#include <LoopMover_CCD.hh>

Inheritance diagram for protocols::loops::loop_mover::refine::LoopMover_Refine_CCD:

[legend]

Public Member Functions
	LoopMover_Refine_CCD ()

	LoopMover_Refine_CCD (protocols::loops::LoopsOP loops_in)

	LoopMover_Refine_CCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn)

	~LoopMover_Refine_CCD () override

protocols::moves::MoverOP	clone () const override
	Clone this object. More...

void	set_default_settings ()

void	set_redesign_loop (bool value=true)

bool	get_redesign_loop ()

void	set_task_factory (core::pack::task::TaskFactoryCOP task_factory_in)

core::pack::task::TaskFactoryCOP	get_task_factory () const

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

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

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

void	outer_cycles (core::Size value)

void	max_inner_cycles (core::Size value)

void	repack_period (core::Size value)

void	temp_initial (core::Real value)

void	temp_final (core::Real value)

void	repack_neighbors (bool s)

void	set_fold_tree_from_loops (bool const s)

bool	set_fold_tree_from_loops () const

core::kinematics::MoveMapOP	move_map () const

void	move_map (core::kinematics::MoveMapOP mm)

protocols::loops::LoopsCOP	get_loops () const

void	set_flank_residue_min (bool value)

bool	flank_residue_min () const

core::Size	inner_cycles () const

core::Size	current_cycle_number () const

core::Size	repack_period () const

bool	repack_neighbors () const

void	setup_movemap (core::pose::Pose const &pose, protocols::loops::Loops const &loops, utility::vector1< bool > const &allow_repack, core::kinematics::MoveMapOP &movemap)
	setup an appropriate movemap for the given loops More...

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

Public Member Functions inherited from protocols::loops::loop_mover::LoopMover
	LoopMover ()

	LoopMover (protocols::loops::LoopsOP loops_in)

	LoopMover (protocols::loops::LoopsFileData const &loops_from_file)

	LoopMover (protocols::loops::GuardedLoopsFromFileOP guarded_loops)

	LoopMover (LoopMover const &rhs)
	copy ctor More...

LoopMover &	operator= (LoopMover const &rhs)
	assignment operator More...

	~LoopMover () override

void	set_guarded_loops_not_in_charge ()
	Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply() More...

void	set_scorefxn (const core::scoring::ScoreFunctionOP score_in)

const core::scoring::ScoreFunctionOP &	scorefxn () const

void	loops (protocols::loops::LoopsOP lptr)
	Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data. More...

void	loops (LoopsFileData const &loop_file_data)
	Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ). More...

void	loops (protocols::loops::loops_definers::LoopsDefinerOP setting)

void	loops (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
	Set the guarded_loops pointer. More...

protocols::loops::LoopsCOP	loops () const
	Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...

protocols::loops::LoopsOP	loops ()
	non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...

const utility::vector1< core::fragment::FragSetOP > &	frag_libs () const

core::conformation::torsion_bin_string	torsion_features_string (core::pose::Pose const &pose) const
	create a string representing the torsion bins (ABEGX) for the loops defined in the guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there's only one Loop object in the guarded_loops_ object). More...

virtual void	set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
	Extend a loop. More...

void	add_fragments (core::fragment::FragSetOP fragset)
	add a fragment set More...

void	clear_fragments ()
	clear the list of fragment sets More...

MoveMapOP const &	false_movemap () const
	explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...

void	false_movemap (MoveMapOP const &mm)
	explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...

checkpoint::CheckPointerOP &	get_checkpoints ()

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

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 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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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
void	read_options ()

basic::Tracer &	tr () const override

Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover
core::Size	enforce_false_movemap (MoveMapOP &mm) const
	import the false_movemap's explicit False settings into the given MoveMap More...

void	set_loops_from_pose_observer_cache (core::pose::Pose const &pose)
	allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step More...

bool	use_loops_from_observer_cache () const

void	set_use_loops_from_observer_cache (bool const loops_from_observer_cache)

void	resolve_loop_indices (core::pose::Pose const &p)
	Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply. 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...

