protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer Class Reference

#include <StepWiseRNA_Clusterer.hh>

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)
virtual	~StepWiseRNA_Clusterer ()
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_job_parameters (protocols::stepwise::sampling::rna::StepWiseRNA_JobParametersCOP &job_parameters)
void	set_job_parameters_exist (bool const job_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::sampling::rna::legacy::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 (Size const &setting)
void	set_VDW_rep_screen_info (utility::vector1< std::string > const &setting)
void	set_user_input_VDW_bin_checker (protocols::stepwise::sampling::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 (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_job_parameters (core::pose::PoseOP const &pose_op, std::string const &tag)
bool	check_for_closeness_without_job_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_
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::sampling::rna::StepWiseRNA_JobParametersCOP	job_parameters_
bool	job_parameters_exist_
bool	distinguish_pucker_
bool	add_lead_zero_to_tag_
bool	quick_alignment_
bool	align_only_over_base_atoms_
bool	optimize_memory_usage_
SlicedPoseJobParameters	sliced_pose_job_params_
bool	verbose_
bool	keep_pose_in_memory_
bool	keep_pose_in_memory_hydrid_
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::sampling::rna::checker::RNA_VDW_BinCheckerOP	user_input_VDW_bin_checker_
bool	perform_VDW_rep_screen_
bool	perform_filters_
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

protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer

(

utility::vector1< std::string > const &

silent_files_in

)

protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer

(

std::string const &

silent_file_in

)

protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer

(

core::io::silent::SilentFileDataOP &

sfd

)

protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::~StepWiseRNA_Clusterer ( )

virtual

Member Function Documentation

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

private

References protocols::stepwise::sampling::rna::align_poses(), alignment_res, and utility_exit_with_message.

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

private

References utility_exit_with_message.

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::check_for_closeness_without_job_parameters ( core::pose::PoseOP const &  pose_op )

private

References all_atom_rmsd(), and rmsd.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::cluster

(

)

References protocols::stepwise::sampling::rna::output_boolean(), protocols::stepwise::sampling::rna::output_title_text(), core::chemical::rna::TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list ( )

private

References protocols::stepwise::sampling::rna::align_poses(), alignment_res, calc_rms_res, protocols::stepwise::sampling::rna::check_for_messed_up_structure(), core::io::silent::SilentStruct::fill_pose(), full_to_sub(), getPoseExtraScores(), protocols::stepwise::sampling::rna::Cluster_Member::ID, protocols::stepwise::sampling::rna::output_title_text(), protocols::stepwise::sampling::rna::Cluster_Member::RMSD, protocols::stepwise::sampling::rna::rmsd_over_residue_list(), score, protocols::stepwise::sampling::rna::Cluster_Member::score, tag, and core::chemical::rna::TR.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list ( )

private

References protocols::stepwise::sampling::rna::apply_full_to_sub_mapping(), protocols::stepwise::sampling::rna::check_for_messed_up_structure(), force_north_sugar_list, force_south_sugar_list, force_syn_chi_res_list, protocols::stepwise::sampling::rna::get_residue_base_state(), protocols::stepwise::sampling::rna::get_residue_pucker_state(), core::chemical::rna::NORTH, protocols::stepwise::sampling::rna::output_seq_num_list(), protocols::stepwise::sampling::rna::output_title_text(), core::chemical::rna::SOUTH, core::chemical::rna::SYN, tag, core::chemical::rna::TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_tags_map ( )

private

References protocols::stepwise::sampling::rna::output_title_text(), tag, core::chemical::rna::TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::do_some_clustering ( )

private

References protocols::stepwise::sampling::rna::check_for_messed_up_structure(), core::io::silent::SilentStruct::fill_pose(), getPoseExtraScores(), score, tag, core::chemical::rna::TR, and utility_exit_with_message.

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

private

References alignment_res.

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

private

References calc_rms_res.

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

private

References full_to_sub().

