#include <LoopGraph.hh>

Inheritance diagram for core::scoring::loop_graph::LoopGraph:

Public Member Functions
	LoopGraph ()

	~LoopGraph () override

void	update (pose::Pose &pose, bool const verbose=false)

evaluator::LoopClosePotentialEvaluatorCOP	loop_score_evaluator (Size const n) const

Size	num_current_pose_loops () const

Real	total_energy () const

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

void	update_loops_and_cycles (utility::vector1< Size > const &pose_domain_map, utility::vector1< Size > const &cutpoint_open)

Size	nmissing (pose::Pose const &pose) const

utility::vector1< char >	missing_residues (pose::Pose const &pose) const

utility::vector1 < utility::vector1< Size > >	loop_suites (bool include_free_loops=true) const
	If include_free_loops is turned off, loops with takeoff_domain == 0 or landing_domain == 0 will not be included. More...

void	set_error_out_on_complex_cycles (bool const &setting)

bool	has_just_simple_cycles () const

void	set_use_6D_potential (bool const &setting)

void	check_loop_cycles_are_disjoint (bool const verbose=false)

utility::vector1< LoopCycle > const &	loop_cycles () const

Private Member Functions
void	figure_out_loop_cycles ()

void	figure_out_loop_cycles_tiernan ()

void	record_loop_cycle (utility::vector1< Size > const &elementary_cycle, Size const &idx, utility::vector1< Loop > const &loops_for_cycle_in)

void	figure_out_loop_cycles_legacy ()

void	look_for_cycles_recursively (Size const current_domain, utility::vector1< Size > parent_domains_in, utility::vector1< Loop > loops_so_far_in)

bool	check_disjoint (LoopCycle loop_cycle1, LoopCycle loop_cycle2) const

void	update_loops (utility::vector1< Size > const &pose_domain_map, utility::vector1< Size > const &cutpoint_open)

void	check_for_unexpected_cutpoints (pose::Pose const &pose) const

Private Attributes
utility::vector1< Loop >	loops_

utility::vector1< LoopCycle >	loop_cycles_

std::map< Size, utility::vector1< Size > >	loops_from_domain_

utility::vector1< bool >	loop_visited_

utility::vector1< bool >	domain_visited_

Real	total_energy_

Real	loop_fixed_cost_

bool	error_out_on_complex_cycles_

bool	has_just_simple_cycles_

bool	use_6D_potential_

utility::vector1 < evaluator::LoopClosePotentialEvaluatorCOP >	current_pose_loop_score_evaluators_

Constructor & Destructor Documentation

core::scoring::loop_graph::LoopGraph::LoopGraph ( )

core::scoring::loop_graph::LoopGraph::~LoopGraph ( )

overridedefault

Member Function Documentation

bool core::scoring::loop_graph::LoopGraph::check_disjoint	(	LoopCycle	loop_cycle1,
		LoopCycle	loop_cycle2
	)		const

private

References error_out_on_complex_cycles_, core::scoring::loop_graph::LoopCycle::loop(), core::scoring::loop_graph::LoopCycle::size(), and core::scoring::TR().

Referenced by check_loop_cycles_are_disjoint().

void core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints ( pose::Pose const & pose ) const

private

References core::chemical::C2_BRANCH_POINT, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by update().

void core::scoring::loop_graph::LoopGraph::check_loop_cycles_are_disjoint ( bool const verbose = false )

References check_disjoint(), has_just_simple_cycles_, loop_cycles_, and core::scoring::TR().

Referenced by figure_out_loop_cycles(), and protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles().

void core::scoring::loop_graph::LoopGraph::figure_out_loop_cycles ( )

private

References check_loop_cycles_are_disjoint(), and figure_out_loop_cycles_tiernan().

Referenced by update_loops_and_cycles().

void core::scoring::loop_graph::LoopGraph::figure_out_loop_cycles_legacy ( )

private

References domain_visited_, look_for_cycles_recursively(), loop_cycles_, loop_visited_, loops_, loops_from_domain_, and core::scoring::TR().

void core::scoring::loop_graph::LoopGraph::figure_out_loop_cycles_tiernan ( )

private

References loop_cycles_, loops_, loops_from_domain_, and record_loop_cycle().

Referenced by figure_out_loop_cycles().

bool core::scoring::loop_graph::LoopGraph::has_just_simple_cycles ( ) const

inline

References has_just_simple_cycles_.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles().

void core::scoring::loop_graph::LoopGraph::look_for_cycles_recursively	(	Size const	current_domain,
		utility::vector1< Size >	parent_domains_in,
		utility::vector1< Loop >	loops_so_far_in
	)

private

References domain_visited_, core::scoring::loop_graph::Loop::landing_domain(), loop_cycles_, loop_visited_, loops_, loops_from_domain_, core::scoring::loop_graph::Loop::takeoff_domain(), and core::scoring::TR().

Referenced by figure_out_loop_cycles_legacy().

utility::vector1< LoopCycle > const& core::scoring::loop_graph::LoopGraph::loop_cycles ( ) const

inline

References loop_cycles_.

LoopClosePotentialEvaluatorCOP core::scoring::loop_graph::LoopGraph::loop_score_evaluator ( Size const n ) const

References current_pose_loop_score_evaluators_.

utility::vector1< utility::vector1< Size > > core::scoring::loop_graph::LoopGraph::loop_suites ( bool include_free_loops = true ) const

If include_free_loops is turned off, loops with takeoff_domain == 0 or landing_domain == 0 will not be included.

Returns a vector of loop_suites

References loops_.

utility::vector1< char > core::scoring::loop_graph::LoopGraph::missing_residues ( pose::Pose const & pose ) const

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::FullModelInfo::input_domain_map(), loops_, and core::pose::full_model_info::FullModelInfo::working_res().

Size core::scoring::loop_graph::LoopGraph::nmissing ( pose::Pose const & pose ) const

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::input_domain_map(), loops_, core::chemical::rings::q, and core::pose::full_model_info::FullModelInfo::working_res().

Size core::scoring::loop_graph::LoopGraph::num_current_pose_loops ( ) const

inline

References current_pose_loop_score_evaluators_.

void core::scoring::loop_graph::LoopGraph::record_loop_cycle	(	utility::vector1< Size > const &	elementary_cycle,
		Size const &	idx,
		utility::vector1< Loop > const &	loops_for_cycle_in
	)

private

References core::scoring::loop_graph::Loop::landing_domain(), loop_cycles_, loops_, loops_from_domain_, and core::scoring::TR().

Referenced by figure_out_loop_cycles_tiernan().

void core::scoring::loop_graph::LoopGraph::set_error_out_on_complex_cycles ( bool const & setting )

inline

References error_out_on_complex_cycles_.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles().

void core::scoring::loop_graph::LoopGraph::set_use_6D_potential ( bool const & setting )

inline

References use_6D_potential_.

Real core::scoring::loop_graph::LoopGraph::total_energy ( ) const

inline

References total_energy_.

void core::scoring::loop_graph::LoopGraph::update	(	pose::Pose &	pose,
		bool const	verbose = `false`
	)

References check_for_unexpected_cutpoints(), core::pose::full_model_info::const_full_model_info(), current_pose_loop_score_evaluators_, core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::figure_out_pose_domain_map(), core::scoring::loop_graph::get_loop_close_potential(), loop_cycles_, loop_fixed_cost_, total_energy_, core::scoring::TR(), update_loops_and_cycles(), and use_6D_potential_.

Referenced by protocols::stepwise::modeler::check_scores_from_parts().

void core::scoring::loop_graph::LoopGraph::update_loops ( core::pose::Pose const & pose )

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), and core::pose::full_model_info::figure_out_pose_domain_map_const().

Referenced by core::pose::full_model_info::get_number_missing_residues_and_connections(), and update_loops_and_cycles().

void core::scoring::loop_graph::LoopGraph::update_loops	(	utility::vector1< Size > const &	pose_domain_map,
		utility::vector1< Size > const &	cutpoint_open
	)

private

References loops_, and loops_from_domain_.

void core::scoring::loop_graph::LoopGraph::update_loops_and_cycles	(	utility::vector1< Size > const &	pose_domain_map,
		utility::vector1< Size > const &	cutpoint_open
	)