A MonteCarlo object for optimizing the interface dG as defined using InterfaceAnalyzer. The dG and Total energy can be weighted. This is so that the interface energy itself can be optimized through a protocol. More...

#include <MonteCarloInterface.hh>

Inheritance diagram for protocols::monte_carlo::MonteCarloInterface:

[legend]

Public Member Functions
	MonteCarloInterface (Pose const &init_pose, ScoreFunction const &scorefxn, Real const temperature, std::string interface, bool detect_disulfide_in_separated_pose=false)
	Constructs a useable MonteCarlo object. More...

	MonteCarloInterface (ScoreFunction const &scorefxn, Real const temperature, std::string interface)
	Constructor without Pose – call reset(pose) before first use. More...

	MonteCarloInterface (MonteCarloInterface const &src)

	~MonteCarloInterface () override

protocols::moves::MonteCarloOP	clone () override

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) override
	Applies the Metropolis Criterion on pose based on the Interface dG and Total Score according to Set weights. More...

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

void	set_interface (std::string const &interface)
	Set the interface that we will be using to calculate interface energy. More...

void	set_pack_interface_separated (bool pack_separated)
	Should we pack the interface while separated? Default TRUE. More...

void	set_dG_weight (core::Real dG_weight)
	Set the weight on the dG component of the energy (Default = 1.0) More...

void	set_total_weight (core::Real total_weight)
	Set the weight on the total component of the enegy (Default = 0.0) More...

void	score_function (ScoreFunction const &scorefxn) override
	Sets the ScoreFunction to <scorefxn> , re-scores last accepted pose and lowest score pose. More...

core::Real	calculate_score (Pose &pose)
	Calculate the score given the pose and the weights. More...

void	set_repack_separated (bool repack_separated)
	Should we repack only the interface residues of a cloned pose on calculating the interface energy? Default TRUE. More...

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 (Pose const &init_pose, Real const init_score, Real const temperature)
	Constructor for external scoring. More...

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

	~MonteCarlo () override
	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...

virtual 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, core::Real const score, 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 externally computes score, 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, 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...

virtual bool	boltzmann (core::Real score, Pose &pose, 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. Updates the Pose Structure accordingly. More...

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

void	set_last_score (core::Real score)
	Set the last score. 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...

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...

core::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	last_score () const
	Returns the score value of the last score. 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...

core::Size	check_frequency () const

void	set_total_score_last_considered (core::Real score)

void	set_last_accepted (core::Real score)

void	set_lowest (core::Real score)

Private Member Functions
void	init_interface_analyzer ()

void	read_cmd_line_options ()

Private Attributes
std::string	interface_definition_ = ""

protocols::analysis::InterfaceAnalyzerMoverOP	analyzer_

core::Real	dG_weight_ = 1.0

core::Real	total_weight_ = 0.0

core::Real	last_dG_ = 0.0

core::Real	last_score_ = 0.0

bool	repack_separated_ = true

bool	detect_disulfide_in_separated_pose_
	detect disulfide in the separated pose in InterfaceAnalyzerMover More...

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

typedef core::Size	Size

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)

Pose &	last_accepted_pose_non_const ()
	Returns the non-const last accepted pose (for subclasses) More...

void	set_last_accepted_score (core::Real score)

void	set_mc_accepted (MCA value)

Detailed Description

A MonteCarlo object for optimizing the interface dG as defined using InterfaceAnalyzer. The dG and Total energy can be weighted. This is so that the interface energy itself can be optimized through a protocol.

Constructor & Destructor Documentation

protocols::monte_carlo::MonteCarloInterface::MonteCarloInterface	(	Pose const &	init_pose,
		ScoreFunction const &	scorefxn,
		Real const	temperature,
		std::string	interface,
		bool	detect_disulfide_in_separated_pose = `false`
	)

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 init_interface_analyzer(), read_cmd_line_options(), reset(), and set_interface().

protocols::monte_carlo::MonteCarloInterface::MonteCarloInterface	(	ScoreFunction const &	scorefxn,
		Real const	temperature,
		std::string	interface
	)

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

References init_interface_analyzer(), read_cmd_line_options(), and set_interface().

protocols::monte_carlo::MonteCarloInterface::MonteCarloInterface ( MonteCarloInterface const & src )

References init_interface_analyzer().

protocols::monte_carlo::MonteCarloInterface::~MonteCarloInterface ( )

override

Member Function Documentation

bool protocols::monte_carlo::MonteCarloInterface::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`
	)

overridevirtual

Applies the Metropolis Criterion on pose based on the Interface dG and Total Score according to Set weights.

Interface dG is calculated using the InterfaceAnalyzer Application.

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.

