core::scoring::loop_graph::LoopGraph Class Reference

#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

LoopGraph()

core::scoring::loop_graph::LoopGraph::LoopGraph

(

)

~LoopGraph()

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

overridedefault

Member Function Documentation

check_disjoint()

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().

check_for_unexpected_cutpoints()

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().

check_loop_cycles_are_disjoint()

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().

figure_out_loop_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().

figure_out_loop_cycles_legacy()

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().

figure_out_loop_cycles_tiernan()

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().

has_just_simple_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().

look_for_cycles_recursively()

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().

loop_cycles()

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

inline

References loop_cycles_.

loop_score_evaluator()

LoopClosePotentialEvaluatorCOP core::scoring::loop_graph::LoopGraph::loop_score_evaluator

(

Size const

n

)

const

References current_pose_loop_score_evaluators_.

loop_suites()

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_.

Referenced by core::pose::full_model_info::get_number_missing_residues_and_connections().

missing_residues()

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().

Referenced by core::pose::full_model_info::get_number_missing_residues_and_connections().

nmissing()

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().

Referenced by core::pose::full_model_info::get_number_missing_residues_and_connections().

num_current_pose_loops()

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

inline

References current_pose_loop_score_evaluators_.

record_loop_cycle()

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().

set_error_out_on_complex_cycles()

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().

set_use_6D_potential()

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

inline

References use_6D_potential_.

total_energy()

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

inline

References total_energy_.

update()

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().

update_loops() [1/2]

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().

update_loops() [2/2]

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_.

update_loops_and_cycles()

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

References figure_out_loop_cycles(), loop_cycles_, loops_, core::scoring::TR(), and update_loops().

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

Member Data Documentation

current_pose_loop_score_evaluators_

utility::vector1< evaluator::LoopClosePotentialEvaluatorCOP > core::scoring::loop_graph::LoopGraph::current_pose_loop_score_evaluators_

private

Referenced by loop_score_evaluator(), num_current_pose_loops(), and update().

domain_visited_

utility::vector1< bool > core::scoring::loop_graph::LoopGraph::domain_visited_

private

Referenced by figure_out_loop_cycles_legacy(), and look_for_cycles_recursively().

error_out_on_complex_cycles_

bool core::scoring::loop_graph::LoopGraph::error_out_on_complex_cycles_

private

Referenced by check_disjoint(), and set_error_out_on_complex_cycles().

has_just_simple_cycles_

bool core::scoring::loop_graph::LoopGraph::has_just_simple_cycles_

private

Referenced by check_loop_cycles_are_disjoint(), and has_just_simple_cycles().

loop_cycles_

utility::vector1< LoopCycle > core::scoring::loop_graph::LoopGraph::loop_cycles_

private

Referenced by check_loop_cycles_are_disjoint(), figure_out_loop_cycles_legacy(), figure_out_loop_cycles_tiernan(), look_for_cycles_recursively(), loop_cycles(), record_loop_cycle(), update(), and update_loops_and_cycles().

loop_fixed_cost_

Real core::scoring::loop_graph::LoopGraph::loop_fixed_cost_

private

Referenced by update().

loop_visited_

utility::vector1< bool > core::scoring::loop_graph::LoopGraph::loop_visited_

private

Referenced by figure_out_loop_cycles_legacy(), and look_for_cycles_recursively().

loops_

utility::vector1< Loop > core::scoring::loop_graph::LoopGraph::loops_

private

Referenced by figure_out_loop_cycles_legacy(), figure_out_loop_cycles_tiernan(), look_for_cycles_recursively(), loop_suites(), missing_residues(), nmissing(), record_loop_cycle(), update_loops(), and update_loops_and_cycles().

loops_from_domain_

std::map< Size, utility::vector1< Size > > core::scoring::loop_graph::LoopGraph::loops_from_domain_

private

Referenced by figure_out_loop_cycles_legacy(), figure_out_loop_cycles_tiernan(), look_for_cycles_recursively(), record_loop_cycle(), and update_loops().

total_energy_

Real core::scoring::loop_graph::LoopGraph::total_energy_

private

Referenced by total_energy(), and update().

use_6D_potential_

bool core::scoring::loop_graph::LoopGraph::use_6D_potential_

private

Referenced by set_use_6D_potential(), and update().

---

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

• src/core/scoring/loop_graph/LoopGraph.hh
• src/core/scoring/loop_graph/LoopGraph.cc