#include <StepWiseMonteCarlo.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::StepWiseMonteCarlo:

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Public Member Functions
	StepWiseMonteCarlo (core::scoring::ScoreFunctionCOP scorefxn)

	~StepWiseMonteCarlo () override

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

void	apply (core::pose::Pose &pose) override
	Apply the loop-rebuild protocol to the input pose. More...

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

void	set_align_pose (core::pose::PoseCOP pose)

void	set_options (options::StepWiseMonteCarloOptionsCOP options)

options::StepWiseMonteCarloOptionsCOP	options () const

void	set_model_tag (std::string const &setting)

std::string	model_tag () const

void	set_out_path (std::string const &setting)

std::string	out_path () const

void	set_move (mover::StepWiseMove const &setting)

mover::StepWiseMove	move () const

void	set_submotif_library (monte_carlo::submotif::SubMotifLibraryCOP setting)

mover::StepWiseMasterMoverCOP	master_mover () const

void	output_checkpoint_file (core::pose::Pose const &pose, core::pose::Pose const &low, core::Size const k) const

void	remove_checkpoint_file () const

bool	checkpoint_file_exists () const

core::pose::Pose	pose_from_checkpoint_file () const

core::pose::Pose	pose_from_checkpoint_file_low () const

void	set_out_file_prefix (std::string const &setting)

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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	initialize ()

void	initialize_scorefunction ()

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

void	do_main_loop (core::pose::Pose &pose)

void	output_movie (core::pose::Pose const &pose, core::Size const k, std::string const &tag, std::string const &movie_file)

core::Real	display_progress (core::pose::Pose &pose, core::Size const cycle_num)

core::Real	show_scores (core::pose::Pose &pose, std::string const &tag)

std::string	checkpoint_file_name () const
	Helper that contains the formula for naming checkpoint files. More...

std::string	checkpoint_file_name_low () const
	Helper that contains the formula for naming checkpoint files. More...

void	anneal_missing (protocols::moves::MonteCarloOP monte_carlo)

Private Attributes
core::scoring::ScoreFunctionCOP	scorefxn_input_

core::scoring::ScoreFunctionOP	scorefxn_

options::StepWiseMonteCarloOptionsCOP	options_

mover::StepWiseMasterMoverOP	master_mover_

core::pose::PoseCOP	align_pose_ = nullptr

core::Real const	max_missing_weight_

core::Real	missing_weight_interval_

core::Real	missing_weight_

std::string	model_tag_

std::string	out_path_

std::string	out_file_prefix_

std::string	movie_file_trial_

std::string	movie_file_accepted_

mover::StepWiseMove	move_

std::clock_t	start_time_

Additional Inherited Members
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

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...

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...

Constructor & Destructor Documentation

◆ StepWiseMonteCarlo()

protocols::stepwise::monte_carlo::StepWiseMonteCarlo::StepWiseMonteCarlo ( core::scoring::ScoreFunctionCOP scorefxn )

◆ ~StepWiseMonteCarlo()

protocols::stepwise::monte_carlo::StepWiseMonteCarlo::~StepWiseMonteCarlo ( )

overridedefault

Member Function Documentation

◆ anneal_missing()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::anneal_missing ( protocols::moves::MonteCarloOP monte_carlo )

private

References core::scoring::missing_res, missing_weight_, and missing_weight_interval_.

Referenced by do_main_loop().

◆ apply()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::apply ( core::pose::Pose & pose )

overridevirtual

Apply the loop-rebuild protocol to the input pose.

Implements protocols::moves::Mover.

References checkpoint_file_exists(), do_main_loop(), initialize(), master_mover_, move_, protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), protocols::stepwise::monte_carlo::mover::NO_MOVE, options_, pose_from_checkpoint_file(), show_scores(), and core::pose::Pose::size().

◆ checkpoint_file_exists()

bool protocols::stepwise::monte_carlo::StepWiseMonteCarlo::checkpoint_file_exists ( ) const

References checkpoint_file_name().

Referenced by apply(), do_main_loop(), pose_from_checkpoint_file(), and pose_from_checkpoint_file_low().

◆ checkpoint_file_name()

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::checkpoint_file_name ( ) const

private

Helper that contains the formula for naming checkpoint files.

References out_file_prefix_, and out_path_.

Referenced by checkpoint_file_exists(), output_checkpoint_file(), pose_from_checkpoint_file(), and remove_checkpoint_file().

◆ checkpoint_file_name_low()

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::checkpoint_file_name_low ( ) const

private

Helper that contains the formula for naming checkpoint files.

References out_file_prefix_, and out_path_.

Referenced by output_checkpoint_file(), pose_from_checkpoint_file_low(), and remove_checkpoint_file().

◆ display_progress()

Real protocols::stepwise::monte_carlo::StepWiseMonteCarlo::display_progress	(	core::pose::Pose &	pose,
		core::Size const	cycle_num
	)

private

References protocols::stepwise::monte_carlo::get_all_res_list(), missing_weight_, options_, show_scores(), and protocols::TR().

