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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer Class Reference

#include <StepWiseRNA_Clusterer.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer:
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Public Member Functions

 StepWiseRNA_Clusterer (utility::vector1< std::string > const &silent_files_in)
 
 StepWiseRNA_Clusterer (std::string const &silent_file_in)
 
 StepWiseRNA_Clusterer (core::io::silent::SilentFileDataOP &sfd)
 
 ~StepWiseRNA_Clusterer () override
 
void set_max_decoys (core::Size const &setting)
 Filter a list of poses by score. More...
 
void set_score_diff_cut (core::Real const &setting)
 
void set_perform_score_diff_cut (bool const &setting)
 
void set_cluster_radius (core::Real const &setting)
 
void set_suite_cluster_radius (core::Real const &setting)
 
void set_loop_cluster_radius (core::Real const &setting)
 
void set_rename_tags (core::Real const &setting)
 
void set_distinguish_pucker (core::Real const &setting)
 
void set_add_lead_zero_to_tag (core::Real const &setting)
 
void set_working_parameters (protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &working_parameters)
 
void set_working_parameters_exist (bool const working_parameters_exist)
 
void set_quick_alignment (bool const &setting)
 
void set_align_only_over_base_atoms (bool const &setting)
 
void set_optimize_memory_usage (bool const &setting)
 
void set_keep_pose_in_memory (bool const &setting)
 
void set_two_stage_clustering (bool const &setting)
 
void set_verbose (bool const &setting)
 
void cluster ()
 
void output_silent_file (std::string const &silent_file)
 
void recalculate_rmsd_and_output_silent_file (std::string const &silent_file, protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup, bool const write_score_only)
 
void get_best_neighboring_shift_RMSD_and_output_silent_file (std::string const &silent_file)
 
void set_PBP_clustering_at_chain_closure (bool const &setting)
 
void set_skip_clustering (bool const &setting)
 
void set_filter_virtual_res_list (utility::vector1< core::Size > const &setting)
 
void set_perform_VDW_rep_screen (bool const &setting)
 
void set_perform_filters (bool const &setting)
 
void set_min_num_south_sugar_filter (core::Size const &setting)
 
void set_VDW_rep_screen_info (utility::vector1< std::string > const &setting)
 
void set_user_input_VDW_bin_checker (protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)
 
void set_full_length_loop_rmsd_clustering (bool const &setting)
 
void set_ignore_FARFAR_no_auto_bulge_tag (bool const &setting)
 
void set_ignore_FARFAR_no_auto_bulge_parent_tag (bool const &setting)
 
void set_ignore_unmatched_virtual_res (bool const &setting)
 
void set_output_pdb (bool const setting)
 

Private Member Functions

void initialize_parameters_and_input ()
 
void create_silent_file_and_tag_list ()
 
void do_some_clustering ()
 
void two_stage_clustering ()
 
void create_large_cluster_centers_member_list ()
 
bool is_old_individual_suite_cluster (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, utility::vector1< core::Size > const &calc_rms_res, std::map< core::Size, core::Size > const &full_to_sub, std::map< core::Size, bool > const &is_prepend_map, core::Real const &cluster_radius) const
 
core::pose::PoseOP get_poseOP (core::Size const n)
 
void setup_fail_triangle_inequailty_list (core::pose::Pose &current_pose, std::string const &tag, utility::vector1< bool > &fail_triangle_inequality_list)
 
bool is_new_cluster_center_with_working_parameters (core::pose::PoseOP const &pose_op, std::string const &tag)
 
bool check_for_closeness_without_working_parameters (core::pose::PoseOP const &pose_op)
 
bool check_for_closeness (core::pose::PoseOP const &pose_op, std::string const &tag)
 
utility::vector1< core::Size > const & get_act_alignment_res () const
 
utility::vector1< core::Size > const & get_act_calc_rms_res () const
 
std::map< core::Size, core::Size > const & get_act_full_to_sub () const
 
std::map< core::Size, bool > const & get_act_is_prepend_map () const
 
void initialize_quick_alignment_pose ()
 
void initialize_max_memory_pose_num ()
 
void align_to_quick_alignment_pose (core::pose::Pose &pose, std::string const &tag) const
 
void initialize_VDW_rep_checker ()
 
void create_tags_map ()
 
bool pass_FARFAR_no_auto_bulge_filter (core::io::silent::SilentStructOP const &silent_struct) const
 

