Central mover of stepwise Monte Carlo protocols, handing work off to special move types. More...

#include <StepWiseMasterMover.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::mover::StepWiseMasterMover:

[legend]

Public Member Functions
	StepWiseMasterMover (core::scoring::ScoreFunctionCOP scorefxn, protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP options)

	~StepWiseMasterMover () override

void	apply (Pose &) override
	Main Method. More...

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

	StepWiseMasterMover (StepWiseMasterMover const &src)

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	apply (core::pose::Pose &pose, StepWiseMove const &stepwise_move, bool const figure_out_all_possible_moves=true)

void	do_the_move (StepWiseMove const &move, core::pose::Pose &pose)

bool	apply_legacy (Pose &)

void	initialize (core::scoring::ScoreFunctionCOP scorefxn, protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP options)

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

void	set_minimize_single_res (bool const minimize_single_res)

bool	do_test_move (StepWiseMove const &move, core::pose::Pose &pose)

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

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

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)

std::string	move_type_string () const

bool	success () const

core::Real const &	proposal_density_ratio () const

void	resample_full_model (core::pose::Pose const &start_pose, core::pose::Pose &output_pose, bool const checkpointing_breadcrumbs)

void	resample_full_model (core::pose::Pose const &start_pose, core::pose::Pose &output_pose, bool const checkpointing_breadcrumbs, utility::vector1< core::Size > const &residues_to_resample, core::Size const resample_round, core::Size const nstruct)

void	build_full_model (core::pose::Pose const &start_pose, core::pose::Pose &full_model_pose, bool const &choose_random=false)

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

StepWiseMoveSelectorCOP	stepwise_move_selector () const

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 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...

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

bool	test_all_moves (core::pose::Pose &pose)

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

utility::vector1< StepWiseMove >	moves_for_pose (core::pose::Pose const &start_pose, utility::vector1< core::Size > const &residues_to_rebuild)

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...

Detailed Description

Central mover of stepwise Monte Carlo protocols, handing work off to special move types.

It's worth noting that one function that for historical reasons is a method of this class is capable of spawning threads. Notably, that method is not called by this Mover's apply function (rather, it calls this Mover's apply function!) and so you don't have to worry. If you are studying this class as an archetypical example of a Mover, for one thing, don't do that because it isn't; for another thing, don't multithread your apply function as a misguided inference from how this Mover has a multithreaded function that's not apply.

Constructor & Destructor Documentation

◆ StepWiseMasterMover() [1/2]

protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::StepWiseMasterMover	(	core::scoring::ScoreFunctionCOP	scorefxn,
		protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP	options
	)

References initialize().

◆ ~StepWiseMasterMover()

protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::~StepWiseMasterMover ( )

overridedefault

◆ StepWiseMasterMover() [2/2]

protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::StepWiseMasterMover ( StepWiseMasterMover const & src )

References initialize(), options_, and scorefxn_.

Member Function Documentation

◆ apply() [1/2]

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply	(	core::pose::Pose &	pose,
		StepWiseMove const &	stepwise_move,
		bool const	figure_out_all_possible_moves = `true`
	)

References protocols::stepwise::monte_carlo::mover::ADD, protocols::stepwise::monte_carlo::mover::ADD_LOOP_RES, protocols::stepwise::monte_carlo::mover::StepWiseMove::attachments(), core::pose::full_model_info::const_full_model_info(), protocols::stepwise::monte_carlo::mover::DELETE_LOOP_RES, do_the_move(), protocols::stepwise::monte_carlo::get_move_type_string(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), move_type_string_, options_, proposal_density_ratio_, scorefxn_, stepwise_move_selector_, protocols::stepwise::modeler::switch_focus_to_other_pose(), and protocols::TR().

◆ apply() [2/2]

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References apply_legacy(), move_type_string_, options_, proposal_density_ratio_, stepwise_move_selector_, and success_.

Referenced by resample_full_model(), and test_all_moves_recursively().

◆ apply_legacy()

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply_legacy ( pose::Pose & pose )

References add_or_delete_mover_, minimize_single_res_, move_type_string_, options_, proposal_density_ratio_, resample_mover_, core::scoring::rg, set_minimize_single_res(), success_, and protocols::stepwise::modeler::switch_focus_among_poses_randomly().

Referenced by apply().

◆ build_full_model()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model	(	core::pose::Pose const &	start_pose,
		core::pose::Pose &	full_model_pose,
		bool const &	choose_random = `false`
	)

References add_mover_, add_or_delete_mover_, core::pose::full_model_info::const_full_model_info(), initialize(), move_type_string(), options_, core::pose::full_model_info::FullModelInfo::res_list(), core::pose::full_model_info::FullModelInfo::rna_bulge_res(), core::pose::stepwise_addable_residue(), protocols::TR(), and core::pose::full_model_info::FullModelInfo::working_res().

Referenced by protocols::stepwise::monte_carlo::build_full_model().