Protected Attributes
core::pack::task::TaskFactoryOP	task_factory_

bool	redesign_loop_

Private Member Functions
core::scoring::ScoreFunctionOP	get_new_ramping_scorefxn ()

core::scoring::ScoreFunctionOP	ramping_scorefxn ()

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

core::pack::task::PackerTaskOP	get_packer_task (core::pose::Pose const &pose)

void	increase_chainbreak_weight_and_update_monte_carlo (core::Size iteration_number, core::scoring::ScoreFunctionOP local_scorefxn, protocols::moves::MonteCarlo &mc, core::pose::Pose &pose)

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

Private Attributes
bool	packing_isolated_to_active_loops_

bool	set_fold_tree_from_loops_

bool	user_defined_move_map_

bool	flank_residue_min_

bool	debug_

bool	repack_neighbors_

core::Size	outer_cycles_

core::Size	max_inner_cycles_

core::Size	inner_cycles_

core::Size	current_cycle_number_

core::Size	repack_period_

core::Real	temp_initial_

core::Real	temp_final_

core::kinematics::FoldTreeOP	original_fold_tree_

core::select::movemap::MoveMapFactoryCOP	move_map_factory_
	If set, the move_map_factory_ will reset the move_map_ (as a user-defined) at the start of every apply() More...

core::kinematics::MoveMapOP	move_map_

core::scoring::ScoreFunctionOP	ramping_scorefxn_

Additional Inherited Members
Public Types inherited from protocols::loops::loop_mover::LoopMover
typedef core::kinematics::MoveMapOP	MoveMapOP

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

Constructor & Destructor Documentation

◆ LoopMover_Refine_CCD() [1/3]

protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD ( )

References protocols::loops::get_fa_scorefxn(), read_options(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

◆ LoopMover_Refine_CCD() [2/3]

protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD ( protocols::loops::LoopsOP loops_in )

References protocols::loops::get_fa_scorefxn(), read_options(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

◆ LoopMover_Refine_CCD() [3/3]

protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD	(	protocols::loops::LoopsOP	loops_in,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References read_options(), protocols::loops::loop_mover::LoopMover::scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

◆ ~LoopMover_Refine_CCD()

protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::~LoopMover_Refine_CCD ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply ( core::pose::Pose & )

overridevirtual

Apply the loop-build protocol to the input pose.

Implements protocols::loops::loop_mover::LoopMover.

References core::scoring::chainbreak, protocols::loops::loop_mover::refine::CHAINBREAK_SCORE_RAMP_FACTOR, current_cycle_number_, debugging_output(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_native_pose(), get_new_ramping_scorefxn(), get_packer_task(), protocols::moves::Mover::get_self_ptr(), protocols::loops::loop_mover::refine::IC_RefineCCDStandard, increase_chainbreak_weight_and_update_monte_carlo(), inner_cycles_, protocols::loops::loop_mover::LoopMover::loops(), max_inner_cycles_, protocols::mean_field::min(), move_map(), move_map_, move_map_factory_, original_fold_tree_, outer_cycles_, core::pack::pack_rotamers(), ramping_scorefxn(), protocols::loops::remove_cutpoint_variants(), protocols::loops::loop_mover::LoopMover::resolve_loop_indices(), set_fold_tree_from_loops_, protocols::loops::loop_mover::LoopMover::set_loops_from_pose_observer_cache(), protocols::moves::Mover::set_native_pose(), setup_foldtree_and_add_cutpoint_variants(), setup_movemap(), task_factory_, temp_final_, temp_initial_, tr(), and protocols::loops::loop_mover::LoopMover::use_loops_from_observer_cache().

Referenced by protocols::LoopRefine::apply(), and protocols::forge::remodel::RemodelMover::confirm_sequence().

◆ clone()

protocols::moves::MoverOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::clone ( ) const

overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

◆ current_cycle_number()

core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::current_cycle_number ( ) const

inline

References current_cycle_number_.

◆ debugging_output()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::debugging_output ( core::pose::Pose & pose )

private

References debug_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::conformation::membrane::out, and ramping_scorefxn().

Referenced by apply().

◆ flank_residue_min()

bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::flank_residue_min ( ) const

inline

References flank_residue_min_.

◆ get_loops()

protocols::loops::LoopsCOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_loops ( void ) const

References protocols::loops::loop_mover::LoopMover::loops().

Referenced by show().

◆ get_name()

std::string protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::loops::loop_mover::LoopMover.

References mover_name().

◆ get_new_ramping_scorefxn()

core::scoring::ScoreFunctionOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_new_ramping_scorefxn ( )

private

References protocols::loops::get_fa_scorefxn(), ramping_scorefxn_, and protocols::loops::loop_mover::LoopMover::scorefxn().

Referenced by apply(), and ramping_scorefxn().

◆ get_packer_task()

core::pack::task::PackerTaskOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_packer_task ( core::pose::Pose const & pose )

private

References protocols::loops::loop_mover::LoopMover::loops(), packing_isolated_to_active_loops_, redesign_loop_, repack_neighbors_, and task_factory_.

Referenced by apply().

◆ get_redesign_loop()

bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_redesign_loop ( )

inline

References redesign_loop_.

◆ get_task_factory()

core::pack::task::TaskFactoryCOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_task_factory ( ) const

References task_factory_.