Private Attributes

utility::vector1< std::string > silent_files_
 
core::import_pose::pose_stream::SilentFilePoseInputStreamOP input_
 
utility::vector1< core::pose::PoseOP > pose_output_list_
 
utility::vector1< std::string > tag_output_list_
 
utility::vector1< core::io::silent::SilentStructOP > silent_struct_output_list_
 
core::Size max_decoys_
 
core::Real score_diff_cut_
 
bool perform_score_diff_cut_
 
core::Real whole_struct_cluster_radius_
 
core::Real suite_cluster_radius_
 
core::Real loop_cluster_radius_
 
bool rename_tags_
 
protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
bool working_parameters_exist_
 
bool distinguish_pucker_
 
bool add_lead_zero_to_tag_
 
bool quick_alignment_
 
bool align_only_over_base_atoms_
 
bool optimize_memory_usage_
 
SlicedPoseWorkingParameters sliced_pose_job_params_
 
bool verbose_
 
bool keep_pose_in_memory_
 
bool keep_pose_in_memory_hydrid_
 
core::Size max_memory_pose_num_
 
bool two_stage_clustering_
 
bool use_triangle_inequality_
 
core::pose::Pose first_pose_
 
utility::vector1< utility::vector1< Cluster_Member > > cluster_centers_neighbor_list_
 
utility::vector1< core::pose::PoseOP > large_cluster_pose_list_
 
utility::vector1< core::Size > all_pose_to_output_pose_ID_map_
 
bool PBP_clustering_at_chain_closure_
 
bool quick_alignment_pose_is_intialized_
 
core::pose::Pose quick_alignment_pose_
 
std::string quick_alignment_tag_
 
bool skip_clustering_
 
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker_
 
bool perform_VDW_rep_screen_
 
bool perform_filters_
 
core::Size min_num_south_sugar_filter_
 
utility::vector1< std::string > VDW_rep_screen_info_
 
bool full_length_loop_rmsd_clustering_
 
utility::vector1< core::Size > filter_virtual_res_list_
 
std::map< std::string, bool > current_tags_map_
 
std::map< std::string, bool > parent_tags_map_
 
bool ignore_FARFAR_no_auto_bulge_parent_tag_
 
bool ignore_FARFAR_no_auto_bulge_tag_
 
bool ignore_unmatched_virtual_res_
 
bool output_pdb_
 
core::chemical::ResidueTypeSetCAP rsd_set_
 

Constructor & Destructor Documentation

◆ StepWiseRNA_Clusterer() [1/3]

protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( utility::vector1< std::string > const &  silent_files_in)

◆ StepWiseRNA_Clusterer() [2/3]

protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( std::string const &  silent_file_in)

◆ StepWiseRNA_Clusterer() [3/3]

protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( core::io::silent::SilentFileDataOP &  sfd)

◆ ~StepWiseRNA_Clusterer()

protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::~StepWiseRNA_Clusterer ( )
overridedefault

Member Function Documentation

◆ align_to_quick_alignment_pose()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::align_to_quick_alignment_pose ( core::pose::Pose &  pose,
std::string const &  tag 
) const
private

References protocols::stepwise::modeler::rna::align_poses().

◆ check_for_closeness()

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::check_for_closeness ( core::pose::PoseOP const &  pose_op,
std::string const &  tag 
)
private

◆ check_for_closeness_without_working_parameters()

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::check_for_closeness_without_working_parameters ( core::pose::PoseOP const &  pose_op)
private

References core::scoring::all_atom_rmsd().

◆ cluster()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::cluster ( )

References core::pose::rna::output_boolean(), protocols::stepwise::modeler::rna::output_title_text(), and core::chemical::rna::TR().