References protocols::moves::MonteCarlo::boltzmann(), calculate_score(), and protocols::hybridization::score.

core::Real protocols::monte_carlo::MonteCarloInterface::calculate_score ( Pose & pose )

Calculate the score given the pose and the weights.

References analyzer_, dG_weight_, last_dG_, last_score_, core::scoring::ScoreFunction::score(), protocols::moves::MonteCarlo::score_function(), core::scoring::total_score, total_weight_, and protocols::TR().

Referenced by boltzmann(), reset(), and score_function().

MonteCarloOP protocols::monte_carlo::MonteCarloInterface::clone ( )

overridevirtual

Reimplemented from protocols::moves::MonteCarlo.

void protocols::monte_carlo::MonteCarloInterface::init_interface_analyzer ( )

private

References analyzer_, core::scoring::ScoreFunction::clone(), detect_disulfide_in_separated_pose_, repack_separated_, protocols::moves::MonteCarlo::score_function(), and protocols::TR().

Referenced by MonteCarloInterface().

void protocols::monte_carlo::MonteCarloInterface::read_cmd_line_options ( )

private

References dG_weight_, and total_weight_.

Referenced by MonteCarloInterface().

void protocols::monte_carlo::MonteCarloInterface::reset ( Pose const & pose )

overridevirtual

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 calculate_score(), protocols::moves::MonteCarlo::last_accepted_pose(), protocols::moves::MonteCarlo::last_accepted_pose_non_const(), protocols::hybridization::score, protocols::moves::MonteCarlo::set_last_accepted(), protocols::moves::MonteCarlo::set_last_accepted_pose(), protocols::moves::MonteCarlo::set_last_score(), and protocols::moves::MonteCarlo::set_lowest_score_pose().

Referenced by MonteCarloInterface().

void protocols::monte_carlo::MonteCarloInterface::score_function ( ScoreFunction const & scorefxn )

overridevirtual

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

Reimplemented from protocols::moves::MonteCarlo.

References analyzer_, calculate_score(), core::scoring::ScoreFunction::clone(), protocols::moves::MonteCarlo::last_accepted_pose_non_const(), protocols::hybridization::score, protocols::moves::MonteCarlo::score_function(), protocols::moves::MonteCarlo::set_last_accepted(), and protocols::moves::MonteCarlo::set_lowest().

void protocols::monte_carlo::MonteCarloInterface::set_dG_weight ( core::Real dG_weight )

Set the weight on the dG component of the energy (Default = 1.0)

References dG_weight_.

void protocols::monte_carlo::MonteCarloInterface::set_interface ( std::string const & interface )

Set the interface that we will be using to calculate interface energy.

References analyzer_, and interface_definition_.

Referenced by MonteCarloInterface().

void protocols::monte_carlo::MonteCarloInterface::set_pack_interface_separated ( bool pack_separated )

Should we pack the interface while separated? Default TRUE.

References analyzer_.

void protocols::monte_carlo::MonteCarloInterface::set_repack_separated ( bool repack_separated )

Should we repack only the interface residues of a cloned pose on calculating the interface energy? Default TRUE.

References analyzer_, and repack_separated_.

void protocols::monte_carlo::MonteCarloInterface::set_total_weight ( core::Real total_weight )

Set the weight on the total component of the enegy (Default = 0.0)

References total_weight_.

Member Data Documentation

protocols::analysis::InterfaceAnalyzerMoverOP protocols::monte_carlo::MonteCarloInterface::analyzer_

private

Referenced by calculate_score(), init_interface_analyzer(), score_function(), set_interface(), set_pack_interface_separated(), and set_repack_separated().

bool protocols::monte_carlo::MonteCarloInterface::detect_disulfide_in_separated_pose_

private

detect disulfide in the separated pose in InterfaceAnalyzerMover

Referenced by init_interface_analyzer().

core::Real protocols::monte_carlo::MonteCarloInterface::dG_weight_ = 1.0

private

Referenced by calculate_score(), read_cmd_line_options(), and set_dG_weight().

std::string protocols::monte_carlo::MonteCarloInterface::interface_definition_ = ""

private

Referenced by set_interface().

core::Real protocols::monte_carlo::MonteCarloInterface::last_dG_ = 0.0

private

Referenced by calculate_score().

core::Real protocols::monte_carlo::MonteCarloInterface::last_score_ = 0.0

private

Referenced by calculate_score().

bool protocols::monte_carlo::MonteCarloInterface::repack_separated_ = true

private

Referenced by init_interface_analyzer(), and set_repack_separated().

core::Real protocols::monte_carlo::MonteCarloInterface::total_weight_ = 0.0

private

Referenced by calculate_score(), read_cmd_line_options(), and set_total_weight().

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

src/protocols/monte_carlo/MonteCarloInterface.hh
src/protocols/monte_carlo/MonteCarloInterface.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation