This object is responsible for all of the major functions needed in a Monte Carlo simulation. Its main purpose is to apply the Metropolis Criterion on a pose, based on a ScoreFunction, temperature, and the previously accepted pose. It stores the lowest-energy pose ecountered, the last-accepted pose in the simulation, and various other statistics. More...

#include <MonteCarlo.hh>

Inheritance diagram for protocols::moves::MonteCarlo:

[legend]

Collaboration diagram for protocols::moves::MonteCarlo:

[legend]

Public Types
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

Public Member Functions
	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	set_temperature (Real const temp)
	Sets the temperature value used in the Metropolis Criterion to <temp> 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 (Pose &pose, std::string const &move_type="unk", core::Real const proposal_density_ratio=1, core::Real const inner_score_temperature_delta=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 bool	boltzmann (core::Real score_delta, std::string const &move_type="unk", core::Real const proposal_density_ratio=1)
	Applies the Metropolis Criterion on the inputted pose based on the supplied score delta. More...

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

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

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...

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

void	set_lowest_score_pose (Pose const &pose)
	Sets the lowest score pose to the score of <pose> 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...

void	score_function (ScoreFunction const &scorefxn)
	Sets the ScoreFunction to <scorefxn> , re-scores last accepted pose and 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
	Returns the total number of trials since the last reset. More...

Real	last_accepted_score () const
	Returns the score value of the last accepted pose. 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...

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

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

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 Member Functions
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)

MonteCarlo const &	operator= (MonteCarlo const &)
	unimplemented – do not use More...

Private Attributes
PoseOP	last_accepted_pose_
	Latest accepted pose. More...

PoseOP	lowest_score_pose_
	Lowest score pose encountered. More...

core::Real	temperature_
	Acceptance criterion temperature. More...

ScoreFunctionOP	score_function_
	Internal scoring function. More...

bool	autotemp_
	For abinitio-style increasing the temperature after a large number of rejects: More...

core::Real	quench_temp_

int	last_accept_

MCA	mc_accepted_
	Result of the last call to boltzmann. More...

TrialCounter	counter_
	diagnostics More...

bool	update_boinc_

Real	total_score_of_last_considered_pose_

Real	last_accepted_score_

Real	lowest_score_

Size	heat_after_cycles_

utility::vector1 < moves::MonteCarloExceptionConvergeOP >	convergence_checks_

Size	last_check_

Size	check_frequency_

Detailed Description

This object is responsible for all of the major functions needed in a Monte Carlo simulation. Its main purpose is to apply the Metropolis Criterion on a pose, based on a ScoreFunction, temperature, and the previously accepted pose. It stores the lowest-energy pose ecountered, the last-accepted pose in the simulation, and various other statistics.

Output Methods: MonteCarlo.show_counters() MonteCarlo.show_scores() MonteCarlo.show_state() Common Methods: MonteCarlo.last_accepted_score MonteCarlo.last_accepted_pose MonteCarlo.lowest_score MonteCarlo.lowest_score_pose MonteCarlo.score_function MonteCarlo.set_temperature MonteCarlo.temperature

Definition at line 74 of file MonteCarlo.hh.

Member Typedef Documentation

typedef core::pose::Pose protocols::moves::MonteCarlo::Pose

Definition at line 79 of file MonteCarlo.hh.

typedef core::pose::PoseCOP protocols::moves::MonteCarlo::PoseCOP

Definition at line 81 of file MonteCarlo.hh.

typedef core::pose::PoseOP protocols::moves::MonteCarlo::PoseOP

Definition at line 80 of file MonteCarlo.hh.

typedef core::Real protocols::moves::MonteCarlo::Real

Definition at line 82 of file MonteCarlo.hh.

typedef core::scoring::ScoreFunction protocols::moves::MonteCarlo::ScoreFunction

Definition at line 76 of file MonteCarlo.hh.

typedef core::scoring::ScoreFunctionCOP protocols::moves::MonteCarlo::ScoreFunctionCOP

Definition at line 78 of file MonteCarlo.hh.

typedef core::scoring::ScoreFunctionOP protocols::moves::MonteCarlo::ScoreFunctionOP

Definition at line 77 of file MonteCarlo.hh.

Constructor & Destructor Documentation

protocols::moves::MonteCarlo::MonteCarlo ( MonteCarlo const & src)

Copy constructor.

The copy constructor does not copy the OPs, but rather creates new objects using the copy constructors or the clone() methods of the objects being pointed at. This is important, since otherwise, a copy of a Monte Carlo object could corrupt the state held in the original MonteCarlo object.

Definition at line 63 of file MonteCarlo.cc.

protocols::moves::MonteCarlo::MonteCarlo	(	Pose const &	init_pose,
		ScoreFunction const &	scorefxn,
		Real const	temperature
	)

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

Definition at line 87 of file MonteCarlo.cc.

References check_frequency_, core::scoring::ScoreFunction::clone(), last_accepted_pose_, last_check_, lowest_score_pose_, reset(), and score_function_.

protocols::moves::MonteCarlo::MonteCarlo	(	ScoreFunction const &	scorefxn,
		Real const	temperature
	)

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

Definition at line 113 of file MonteCarlo.cc.

References check_frequency_, core::scoring::ScoreFunction::clone(), last_accepted_pose_, last_check_, lowest_score_pose_, and score_function_.

protocols::moves::MonteCarlo::~MonteCarlo ( )

virtual

Empty destructor in C++ file to reduce number of necessary includes.

Definition at line 137 of file MonteCarlo.cc.

Member Function Documentation

template<typename ConformationObserver >

void protocols::moves::MonteCarlo::attach_observer_to_last_accepted_conformation ( ConformationObserver & obs)

attach observer to last accepted conformation

Template Parameters

ConformationObserver any class implementing void attach_to( Conformation & )

Definition at line 109 of file MonteCarlo.tmpl.hh.

References last_accepted_pose_.

template<typename PoseObserver >

void protocols::moves::MonteCarlo::attach_observer_to_last_accepted_pose ( PoseObserver & obs)

attach observer to last accepted pose

Template Parameters

PoseObserver any class implementing void attach_to( Pose & )

Definition at line 127 of file MonteCarlo.tmpl.hh.

References last_accepted_pose_.

Referenced by protocols::viewer::add_monte_carlo_silent_viewer().

template<typename ConformationObserver >

void protocols::moves::MonteCarlo::attach_observer_to_lowest_score_conformation ( ConformationObserver & obs)

attach observer to lowest score conformation

Template Parameters

ConformationObserver any class implementing void attach_to( Conformation & )

Definition at line 118 of file MonteCarlo.tmpl.hh.

References lowest_score_pose_.

template<typename PoseObserver >

void protocols::moves::MonteCarlo::attach_observer_to_lowest_score_pose ( PoseObserver & obs)

attach observer to lowest score pose

Template Parameters

PoseObserver any class implementing void attach_to( Pose & )

Definition at line 136 of file MonteCarlo.tmpl.hh.

References lowest_score_pose_.

Referenced by protocols::viewer::add_monte_carlo_silent_viewer().

void protocols::moves::MonteCarlo::autotemp_accept ( )

private

Definition at line 614 of file MonteCarlo.cc.

References autotemp_, last_accept_, quench_temp_, temperature_, and protocols::moves::TR().

Referenced by boltzmann().

void protocols::moves::MonteCarlo::autotemp_reject ( )

private

for managing the temperature, if we need to do so

Definition at line 595 of file MonteCarlo.cc.

References autotemp_, heat_after_cycles_, last_accept_, quench_temp_, temperature_, and protocols::moves::TR().

Referenced by boltzmann().

bool protocols::moves::MonteCarlo::boltzmann	(	Pose &	pose,
		std::string const &	move_type = `"unk"`,
		core::Real const	proposal_density_ratio = `1`,
		core::Real const	inner_score_temperature_delta = `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

Definition at line 320 of file MonteCarlo.cc.

References autotemp_accept(), autotemp_reject(), core::scoring::Energies::clear(), protocols::moves::TrialCounter::count_accepted(), protocols::moves::TrialCounter::count_energy_drop(), protocols::moves::TrialCounter::count_trial(), counter_, protocols::comparative_modeling::features::E, core::pose::Pose::energies(), evaluate_convergence_checks(), last_accepted_pose_, last_accepted_score(), last_accepted_score_, lowest_score(), lowest_score_, lowest_score_pose_, mc_accepted_, mc_RG(), protocols::moves::MCA_accepted_score_beat_last, protocols::moves::MCA_accepted_score_beat_low, protocols::moves::MCA_accepted_thermally, protocols::moves::MCA_rejected, score_function_, core::scoring::EMapVector::show_if_nonzero_weight(), temperature_, core::scoring::Energies::total_energies(), total_score_of_last_considered_pose_, protocols::moves::TR(), protocols::moves::TrialCounter::trial(), and update_boinc_.

