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

#include <LoopGraph.hh>

Inheritance diagram for core::scoring::loop_graph::LoopGraph:
Inheritance graph
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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< Looploops_
 
utility::vector1< LoopCycleloop_cycles_
 
std::map< Size,
utility::vector1< Size > > 
loops_from_domain_
 
utility::vector1< boolloop_visited_
 
utility::vector1< booldomain_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
void core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints ( pose::Pose const &  pose) const
private
void core::scoring::loop_graph::LoopGraph::check_loop_cycles_are_disjoint ( bool const  verbose = false)
void core::scoring::loop_graph::LoopGraph::figure_out_loop_cycles ( )
private
void core::scoring::loop_graph::LoopGraph::figure_out_loop_cycles_legacy ( )
private
void core::scoring::loop_graph::LoopGraph::figure_out_loop_cycles_tiernan ( )
private
bool core::scoring::loop_graph::LoopGraph::has_just_simple_cycles ( ) const
inline
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
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
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
Size core::scoring::loop_graph::LoopGraph::nmissing ( pose::Pose const &  pose) const
Size core::scoring::loop_graph::LoopGraph::num_current_pose_loops ( ) const
inline
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
void core::scoring::loop_graph::LoopGraph::set_error_out_on_complex_cycles ( bool const &  setting)
inline
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 
)
void core::scoring::loop_graph::LoopGraph::update_loops ( core::pose::Pose const &  pose)
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 
)

Member Data Documentation

utility::vector1< evaluator::LoopClosePotentialEvaluatorCOP > core::scoring::loop_graph::LoopGraph::current_pose_loop_score_evaluators_
private
utility::vector1< bool > core::scoring::loop_graph::LoopGraph::domain_visited_
private
bool core::scoring::loop_graph::LoopGraph::error_out_on_complex_cycles_
private
bool core::scoring::loop_graph::LoopGraph::has_just_simple_cycles_
private
utility::vector1< LoopCycle > core::scoring::loop_graph::LoopGraph::loop_cycles_
private
Real core::scoring::loop_graph::LoopGraph::loop_fixed_cost_
private

Referenced by update().

utility::vector1< bool > core::scoring::loop_graph::LoopGraph::loop_visited_
private
utility::vector1< Loop > core::scoring::loop_graph::LoopGraph::loops_
private
std::map< Size, utility::vector1< Size > > core::scoring::loop_graph::LoopGraph::loops_from_domain_
private
Real core::scoring::loop_graph::LoopGraph::total_energy_
private

Referenced by total_energy(), and update().

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: