#include <StepWiseLegacyClusterer.hh>

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

Public Member Functions
	StepWiseLegacyClusterer (utility::vector1< core::pose::PoseOP > const &pose_list)

	StepWiseLegacyClusterer (utility::vector1< core::pose::PoseOP > const &pose_list, utility::vector1< core::Size > const &moving_res_list, options::StepWiseModelerOptionsCOP options, bool const force_align)

	~StepWiseLegacyClusterer () override

void	set_max_decoys (core::Size const &setting)
	Filter a list of poses by score. More...

void	set_cluster_radius (core::Real const &setting)

void	set_cluster_by_all_atom_rmsd (core::Real const &setting)

void	set_rename_tags (core::Real const &setting)

void	set_score_diff_cut (core::Real const &setting)

void	set_auto_tune (bool const auto_tune)

void	set_force_align (bool const force_align)

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

void	cluster ()

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

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

Private Member Functions
void	initialize_parameters_and_input ()

void	initialize_cluster_list ()

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

void	do_some_clustering ()

core::Size	check_for_closeness (core::pose::PoseOP rms_pose)

void	cluster_with_auto_tune ()

void	recluster_current_pose_list ()

void	initialize_auto_tune_cluster_rmsds ()

core::io::silent::SilentStructOP	setup_silent_struct (core::Size const n)

Private Attributes
core::Size	max_decoys_

core::Real	cluster_radius_

bool	cluster_by_all_atom_rmsd_

core::Real	score_diff_cut_

bool	auto_tune_

bool	rename_tags_

bool	force_align_

core::Real	score_min_

utility::vector1< core::pose::PoseOP >	input_pose_list_

utility::vector1< core::pose::PoseOP >	rms_pose_list_

utility::vector1< core::pose::PoseOP >	output_pose_list_

utility::vector1< core::Size >	num_pose_in_cluster_

utility::vector1< core::Real >	cluster_rmsds_to_try_with_auto_tune_

core::Size	input_pose_counter_

bool	hit_score_cutoff_

bool	initialized_atom_id_map_for_rmsd_

utility::vector1< core::Size >	calc_rms_res_

std::map< core::id::AtomID, core::id::AtomID >	corresponding_atom_id_map_

Constructor & Destructor Documentation

◆ StepWiseLegacyClusterer() [1/2]

protocols::stepwise::modeler::align::StepWiseLegacyClusterer::StepWiseLegacyClusterer ( utility::vector1< core::pose::PoseOP > const & pose_list )

References initialize_parameters_and_input().

◆ StepWiseLegacyClusterer() [2/2]

protocols::stepwise::modeler::align::StepWiseLegacyClusterer::StepWiseLegacyClusterer	(	utility::vector1< core::pose::PoseOP > const &	pose_list,
		utility::vector1< core::Size > const &	moving_res_list,
		options::StepWiseModelerOptionsCOP	options,
		bool const	force_align
	)

References initialize_parameters_and_input(), set_calc_rms_res(), set_cluster_by_all_atom_rmsd(), set_cluster_radius(), set_force_align(), set_max_decoys(), and set_rename_tags().

◆ ~StepWiseLegacyClusterer()

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

overridedefault

Member Function Documentation

◆ check_for_closeness()

Size protocols::stepwise::modeler::align::StepWiseLegacyClusterer::check_for_closeness ( core::pose::PoseOP rms_pose )

private

References calc_rms_res_, cluster_radius_, corresponding_atom_id_map_, force_align_, initialize_corresponding_atom_id_map(), initialized_atom_id_map_for_rmsd_, core::scoring::rms_at_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms_no_super(), and rms_pose_list_.

Referenced by do_some_clustering(), and recluster_current_pose_list().

◆ cluster()

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

References auto_tune_, cluster_with_auto_tune(), do_some_clustering(), initialize_cluster_list(), and protocols::TR().

Referenced by protocols::stepwise::legacy::screener::SimplePoseSelection::finalize().

◆ cluster_with_auto_tune()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_with_auto_tune ( )

private

References cluster_radius_, cluster_rmsds_to_try_with_auto_tune_, do_some_clustering(), hit_score_cutoff_, input_pose_counter_, input_pose_list_, recluster_current_pose_list(), score_diff_cut_, and protocols::TR().

Referenced by cluster().

