GenericSimulatedAnnealer mover for performing simulated annealing trajectories. More...

#include <GenericSimulatedAnnealer.hh>

Inheritance diagram for protocols::monte_carlo::GenericSimulatedAnnealer:

Public Member Functions
	GenericSimulatedAnnealer ()
	default constructor More...

	~GenericSimulatedAnnealer () override
	destructor More...

protocols::moves::MoverOP	clone () const override
	create copy constructor More...

protocols::moves::MoverOP	fresh_instance () const override
	create this type of objectt More...

void	apply (Pose &pose) override
	apply GenericSimulatedAnnealer (Mover) More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	XML interface to this mover. More...

virtual void	reset (Pose &pose)
	Clears accepted data and initialize with new pose. More...

AcceptedScores	score_pose (core::pose::Pose const &pose) const
	given a pose, score the result More...

void	save_checkpoint_file () const
	Saves the current state of the mover into checkpoint files. More...

void	remove_checkpoint_file () const
	Deletes the checkpoint files. More...

bool	checkpoint_exists () const
	tests to see if the checkpoint files exist and have been generated More...

AcceptedScores const &	accepted_scores (core::Size const i) const
	gets a list of scores for acceptance number i More...

core::Size	num_accepted_scores () const
	number of acceptances More...

core::Real	calc_boltz_score (utility::vector1< core::Real > const &scores) const
	if boltz_rank is used, this will calculate the ranking score from a list of filter scores More...

std::string	create_tag (std::string const &suffix) const
	create a silent struct tag for checkpointing with the given suffix More...

void	load_checkpoint_file (core::pose::Pose &pose)
	loads checkpoint data and attempts to resume a run with pose as the pose More...

void	checkpoint_file (std::string const &check_file)
	set the checkpoint file name More...

void	keep_checkpoint_file (bool const keep_checkpoint)
	sets whether or not to delete checkpoint files when done – useful for debugging More...

void	scale_temperatures (core::Real const temp_factor)
	scales temperatures by the factor provided More...

TrialResult	boltzmann_result (core::pose::Pose &pose)
	given a modified pose, determines whether we should accept or not, and updates internal class data accordingly uses randomly generated numbers to assess acceptance of scores with temperatures More...

TrialResult	boltzmann_result (core::pose::Pose &pose, utility::vector1< core::Real > const &random_nums)
	given a modified pose, determines whether we should accept or not, and updates internal class data accordingly More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::monte_carlo::GenericMonteCarloMover
	GenericMonteCarloMover ()
	default constructor More...

	GenericMonteCarloMover (core::Size const maxtrials, core::Size const max_accepted_trials, core::Size const task_scaling, MoverOP const &mover, Real const temperature=0.0, String const &sample_type="low", bool const drift=true)
	value constructor without score function More...

	GenericMonteCarloMover (core::Size const maxtrials, core::Size const max_accepted_trials, core::Size const task_scaling, MoverOP const &mover, TaskFactoryOP factory_in, Real const temperature=0.0, String const &sample_type="low", bool const drift=true)
	value constructor with score function More...

	~GenericMonteCarloMover () override
	destructor More...

void	initialize ()
	initialize object used in constructor More...

void	reset (Pose &pose)
	reset MC iterations, with pose used for the last & best structures More...

void	recover_low (Pose &pose)
	return the simulation state to the lowest energy structure we've seen More...

bool	boltzmann (Pose &pose)
	core of MC More...

virtual bool	boltzmann (Pose &pose, utility::vector1< core::Real > const &random_nums)
	core of MC – evaulates a pose based on the scores/filters + temperatures. random_num is a vector of random numbers between 0 and 1 with size equal to the number of MC criteria More...

void	accept (Pose &pose, utility::vector1< core::Real > const &provisional_scores, protocols::moves::MCA const mca_status)
	Does what the mover needs to do when a pose is accepted, given a pose and scores. More...

core::Size	num_designable (Pose &pose, PackerTaskOP &task)

PoseOP	last_accepted_pose () const
	return the last accepted pose More...

Real	last_accepted_score () const
	return the last accepted score More...

PoseOP	lowest_score_pose () const
	return the lowest score pose More...