Referenced by protocols::enzdes::BackboneSampler::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::moves::ReplicaExchangeMC::boltzmann(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

bool protocols::moves::MonteCarlo::boltzmann	(	core::Real	score_delta,
		std::string const &	move_type = `"unk"`,
		core::Real const	proposal_density_ratio = `1`
	)

virtual

Applies the Metropolis Criterion on the inputted pose based on the supplied score delta.

example(s):

See also: MonteCarlo

Definition at line 435 of file MonteCarlo.cc.

References autotemp_accept(), autotemp_reject(), protocols::moves::TrialCounter::count_accepted(), protocols::moves::TrialCounter::count_energy_drop(), protocols::moves::TrialCounter::count_trial(), counter_, last_accepted_score(), last_accepted_score_, lowest_score(), lowest_score_, mc_accepted_, mc_RG(), protocols::moves::MCA_accepted_score_beat_last, protocols::moves::MCA_accepted_score_beat_low, protocols::moves::MCA_accepted_thermally, protocols::moves::MCA_rejected, temperature_, and total_score_of_last_considered_pose_.

Size protocols::moves::MonteCarlo::check_frequency ( ) const

inline

Definition at line 542 of file MonteCarlo.hh.

References check_frequency_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::Heat_ConvergenceCheck::operator()().

void protocols::moves::MonteCarlo::clear_poses ( )

Removes last accepted pose and lowest score pose.

example(s): mc.clear_poses() See also: MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.lowest_score_pose MonteCarlo.recover_low MonteCarlo.reset MonteCarlo.set_last_accepted_pose MonteCarlo.set_lowest_score_pose

Definition at line 142 of file MonteCarlo.cc.

References last_accepted_pose_, and lowest_score_pose_.

Referenced by protocols::abinitio::ConstraintFragmentSampler::apply(), and protocols::abinitio::FragmentSampler::apply().

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

private

Definition at line 626 of file MonteCarlo.cc.

References check_frequency_, convergence_checks_, last_check_, and protocols::hotspot_hashing::reject.

Referenced by boltzmann().

core::Size protocols::moves::MonteCarlo::heat_after_cycles ( ) const

inline

no brief for now

Definition at line 513 of file MonteCarlo.hh.

References heat_after_cycles_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::Heat_ConvergenceCheck::operator()().

core::Size protocols::moves::MonteCarlo::last_accept ( ) const

inline

Returns the number of trials since last acceptance.

example(s): mc.last_accept() See also: MonteCarlo MonteCarlo.show_counters MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score

Definition at line 507 of file MonteCarlo.hh.

References last_accept_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::Heat_ConvergenceCheck::operator()().

Pose const& protocols::moves::MonteCarlo::last_accepted_pose ( ) const

inline

Returns the last accepted pose.

example(s): mc.last_accepted_pose() See also: MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_score

Definition at line 233 of file MonteCarlo.hh.

References last_accepted_pose_.

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::checkpoint::CheckPointer::checkpoint(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::canonical_sampling::PDBTrajectoryRecorder::reset(), and protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann().

Real protocols::moves::MonteCarlo::last_accepted_score ( ) const

Returns the score value of the last accepted pose.

example(s): mc.last_accepted_score() See also: MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.show_state

Definition at line 562 of file MonteCarlo.cc.

References last_accepted_score_.

Referenced by protocols::moves::ReplicaExchangeMC::boltzmann(), boltzmann(), protocols::moves::operator<<(), score_function(), show_scores(), and show_state().

Real protocols::moves::MonteCarlo::lowest_score ( ) const

Returns the score value of the lowest score pose encountered.

example(s): mc.lowest_score() See also: MonteCarlo MonteCarlo.lowest_score_pose MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.show_state

Definition at line 573 of file MonteCarlo.cc.

References lowest_score_.

Referenced by boltzmann(), protocols::moves::operator<<(), score_function(), show_scores(), and show_state().

Pose const& protocols::moves::MonteCarlo::lowest_score_pose ( ) const

inline

Returns the lowest score pose encountered.

example(s): mc.lowest_score_pose() See also: MonteCarlo MonteCarlo.last_accepted_pose MonteCarlo.lowest_score

Definition at line 248 of file MonteCarlo.hh.

