanOptionKey const run::randomize_missing_coords

(

"run:randomize_missing_coords"

)

rebuild_disulf()

BooleanOptionKey const run::rebuild_disulf

(

"run:rebuild_disulf"

)

reinitialize_mover_for_each_job()

BooleanOptionKey const run::reinitialize_mover_for_each_job

(

"run:reinitialize_mover_for_each_job"

)

reinitialize_mover_for_new_input()

BooleanOptionKey const run::reinitialize_mover_for_new_input

(

"run:reinitialize_mover_for_new_input"

)

remove_ss_length_screen()

BooleanOptionKey const run::remove_ss_length_screen

(

"run:remove_ss_length_screen"

)

repack_rate()

IntegerOptionKey const run::repack_rate

(

"run:repack_rate"

)

repeat()

IntegerOptionKey const run::repeat

(

"run:repeat"

)

rng()

StringOptionKey const run::rng

(

"run:rng"

)

Referenced by basic::random::RandomGeneratorSettings::initialize_from_options(), and basic::random::RandomGeneratorSettings::list_options_read().

rng_seed_device()

StringOptionKey const run::rng_seed_device

(

"run:rng_seed_device"

)

Referenced by basic::random::RandomGeneratorSettings::initialize_from_options(), and basic::random::RandomGeneratorSettings::list_options_read().

run()

BooleanOptionKey const run::run

(

"run"

)

score_only()

BooleanOptionKey const run::score_only

(

"run:score_only"

)

Referenced by cst_relax_test().

seed_offset()

IntegerOptionKey const run::seed_offset

(

"run:seed_offset"

)

Referenced by basic::random::RandomGeneratorSettings::initialize_from_options(), and basic::random::RandomGeneratorSettings::list_options_read().

show_simulation_in_pymol()

RealOptionKey const run::show_simulation_in_pymol

(

"run:show_simulation_in_pymol"

)

Referenced by stepwise_monte_carlo_legacy().

shuffle()

BooleanOptionKey const run::shuffle

(

"run:shuffle"

)

skip_set_reasonable_fold_tree()

BooleanOptionKey const run::skip_set_reasonable_fold_tree

(

"run:skip_set_reasonable_fold_tree"

)

suppress_checkpoints()

BooleanOptionKey const run::suppress_checkpoints

(

"run:suppress_checkpoints"

)

test_cycles()

BooleanOptionKey const run::test_cycles

(

"run:test_cycles"

)

Referenced by register_options_broker().

timer()

BooleanOptionKey const run::timer

(

"run:timer"

)

Referenced by distribute_jobs().

update_pymol_on_conformation_changes_only()

BooleanOptionKey const run::update_pymol_on_conformation_changes_only

(

"run:update_pymol_on_conformation_changes_only"

)

update_pymol_on_energy_changes_only()

BooleanOptionKey const run::update_pymol_on_energy_changes_only

(

"run:update_pymol_on_energy_changes_only"

)

use_time_as_seed()

BooleanOptionKey const run::use_time_as_seed

(

"run:use_time_as_seed"

)

Referenced by basic::random::RandomGeneratorSettings::initialize_from_options(), and basic::random::RandomGeneratorSettings::list_options_read().

version()

BooleanOptionKey const run::version

(

"run:version"

)

wide_nblist_extension()

RealOptionKey const run::wide_nblist_extension

(

"run:wide_nblist_extension"

)

write_failures()

BooleanOptionKey const run::write_failures

(

"run:write_failures"

)