NativeEnsemble Class Reference

Inheritance diagram for NativeEnsemble:

Public Member Functions
	NativeEnsemble ()
void	apply (Pose &pose)
string	get_name () const
MoverOP	fresh_instance () const
void	set_loop (Loop loop)
void	set_loop (IndexList values)
void	set_algorithm (string value)
void	set_iterations (Size value)
void	set_temperature (Real value)
void	set_weights (Real bb, Real sc)
void	set_weights (IndexList values)
void	set_dump_frequency (Size value)
void	set_input_file (string value)
void	set_description (string value)
void	set_quiet (bool value)

Static Public Member Functions
static void	register_options ()

Private Member Functions
void	show_header () const
void	show_progress (Size current_iteration) const
void	show_footer () const
void	write_schema_to_db () const
Size	write_job_to_db () const
void	write_stop_time_to_db (Size id) const
void	write_temperatures_to_db (Size id, TemperatureControllerCOP tc) const
void	write_stats_to_db (Size id, MultiTempTrialCounterCOP counter) const
bool	ok_to_use_db () const

Private Attributes
Loop	loop_
string	algorithm_
Size	iterations_
Real	temperature_
Real	backbone_weight_
Real	sidechain_weight_
Size	dump_frequency_
string	input_file_
string	description_
bool	quiet_

Constructor & Destructor Documentation

NativeEnsemble()

NativeEnsemble::NativeEnsemble ( )

inline

Member Function Documentation

apply()

void NativeEnsemble::apply

(

Pose &

pose

)

References basic::options::OptionKeys::coupled_moves::backbone_mover, create_a3b_hbs::i, basic::options::OptionKeys::magnesium::monte_carlo, basic::options::OptionKeys::MonteCarlo::MonteCarlo, beta_nonlocal::pose, basic::options::OptionKeys::packing::prevent_repacking, basic::options::OptionKeys::dna::specificity::score_function, select_loop_residues(), utility_exit_with_message, and write_schema_to_db().

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

fresh_instance()

MoverOP NativeEnsemble::fresh_instance ( ) const

inline

get_name()

string NativeEnsemble::get_name ( ) const

inline

ok_to_use_db()

bool NativeEnsemble::ok_to_use_db ( ) const

private

References basic::options::OptionKeys::legacy_sewing::rank.

register_options()

void NativeEnsemble::register_options ( )

static

References register_options().

Referenced by main().

set_algorithm()

void NativeEnsemble::set_algorithm ( string  value )

inline

References value.

set_description()

void NativeEnsemble::set_description ( string  value )

inline

References value.

set_dump_frequency()

void NativeEnsemble::set_dump_frequency ( Size  value )

inline

References value.

set_input_file()

void NativeEnsemble::set_input_file ( string  value )

inline

References value.

set_iterations()

void NativeEnsemble::set_iterations ( Size  value )

inline

References value.

set_loop() [1/2]

void NativeEnsemble::set_loop ( IndexList  values )

inline

References set_loop(), and test.T040_Types::values.

Referenced by set_loop().

set_loop() [2/2]

void NativeEnsemble::set_loop ( Loop  loop )

inline

References internal_coordinates::loop.

set_quiet()

void NativeEnsemble::set_quiet ( bool  value )

inline

References value.

set_temperature()

void NativeEnsemble::set_temperature ( Real  value )

inline

References value.

set_weights() [1/2]

void NativeEnsemble::set_weights ( IndexList  values )

inline

References set_weights(), and test.T040_Types::values.

Referenced by set_weights().

set_weights() [2/2]

void NativeEnsemble::set_weights ( Real  bb, Real  sc  )

inline

References basic::options::OptionKeys::canonical_sampling::probabilities::sc.

show_footer()

void NativeEnsemble::show_footer ( ) const

private

References utility::io::oc::cerr.

show_header()

void NativeEnsemble::show_header ( ) const

private

References tr.

show_progress()

void NativeEnsemble::show_progress ( Size  current_iteration ) const

private

References utility::io::oc::cerr.

write_job_to_db()

Size NativeEnsemble::write_job_to_db ( ) const

private

References execute::command, basic::database::get_db_session(), kic_runner::job_id, option, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), and rna_rosetta_ready_set::start_time.

write_schema_to_db()

void NativeEnsemble::write_schema_to_db ( ) const

private

References basic::database::schema_generator::Schema::add_column(), execute::command, score_vs_rmsd::frames, basic::database::get_db_session(), input_file, autocorrelation::iterations, kic_runner::job_id, demo.D060_Folding::jobs, basic::options::OptionKeys::out::level, demo.D080_Loop_modeling::loop_begin, pivot_selection::loop_end, utility::tools::make_vector1(), local::num_trials, rna_rosetta_ready_set::start_time, local::temperature, and basic::database::schema_generator::Schema::write().

write_stats_to_db()

void NativeEnsemble::write_stats_to_db ( Size  id, MultiTempTrialCounterCOP  counter  ) const

private

References demo.D060_Folding::counter, basic::database::get_db_session(), local::num_trials, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), and tag.

write_stop_time_to_db()

void NativeEnsemble::write_stop_time_to_db ( Size  id ) const

private

References basic::database::get_db_session(), basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

write_temperatures_to_db()

void NativeEnsemble::write_temperatures_to_db ( Size  id, TemperatureControllerCOP  tc  ) const

private

References basic::database::get_db_session(), basic::options::OptionKeys::out::level, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Member Data Documentation

algorithm_

string NativeEnsemble::algorithm_

private

backbone_weight_

Real NativeEnsemble::backbone_weight_

private

description_

string NativeEnsemble::description_

private

dump_frequency_

Size NativeEnsemble::dump_frequency_

private

input_file_

string NativeEnsemble::input_file_

private

iterations_

Size NativeEnsemble::iterations_

private

loop_

Loop NativeEnsemble::loop_

private

quiet_

bool NativeEnsemble::quiet_

private

sidechain_weight_

Real NativeEnsemble::sidechain_weight_

private

temperature_

Real NativeEnsemble::temperature_

private

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The documentation for this class was generated from the following file:

• src/apps/pilot/kale/native_ensemble/native_ensemble.cc