A wrapper class around MonteCarlo that uses both centroid and FA scorefxns. More...

#include <MixedMonteCarlo.hh>

Inheritance diagram for protocols::moves::MixedMonteCarlo:

Public Member Functions
	MixedMonteCarlo (core::pose::Pose const &low_pose, core::pose::Pose const &high_pose, core::scoring::ScoreFunction const &low_scorefxn, core::scoring::ScoreFunction const &high_scorefxn, core::Real const tuning_param, core::Real const temperature)
	Default constructor. More...

	~MixedMonteCarlo () override
	Destructor. More...

bool	boltzmann (core::pose::Pose &low_pose, core::pose::Pose &high_pose, std::string const &move_type="unk")
	This method should evaluate net score from CG and AA modes. More...

void	reset (core::pose::Pose const &low_pose, core::pose::Pose const &high_pose)
	Sets the lowest and last accepted poses to pose and calls MC reset. More...

core::pose::Pose const &	last_accepted_pose () const
	this gets you only the low-res pose More...

core::pose::Pose const &	lowest_score_pose () const
	this gets you only the low-res pose More...

void	recover_low (core::pose::Pose &high_pose)
	Copies the lowest_score_ pose into the input pose as well as in the last_accepted_ pose. More...

void	recover_low (core::pose::Pose &low_pose, core::pose::Pose &high_pose)
	Copies the lowest_score_ pose into the input pose as well as in the last_accepted_ pose. Returns the highres pose. More...

core::scoring::ScoreFunction const &	highres_score_function () const
	Returns the highres scorefxn. More...

core::scoring::ScoreFunction const &	lowres_score_function () const
	Returns the lowres scorefxn. More...

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

core::Real	last_accepted_score () const
	Resets the mover counters. More...

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

protocols::moves::MonteCarlo const &	MC () const
	Const access to the MC object. More...

Private Member Functions
void	reset_mmc (core::pose::Pose const &high_pose)
	Clone operation: make a copy of this object, and return an owning pointer to the copy. More...

core::Real	score_mixed_res (core::pose::Pose const &low_pose, core::pose::Pose const &high_pose)
	Returns the mixed resolution score. More...

MixedMonteCarlo &	operator= (MixedMonteCarlo const &rhs)
	Assignment operator. More...

	MixedMonteCarlo ()
	Declared only for the #inclusion drive. More...

	MixedMonteCarlo (MixedMonteCarlo const &rhs)
	Declared only for the #inclusion drive. More...

Private Attributes
core::pose::PoseOP	last_accepted_pose_
	accepted structure More...

core::pose::PoseOP	lowest_score_pose_
	Lowest structure we have seen. More...

core::scoring::ScoreFunctionOP	lowres_scorefxn_
	Internal scoring functions for force calls if not set. More...

core::scoring::ScoreFunctionOP	highres_scorefxn_

core::Real	tuning_param_
	Tuning parameter for scorefxns. More...

protocols::moves::MonteCarlo	MC_
	Getting the MC object. More...

Detailed Description

A wrapper class around MonteCarlo that uses both centroid and FA scorefxns.

A Hybrid Monte Carlo mover that employs both centroid and ful-atom score functions. The purpose of this object is to use a combination of centroid and full-atom scorefxn for Boltzmann scoring but only use only the full-atom pose for bookkeeping. This object is particularly important for Resolution Exchange MC based docking.

Author: AmeyaHarmalkar (harma.nosp@m.lkar.nosp@m..amey.nosp@m.a24@.nosp@m.gmail.nosp@m..com)

Constructor & Destructor Documentation

◆ MixedMonteCarlo() [1/3]

protocols::moves::MixedMonteCarlo::MixedMonteCarlo	(	core::pose::Pose const &	low_pose,
		core::pose::Pose const &	high_pose,
		core::scoring::ScoreFunction const &	low_scorefxn,
		core::scoring::ScoreFunction const &	high_scorefxn,
		core::Real const	tuning_param,
		core::Real const	temperature
	)

Default constructor.

Constructors ///.