◆ clone()

protocols::moves::MoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ do_test_move()

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::do_test_move	(	StepWiseMove const &	move,
		core::pose::Pose &	pose
	)

References do_the_move(), core::pose::Pose::dump_pdb(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), protocols::stepwise::monte_carlo::mover::NO_MOVE, options_, preminimize_pose(), core::pose::tag_from_pose(), test_all_moves(), and protocols::TR().

◆ do_the_move()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::do_the_move	(	StepWiseMove const &	move,
		core::pose::Pose &	pose
	)

Referenced by apply(), and do_test_move().

◆ get_name()

std::string protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ initialize() [1/2]

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::initialize ( )

private

References add_mover_, add_or_delete_mover_, delete_mover_, from_scratch_mover_, protocols::moves::Mover::get_native_pose(), options_, resample_mover_, scorefxn_, protocols::stepwise::monte_carlo::mover::setup_unified_stepwise_modeler(), stepwise_modeler_, stepwise_move_selector_, submotif_library_, and vary_loop_length_mover_.

Referenced by build_full_model(), initialize(), resample_full_model(), set_options(), and StepWiseMasterMover().

◆ initialize() [2/2]

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::initialize	(	core::scoring::ScoreFunctionCOP	scorefxn,
		protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP	options
	)

References initialize(), options_, and scorefxn_.

◆ initialize_pose_if_empty()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::initialize_pose_if_empty ( core::pose::Pose & pose )

References add_or_delete_mover_, options_, and core::pose::Pose::size().

◆ move_type_string()

std::string protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::move_type_string ( ) const

inline

References move_type_string_.

Referenced by build_full_model().

◆ moves_for_pose()

utility::vector1< StepWiseMove > protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose	(	core::pose::Pose const &	start_pose,
		utility::vector1< core::Size > const &	residues_to_rebuild
	)

private

Referenced by resample_full_model().

◆ preminimize_pose()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::preminimize_pose ( core::pose::Pose & pose )

References core::pose::fix_up_residue_type_variants(), protocols::stepwise::modeler::get_all_residues(), core::pose::full_model_info::get_moving_res_from_full_model_info(), core::pose::full_model_info::nonconst_full_model_info(), core::pose::full_model_info::FullModelInfo::other_pose_list(), and stepwise_modeler_.

Referenced by do_test_move().

◆ proposal_density_ratio()

core::Real const& protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::proposal_density_ratio ( ) const

inline

References proposal_density_ratio_.

◆ resample_full_model() [1/2]

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model	(	core::pose::Pose const &	start_pose,
		core::pose::Pose &	output_pose,
		bool const	checkpointing_breadcrumbs
	)

References core::pose::Pose::size().

Referenced by protocols::rna::movers::ERRASER2Protocol::resample_full_model().

◆ resample_full_model() [2/2]

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model	(	core::pose::Pose const &	start_pose,
		core::pose::Pose &	output_pose,
		bool const	checkpointing_breadcrumbs,
		utility::vector1< core::Size > const &	residues_to_resample,
		core::Size const	resample_round,
		core::Size const	nstruct
	)

References core::pose::addVirtualResAsRoot(), apply(), core::pose::Pose::dump_pdb(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), core::chemical::FA_STANDARD, core::import_pose::pose_stream::PDBPoseInputStream::fill_pose(), core::pose::Pose::fold_tree(), initialize(), moves_for_pose(), core::pose::full_model_info::nonconst_full_model_info(), protocols::stepwise::monte_carlo::mover::read_checkpoint_log(), protocols::stepwise::monte_carlo::mover::residue_rebuild_checkpoint_namer(), protocols::stepwise::monte_carlo::mover::residue_rebuild_log_namer(), core::pose::full_model_info::SAMPLE, scorefxn_, protocols::stepwise::monte_carlo::mover::set_up_params_for_move(), stepwise_move_selector_, protocols::TR(), and protocols::stepwise::monte_carlo::mover::write_checkpoint().

◆ set_minimize_single_res()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_minimize_single_res ( bool const minimize_single_res )

References add_or_delete_mover_, minimize_single_res_, and resample_mover_.

Referenced by apply_legacy().

◆ set_options()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_options ( protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP options )

References initialize(), and options_.

◆ set_scorefxn()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

inline

References scorefxn_.

◆ set_submotif_library()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_submotif_library ( monte_carlo::submotif::SubMotifLibraryCOP setting )

inline

References submotif_library_.

◆ stepwise_move_selector()

StepWiseMoveSelectorCOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::stepwise_move_selector ( ) const

inline

References stepwise_move_selector_.

◆ success()

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::success ( ) const

inline

References success_.

◆ test_all_moves()

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::test_all_moves ( core::pose::Pose & pose )

private

References num_tested_moves_, and test_all_moves_recursively().

Referenced by do_test_move().

◆ test_all_moves_recursively()

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::test_all_moves_recursively ( core::pose::Pose & pose )

private

References protocols::stepwise::monte_carlo::mover::ADD, add_mover_, apply(), protocols::stepwise::monte_carlo::get_all_res_list(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), num_tested_moves_, options_, stepwise_move_selector_, success_, and protocols::TR().

