#include <BiasedMonteCarlo.hh>

Inheritance diagram for protocols::canonical_sampling::BiasedMonteCarlo:

Public Member Functions
	BiasedMonteCarlo (Pose const &init_pose, ScoreFunction const &scorefxn, Real const temperature, BiasEnergyOP bias_energy)
	Constructs a useable MonteCarlo object. More...

	BiasedMonteCarlo (ScoreFunction const &scorefxn, Real const temperature, BiasEnergyOP bias_energy)
	Constructor without Pose – call reset(pose) before first use. More...

	BiasedMonteCarlo (BiasedMonteCarlo const &)

virtual protocols::moves::MonteCarloOP	clone ()

virtual bool	boltzmann (Pose &pose, std::string const &move_type="unk", core::Real const proposal_density_ratio=1, core::Real const inner_score_delta_over_temperature=0)
	Applies the Metropolis Criterion on pose based on the ScoreFunction, temperature, and the last accepted pose. This method evaluates the change in score, compares the trial pose to the last accepted pose, and updates the pose structure and simulation statistics appropriately. More...

virtual void	reset (Pose const &pose)
	Sets lowest score pose and last accepted pose to the score of <pose> More...

virtual void	score_function (ScoreFunction const &scorefxn)
	set the scorefxn, re-scores last-accepted and lowest-score pose More...

virtual void	set_temperature (Real const temp)
	Sets the temperature value used in the Metropolis Criterion to <temp> More...

BiasEnergyOP	bias_energy ()

Public Member Functions inherited from protocols::moves::MonteCarlo
	MonteCarlo (MonteCarlo const &)
	Copy constructor. More...

	MonteCarlo (Pose const &init_pose, ScoreFunction const &scorefxn, Real const temperature)
	Constructs a useable MonteCarlo object. More...

	MonteCarlo (ScoreFunction const &scorefxn, Real const temperature)
	Constructor without Pose – call reset(pose) before first use. More...

virtual	~MonteCarlo ()
	Empty destructor in C++ file to reduce number of necessary includes. More...

void	reset_scorefxn (Pose const &init_pose, ScoreFunction const &scorefxn)
	Resets the ScoreFunction. More...

void	change_weight (core::scoring::ScoreType const &t, Real const &setting)
	Change the weight on a score term in the object's scorefunction. Useful when we don't want to reset the whole scorefunction during an annealing step. More...

Real	temperature () const
	Returns the temperature value used in the Metropolis Criterion. More...

void	set_autotemp (bool const setting, core::Real const quench_temp)
	Sets autotemp to quench_temp example(s): See also: MonteCarlo MonteCarlo.autotemp MonteCarlo.show_state. More...

virtual bool	boltzmann (core::Real score, std::string const &move_type="unk", core::Real const proposal_density_ratio=1, core::Real const inner_score_delta_over_temperature=0, bool check_lowest_score=true)
	Applies the Metropolis Criterion on the inputted pose based on the supplied score delta. More...

void	set_last_accepted_pose (Pose const &pose)
	Sets the last accepted pose to the score of <pose> More...

void	set_last_accepted_pose (core::pose::Pose const &pose, core::Real score)
	Sets the last accepted pose and last accepted score. More...

void	set_lowest_score_pose (core::pose::Pose const &pose)

void	set_lowest_score_pose (core::pose::Pose const &pose, core::Real score)

Pose const &	last_accepted_pose () const
	Returns the last accepted pose. More...

Pose const &	lowest_score_pose () const
	Returns the lowest score pose encountered. More...

bool	eval_lowest_score_pose (Pose &pose, bool score_pose=true, bool update_stats=false, std::string const &move_type="unk")
	Compares score of <pose> to the lowest score found. If lower, sets the current lowest score pose and lowest score. Use internal pose energies if score_pose is false. Used to evaluate lowest score without boltzmann. Does not change pose structure. More...

template<typename ConformationObserver >
void	attach_observer_to_last_accepted_conformation (ConformationObserver &obs)
	attach observer to last accepted conformation More...

template<typename ConformationObserver >
void	attach_observer_to_lowest_score_conformation (ConformationObserver &obs)
	attach observer to lowest score conformation More...

template<typename PoseObserver >
void	attach_observer_to_last_accepted_pose (PoseObserver &obs)
	attach observer to last accepted pose More...

template<typename PoseObserver >
void	attach_observer_to_lowest_score_pose (PoseObserver &obs)
	attach observer to lowest score pose More...

void	recover_low (Pose &pose)
	Sets the input <pose> and last accepted pose to the lowest score pose. More...

ScoreFunction const &	score_function () const
	Returns the MonteCarlo ScoreFunction. More...

void	show_scores () const
	Displays the last accepted score and the lowest score. More...

void	reset_counters ()
	Resets the mover counters. More...

void	show_state () const
	Displays the entire MonteCarlo state temperature, scores, annealing settings, move statistics, move counters (show_counters) More...

void	show_counters () const
	Displays the number of trials performed, fraction of trial moves accepted, and the average energy drop per accepted trial by mover types applied (unknown movers or perturbations are listed as "unktrials") More...

Size	total_trials () const
	Set the counter to be used for this simulation. More...