Real	lowest_score () const
	return the lowest score More...

Real	current_score () const
	return the lowest score More...

protocols::moves::MCA	mc_accpeted () const
	return mc_accepted More...

ScoreFunctionOP	score_function () const
	Return the score function in use. More...

core::Size	add_trigger (const GenericMonteCarloMoverTrigger &trigger)
	Adds a new trigger, returning its id. More...

core::Size	num_triggers () const
	Returns the number of triggers. More...

core::Size	maxtrials () const
	Returns maximum number of trials. More...

core::Size	max_accepted_trials () const
	Returns maximum number of accepted trials. More...

core::Size	task_scaling () const
	Returns the task scaling value. More...

void	remove_trigger (core::Size trigger_id)
	Removes the trigger with the specified id. More...

void	set_maxtrials (core::Size const ntrial)
	set max trials of MC trials More...

void	set_max_accepted_trials (core::Size const n_max_accepted_trial)
	set max accepted trials of MC trials More...

void	set_task_scaling (core::Size const scaling)
	set task multiplier to calculate trials from task More...

void	set_mover (MoverOP mover) override
	set mover More...

void	set_scorefxn (ScoreFunctionOP const &sfxn)
	Pose is evaluated by ScoreFunctionOP during MC trials. More...

void	set_temperature (Real const temp)
	set temperature More...

void	set_sampletype (String const &type)
	set sample type, max or min when sample_type == max, sample pose which have higher score when sample_type == min, sample pose which have lower score More...

void	set_drift (bool const drift)
	if drift=false, the pose is set back to the initial pose at each MC trial Of course, this is not MC sampling. More...

void	set_stop_sampling (bool const stop_sampling)
	if set to true, the MC mover will stop sampling More...

void	set_preapply (bool const preapply=false)
	if preapply=true, auto-accept the first application of the submover, ignoring boltzman criteria. More...

void	set_recover_low (bool const recover_low)
	if recover_low=true, after apply() the structure is the lowest energy structure, rather than the last accepted structure. More...

void	set_boltz_rank (bool const boltz_rank)
	if boltz_rank=true, rank structures by the temperature-weighted sum of scores, rather than a single filter More...

void	show_scores (std::ostream &out) const
	show scores of last_accepted_score and "best_score" ( = flip_sign_ * lowest_score ) More...

void	show_counters (std::ostream &out) const
	show counters of ntrial and acceptance ratio More...

virtual void	parse_task_operations (TagCOP, basic::datacache::DataMap const &)
	parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...

void	add_filter (FilterOP filter, bool const adaptive, Real const temp, String const &sample_type, bool rank_by=false)
	set filter Pose is evaluated by FilterOP which can do report_sm() or ScoreFunctionOP during MC trials You can choose either way FilterOP or ScoreFunction. More...

void	stopping_condition (protocols::filters::FilterOP filter)

protocols::filters::FilterOP	stopping_condition () const

void	adaptive_movers (bool const a)

bool	adaptive_movers () const

void	adaptation_period (core::Size const a)

core::Size	adaptation_period () const

std::string	saved_accept_file_name () const

void	saved_accept_file_name (std::string const )

std::string	saved_trial_number_file () const

void	saved_trial_number_file (std::string const )

core::Size	load_trial_number_from_checkpoint (core::pose::Pose &)

void	save_trial_number_to_checkpoint (core::Size const i) const

void	reset_baselines (bool const r)

bool	reset_baselines () const

void	set_keep_filters (bool const k)

bool	keep_filters () const

void	task_factory (core::pack::task::TaskFactoryOP tf)

core::pack::task::TaskFactoryOP	task_factory () const

core::Size	trial_counter () const

void	trial_counter (core::Size const i)

core::Size	accept_counter () const

utility::vector1< Real >	temperatures () const

void	temperatures (utility::vector1< Real > const &temps)

bool	recover_low () const

MoverOP	mover () const override

utility::vector1< FilterOP > const &	filters () const

utility::vector1< bool > const &	adaptive () const

utility::vector1< core::Size > const &	num_rejections () const

ScoreFunctionOP	scorefxn () const

utility::pointer::shared_ptr < basic::datacache::DataMapObj < bool > >	mover_stopping_condition () const