◆ create_large_cluster_centers_member_list()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list ( )
private

References protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::pose::full_model_info::full_to_sub(), core::pose::getPoseExtraScore(), protocols::stepwise::legacy::modeler::rna::Cluster_Member::ID, protocols::stepwise::modeler::rna::output_title_text(), protocols::cluster::calibur::RMSD(), protocols::stepwise::legacy::modeler::rna::Cluster_Member::RMSD, protocols::stepwise::modeler::rna::rmsd_over_residue_list(), protocols::hybridization::score, protocols::stepwise::legacy::modeler::rna::Cluster_Member::score, and core::chemical::rna::TR().

◆ create_silent_file_and_tag_list()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list ( )
private

References core::chemical::rna::ANTI, protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), core::chemical::BULGE, protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::pose::rna::get_residue_base_state(), core::pose::rna::get_residue_pucker_state(), core::chemical::rna::NORTH, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::rna::remove_bracketed(), core::chemical::rna::SOUTH, core::chemical::rna::SYN, core::chemical::rna::TR(), core::chemical::VIRTUAL_RIBOSE, and core::chemical::VIRTUAL_RNA_RESIDUE.

◆ create_tags_map()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_tags_map ( )
private

References protocols::stepwise::modeler::rna::output_title_text(), and core::chemical::rna::TR().

◆ do_some_clustering()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::do_some_clustering ( )
private

References protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::pose::getPoseExtraScore(), core::pose::rna::remove_bracketed(), protocols::hybridization::score, and core::chemical::rna::TR().

◆ get_act_alignment_res()

utility::vector1< core::Size > const & protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_act_alignment_res ( ) const
private

◆ get_act_calc_rms_res()

utility::vector1< core::Size > const & protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_act_calc_rms_res ( ) const
private

◆ get_act_full_to_sub()

std::map< core::Size, core::Size > const & protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_act_full_to_sub ( ) const
private

References core::pose::full_model_info::full_to_sub().

◆ get_act_is_prepend_map()

std::map< core::Size, bool > const & protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_act_is_prepend_map ( ) const
private

◆ get_best_neighboring_shift_RMSD_and_output_silent_file()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file ( std::string const &  silent_file)

References protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), core::pose::full_model_info::full_to_sub(), core::pose::getPoseExtraScore(), protocols::loops::loop_rmsd(), core::scoring::other_pose, core::pose::rna::output_boolean(), protocols::stepwise::modeler::rna::output_title_text(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), core::pose::Pose::size(), core::chemical::rna::TR(), and core::io::silent::SilentFileData::write_silent_struct().

◆ get_poseOP()

core::pose::PoseOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_poseOP ( core::Size const  n)
private

◆ initialize_max_memory_pose_num()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num ( )
private

References protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::pose::rna::output_boolean(), core::pose::Pose::size(), and core::chemical::rna::TR().

◆ initialize_parameters_and_input()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_parameters_and_input ( )
private

References core::chemical::FA_STANDARD.

◆ initialize_quick_alignment_pose()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose ( )
private

References protocols::stepwise::modeler::rna::check_for_messed_up_structure(), protocols::stepwise::modeler::rna::output_seq_num_list(), and core::chemical::rna::TR().

◆ initialize_VDW_rep_checker()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_VDW_rep_checker ( )
private

References protocols::stepwise::modeler::rna::check_for_messed_up_structure().

◆ is_new_cluster_center_with_working_parameters()

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters ( core::pose::PoseOP const &  pose_op,
std::string const &  tag 
)
private

References protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), core::pose::full_model_info::full_to_sub(), protocols::loops::loop_rmsd(), core::pose::rna::output_boolean(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), and core::chemical::rna::TR().