Referenced by do_main_loop().

◆ do_main_loop()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop ( core::pose::Pose & pose )

private

References core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_base_pairs(), anneal_missing(), protocols::stepwise::monte_carlo::build_full_model(), core::pose::full_model_info::check_all_residues_sampled(), checkpoint_file_exists(), core::pose::clearPoseExtraScores(), core::pose::full_model_info::const_full_model_info(), display_progress(), core::pose::Pose::energies(), protocols::stepwise::monte_carlo::get_all_res_list(), protocols::moves::Mover::get_native_pose(), core::pose::getPoseExtraScore(), core::pose::hasPoseExtraScore(), initialize_for_movie(), master_mover_, core::scoring::missing_res, movie_file_accepted_, movie_file_trial_, options_, output_checkpoint_file(), output_movie(), pose_from_checkpoint_file_low(), remove_checkpoint_file(), core::scoring::rms, core::pose::full_model_info::FullModelInfo::rna_bulge_res(), scorefxn_, core::pose::setPoseExtraScore(), show_scores(), start_time_, protocols::stepwise::modeler::align::superimpose_with_stepwise_aligner(), protocols::stepwise::modeler::switch_focus_among_poses_randomly(), core::scoring::Energies::total_energies(), protocols::TR(), and core::scoring::Energies::weights().

Referenced by apply().

◆ get_name()

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ initialize()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::initialize ( )

private

References align_pose_, protocols::moves::Mover::get_native_pose(), initialize_scorefunction(), master_mover_, options_, scorefxn_, and start_time_.

Referenced by apply().

◆ initialize_for_movie()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::initialize_for_movie ( core::pose::Pose const & pose )

private

References model_tag_, movie_file_accepted_, movie_file_trial_, options_, out_path_, output_movie(), core::pose::setPoseExtraScore(), and protocols::TR().

Referenced by do_main_loop().

◆ initialize_scorefunction()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::initialize_scorefunction ( )

private

References core::scoring::loop_close, master_mover_, max_missing_weight_, core::scoring::missing_res, missing_weight_, missing_weight_interval_, options_, scorefxn_, and scorefxn_input_.

Referenced by initialize().

◆ master_mover()

mover::StepWiseMasterMoverCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::master_mover ( ) const

inline

References master_mover_.

◆ model_tag()

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::model_tag ( ) const

inline

References model_tag_.

◆ move()

mover::StepWiseMove protocols::stepwise::monte_carlo::StepWiseMonteCarlo::move ( ) const

inline

References move_.

◆ options()

options::StepWiseMonteCarloOptionsCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::options ( ) const

inline

References options_.

Referenced by set_options().

◆ out_path()

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::out_path ( ) const

inline

References out_path_.

◆ output_checkpoint_file()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::output_checkpoint_file	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	low,
		core::Size const	k
	)		const

References checkpoint_file_name(), checkpoint_file_name_low(), protocols::moves::Mover::get_native_pose(), model_tag_, protocols::stepwise::monte_carlo::output_to_silent_file(), and core::pose::setPoseExtraScore().

Referenced by do_main_loop().

◆ output_movie()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::output_movie	(	core::pose::Pose const &	pose,
		core::Size const	k,
		std::string const &	tag,
		std::string const &	movie_file
	)

private

References protocols::moves::Mover::get_native_pose(), options_, protocols::stepwise::monte_carlo::output_to_silent_file(), and core::pose::setPoseExtraScore().

Referenced by do_main_loop(), and initialize_for_movie().

◆ pose_from_checkpoint_file()

core::pose::Pose protocols::stepwise::monte_carlo::StepWiseMonteCarlo::pose_from_checkpoint_file ( ) const

References checkpoint_file_exists(), and checkpoint_file_name().

Referenced by apply().

◆ pose_from_checkpoint_file_low()

core::pose::Pose protocols::stepwise::monte_carlo::StepWiseMonteCarlo::pose_from_checkpoint_file_low ( ) const

References checkpoint_file_exists(), and checkpoint_file_name_low().

Referenced by do_main_loop().

◆ remove_checkpoint_file()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::remove_checkpoint_file ( ) const

References checkpoint_file_name(), checkpoint_file_name_low(), and core::io::silent::remove_silent_file_if_it_exists().

Referenced by do_main_loop().

◆ set_align_pose()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_align_pose ( core::pose::PoseCOP pose )

inline

References align_pose_.

◆ set_model_tag()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_model_tag ( std::string const & setting )

inline

References model_tag_.

◆ set_move()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_move ( mover::StepWiseMove const & setting )

inline

References move_.

◆ set_native_pose()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_native_pose ( core::pose::PoseCOP pose )

overridevirtual

setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe

Reimplemented from protocols::moves::Mover.