bool	preapply () const

bool	drift () const

bool	stop_sampling () const

bool	boltz_rank () const

utility::vector1< String > const &	sample_types () const

utility::vector1< core::Real > const &	last_accepted_scores () const

void	last_accepted_scores (utility::vector1< core::Real > const &scores)

utility::vector1< core::Real > const &	last_tested_scores () const

utility::vector1< core::Real > const &	lowest_scores () const

void	lowest_scores (utility::vector1< core::Real > const &scores)

void	lowest_score (core::Real const score)

void	last_accepted_score (core::Real const score)

void	lowest_score_pose (core::pose::PoseOP pose)
	Set the lowest scoring pose. More...

void	last_accepted_pose (core::pose::PoseOP pose)
	Set the last pose that was accepted. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from protocols::moves::MoverApplyingMover
	MoverApplyingMover (std::string const &name)

	MoverApplyingMover (MoverApplyingMover const &)=default

	~MoverApplyingMover () override=default

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::monte_carlo::GenericMonteCarloMover
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static utility::tag::XMLSchemaComplexTypeGeneratorOP	define_composition_schema (utility::tag::XMLSchemaDefinition &)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
TrialResult	apply_mover (core::pose::Pose &pose)
	calls a round of monte carlo – basically copied from GenericMonteCarloMover More...

void	calculate_temps ()
	computes the appropriately scaled temperatures and sets them More...

utility::vector1< core::Real >	calculate_standardized_scores (core::Size const filterid) const

core::Real	calc_temp_factor () const
	calculates multiplier for temperatures based on which anneal step we are no More...

AcceptedScores	read_checkpoint_line (std::istream &is) const

void	recompute_rank_scores ()

Private Attributes
core::Size	history_
	counter for how many accepts it takes to reach equilibrium at a given temperature More...

protocols::moves::MoverOP	periodic_mover_
	mover to be called every eval_period steps More...

core::Size	eval_period_
	how many steps in between running the periodic mover? More...

std::string	checkpoint_file_
	what name should be used to store checkpoint information so that the run can be resumed? More...

bool	keep_checkpoint_file_
	if true, the checkpoint files will not be cleaned up after the apply() terminates. Useful for debugging/gathering statistics More...

utility::vector1< AcceptedScores >	accepted_scores_
	a history of accepted scores, used for adapting temperature More...

utility::vector1< core::Real >	start_temperatures_
	the initial temperatures, used for adapting temperature More...

core::Size	anneal_step_
	counter that tells which annealing step we are on More...

core::Size	temp_step_
	which step in this temperature are we on More...

core::Size	current_trial_
	what is the current trial number More...

Additional Inherited Members
Public Types inherited from protocols::monte_carlo::GenericMonteCarloMover
typedef std::string	String

typedef core::Size	Size

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef protocols::filters::FilterOP	FilterOP

typedef protocols::moves::MoverOP	MoverOP

typedef core::pack::task::PackerTask	PackerTask

typedef core::pack::task::PackerTaskOP	PackerTaskOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryOP	TaskFactoryOP

typedef protocols::rosetta_scripts::ParsedProtocolOP	ParsedProtocolOP

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::monte_carlo::GenericMonteCarloMover
Real	scoring (Pose &pose)
	evalute pose by ScoreFunctionOP or FilterOP More...

void	fire_all_triggers (core::Size cycle, core::Size num_cycles, const Pose &pose, ScoreFunctionOP scoring)
	Executes all triggers. The order of trigger execution is undefined. Do not assume, depend, or in any way rely on a particular ordering. More...

utility::vector1< core::Real >	generate_random () const
	generate a set of random numbers to accompany the filters or scorefxn More...

std::string	progress_file () const

void	progress_file (std::string const &s)

void	set_mc_accepted (moves::MCA const m)
	Sets mc_accpeted. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Protected Attributes inherited from protocols::monte_carlo::GenericMonteCarloMover
int	trial_counter_ = 0

utility::vector1< core::Size >	num_rejections_
	Count the number of rejections each filter resulted in. More...

Detailed Description

GenericSimulatedAnnealer mover for performing simulated annealing trajectories.

This class extends GenericMonteCarloMover to provide temperature scaling

Constructor & Destructor Documentation

protocols::monte_carlo::GenericSimulatedAnnealer::GenericSimulatedAnnealer ( )

default constructor

References accepted_scores_, and start_temperatures_.

protocols::monte_carlo::GenericSimulatedAnnealer::~GenericSimulatedAnnealer ( )

overridedefault

destructor

Member Function Documentation

AcceptedScores const& protocols::monte_carlo::GenericSimulatedAnnealer::accepted_scores ( core::Size const i ) const

inline

gets a list of scores for acceptance number i

References accepted_scores_.

void protocols::monte_carlo::GenericSimulatedAnnealer::apply ( Pose & pose )

overridevirtual

apply GenericSimulatedAnnealer (Mover)

applies the mover

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

Referenced by boltzmann_result().

TrialResult protocols::monte_carlo::GenericSimulatedAnnealer::apply_mover ( core::pose::Pose & pose )

private

calls a round of monte carlo – basically copied from GenericMonteCarloMover

References boltzmann_result(), protocols::moves::FAIL_BAD_INPUT, protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, protocols::monte_carlo::FAILED, protocols::moves::Mover::get_last_move_status(), protocols::monte_carlo::GenericMonteCarloMover::mover(), protocols::monte_carlo::REJECTED, and protocols::TR().

Referenced by apply().

TrialResult protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result ( core::pose::Pose & pose )

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly uses randomly generated numbers to assess acceptance of scores with temperatures

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly

uses randomly generated numbers to assess acceptance of scores with temperatures

References protocols::monte_carlo::GenericMonteCarloMover::filters(), and core::scoring::rg.

Referenced by apply_mover().

TrialResult protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result	(	core::pose::Pose &	pose,
		utility::vector1< core::Real > const &	random_nums
	)

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly

References protocols::monte_carlo::ACCEPTED, accepted_scores_, apply(), protocols::monte_carlo::GenericMonteCarloMover::boltzmann(), calc_boltz_score(), calculate_temps(), current_trial_, protocols::monte_carlo::FINISHED, protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose(), protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(), protocols::monte_carlo::GenericMonteCarloMover::mover_stopping_condition(), protocols::monte_carlo::REJECTED, protocols::loops::stop, protocols::monte_carlo::GenericMonteCarloMover::stopping_condition(), and protocols::TR().

core::Real protocols::monte_carlo::GenericSimulatedAnnealer::calc_boltz_score ( utility::vector1< core::Real > const & scores ) const

if boltz_rank is used, this will calculate the ranking score from a list of filter scores

References protocols::monte_carlo::GenericMonteCarloMover::filters(), and protocols::monte_carlo::GenericMonteCarloMover::temperatures().

Referenced by boltzmann_result(), recompute_rank_scores(), reset(), save_checkpoint_file(), scale_temperatures(), and score_pose().

core::Real protocols::monte_carlo::GenericSimulatedAnnealer::calc_temp_factor ( ) const

private

calculates multiplier for temperatures based on which anneal step we are no

References anneal_step_, and protocols::monte_carlo::GenericMonteCarloMover::filters().

Referenced by calculate_temps(), and load_checkpoint_file().

utility::vector1< core::Real > protocols::monte_carlo::GenericSimulatedAnnealer::calculate_standardized_scores ( core::Size const filterid ) const

private

References accepted_scores_, core::sequence::end, protocols::monte_carlo::GenericMonteCarloMover::filters(), history_, core::simple_metrics::metrics::mean, and protocols::loops::start.

void protocols::monte_carlo::GenericSimulatedAnnealer::calculate_temps ( )

private

computes the appropriately scaled temperatures and sets them

References accepted_scores_, anneal_step_, calc_temp_factor(), core::sequence::end, protocols::monte_carlo::GenericMonteCarloMover::filters(), history_, protocols::monte_carlo::linear_regression(), scale_temperatures(), protocols::loops::start, temp_step_, and protocols::TR().