Real	last_accepted_score () const
	Manually record that a move was attempted. More...

Real	lowest_score () const
	Returns the score value of the lowest score pose encountered. More...

MCA	mc_accepted () const
	Returns mc_accepted, informative of the last move applied. More...

std::string	mc_accepted_string () const
	Returns mc_accepted as a human-readable string, informative of the last move applied. More...

void	clear_poses ()
	Removes last accepted pose and lowest score pose. More...

void	set_update_boinc (bool setting)
	no brief for now More...

bool	get_update_boinc () const

Real	total_score_of_last_considered_pose () const

core::Size	last_accept () const
	Returns the number of trials since last acceptance. More...

core::Size	heat_after_cycles () const
	no brief for now More...

void	set_heat_after_cycles (core::Size setting)
	no brief for now More...

void	push_back (moves::MonteCarloExceptionConvergeOP)
	no brief for now More...

Size	check_frequency () const

Private Types
typedef protocols::moves::MonteCarlo	Parent

Private Attributes
BiasEnergyOP	bias_energy_

Additional Inherited Members
Public Types inherited from protocols::moves::MonteCarlo
typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef core::pose::PoseCOP	PoseCOP

typedef core::Real	Real

Protected Member Functions inherited from protocols::moves::MonteCarlo
void	autotemp_reject ()
	for managing the temperature, if we need to do so More...

void	autotemp_accept ()

void	evaluate_convergence_checks (core::pose::Pose const &pose, bool reject, bool final)

void	set_last_accepted_score (core::Real score)

void	set_mc_accepted (MCA value)

Member Typedef Documentation

typedef protocols::moves::MonteCarlo protocols::canonical_sampling::BiasedMonteCarlo::Parent

private

Constructor & Destructor Documentation

protocols::canonical_sampling::BiasedMonteCarlo::BiasedMonteCarlo	(	Pose const &	init_pose,
		ScoreFunction const &	scorefxn,
		Real const	temperature,
		BiasEnergyOP	bias_energy
	)

Constructs a useable MonteCarlo object.

mc = MonteCarlo( init_pose , scorefxn , temp )

Pose init_pose /manipulated during the simulation ScoreFunction scorefxn /evaluates pose scores Real (float) temp /used in the Metropolis Criterion

References bias_energy_.

Referenced by clone().

protocols::canonical_sampling::BiasedMonteCarlo::BiasedMonteCarlo	(	ScoreFunction const &	scorefxn,
		Real const	temperature,
		BiasEnergyOP	bias_energy
	)

Constructor without Pose – call reset(pose) before first use.

References bias_energy_.

protocols::canonical_sampling::BiasedMonteCarlo::BiasedMonteCarlo ( BiasedMonteCarlo const & src )

Member Function Documentation

BiasEnergyOP protocols::canonical_sampling::BiasedMonteCarlo::bias_energy ( )

inline

bool protocols::canonical_sampling::BiasedMonteCarlo::boltzmann	(	Pose &	pose,
		std::string const &	move_type = `"unk"`,
		core::Real const	proposal_density_ratio = `1`,
		core::Real const	inner_score_delta_over_temperature = `0`
	)

virtual

Applies the Metropolis Criterion on pose based on the ScoreFunction, temperature, and the last accepted pose. This method evaluates the change in score, compares the trial pose to the last accepted pose, and updates the pose structure and simulation statistics appropriately.

example(s): mc.boltzmann( pose ) See also: MonteCarlo MonteCarlo.last_accepted_score MonteCarlo.lowest_score

Reimplemented from protocols::moves::MonteCarlo.

virtual protocols::moves::MonteCarloOP protocols::canonical_sampling::BiasedMonteCarlo::clone ( )

inlinevirtual

Reimplemented from protocols::moves::MonteCarlo.

References BiasedMonteCarlo().

void protocols::canonical_sampling::BiasedMonteCarlo::reset ( Pose const & pose )

virtual

Sets lowest score pose and last accepted pose to the score of <pose>

Note: (does not reset counters)

example(s): mc.reset(pose) See also: MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.lowest_scored_pose

Reimplemented from protocols::moves::MonteCarlo.

References bias_energy_, protocols::moves::MonteCarlo::last_accepted_pose(), protocols::moves::MonteCarlo::reset(), and protocols::moves::MonteCarlo::set_last_accepted_score().

void protocols::canonical_sampling::BiasedMonteCarlo::score_function ( ScoreFunction const & scorefxn )

virtual

set the scorefxn, re-scores last-accepted and lowest-score pose

Reimplemented from protocols::moves::MonteCarlo.

References bias_energy_, protocols::moves::MonteCarlo::last_accepted_pose(), protocols::moves::MonteCarlo::score_function(), and protocols::moves::MonteCarlo::set_last_accepted_score().

void protocols::canonical_sampling::BiasedMonteCarlo::set_temperature ( Real const temp )

virtual

Sets the temperature value used in the Metropolis Criterion to <temp>

example(s): mc.set_temperature( temp ) See also: MonteCarlo MonteCarlo.temperature MonteCarlo.show_state

Reimplemented from protocols::moves::MonteCarlo.