◆ do_some_clustering()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering ( )

private

References calc_rms_res_, check_for_closeness(), hit_score_cutoff_, input_pose_counter_, input_pose_list_, max_decoys_, num_pose_in_cluster_, output_pose_list_, core::pose::pdbslice(), rms_pose_list_, protocols::hybridization::score, score_diff_cut_, score_min_, core::pose::tag_from_pose(), core::pose::total_energy_from_pose(), and protocols::TR().

Referenced by cluster(), and cluster_with_auto_tune().

◆ get_pose_list()

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::get_pose_list ( )

inline

References output_pose_list_.

Referenced by protocols::stepwise::legacy::screener::SimplePoseSelection::finalize().

◆ initialize_auto_tune_cluster_rmsds()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_auto_tune_cluster_rmsds ( )

private

References cluster_rmsds_to_try_with_auto_tune_.

Referenced by initialize_parameters_and_input().

◆ initialize_cluster_list()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_cluster_list ( )

private

References hit_score_cutoff_, input_pose_counter_, num_pose_in_cluster_, output_pose_list_, and rms_pose_list_.

Referenced by cluster().

◆ initialize_corresponding_atom_id_map()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_corresponding_atom_id_map ( core::pose::Pose const & pose )

private

References cluster_by_all_atom_rmsd_, corresponding_atom_id_map_, initialized_atom_id_map_for_rmsd_, core::scoring::setup_matching_heavy_atoms(), and core::scoring::setup_matching_protein_backbone_heavy_atoms().

Referenced by check_for_closeness().

◆ initialize_parameters_and_input()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_parameters_and_input ( )

private

References auto_tune_, cluster_by_all_atom_rmsd_, cluster_radius_, force_align_, hit_score_cutoff_, initialize_auto_tune_cluster_rmsds(), initialized_atom_id_map_for_rmsd_, input_pose_counter_, input_pose_list_, max_decoys_, rename_tags_, score_diff_cut_, score_min_, core::pose::sort_pose_by_score(), and core::pose::total_energy_from_pose().

Referenced by StepWiseLegacyClusterer().

◆ recluster_current_pose_list()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::recluster_current_pose_list ( )

private

References check_for_closeness(), cluster_radius_, num_pose_in_cluster_, output_pose_list_, rms_pose_list_, and protocols::TR().

Referenced by cluster_with_auto_tune().

◆ rms_pose_list()

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::rms_pose_list ( )

inline

References rms_pose_list_.

◆ set_auto_tune()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_auto_tune ( bool const auto_tune )

inline

References auto_tune_.

◆ set_calc_rms_res()

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

References calc_rms_res_.

Referenced by StepWiseLegacyClusterer().

◆ set_cluster_by_all_atom_rmsd()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_cluster_by_all_atom_rmsd ( core::Real const & setting )

inline

References cluster_by_all_atom_rmsd_.

Referenced by StepWiseLegacyClusterer().

◆ set_cluster_radius()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_cluster_radius ( core::Real const & setting )

inline

References cluster_radius_.

Referenced by StepWiseLegacyClusterer().

◆ set_force_align()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_force_align ( bool const force_align )

inline

References force_align_.

Referenced by StepWiseLegacyClusterer().

◆ set_max_decoys()

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

inline

Filter a list of poses by score.

References max_decoys_.

Referenced by StepWiseLegacyClusterer().

◆ set_rename_tags()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_rename_tags ( core::Real const & setting )

inline

References rename_tags_.

Referenced by StepWiseLegacyClusterer().

◆ set_score_diff_cut()

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_score_diff_cut ( core::Real const & setting )

inline

References score_diff_cut_.

◆ setup_silent_struct()

core::io::silent::SilentStructOP protocols::stepwise::modeler::align::StepWiseLegacyClusterer::setup_silent_struct ( core::Size const n )

private

Member Data Documentation

◆ auto_tune_

bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::auto_tune_

private

Referenced by cluster(), initialize_parameters_and_input(), and set_auto_tune().

◆ calc_rms_res_

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

private

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

◆ cluster_by_all_atom_rmsd_

bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_by_all_atom_rmsd_

private

Referenced by initialize_corresponding_atom_id_map(), initialize_parameters_and_input(), and set_cluster_by_all_atom_rmsd().