Default Constructor. This would call the MC Constructor as well.

References core::scoring::ScoreFunction::clone(), highres_scorefxn_, lowres_scorefxn_, reset(), and tuning_param_.

◆ ~MixedMonteCarlo()

protocols::moves::MixedMonteCarlo::~MixedMonteCarlo ( )

overridedefault

Destructor.

◆ MixedMonteCarlo() [2/3]

protocols::moves::MixedMonteCarlo::MixedMonteCarlo ( )

private

Declared only for the #inclusion drive.

◆ MixedMonteCarlo() [3/3]

protocols::moves::MixedMonteCarlo::MixedMonteCarlo ( MixedMonteCarlo const & rhs )

private

Declared only for the #inclusion drive.

Member Function Documentation

◆ boltzmann()

bool protocols::moves::MixedMonteCarlo::boltzmann	(	core::pose::Pose &	low_pose,
		core::pose::Pose &	high_pose,
		std::string const &	move_type = `"unk"`
	)

This method should evaluate net score from CG and AA modes.

Boltzmann for MixedMC. Gets the score and passes to the MC boltzman.

Returns true for an accept, and false otherwise MC_accepted 3 = accepted : score beats low_score and last_accepted score 2 = accepted : score beats last_accepted score 1 = thermally accepted: score worse than last_accepted score 0 = not accepted

References protocols::moves::MonteCarlo::boltzmann(), last_accepted_pose_, MC_, protocols::moves::MonteCarlo::mc_accepted(), protocols::moves::MCA_accepted_score_beat_last, protocols::moves::MCA_accepted_score_beat_low, protocols::moves::MCA_accepted_thermally, protocols::moves::MCA_rejected, reset_mmc(), protocols::hybridization::score, and score_mixed_res().

◆ highres_score_function()

core::scoring::ScoreFunction const & protocols::moves::MixedMonteCarlo::highres_score_function ( ) const

Returns the highres scorefxn.

References highres_scorefxn_.

◆ last_accepted_pose()

core::pose::Pose const& protocols::moves::MixedMonteCarlo::last_accepted_pose ( ) const

inline

this gets you only the low-res pose

References last_accepted_pose_.

◆ last_accepted_score()

core::Real protocols::moves::MixedMonteCarlo::last_accepted_score ( ) const

Resets the mover counters.

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")

Returns the total number of trials since the last reset

Note: : MonteCarlo.boltzmann(pose) updates the number of trials

Returns the score value of the last accepted pose

References protocols::moves::MonteCarlo::last_accepted_score(), and MC_.

Referenced by show_scores().

◆ lowest_score()

core::Real protocols::moves::MixedMonteCarlo::lowest_score ( ) const

Returns the score value of the lowest score pose encountered.

References protocols::moves::MonteCarlo::lowest_score(), and MC_.

Referenced by show_scores().

◆ lowest_score_pose()

core::pose::Pose const& protocols::moves::MixedMonteCarlo::lowest_score_pose ( ) const

inline

this gets you only the low-res pose

References lowest_score_pose_.

◆ lowres_score_function()

core::scoring::ScoreFunction const & protocols::moves::MixedMonteCarlo::lowres_score_function ( ) const

Returns the lowres scorefxn.

References lowres_scorefxn_.

◆ MC()

protocols::moves::MonteCarlo const & protocols::moves::MixedMonteCarlo::MC ( ) const

Const access to the MC object.

References MC_.

◆ operator=()

MixedMonteCarlo& protocols::moves::MixedMonteCarlo::operator= ( MixedMonteCarlo const & rhs )

private

Assignment operator.

◆ recover_low() [1/2]

void protocols::moves::MixedMonteCarlo::recover_low ( core::pose::Pose & high_pose )

Copies the lowest_score_ pose into the input pose as well as in the last_accepted_ pose.

Copies the lowest_score_ pose into the input pose as well as in the last_accepted_ pose. Copies action for underlying MC but does not return that pose.

◆ recover_low() [2/2]

void protocols::moves::MixedMonteCarlo::recover_low	(	core::pose::Pose &	low_pose,
		core::pose::Pose &	high_pose
	)

Copies the lowest_score_ pose into the input pose as well as in the last_accepted_ pose. Returns the highres pose.

Returns simulation state to the lowest energy structure that has been observed.

References last_accepted_pose_, lowest_score_pose_, MC_, and protocols::moves::MonteCarlo::recover_low().

◆ reset()

void protocols::moves::MixedMonteCarlo::reset	(	core::pose::Pose const &	low_pose,
		core::pose::Pose const &	high_pose
	)

Sets the lowest and last accepted poses to pose and calls MC reset.

References MC_, protocols::moves::MonteCarlo::reset(), reset_mmc(), protocols::hybridization::score, and score_mixed_res().

Referenced by MixedMonteCarlo().

◆ reset_mmc()

void protocols::moves::MixedMonteCarlo::reset_mmc ( core::pose::Pose const & high_pose )

private

Clone operation: make a copy of this object, and return an owning pointer to the copy.

Bookkeeping with highres pose.

Methods

Sets the lowest and last accepted low pose to pose

References last_accepted_pose_, and lowest_score_pose_.

Referenced by boltzmann(), and reset().

◆ score_mixed_res()

core::Real protocols::moves::MixedMonteCarlo::score_mixed_res	(	core::pose::Pose const &	low_pose,
		core::pose::Pose const &	high_pose
	)

private

Returns the mixed resolution score.

References highres_scorefxn_, lowres_scorefxn_, protocols::hybridization::score, and tuning_param_.

Referenced by boltzmann(), and reset().

◆ show_scores()

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

Displays the last accepted and lowest scores.

Shows the current scores.

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

Member Data Documentation

◆ highres_scorefxn_

core::scoring::ScoreFunctionOP protocols::moves::MixedMonteCarlo::highres_scorefxn_

private

Referenced by highres_score_function(), MixedMonteCarlo(), and score_mixed_res().

◆ last_accepted_pose_

core::pose::PoseOP protocols::moves::MixedMonteCarlo::last_accepted_pose_

private

accepted structure

Referenced by boltzmann(), last_accepted_pose(), recover_low(), and reset_mmc().

◆ lowest_score_pose_

core::pose::PoseOP protocols::moves::MixedMonteCarlo::lowest_score_pose_

private

Lowest structure we have seen.

Referenced by lowest_score_pose(), recover_low(), and reset_mmc().

◆ lowres_scorefxn_

core::scoring::ScoreFunctionOP protocols::moves::MixedMonteCarlo::lowres_scorefxn_

private

Internal scoring functions for force calls if not set.

Referenced by lowres_score_function(), MixedMonteCarlo(), and score_mixed_res().

◆ MC_

protocols::moves::MonteCarlo protocols::moves::MixedMonteCarlo::MC_

private

Getting the MC object.

Referenced by boltzmann(), last_accepted_score(), lowest_score(), MC(), recover_low(), and reset().

◆ tuning_param_

core::Real protocols::moves::MixedMonteCarlo::tuning_param_

private

Tuning parameter for scorefxns.

Referenced by MixedMonteCarlo(), and score_mixed_res().

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

src/protocols/moves/MixedMonteCarlo.hh
src/protocols/moves/MixedMonteCarlo.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MixedMonteCarlo() [1/3]

◆ ~MixedMonteCarlo()

◆ MixedMonteCarlo() [2/3]

◆ MixedMonteCarlo() [3/3]

Member Function Documentation

◆ boltzmann()

◆ highres_score_function()

◆ last_accepted_pose()

◆ last_accepted_score()

◆ lowest_score()

◆ lowest_score_pose()

◆ lowres_score_function()

◆ MC()

◆ operator=()

◆ recover_low() [1/2]

◆ recover_low() [2/2]

◆ reset()

◆ reset_mmc()

◆ score_mixed_res()

◆ show_scores()

Member Data Documentation

◆ highres_scorefxn_

◆ last_accepted_pose_

◆ lowest_score_pose_

◆ lowres_scorefxn_

◆ MC_

◆ tuning_param_