Referenced by test_all_moves().

Member Data Documentation

◆ add_mover_

AddMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::add_mover_

private

Referenced by build_full_model(), initialize(), and test_all_moves_recursively().

◆ add_or_delete_mover_

AddOrDeleteMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::add_or_delete_mover_

private

Referenced by apply_legacy(), build_full_model(), do_the_move(), initialize(), initialize_pose_if_empty(), and set_minimize_single_res().

◆ delete_mover_

DeleteMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::delete_mover_

private

Referenced by initialize().

◆ from_scratch_mover_

FromScratchMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::from_scratch_mover_

private

Referenced by initialize().

◆ minimize_single_res_

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::minimize_single_res_

private

Referenced by apply_legacy(), and set_minimize_single_res().

◆ move_type_string_

std::string protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::move_type_string_

private

Referenced by apply(), apply_legacy(), do_the_move(), and move_type_string().

◆ num_tested_moves_

core::Size protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::num_tested_moves_

private

Referenced by test_all_moves(), and test_all_moves_recursively().

◆ options_

protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::options_

private

Referenced by apply(), apply_legacy(), build_full_model(), do_test_move(), initialize(), initialize_pose_if_empty(), set_options(), StepWiseMasterMover(), and test_all_moves_recursively().

◆ proposal_density_ratio_

core::Real protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::proposal_density_ratio_

private

Referenced by apply(), apply_legacy(), and proposal_density_ratio().

◆ resample_mover_

ResampleMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_mover_

private

Referenced by apply_legacy(), do_the_move(), initialize(), and set_minimize_single_res().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::scorefxn_

private

Referenced by apply(), initialize(), resample_full_model(), set_scorefxn(), and StepWiseMasterMover().

◆ stepwise_modeler_

modeler::StepWiseModelerOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::stepwise_modeler_

private

Referenced by initialize(), and preminimize_pose().

◆ stepwise_move_selector_

StepWiseMoveSelectorOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::stepwise_move_selector_

private

Referenced by apply(), initialize(), resample_full_model(), stepwise_move_selector(), and test_all_moves_recursively().

◆ submotif_library_

monte_carlo::submotif::SubMotifLibraryCOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::submotif_library_

private

Referenced by initialize(), and set_submotif_library().

◆ success_

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::success_

private

Referenced by apply(), apply_legacy(), success(), and test_all_moves_recursively().

◆ vary_loop_length_mover_

VaryLoopLengthMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::vary_loop_length_mover_

private

Referenced by do_the_move(), and initialize().

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

src/protocols/stepwise/monte_carlo/mover/StepWiseMasterMover.hh
src/protocols/stepwise/monte_carlo/mover/StepWiseMasterMover.cc

Private Attributes
bool	minimize_single_res_

core::scoring::ScoreFunctionCOP	scorefxn_

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

modeler::StepWiseModelerOP	stepwise_modeler_

DeleteMoverOP	delete_mover_

AddMoverOP	add_mover_

FromScratchMoverOP	from_scratch_mover_

AddOrDeleteMoverOP	add_or_delete_mover_

ResampleMoverOP	resample_mover_

VaryLoopLengthMoverOP	vary_loop_length_mover_

monte_carlo::submotif::SubMotifLibraryCOP	submotif_library_

StepWiseMoveSelectorOP	stepwise_move_selector_

bool	success_

std::string	move_type_string_

core::Real	proposal_density_ratio_

core::Size	num_tested_moves_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ StepWiseMasterMover() [1/2]

◆ ~StepWiseMasterMover()

◆ StepWiseMasterMover() [2/2]

Member Function Documentation

◆ apply() [1/2]

◆ apply() [2/2]

◆ apply_legacy()

◆ build_full_model()

◆ clone()

◆ do_test_move()

◆ do_the_move()

◆ get_name()

◆ initialize() [1/2]

◆ initialize() [2/2]

◆ initialize_pose_if_empty()

◆ move_type_string()

◆ moves_for_pose()

◆ preminimize_pose()

◆ proposal_density_ratio()

◆ resample_full_model() [1/2]

◆ resample_full_model() [2/2]

◆ set_minimize_single_res()

◆ set_options()

◆ set_scorefxn()

◆ set_submotif_library()

◆ stepwise_move_selector()

◆ success()

◆ test_all_moves()

◆ test_all_moves_recursively()

Member Data Documentation

◆ add_mover_

◆ add_or_delete_mover_

◆ delete_mover_

◆ from_scratch_mover_

◆ minimize_single_res_

◆ move_type_string_

◆ num_tested_moves_

◆ options_

◆ proposal_density_ratio_

◆ resample_mover_

◆ scorefxn_

◆ stepwise_modeler_

◆ stepwise_move_selector_

◆ submotif_library_

◆ success_

◆ vary_loop_length_mover_