protocols::stepwise::monte_carlo::mover::StepWiseMasterMover Class Reference

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:

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< Size > const &residues_to_resample, Size const resample_round, 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, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...
virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...
virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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< Size > const &residues_to_rebuild)

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_
Size	num_tested_moves_

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 protocols::filters::Filters_map	Filters_map
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

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

References initialize().

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

overridedefault

protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::StepWiseMasterMover

(

StepWiseMasterMover const &

src

)

References initialize(), options_, and scorefxn_.

Member Function Documentation

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().

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().

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().

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().

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.

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().

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

References protocols::stepwise::monte_carlo::mover::ADD, protocols::stepwise::monte_carlo::mover::ADD_LOOP_RES, add_or_delete_mover_, protocols::stepwise::monte_carlo::mover::ADD_SUBMOTIF, protocols::stepwise::monte_carlo::mover::DELETE, protocols::stepwise::monte_carlo::mover::DELETE_LOOP_RES, protocols::stepwise::monte_carlo::mover::FROM_SCRATCH, protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), move_type_string_, protocols::stepwise::monte_carlo::mover::RESAMPLE, protocols::stepwise::monte_carlo::mover::RESAMPLE_INTERNAL_LOCAL, resample_mover_, and vary_loop_length_mover_.

Referenced by apply(), and do_test_move().

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.

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

References initialize(), options_, and scorefxn_.

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().

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().

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

inline

References move_type_string_.

Referenced by build_full_model().

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

private

References protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, core::conformation::Residue::connection_incomplete(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_virtual_residue(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, core::chemical::ResidueType::lower_connect_id(), core::chemical::LOWER_TERMINUS_VARIANT, core::conformation::Residue::name(), protocols::stepwise::monte_carlo::mover::RESAMPLE, protocols::stepwise::monte_carlo::mover::RESAMPLE_INTERNAL_LOCAL, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), core::conformation::Residue::type(), core::chemical::ResidueType::upper_connect_id(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by resample_full_model().

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().

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

inline

References proposal_density_ratio_.

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().

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< Size > const &	residues_to_resample,
		Size const	resample_round,
		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().

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().

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_options

(

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

options

)

References initialize(), and options_.

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

inline

References scorefxn_.

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

inline

References submotif_library_.

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

inline

References stepwise_move_selector_.

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

inline

References success_.

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().

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

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

private

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

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().

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

private

Referenced by initialize().

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

private

Referenced by initialize().

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

private

Referenced by apply_legacy(), and set_minimize_single_res().

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

private

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

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

private

Referenced by test_all_moves(), and test_all_moves_recursively().

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().

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

private

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

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

private

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

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

private

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

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

private

Referenced by initialize(), and preminimize_pose().

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().

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

private

Referenced by initialize(), and set_submotif_library().

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

private

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

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