Referenced by boltzmann_result().

bool protocols::monte_carlo::GenericSimulatedAnnealer::checkpoint_exists ( ) const

tests to see if the checkpoint files exist and have been generated

References checkpoint_file_.

Referenced by apply().

void protocols::monte_carlo::GenericSimulatedAnnealer::checkpoint_file ( std::string const & check_file )

inline

set the checkpoint file name

References checkpoint_file_.

protocols::moves::MoverOP protocols::monte_carlo::GenericSimulatedAnnealer::clone ( ) const

overridevirtual

create copy constructor

clone this object

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

std::string protocols::monte_carlo::GenericSimulatedAnnealer::create_tag ( std::string const & suffix ) const

create a silent struct tag for checkpointing with the given suffix

References core::pack::dunbrack::c, and checkpoint_file_.

Referenced by load_checkpoint_file(), and save_checkpoint_file().

protocols::moves::MoverOP protocols::monte_carlo::GenericSimulatedAnnealer::fresh_instance ( ) const

overridevirtual

create this type of objectt

create this type of object

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

std::string protocols::monte_carlo::GenericSimulatedAnnealer::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

References mover_name().

void protocols::monte_carlo::GenericSimulatedAnnealer::keep_checkpoint_file ( bool const keep_checkpoint )

inline

sets whether or not to delete checkpoint files when done – useful for debugging

References keep_checkpoint_file_.

void protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file ( core::pose::Pose & pose )

loads checkpoint data and attempts to resume a run with pose as the pose

References accepted_scores_, anneal_step_, calc_temp_factor(), checkpoint_file_, create_tag(), current_trial_, core::io::silent::SilentStruct::fill_pose(), core::io::silent::SilentFileData::get_structure(), core::io::silent::SilentFileData::has_tag(), protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose(), protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(), protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose(), protocols::monte_carlo::GenericMonteCarloMover::lowest_scores(), read_checkpoint_line(), core::io::silent::SilentFileData::read_file(), scale_temperatures(), temp_step_, and protocols::TR().

Referenced by apply().

std::string protocols::monte_carlo::GenericSimulatedAnnealer::mover_name ( )

static

Referenced by get_name(), protocols::monte_carlo::GenericSimulatedAnnealerCreator::keyname(), parse_my_tag(), and provide_xml_schema().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::num_accepted_scores ( ) const

inline

number of acceptances

References accepted_scores_.

void protocols::monte_carlo::GenericSimulatedAnnealer::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

XML interface to this mover.

parse xml file

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

References checkpoint_file_, eval_period_, history_, keep_checkpoint_file_, mover_name(), protocols::rosetta_scripts::parse_mover(), protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag(), and periodic_mover_.

void protocols::monte_carlo::GenericSimulatedAnnealer::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::monte_carlo::GenericMonteCarloMover::define_composition_schema(), and mover_name().

Referenced by protocols::monte_carlo::GenericSimulatedAnnealerCreator::provide_xml_schema().

AcceptedScores protocols::monte_carlo::GenericSimulatedAnnealer::read_checkpoint_line ( std::istream & is ) const

private

References protocols::monte_carlo::GenericMonteCarloMover::filters(), protocols::hybridization::score, and protocols::TR().

Referenced by load_checkpoint_file().

void protocols::monte_carlo::GenericSimulatedAnnealer::recompute_rank_scores ( )

private

References accepted_scores_, and calc_boltz_score().

Referenced by scale_temperatures().

void protocols::monte_carlo::GenericSimulatedAnnealer::remove_checkpoint_file ( ) const

Deletes the checkpoint files.

References checkpoint_file_, and protocols::TR().

Referenced by apply().

void protocols::monte_carlo::GenericSimulatedAnnealer::reset ( Pose & pose )

virtual

Clears accepted data and initialize with new pose.

References accepted_scores_, anneal_step_, calc_boltz_score(), current_trial_, protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(), protocols::monte_carlo::GenericMonteCarloMover::reset(), start_temperatures_, temp_step_, and protocols::monte_carlo::GenericMonteCarloMover::temperatures().

Referenced by apply().

void protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file ( ) const

Saves the current state of the mover into checkpoint files.

References accepted_scores_, core::io::silent::SilentFileData::add_structure_replace_tag_if_necessary(), anneal_step_, calc_boltz_score(), checkpoint_file_, create_tag(), current_trial_, protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose(), protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(), protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose(), protocols::monte_carlo::GenericMonteCarloMover::lowest_scores(), protocols::monte_carlo::replace_file(), temp_step_, core::id::to_string(), and core::io::silent::SilentFileData::write_all().

Referenced by apply().

void protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures ( core::Real const temp_factor )

scales temperatures by the factor provided

References protocols::monte_carlo::GenericMonteCarloMover::boltz_rank(), calc_boltz_score(), protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score(), protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(), protocols::monte_carlo::GenericMonteCarloMover::lowest_score(), protocols::monte_carlo::GenericMonteCarloMover::lowest_scores(), recompute_rank_scores(), start_temperatures_, protocols::monte_carlo::GenericMonteCarloMover::temperatures(), and protocols::TR().

Referenced by calculate_temps(), and load_checkpoint_file().

AcceptedScores protocols::monte_carlo::GenericSimulatedAnnealer::score_pose ( core::pose::Pose const & pose ) const

given a pose, score the result

References calc_boltz_score(), current_trial_, protocols::monte_carlo::GenericMonteCarloMover::filters(), protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(), protocols::monte_carlo::GenericMonteCarloMover::lowest_scores(), protocols::monte_carlo::GenericMonteCarloMover::sample_types(), protocols::monte_carlo::AcceptedScores::set_rank_score(), and protocols::TR().

Referenced by apply().

Member Data Documentation

utility::vector1< AcceptedScores > protocols::monte_carlo::GenericSimulatedAnnealer::accepted_scores_

private

a history of accepted scores, used for adapting temperature

Referenced by accepted_scores(), boltzmann_result(), calculate_standardized_scores(), calculate_temps(), GenericSimulatedAnnealer(), load_checkpoint_file(), num_accepted_scores(), recompute_rank_scores(), reset(), and save_checkpoint_file().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::anneal_step_

private

counter that tells which annealing step we are on

Referenced by calc_temp_factor(), calculate_temps(), load_checkpoint_file(), reset(), and save_checkpoint_file().

std::string protocols::monte_carlo::GenericSimulatedAnnealer::checkpoint_file_

private

what name should be used to store checkpoint information so that the run can be resumed?

Referenced by apply(), checkpoint_exists(), checkpoint_file(), create_tag(), load_checkpoint_file(), parse_my_tag(), remove_checkpoint_file(), and save_checkpoint_file().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::current_trial_

private

what is the current trial number

Referenced by apply(), boltzmann_result(), load_checkpoint_file(), reset(), save_checkpoint_file(), and score_pose().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::eval_period_

private

how many steps in between running the periodic mover?

Referenced by apply(), and parse_my_tag().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::history_

private

counter for how many accepts it takes to reach equilibrium at a given temperature

Referenced by calculate_standardized_scores(), calculate_temps(), and parse_my_tag().

bool protocols::monte_carlo::GenericSimulatedAnnealer::keep_checkpoint_file_

private

if true, the checkpoint files will not be cleaned up after the apply() terminates. Useful for debugging/gathering statistics

Referenced by apply(), keep_checkpoint_file(), and parse_my_tag().

protocols::moves::MoverOP protocols::monte_carlo::GenericSimulatedAnnealer::periodic_mover_

private

mover to be called every eval_period steps

Referenced by apply(), and parse_my_tag().

utility::vector1< core::Real > protocols::monte_carlo::GenericSimulatedAnnealer::start_temperatures_

private

the initial temperatures, used for adapting temperature

Referenced by apply(), GenericSimulatedAnnealer(), reset(), and scale_temperatures().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::temp_step_

private

which step in this temperature are we on

Referenced by calculate_temps(), load_checkpoint_file(), reset(), and save_checkpoint_file().

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

src/protocols/monte_carlo/GenericSimulatedAnnealer.hh
src/protocols/monte_carlo/GenericSimulatedAnnealer.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation