#include <StepWiseClusterer.hh>

Inheritance diagram for protocols::stepwise::modeler::align::StepWiseClusterer:

Public Member Functions
	StepWiseClusterer ()

	StepWiseClusterer (options::StepWiseModelerOptionsCOP options)

	~StepWiseClusterer () override

void	cluster ()

core::Size	size () const

void	set_max_decoys (core::Size const &setting)

void	set_pose_list (utility::vector1< core::pose::PoseOP > const &setting)

utility::vector1< core::pose::PoseOP >	pose_list ()

void	set_calc_rms_res (utility::vector1< core::Size > const &setting)

void	set_silent_file (std::string const &setting)

void	set_do_checks (core::Size const &setting)

void	set_assume_atom_ids_invariant (core::Size const &setting)

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

core::Real	cluster_rmsd () const

Private Member Functions
void	initialize_parameters (core::pose::Pose const &pose)

void	sort_pose_list ()

bool	check_screen_and_kick_out_displaced_model (core::pose::Pose const &pose)

void	kick_out_pose_at_idx (core::Size const n)

bool	check_for_closeness (core::pose::Pose const &pose1, core::pose::Pose const &pose2)

Private Attributes
utility::vector1< core::pose::PoseOP >	pose_list_

utility::vector1< core::Size >	calc_rms_res_

core::Size	max_decoys_

core::Real	rmsd_

core::Real	cluster_rmsd_

core::Real	score_diff_cut_

bool	do_checks_

bool	assume_atom_ids_invariant_

bool	initialized_

core::Size	count_

core::Real	cluster_size_

bool	output_cluster_size_

std::string	silent_file_

StepWisePoseAlignerOP	pose_aligner_

Constructor & Destructor Documentation

◆ StepWiseClusterer() [1/2]

protocols::stepwise::modeler::align::StepWiseClusterer::StepWiseClusterer ( )

◆ StepWiseClusterer() [2/2]

protocols::stepwise::modeler::align::StepWiseClusterer::StepWiseClusterer ( options::StepWiseModelerOptionsCOP options )

◆ ~StepWiseClusterer()

protocols::stepwise::modeler::align::StepWiseClusterer::~StepWiseClusterer ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::stepwise::modeler::align::StepWiseClusterer::apply ( core::pose::Pose const & pose )

References check_screen_and_kick_out_displaced_model(), core::pose::Pose::clone(), cluster_size_, count_, initialize_parameters(), output_cluster_size_, protocols::stepwise::monte_carlo::output_to_silent_file(), pose_list_, core::pose::setPoseExtraScore(), silent_file_, and sort_pose_list().

◆ check_for_closeness()

bool protocols::stepwise::modeler::align::StepWiseClusterer::check_for_closeness	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

private

References assume_atom_ids_invariant_, calc_rms_res_, cluster_rmsd_, do_checks_, protocols::stepwise::modeler::figure_out_root_partition_res(), protocols::stepwise::modeler::align::get_rmsd(), pose_aligner_, and rmsd_.

Referenced by check_screen_and_kick_out_displaced_model().

◆ check_screen_and_kick_out_displaced_model()

bool protocols::stepwise::modeler::align::StepWiseClusterer::check_screen_and_kick_out_displaced_model ( core::pose::Pose const & pose )

private

References check_for_closeness(), cluster_size_, core::pose::getPoseExtraScore(), core::pose::hasPoseExtraScore(), kick_out_pose_at_idx(), max_decoys_, output_cluster_size_, pose_list_, score_diff_cut_, core::pose::setPoseExtraScore(), size(), and core::pose::total_energy_from_pose().

Referenced by apply(), and cluster().

◆ cluster()

void protocols::stepwise::modeler::align::StepWiseClusterer::cluster ( )

References check_screen_and_kick_out_displaced_model(), pose_list_, and sort_pose_list().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_clustering().

◆ cluster_rmsd()

core::Real protocols::stepwise::modeler::align::StepWiseClusterer::cluster_rmsd ( ) const

inline

References cluster_rmsd_.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_clustering().

◆ initialize_parameters()

void protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters ( core::pose::Pose const & pose )

private

References calc_rms_res_, cluster_rmsd_, initialized_, core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_TNA(), max_decoys_, and core::pose::Pose::residue_type().

Referenced by apply().

◆ kick_out_pose_at_idx()

void protocols::stepwise::modeler::align::StepWiseClusterer::kick_out_pose_at_idx ( core::Size const n )

private

References pose_list_, and size().

Referenced by check_screen_and_kick_out_displaced_model().

◆ pose_list()

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseClusterer::pose_list ( )

inline

References pose_list_.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_clustering().

◆ set_assume_atom_ids_invariant()

void protocols::stepwise::modeler::align::StepWiseClusterer::set_assume_atom_ids_invariant ( core::Size const & setting )

inline

References assume_atom_ids_invariant_.

◆ set_calc_rms_res()

void protocols::stepwise::modeler::align::StepWiseClusterer::set_calc_rms_res ( utility::vector1< core::Size > const & setting )

inline

References calc_rms_res_.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_clustering().

◆ set_do_checks()

void protocols::stepwise::modeler::align::StepWiseClusterer::set_do_checks ( core::Size const & setting )

inline

References do_checks_.

◆ set_max_decoys()

void protocols::stepwise::modeler::align::StepWiseClusterer::set_max_decoys ( core::Size const & setting )

inline

References max_decoys_.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_clustering().

◆ set_pose_list()

void protocols::stepwise::modeler::align::StepWiseClusterer::set_pose_list ( utility::vector1< core::pose::PoseOP > const & setting )

inline

References pose_list_.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_clustering().

◆ set_silent_file()

void protocols::stepwise::modeler::align::StepWiseClusterer::set_silent_file ( std::string const & setting )

inline

References silent_file_.

◆ size()

core::Size protocols::stepwise::modeler::align::StepWiseClusterer::size ( ) const

inline

References pose_list_.

Referenced by check_screen_and_kick_out_displaced_model(), and kick_out_pose_at_idx().

◆ sort_pose_list()

void protocols::stepwise::modeler::align::StepWiseClusterer::sort_pose_list ( )

private

References pose_list_, and core::pose::sort_pose_by_score().

Referenced by apply(), and cluster().

Member Data Documentation

◆ assume_atom_ids_invariant_

bool protocols::stepwise::modeler::align::StepWiseClusterer::assume_atom_ids_invariant_

private

Referenced by check_for_closeness(), and set_assume_atom_ids_invariant().

◆ calc_rms_res_

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseClusterer::calc_rms_res_

private

Referenced by check_for_closeness(), initialize_parameters(), and set_calc_rms_res().

◆ cluster_rmsd_

core::Real protocols::stepwise::modeler::align::StepWiseClusterer::cluster_rmsd_

private

Referenced by check_for_closeness(), cluster_rmsd(), and initialize_parameters().

◆ cluster_size_

core::Real protocols::stepwise::modeler::align::StepWiseClusterer::cluster_size_

private

Referenced by apply(), and check_screen_and_kick_out_displaced_model().

◆ count_

core::Size protocols::stepwise::modeler::align::StepWiseClusterer::count_

private

Referenced by apply().

◆ do_checks_

bool protocols::stepwise::modeler::align::StepWiseClusterer::do_checks_

private

Referenced by check_for_closeness(), and set_do_checks().

◆ initialized_

bool protocols::stepwise::modeler::align::StepWiseClusterer::initialized_

private

Referenced by initialize_parameters().

◆ max_decoys_

core::Size protocols::stepwise::modeler::align::StepWiseClusterer::max_decoys_

private

Referenced by check_screen_and_kick_out_displaced_model(), initialize_parameters(), and set_max_decoys().

◆ output_cluster_size_

bool protocols::stepwise::modeler::align::StepWiseClusterer::output_cluster_size_

private

Referenced by apply(), and check_screen_and_kick_out_displaced_model().

◆ pose_aligner_

StepWisePoseAlignerOP protocols::stepwise::modeler::align::StepWiseClusterer::pose_aligner_

private

Referenced by check_for_closeness().

◆ pose_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseClusterer::pose_list_

private

Referenced by apply(), check_screen_and_kick_out_displaced_model(), cluster(), kick_out_pose_at_idx(), pose_list(), set_pose_list(), size(), and sort_pose_list().

◆ rmsd_

core::Real protocols::stepwise::modeler::align::StepWiseClusterer::rmsd_

private

Referenced by check_for_closeness().

◆ score_diff_cut_

core::Real protocols::stepwise::modeler::align::StepWiseClusterer::score_diff_cut_

private

Referenced by check_screen_and_kick_out_displaced_model().

◆ silent_file_

std::string protocols::stepwise::modeler::align::StepWiseClusterer::silent_file_

private

Referenced by apply(), and set_silent_file().

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

src/protocols/stepwise/modeler/align/StepWiseClusterer.hh
src/protocols/stepwise/modeler/align/StepWiseClusterer.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ StepWiseClusterer() [1/2]

◆ StepWiseClusterer() [2/2]

◆ ~StepWiseClusterer()

Member Function Documentation

◆ apply()

◆ check_for_closeness()

◆ check_screen_and_kick_out_displaced_model()

◆ cluster()

◆ cluster_rmsd()

◆ initialize_parameters()

◆ kick_out_pose_at_idx()

◆ pose_list()

◆ set_assume_atom_ids_invariant()

◆ set_calc_rms_res()

◆ set_do_checks()

◆ set_max_decoys()

◆ set_pose_list()

◆ set_silent_file()

◆ size()

◆ sort_pose_list()

Member Data Documentation

◆ assume_atom_ids_invariant_

◆ calc_rms_res_

◆ cluster_rmsd_

◆ cluster_size_

◆ count_

◆ do_checks_

◆ initialized_

◆ max_decoys_

◆ output_cluster_size_

◆ pose_aligner_

◆ pose_list_

◆ rmsd_

◆ score_diff_cut_

◆ silent_file_