◆ cluster_radius_

core::Real protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_radius_

private

Referenced by check_for_closeness(), cluster_with_auto_tune(), initialize_parameters_and_input(), recluster_current_pose_list(), and set_cluster_radius().

◆ cluster_rmsds_to_try_with_auto_tune_

utility::vector1< core::Real > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_rmsds_to_try_with_auto_tune_

private

Referenced by cluster_with_auto_tune(), and initialize_auto_tune_cluster_rmsds().

◆ corresponding_atom_id_map_

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::corresponding_atom_id_map_

private

Referenced by check_for_closeness(), and initialize_corresponding_atom_id_map().

◆ force_align_

bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::force_align_

private

Referenced by check_for_closeness(), initialize_parameters_and_input(), and set_force_align().

◆ hit_score_cutoff_

bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::hit_score_cutoff_

private

Referenced by cluster_with_auto_tune(), do_some_clustering(), initialize_cluster_list(), and initialize_parameters_and_input().

◆ initialized_atom_id_map_for_rmsd_

bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialized_atom_id_map_for_rmsd_

private

Referenced by check_for_closeness(), initialize_corresponding_atom_id_map(), and initialize_parameters_and_input().

◆ input_pose_counter_

core::Size protocols::stepwise::modeler::align::StepWiseLegacyClusterer::input_pose_counter_

private

Referenced by cluster_with_auto_tune(), do_some_clustering(), initialize_cluster_list(), and initialize_parameters_and_input().

◆ input_pose_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::input_pose_list_

private

Referenced by cluster_with_auto_tune(), do_some_clustering(), and initialize_parameters_and_input().

◆ max_decoys_

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

private

Referenced by do_some_clustering(), initialize_parameters_and_input(), and set_max_decoys().

◆ num_pose_in_cluster_

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::num_pose_in_cluster_

private

Referenced by do_some_clustering(), initialize_cluster_list(), and recluster_current_pose_list().

◆ output_pose_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::output_pose_list_

private

Referenced by do_some_clustering(), get_pose_list(), initialize_cluster_list(), and recluster_current_pose_list().

◆ rename_tags_

bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::rename_tags_

private

Referenced by initialize_parameters_and_input(), and set_rename_tags().

◆ rms_pose_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::rms_pose_list_

private

Referenced by check_for_closeness(), do_some_clustering(), initialize_cluster_list(), recluster_current_pose_list(), and rms_pose_list().

◆ score_diff_cut_

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

private

Referenced by cluster_with_auto_tune(), do_some_clustering(), initialize_parameters_and_input(), and set_score_diff_cut().

◆ score_min_

core::Real protocols::stepwise::modeler::align::StepWiseLegacyClusterer::score_min_

private

Referenced by do_some_clustering(), and initialize_parameters_and_input().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ StepWiseLegacyClusterer() [1/2]

◆ StepWiseLegacyClusterer() [2/2]

◆ ~StepWiseLegacyClusterer()

Member Function Documentation

◆ check_for_closeness()

◆ cluster()

◆ cluster_with_auto_tune()

◆ do_some_clustering()

◆ get_pose_list()

◆ initialize_auto_tune_cluster_rmsds()

◆ initialize_cluster_list()

◆ initialize_corresponding_atom_id_map()

◆ initialize_parameters_and_input()

◆ recluster_current_pose_list()

◆ rms_pose_list()

◆ set_auto_tune()

◆ set_calc_rms_res()

◆ set_cluster_by_all_atom_rmsd()

◆ set_cluster_radius()

◆ set_force_align()

◆ set_max_decoys()

◆ set_rename_tags()

◆ set_score_diff_cut()

◆ setup_silent_struct()

Member Data Documentation

◆ auto_tune_

◆ calc_rms_res_

◆ cluster_by_all_atom_rmsd_

◆ cluster_radius_

◆ cluster_rmsds_to_try_with_auto_tune_

◆ corresponding_atom_id_map_

◆ force_align_

◆ hit_score_cutoff_

◆ initialized_atom_id_map_for_rmsd_

◆ input_pose_counter_

◆ input_pose_list_

◆ max_decoys_

◆ num_pose_in_cluster_

◆ output_pose_list_

◆ rename_tags_

◆ rms_pose_list_

◆ score_diff_cut_

◆ score_min_