◆ is_old_individual_suite_cluster()

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster ( core::pose::Pose const &  current_pose,
core::pose::Pose const &  cluster_center_pose,
utility::vector1< core::Size > const &  calc_rms_res,
std::map< core::Size, core::Size > const &  full_to_sub,
std::map< core::Size, bool > const &  is_prepend_map,
core::Real const &  cluster_radius 
) const
private

References core::pose::full_model_info::full_to_sub(), core::pose::rna::get_residue_pucker_state(), core::conformation::Residue::has_variant_type(), protocols::stepwise::legacy::modeler::rna::is_same_sugar_pucker(), core::pose::rna::output_boolean(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_rmsd(), protocols::stepwise::modeler::rna::print_sugar_pucker_state(), core::pose::Pose::residue(), protocols::stepwise::modeler::rna::suite_rmsd(), core::chemical::rna::TR(), core::chemical::VIRTUAL_RIBOSE, and core::chemical::VIRTUAL_RNA_RESIDUE.

◆ output_silent_file()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::output_silent_file ( std::string const &  silent_file)

References core::io::silent::SilentFileData::write_silent_struct().

◆ pass_FARFAR_no_auto_bulge_filter()

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::pass_FARFAR_no_auto_bulge_filter ( core::io::silent::SilentStructOP const &  silent_struct) const
private

References core::chemical::rna::TR().

◆ recalculate_rmsd_and_output_silent_file()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file ( std::string const &  silent_file,
protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetupOP &  stepwise_rna_pose_setup,
bool const  write_score_only 
)

References protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), core::pose::full_model_info::full_to_sub(), core::pose::getPoseExtraScore(), core::pose::rna::output_boolean(), protocols::stepwise::modeler::rna::output_title_text(), protocols::stepwise::modeler::rna::remove_all_variant_types(), core::scoring::rms_at_corresponding_heavy_atoms(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), protocols::hybridization::score, core::pose::Pose::size(), core::chemical::rna::TR(), and core::io::silent::SilentFileData::write_silent_struct().

◆ set_add_lead_zero_to_tag()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_add_lead_zero_to_tag ( core::Real const &  setting)
inline

References add_lead_zero_to_tag_.

◆ set_align_only_over_base_atoms()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_align_only_over_base_atoms ( bool const &  setting)
inline

References align_only_over_base_atoms_.

◆ set_cluster_radius()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_cluster_radius ( core::Real const &  setting)
inline

References whole_struct_cluster_radius_.

◆ set_distinguish_pucker()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_distinguish_pucker ( core::Real const &  setting)
inline

References distinguish_pucker_.

◆ set_filter_virtual_res_list()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_filter_virtual_res_list ( utility::vector1< core::Size > const &  setting)
inline

References filter_virtual_res_list_.

◆ set_full_length_loop_rmsd_clustering()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_full_length_loop_rmsd_clustering ( bool const &  setting)
inline

References full_length_loop_rmsd_clustering_.

◆ set_ignore_FARFAR_no_auto_bulge_parent_tag()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_ignore_FARFAR_no_auto_bulge_parent_tag ( bool const &  setting)
inline

References ignore_FARFAR_no_auto_bulge_parent_tag_.

◆ set_ignore_FARFAR_no_auto_bulge_tag()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_ignore_FARFAR_no_auto_bulge_tag ( bool const &  setting)
inline

References ignore_FARFAR_no_auto_bulge_tag_.

◆ set_ignore_unmatched_virtual_res()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_ignore_unmatched_virtual_res ( bool const &  setting)
inline

References ignore_unmatched_virtual_res_.

◆ set_keep_pose_in_memory()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_keep_pose_in_memory ( bool const &  setting)
inline

References keep_pose_in_memory_.

◆ set_loop_cluster_radius()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_loop_cluster_radius ( core::Real const &  setting)
inline

References loop_cluster_radius_.

◆ set_max_decoys()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_max_decoys ( core::Size const &  setting)
inline

Filter a list of poses by score.

References max_decoys_.

◆ set_min_num_south_sugar_filter()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_min_num_south_sugar_filter ( core::Size const &  setting)
inline

References min_num_south_sugar_filter_.

◆ set_optimize_memory_usage()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_optimize_memory_usage ( bool const &  setting)
inline

References optimize_memory_usage_.