◆ increase_chainbreak_weight_and_update_monte_carlo()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::increase_chainbreak_weight_and_update_monte_carlo	(	core::Size	iteration_number,
		core::scoring::ScoreFunctionOP	local_scorefxn,
		protocols::moves::MonteCarlo &	mc,
		core::pose::Pose &	pose
	)

private

References core::scoring::chainbreak, protocols::loops::loop_mover::refine::CHAINBREAK_SCORE_RAMP_FACTOR, protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::score_function(), and tr().

Referenced by apply().

◆ inner_cycles()

core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::inner_cycles ( ) const

inline

References inner_cycles_.

◆ max_inner_cycles()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::max_inner_cycles ( core::Size value )

inline

References max_inner_cycles_.

◆ move_map() [1/2]

loop_mover::LoopMover::MoveMapOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map ( ) const

References move_map_.

Referenced by apply(), and show().

◆ move_map() [2/2]

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map ( core::kinematics::MoveMapOP mm )

References move_map_, and user_defined_move_map_.

◆ mover_name()

std::string protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::mover_name ( )

static

Referenced by get_name(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator::keyname(), and provide_xml_schema().

◆ outer_cycles()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::outer_cycles ( core::Size value )

inline

References outer_cycles_.

◆ parse_my_tag()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::scoring::ScoreFunction::clone(), protocols::loops::loops_definers::load_loop_definitions(), protocols::loops::loop_mover::LoopMover::loops(), max_inner_cycles_, move_map_factory_, outer_cycles_, packing_isolated_to_active_loops_, protocols::rosetta_scripts::parse_movemap_factory_legacy(), core::pack::task::parse_task_operations(), set_fold_tree_from_loops(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), set_task_factory(), protocols::loops::loop_mover::LoopMover::set_use_loops_from_observer_cache(), task_factory_, temp_final(), and temp_initial().

◆ provide_xml_schema()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), protocols::loops::loops_definers::attributes_for_load_loop_definitions(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator::provide_xml_schema().

◆ ramping_scorefxn()

core::scoring::ScoreFunctionOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::ramping_scorefxn ( )

private

References get_new_ramping_scorefxn(), and ramping_scorefxn_.

Referenced by apply(), and debugging_output().

◆ read_options()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::read_options ( )

protected

References core::pack::interaction_graph::debug, debug_, max_inner_cycles_, outer_cycles_, repack_neighbors_, repack_period_, temp_final_, and temp_initial_.

Referenced by LoopMover_Refine_CCD().

◆ repack_neighbors() [1/2]

bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_neighbors ( ) const

inline

References repack_neighbors_.

◆ repack_neighbors() [2/2]

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_neighbors ( bool s )

inline

References repack_neighbors_.

◆ repack_period() [1/2]

core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period ( ) const

inline

References repack_period_.

◆ repack_period() [2/2]

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period ( core::Size value )

inline

References repack_period_.

◆ set_default_settings()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_default_settings ( )

References current_cycle_number_, flank_residue_min_, inner_cycles_, max_inner_cycles_, move_map_, original_fold_tree_, packing_isolated_to_active_loops_, and redesign_loop_.

Referenced by LoopMover_Refine_CCD().

◆ set_flank_residue_min()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_flank_residue_min ( bool value )

inline

References flank_residue_min_.

◆ set_fold_tree_from_loops() [1/2]

bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops ( ) const

inline

References set_fold_tree_from_loops_.

Referenced by parse_my_tag().

◆ set_fold_tree_from_loops() [2/2]

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops ( bool const s )

inline

References set_fold_tree_from_loops_.

◆ set_redesign_loop()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_redesign_loop ( bool value = true )

inline

References redesign_loop_.

◆ set_task_factory()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory ( core::pack::task::TaskFactoryCOP task_factory_in )

References task_factory_.

Referenced by protocols::forge::remodel::RemodelMover::confirm_sequence(), and parse_my_tag().

◆ setup_foldtree_and_add_cutpoint_variants()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_foldtree_and_add_cutpoint_variants ( core::pose::Pose & pose )

private

References protocols::loops::add_cutpoint_variants(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::loops::loop_mover::LoopMover::loops(), original_fold_tree_, and set_fold_tree_from_loops_.

Referenced by apply().

◆ setup_movemap()

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap	(	core::pose::Pose const &	pose,
		protocols::loops::Loops const &	loops,
		utility::vector1< bool > const &	allow_repack,
		core::kinematics::MoveMapOP &	movemap
	)

setup an appropriate movemap for the given loops

Parameters

[in]	loops	The loops to model.
[in]	allow_repack	Indicates whether or not to allow a position to repack.
[out]	movemap	Output movemap, all settings added here.