References lowest_score_pose_.

Referenced by protocols::enzdes::BackboneSampler::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::checkpoint::CheckPointer::checkpoint(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::simple_moves::EnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::simple_moves::EnergyCutRotamerTrialsMinMover::setup_energycut_task(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

MCA protocols::moves::MonteCarlo::mc_accepted ( ) const

Returns mc_accepted, informative of the last move applied.

Note: Returns true for an accept, false otherwise 3 = accepted:score beat low score and last_accepted score 2 = accepted:score beat last_accepted score 1 = thermally accepted: score worse than last_accepted score 0 = not accepted example(s): mc.mc_accepted() See also: MonteCarlo MonteCarlo.show_state

Definition at line 584 of file MonteCarlo.cc.

References mc_accepted_.

MonteCarlo const& protocols::moves::MonteCarlo::operator= ( MonteCarlo const & )

private

unimplemented – do not use

void protocols::moves::MonteCarlo::push_back ( moves::MonteCarloExceptionConvergeOP check)

no brief for now

Definition at line 635 of file MonteCarlo.cc.

References convergence_checks_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::setup_convergence_checks_from_cmdline().

void protocols::moves::MonteCarlo::recover_low ( Pose & pose)

Sets the input <pose> and last accepted pose to the lowest score pose.

return the simulation state to the lowest energy structure we've seen

example(s): mc.recover_low( pose ) See also: MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.lowest_score_pose

Definition at line 165 of file MonteCarlo.cc.

References last_accepted_pose_, last_accepted_score_, and lowest_score_pose_.

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::abinitio::FragmentSampler::apply(), protocols::abinitio::MembraneAbinitio::apply(), protocols::abinitio::FoldConstraints::do_stage2_cycles(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::increase_chainbreak_weight_and_update_monte_carlo(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::abinitio::FoldConstraints::set_max_seq_sep(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().

void protocols::moves::MonteCarlo::reset ( Pose const & pose)

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

Definition at line 487 of file MonteCarlo.cc.

References last_accepted_pose_, last_accepted_score_, lowest_score_, lowest_score_pose_, and score_function_.

void protocols::moves::MonteCarlo::reset_counters ( )

Resets the mover counters.

example(s): mc.reset_counters() See alse: MonteCarlo MonteCarlo.show_counters

Definition at line 200 of file MonteCarlo.cc.

References counter_, and protocols::moves::TrialCounter::reset().

Referenced by protocols::abinitio::MembraneAbinitio::apply(), protocols::abinitio::ClassicAbinitio::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

void protocols::moves::MonteCarlo::reset_last_accepted ( Pose const & pose)

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

Note: (does not reset counters)

example(s): mc.reset_last_accepted( pose ) See also: MonteCarlo MonteCarlo.reset

Definition at line 506 of file MonteCarlo.cc.

References last_accepted_pose_, last_accepted_score_, lowest_score_pose_, and score_function_.

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply().

void protocols::moves::MonteCarlo::reset_scorefxn	(	Pose const &	init_pose,
		ScoreFunction const &	scorefxn
	)

Resets the ScoreFunction.

Definition at line 148 of file MonteCarlo.cc.

References core::scoring::ScoreFunction::clone(), reset(), and score_function_.

void protocols::moves::MonteCarlo::score_function ( ScoreFunction const & scorefxn)

Sets the ScoreFunction to <scorefxn> , re-scores last accepted pose and lowest score pose.

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

example(s): mc.score_function( scorefxn ) See also: MonteCarlo MonteCarlo.boltzmann MonteCarlo.set_temperature MonteCarlo.temperature ScoreFunction create_score_function

Definition at line 219 of file MonteCarlo.cc.

References core::scoring::Energies::clear(), core::scoring::ScoreFunction::clone(), protocols::comparative_modeling::features::E, core::pose::Pose::energies(), last_accepted_pose_, last_accepted_score(), last_accepted_score_, lowest_score(), lowest_score_, lowest_score_pose_, score_function_, core::scoring::EMapVector::show_if_nonzero_weight(), core::scoring::Energies::total_energies(), and protocols::moves::TR().

core::scoring::ScoreFunction const & protocols::moves::MonteCarlo::score_function ( ) const

Returns the MonteCarlo ScoreFunction.

example(s): mc.score_function() mc.score_function()( pose ) See also: MonteCarlo MonteCarlo.boltzmann MonteCarlo.set_temperature MonteCarlo.temperature ScoreFunction create_score_function

Definition at line 556 of file MonteCarlo.cc.

References score_function_.

void protocols::moves::MonteCarlo::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.

Definition at line 528 of file MonteCarlo.cc.

References autotemp_, last_accept_, and quench_temp_.

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply().

void protocols::moves::MonteCarlo::set_heat_after_cycles ( core::Size setting)

inline

no brief for now

Definition at line 519 of file MonteCarlo.hh.

References heat_after_cycles_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::setup_convergence_checks_from_cmdline().

void protocols::moves::MonteCarlo::set_last_accepted_pose ( Pose const & pose)

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

Note: (for recovering from a checkpoint)

example(s): mc.set_last_accepted_pose( pose ) See also: MonteCarlo MonteCarlo.last_accept MonteCarlo.last_accepted_pose MonteCarlo.last_accepted_score

Definition at line 541 of file MonteCarlo.cc.

References last_accepted_pose_, and last_accepted_score_.

Referenced by protocols::checkpoint::CheckPointer::recover_checkpoint().

void protocols::moves::MonteCarlo::set_lowest_score_pose ( Pose const & pose)

Sets the lowest score pose to the score of <pose>

Note: (for recovering from a checkpoint)

example(s): mc.set_lowest_score_pose(pose) See also: MonteCarlo MonteCarlo.lowest_score MonteCarlo.lowest_score_pose

Definition at line 549 of file MonteCarlo.cc.

References lowest_score_, and lowest_score_pose_.

Referenced by protocols::checkpoint::CheckPointer::recover_checkpoint().

void protocols::moves::MonteCarlo::set_temperature ( Real const temp)

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

Definition at line 158 of file MonteCarlo.cc.

References temperature_.

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::moves::ReplicaExchangeMC::boltzmann(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(), protocols::moves::ReplicaExchangeMC::init(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

void protocols::moves::MonteCarlo::set_update_boinc ( bool setting)

inline

no brief for now

Definition at line 493 of file MonteCarlo.hh.

References update_boinc_.

void protocols::moves::MonteCarlo::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")

example(s): mc.show_counters() Output as: protocols.moves.MonteCarlo: unk trials= X; accepts= Y; energy_drop/trial= Z See also: MonteCarlo MonteCarlo.show_scores MonteCarlo.show_state

Definition at line 212 of file MonteCarlo.cc.

References counter_, and protocols::moves::TrialCounter::show().

Referenced by protocols::enzdes::BackboneSampler::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::abinitio::MembraneAbinitio::apply(), protocols::abinitio::ClassicAbinitio::apply(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(), protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(), and show_state().

void protocols::moves::MonteCarlo::show_scores ( ) const

Displays the last accepted score and the lowest score.

example(s): mc.show_scores() Output as: protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: X Y See also: MonteCarlo MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.show_counters MonteCarlo.show_state

Definition at line 193 of file MonteCarlo.cc.

References last_accepted_score(), lowest_score(), and protocols::moves::TR().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

void protocols::moves::MonteCarlo::show_state ( ) const

Displays the entire MonteCarlo state temperature, scores, annealing settings, move statistics, move counters (show_counters)

example(s): mc.show_state() Output as: protocols.moves.MonteCarlo: MC: t l1 l2 las lws la au qu mca t= temperature l1= (*score_function_)(*last_accepted_pose_) l2= (*score_function_)(*lowest_score_pose_) las= last accepted score lws= lowest score la= last_accept_ au= autotemp_ qu= quench_temp_ mca= mc_accepted_ See also: MonteCarlo MonteCarlo.show_counters MonteCarlo.show_scores MonteCarlo.last_accepted_score MonteCarlo.lowest_score MonteCarlo.temperature

Definition at line 175 of file MonteCarlo.cc.

References autotemp_, last_accept_, last_accepted_score(), lowest_score(), mc_accepted_, quench_temp_, show_counters(), temperature_, and protocols::moves::TR().

Referenced by protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

Real protocols::moves::MonteCarlo::temperature ( ) const

inline

Returns the temperature value used in the Metropolis Criterion.

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

Definition at line 142 of file MonteCarlo.hh.

References temperature_.

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::abinitio::KinematicAbinitio::create_bb_moves(), and protocols::moves::operator<<().

Real protocols::moves::MonteCarlo::total_score_of_last_considered_pose ( ) const

inline