◆ set_output_pdb()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_output_pdb ( bool const  setting)
inline

References output_pdb_.

◆ set_PBP_clustering_at_chain_closure()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_PBP_clustering_at_chain_closure ( bool const &  setting)
inline

References PBP_clustering_at_chain_closure_.

◆ set_perform_filters()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_perform_filters ( bool const &  setting)
inline

References perform_filters_.

◆ set_perform_score_diff_cut()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_perform_score_diff_cut ( bool const &  setting)
inline

References perform_score_diff_cut_.

◆ set_perform_VDW_rep_screen()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_perform_VDW_rep_screen ( bool const &  setting)
inline

References perform_VDW_rep_screen_.

◆ set_quick_alignment()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_quick_alignment ( bool const &  setting)
inline

References quick_alignment_.

◆ set_rename_tags()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_rename_tags ( core::Real const &  setting)
inline

References rename_tags_.

◆ set_score_diff_cut()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_score_diff_cut ( core::Real const &  setting)
inline

References score_diff_cut_.

◆ set_skip_clustering()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_skip_clustering ( bool const &  setting)
inline

References skip_clustering_.

◆ set_suite_cluster_radius()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_suite_cluster_radius ( core::Real const &  setting)
inline

References suite_cluster_radius_.

◆ set_two_stage_clustering()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_two_stage_clustering ( bool const &  setting)
inline

References two_stage_clustering_.

◆ set_user_input_VDW_bin_checker()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_user_input_VDW_bin_checker ( protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP const &  user_input_VDW_bin_checker)
inline

References user_input_VDW_bin_checker_.

◆ set_VDW_rep_screen_info()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_VDW_rep_screen_info ( utility::vector1< std::string > const &  setting)
inline

References VDW_rep_screen_info_.

◆ set_verbose()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_verbose ( bool const &  setting)
inline

References verbose_.

◆ set_working_parameters()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_working_parameters ( protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &  working_parameters)

◆ set_working_parameters_exist()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_working_parameters_exist ( bool const  working_parameters_exist)

◆ setup_fail_triangle_inequailty_list()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list ( core::pose::Pose &  current_pose,
std::string const &  tag,
utility::vector1< bool > &  fail_triangle_inequality_list 
)
private

References protocols::stepwise::modeler::rna::align_poses(), core::pose::full_model_info::full_to_sub(), core::pose::getPoseExtraScore(), protocols::cluster::calibur::RMSD(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), and core::chemical::rna::TR().

◆ two_stage_clustering()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::two_stage_clustering ( )
private

References protocols::stepwise::modeler::rna::output_title_text(), and core::chemical::rna::TR().

Member Data Documentation

◆ add_lead_zero_to_tag_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::add_lead_zero_to_tag_
private

Referenced by set_add_lead_zero_to_tag().

◆ align_only_over_base_atoms_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::align_only_over_base_atoms_
private

Referenced by set_align_only_over_base_atoms().

◆ all_pose_to_output_pose_ID_map_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::all_pose_to_output_pose_ID_map_
private

◆ cluster_centers_neighbor_list_

utility::vector1< utility::vector1< Cluster_Member > > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::cluster_centers_neighbor_list_
private

◆ current_tags_map_

std::map< std::string, bool > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::current_tags_map_
private

◆ distinguish_pucker_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::distinguish_pucker_
private

Referenced by set_distinguish_pucker().

◆ filter_virtual_res_list_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::filter_virtual_res_list_
private

Referenced by set_filter_virtual_res_list().

◆ first_pose_

core::pose::Pose protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::first_pose_
private

◆ full_length_loop_rmsd_clustering_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::full_length_loop_rmsd_clustering_
private

Referenced by set_full_length_loop_rmsd_clustering().

◆ ignore_FARFAR_no_auto_bulge_parent_tag_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::ignore_FARFAR_no_auto_bulge_parent_tag_
private

Referenced by set_ignore_FARFAR_no_auto_bulge_parent_tag().

◆ ignore_FARFAR_no_auto_bulge_tag_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::ignore_FARFAR_no_auto_bulge_tag_
private

Referenced by set_ignore_FARFAR_no_auto_bulge_tag().

◆ ignore_unmatched_virtual_res_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::ignore_unmatched_virtual_res_
private

Referenced by set_ignore_unmatched_virtual_res().

◆ input_

core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::input_
private

◆ keep_pose_in_memory_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::keep_pose_in_memory_
private

Referenced by set_keep_pose_in_memory().

◆ keep_pose_in_memory_hydrid_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::keep_pose_in_memory_hydrid_
private

◆ large_cluster_pose_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::large_cluster_pose_list_
private

◆ loop_cluster_radius_

core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::loop_cluster_radius_
private

Referenced by set_loop_cluster_radius().

◆ max_decoys_

core::Size protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::max_decoys_
private

Referenced by set_max_decoys().

◆ max_memory_pose_num_

core::Size protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::max_memory_pose_num_
private

◆ min_num_south_sugar_filter_

core::Size protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::min_num_south_sugar_filter_
private

Referenced by set_min_num_south_sugar_filter().

◆ optimize_memory_usage_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::optimize_memory_usage_
private

Referenced by set_optimize_memory_usage().

◆ output_pdb_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::output_pdb_
private

Referenced by set_output_pdb().

◆ parent_tags_map_

std::map< std::string, bool > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::parent_tags_map_
private

◆ PBP_clustering_at_chain_closure_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::PBP_clustering_at_chain_closure_
private

Referenced by set_PBP_clustering_at_chain_closure().

◆ perform_filters_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::perform_filters_
private

Referenced by set_perform_filters().

◆ perform_score_diff_cut_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::perform_score_diff_cut_
private

Referenced by set_perform_score_diff_cut().

◆ perform_VDW_rep_screen_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::perform_VDW_rep_screen_
private

Referenced by set_perform_VDW_rep_screen().

◆ pose_output_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::pose_output_list_
private

◆ quick_alignment_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::quick_alignment_
private

Referenced by set_quick_alignment().

◆ quick_alignment_pose_

core::pose::Pose protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::quick_alignment_pose_
private

◆ quick_alignment_pose_is_intialized_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::quick_alignment_pose_is_intialized_
private

◆ quick_alignment_tag_

std::string protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::quick_alignment_tag_
private

◆ rename_tags_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::rename_tags_
private

Referenced by set_rename_tags().

◆ rsd_set_

core::chemical::ResidueTypeSetCAP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::rsd_set_
private

◆ score_diff_cut_

core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::score_diff_cut_
private

Referenced by set_score_diff_cut().

◆ silent_files_

utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::silent_files_
private

◆ silent_struct_output_list_

utility::vector1< core::io::silent::SilentStructOP > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::silent_struct_output_list_
private

◆ skip_clustering_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::skip_clustering_
private

Referenced by set_skip_clustering().

◆ sliced_pose_job_params_

SlicedPoseWorkingParameters protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::sliced_pose_job_params_
private

◆ suite_cluster_radius_

core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::suite_cluster_radius_
private

Referenced by set_suite_cluster_radius().

◆ tag_output_list_

utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::tag_output_list_
private

◆ two_stage_clustering_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::two_stage_clustering_
private

Referenced by set_two_stage_clustering().

◆ use_triangle_inequality_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::use_triangle_inequality_
private

◆ user_input_VDW_bin_checker_

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::user_input_VDW_bin_checker_
private

Referenced by set_user_input_VDW_bin_checker().

◆ VDW_rep_screen_info_

utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::VDW_rep_screen_info_
private

Referenced by set_VDW_rep_screen_info().

◆ verbose_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::verbose_
private

Referenced by set_verbose().

◆ whole_struct_cluster_radius_

core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::whole_struct_cluster_radius_
private

Referenced by set_cluster_radius().

◆ working_parameters_

protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::working_parameters_
private

◆ working_parameters_exist_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::working_parameters_exist_
private
The documentation for this class was generated from the following files:
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