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

#include <LoopGraph.hh>

Public Member Functions
	LoopGraph ()
	~LoopGraph ()
void	update (pose::Pose &pose)
LoopScoreInfoOP	loop_score_info (Size const n) const
Size	num_loops () const
Real	total_energy () const

Private Member Functions
void	get_loop_atom (Size const &res, core::pose::Pose const &pose, bool const takeoff, id::AtomID &atom_id, Vector &xyz)
void	update_loops_and_cycles (utility::vector1< Size > const &pose_domain_map, utility::vector1< Size > const &cutpoint_open)
void	figure_out_loop_cycles ()
void	look_for_cycles_recursively (Size const current_domain, utility::vector1< Size > parent_domains_in, utility::vector1< Loop > loops_so_far_in)
void	check_loop_cycles_are_disjoint ()
bool	check_disjoint (LoopCycle loop_cycle1, LoopCycle loop_cycle2)
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_
utility::vector1< LoopScoreInfoOP >	current_pose_loop_score_info_
std::map< Size, utility::vector1< Size > >	loops_from_domain_
utility::vector1< bool >	loop_visited_
utility::vector1< bool >	domain_visited_
Real const	rna_gaussian_variance_per_residue_
Real const	protein_gaussian_variance_per_residue_
Real const	loop_fixed_cost_
Real	total_energy_

Constructor & Destructor Documentation

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

(

)

References loop_fixed_cost, option, options, and score.

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

(

)

Member Function Documentation

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

private

References j, core::scoring::loop_graph::LoopCycle::loop(), core::scoring::loop_graph::LoopCycle::size(), and utility_exit_with_message.

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::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(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by update().

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

private

References check_disjoint(), j, and loop_cycles_.

Referenced by figure_out_loop_cycles().

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

private

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

Referenced by update_loops_and_cycles().

void core::scoring::loop_graph::LoopGraph::get_loop_atom ( Size const &  res, core::pose::Pose const &  pose, bool const  takeoff, id::AtomID &  atom_id, Vector &  xyz  )

private

References core::pose::full_model_info::get_residue(), and runtime_assert.

Referenced by update().

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_, utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), core::scoring::loop_graph::Loop::landing_domain(), loop_cycles_, loop_visited_, loops_, loops_from_domain_, runtime_assert, core::scoring::loop_graph::Loop::takeoff_domain(), and core::scoring::TR.

Referenced by figure_out_loop_cycles().

LoopScoreInfoOP core::scoring::loop_graph::LoopGraph::loop_score_info

(

Size const

n

)

const

References current_pose_loop_score_info_.

Referenced by update().

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

inline

References current_pose_loop_score_info_.

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

inline

References total_energy_.

void core::scoring::loop_graph::LoopGraph::update

(

pose::Pose &

pose

)

References check_for_unexpected_cutpoints(), core::pose::full_model_info::const_full_model_info(), current_pose_loop_score_info_, cutpoint_open, 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::LoopCycle::find_index_for_loop_landing_at_domain(), get_loop_atom(), core::pose::full_model_info::get_residue(), core::io::pdb::is_NA(), core::scoring::loop_graph::Loop::landing_domain(), core::scoring::loop_graph::Loop::landing_pos(), length, core::scoring::loop_graph::LoopCycle::loop(), loop_cycles_, loop_fixed_cost_, loop_score_info(), protein_gaussian_variance_per_residue_, rna_gaussian_variance_per_residue_, runtime_assert, core::scoring::loop_graph::LoopCycle::size(), core::scoring::loop_graph::Loop::takeoff_domain(), core::scoring::loop_graph::Loop::takeoff_pos(), total_energy_, update_loops_and_cycles(), and utility_exit_with_message.

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

private

References utility::vector1< T, class >::has_value(), loops_, loops_from_domain_, and nres.

Referenced by 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  )

private

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

Referenced by update().

Member Data Documentation

utility::vector1< LoopScoreInfoOP > core::scoring::loop_graph::LoopGraph::current_pose_loop_score_info_

private

Referenced by loop_score_info(), num_loops(), and update().

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

private

Referenced by figure_out_loop_cycles(), and look_for_cycles_recursively().

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

private

Referenced by check_loop_cycles_are_disjoint(), figure_out_loop_cycles(), look_for_cycles_recursively(), update(), and update_loops_and_cycles().

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

private

Referenced by update().

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

private

Referenced by figure_out_loop_cycles(), and look_for_cycles_recursively().

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

private

Referenced by figure_out_loop_cycles(), look_for_cycles_recursively(), update_loops(), and update_loops_and_cycles().

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

private

Referenced by figure_out_loop_cycles(), look_for_cycles_recursively(), and update_loops().

Real const core::scoring::loop_graph::LoopGraph::protein_gaussian_variance_per_residue_

private

Referenced by update().

Real const core::scoring::loop_graph::LoopGraph::rna_gaussian_variance_per_residue_

private

Referenced by update().

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

private

Referenced by total_energy(), and update().

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

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