References master_mover_.

◆ set_options()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_options ( options::StepWiseMonteCarloOptionsCOP options )

References master_mover_, options(), and options_.

◆ set_out_file_prefix()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_out_file_prefix ( std::string const & setting )

inline

References out_file_prefix_.

◆ set_out_path()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_out_path ( std::string const & setting )

inline

References out_path_.

◆ set_submotif_library()

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_submotif_library ( monte_carlo::submotif::SubMotifLibraryCOP setting )

References master_mover_.

◆ show_scores()

Real protocols::stepwise::monte_carlo::StepWiseMonteCarlo::show_scores	(	core::pose::Pose &	pose,
		std::string const &	tag
	)

private

References options_, scorefxn_, and protocols::TR().

Referenced by apply(), display_progress(), and do_main_loop().

Member Data Documentation

◆ align_pose_

core::pose::PoseCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::align_pose_ = nullptr

private

Referenced by initialize(), and set_align_pose().

◆ master_mover_

mover::StepWiseMasterMoverOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::master_mover_

private

Referenced by apply(), do_main_loop(), initialize(), initialize_scorefunction(), master_mover(), set_native_pose(), set_options(), and set_submotif_library().

◆ max_missing_weight_

core::Real const protocols::stepwise::monte_carlo::StepWiseMonteCarlo::max_missing_weight_

private

Referenced by initialize_scorefunction().

◆ missing_weight_

core::Real protocols::stepwise::monte_carlo::StepWiseMonteCarlo::missing_weight_

private

Referenced by anneal_missing(), display_progress(), and initialize_scorefunction().

◆ missing_weight_interval_

core::Real protocols::stepwise::monte_carlo::StepWiseMonteCarlo::missing_weight_interval_

private

Referenced by anneal_missing(), and initialize_scorefunction().

◆ model_tag_

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::model_tag_

private

Referenced by initialize_for_movie(), model_tag(), output_checkpoint_file(), and set_model_tag().

◆ move_

mover::StepWiseMove protocols::stepwise::monte_carlo::StepWiseMonteCarlo::move_

private

Referenced by apply(), move(), and set_move().

◆ movie_file_accepted_

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::movie_file_accepted_

private

Referenced by do_main_loop(), and initialize_for_movie().

◆ movie_file_trial_

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::movie_file_trial_

private

Referenced by do_main_loop(), and initialize_for_movie().

◆ options_

options::StepWiseMonteCarloOptionsCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::options_

private

Referenced by apply(), display_progress(), do_main_loop(), initialize(), initialize_for_movie(), initialize_scorefunction(), options(), output_movie(), set_options(), and show_scores().

◆ out_file_prefix_

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::out_file_prefix_

private

Referenced by checkpoint_file_name(), checkpoint_file_name_low(), and set_out_file_prefix().

◆ out_path_

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::out_path_

private

Referenced by checkpoint_file_name(), checkpoint_file_name_low(), initialize_for_movie(), out_path(), and set_out_path().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::scorefxn_

private

Referenced by do_main_loop(), initialize(), initialize_scorefunction(), and show_scores().

◆ scorefxn_input_

core::scoring::ScoreFunctionCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::scorefxn_input_

private

Referenced by initialize_scorefunction().

◆ start_time_

std::clock_t protocols::stepwise::monte_carlo::StepWiseMonteCarlo::start_time_

private

Referenced by do_main_loop(), and initialize().

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

src/protocols/stepwise/monte_carlo/StepWiseMonteCarlo.hh
src/protocols/stepwise/monte_carlo/StepWiseMonteCarlo.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StepWiseMonteCarlo()

◆ ~StepWiseMonteCarlo()

Member Function Documentation

◆ anneal_missing()

◆ apply()

◆ checkpoint_file_exists()

◆ checkpoint_file_name()

◆ checkpoint_file_name_low()

◆ display_progress()

◆ do_main_loop()

◆ get_name()

◆ initialize()

◆ initialize_for_movie()

◆ initialize_scorefunction()

◆ master_mover()

◆ model_tag()

◆ move()

◆ options()

◆ out_path()

◆ output_checkpoint_file()

◆ output_movie()

◆ pose_from_checkpoint_file()

◆ pose_from_checkpoint_file_low()

◆ remove_checkpoint_file()

◆ set_align_pose()

◆ set_model_tag()

◆ set_move()

◆ set_native_pose()

◆ set_options()

◆ set_out_file_prefix()

◆ set_out_path()

◆ set_submotif_library()

◆ show_scores()

Member Data Documentation

◆ align_pose_

◆ master_mover_

◆ max_missing_weight_

◆ missing_weight_

◆ missing_weight_interval_

◆ model_tag_

◆ move_

◆ movie_file_accepted_

◆ movie_file_trial_

◆ options_

◆ out_file_prefix_

◆ out_path_

◆ scorefxn_

◆ scorefxn_input_

◆ start_time_