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

private

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file

(

std::string const &

silent_file

)

References protocols::stepwise::sampling::rna::align_poses(), calc_rms_res, protocols::stepwise::sampling::rna::check_for_messed_up_structure(), core::io::silent::SilentStruct::clone(), protocols::stepwise::sampling::rna::full_length_rmsd_over_residue_list(), full_to_sub(), getPoseExtraScores(), protocols::loops::loop_rmsd(), other_pose, protocols::stepwise::sampling::rna::output_boolean(), protocols::stepwise::sampling::rna::output_title_text(), protocols::stepwise::sampling::rna::rmsd_over_residue_list(), s, tag, core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

core::pose::PoseOP protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::get_poseOP ( Size const  n )

private

References utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num ( )

private

References protocols::stepwise::sampling::rna::check_for_messed_up_structure(), protocols::stepwise::sampling::rna::output_boolean(), tag, and core::chemical::rna::TR.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::initialize_parameters_and_input ( )

private

References core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::residue_type_set(), and core::chemical::RNA.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose ( )

private

References protocols::stepwise::sampling::rna::check_for_messed_up_structure(), core::io::silent::SilentStruct::fill_pose(), protocols::stepwise::sampling::rna::output_seq_num_list(), tag, core::chemical::rna::TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::initialize_VDW_rep_checker ( )

private

References protocols::stepwise::sampling::rna::check_for_messed_up_structure(), core::io::silent::SilentStruct::fill_pose(), tag, and utility_exit_with_message.

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_job_parameters ( core::pose::PoseOP const &  pose_op, std::string const &  tag  )

private

References protocols::stepwise::sampling::rna::align_poses(), alignment_res, calc_rms_res, protocols::stepwise::sampling::rna::full_length_rmsd_over_residue_list(), full_to_sub(), protocols::loops::loop_rmsd(), protocols::stepwise::sampling::rna::output_boolean(), protocols::stepwise::sampling::rna::rmsd_over_residue_list(), core::chemical::rna::TR, and utility_exit_with_message.

bool protocols::stepwise::sampling::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 protocols::stepwise::sampling::rna::get_residue_pucker_state(), core::conformation::Residue::has_variant_type(), protocols::stepwise::sampling::rna::is_same_sugar_pucker(), protocols::stepwise::sampling::rna::output_boolean(), protocols::stepwise::sampling::rna::phosphate_base_phosphate_rmsd(), protocols::stepwise::sampling::rna::print_sugar_pucker_state(), core::pose::Pose::residue(), protocols::stepwise::sampling::rna::suite_rmsd(), core::chemical::rna::TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::output_silent_file

(

std::string const &

silent_file

)

References s, and tag.

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

private

References tag, core::chemical::rna::TR, and utility_exit_with_message.

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

References protocols::stepwise::sampling::rna::align_poses(), calc_rms_res, protocols::stepwise::sampling::rna::check_for_messed_up_structure(), protocols::stepwise::sampling::rna::full_length_rmsd_over_residue_list(), full_to_sub(), getPoseExtraScores(), native, protocols::stepwise::sampling::rna::output_boolean(), protocols::stepwise::sampling::rna::output_title_text(), protocols::stepwise::sampling::rna::remove_all_variant_types(), rms_at_corresponding_heavy_atoms(), protocols::stepwise::sampling::rna::rmsd_over_residue_list(), s, score, tag, core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_add_lead_zero_to_tag ( core::Real const &  setting )

inline

References add_lead_zero_to_tag_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_align_only_over_base_atoms ( bool const &  setting )

inline

References align_only_over_base_atoms_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_cluster_radius ( core::Real const &  setting )

inline

References whole_struct_cluster_radius_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_distinguish_pucker ( core::Real const &  setting )

inline

References distinguish_pucker_.

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

inline

References filter_virtual_res_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_full_length_loop_rmsd_clustering ( bool const &  setting )

inline

References full_length_loop_rmsd_clustering_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_ignore_FARFAR_no_auto_bulge_parent_tag ( bool const &  setting )

inline

References ignore_FARFAR_no_auto_bulge_parent_tag_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_ignore_FARFAR_no_auto_bulge_tag ( bool const &  setting )

inline

References ignore_FARFAR_no_auto_bulge_tag_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_ignore_unmatched_virtual_res ( bool const &  setting )

inline

References ignore_unmatched_virtual_res_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_job_parameters

(

protocols::stepwise::sampling::rna::StepWiseRNA_JobParametersCOP &

job_parameters

)

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_job_parameters_exist

(

bool const

job_parameters_exist

)

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_keep_pose_in_memory ( bool const &  setting )

inline

References keep_pose_in_memory_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_loop_cluster_radius ( core::Real const &  setting )

inline

References loop_cluster_radius_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_max_decoys ( core::Size const &  setting )

inline

Filter a list of poses by score.

References max_decoys_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_min_num_south_sugar_filter ( Size const &  setting )

inline

References min_num_south_sugar_filter_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_optimize_memory_usage ( bool const &  setting )

inline

References optimize_memory_usage_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_output_pdb ( bool const  setting )

inline

References output_pdb_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_PBP_clustering_at_chain_closure ( bool const &  setting )

inline

References PBP_clustering_at_chain_closure_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_perform_filters ( bool const &  setting )

inline

References perform_filters_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_perform_score_diff_cut ( bool const &  setting )

inline

References perform_score_diff_cut_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_perform_VDW_rep_screen ( bool const &  setting )

inline

References perform_VDW_rep_screen_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_quick_alignment ( bool const &  setting )

inline

References quick_alignment_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_rename_tags ( core::Real const &  setting )

inline

References rename_tags_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_score_diff_cut ( core::Real const &  setting )

inline

References score_diff_cut_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_skip_clustering ( bool const &  setting )

inline

References skip_clustering_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_suite_cluster_radius ( core::Real const &  setting )

inline

References suite_cluster_radius_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_two_stage_clustering ( bool const &  setting )

inline

References two_stage_clustering_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_user_input_VDW_bin_checker ( protocols::stepwise::sampling::rna::checker::RNA_VDW_BinCheckerOP const &  user_input_VDW_bin_checker )

inline

References user_input_VDW_bin_checker_.

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

inline

References VDW_rep_screen_info_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::set_verbose ( bool const &  setting )

inline

References verbose_.

void protocols::stepwise::sampling::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::sampling::rna::align_poses(), alignment_res, calc_rms_res, full_to_sub(), getPoseExtraScores(), protocols::stepwise::sampling::rna::Cluster_Member::ID, protocols::stepwise::sampling::rna::Cluster_Member::RMSD, protocols::stepwise::sampling::rna::rmsd_over_residue_list(), protocols::stepwise::sampling::rna::Cluster_Member::score, core::chemical::rna::TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::two_stage_clustering ( )

private

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

Member Data Documentation

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::add_lead_zero_to_tag_

private

Referenced by set_add_lead_zero_to_tag().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::align_only_over_base_atoms_

private

Referenced by set_align_only_over_base_atoms().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::all_pose_to_output_pose_ID_map_

private

utility::vector1< utility::vector1< Cluster_Member > > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::cluster_centers_neighbor_list_

private

std::map< std::string, bool > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::current_tags_map_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::distinguish_pucker_

private

Referenced by set_distinguish_pucker().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::filter_virtual_res_list_

private

Referenced by set_filter_virtual_res_list().

core::pose::Pose protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::first_pose_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::full_length_loop_rmsd_clustering_

private

Referenced by set_full_length_loop_rmsd_clustering().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::ignore_FARFAR_no_auto_bulge_parent_tag_

private

Referenced by set_ignore_FARFAR_no_auto_bulge_parent_tag().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::ignore_FARFAR_no_auto_bulge_tag_

private

Referenced by set_ignore_FARFAR_no_auto_bulge_tag().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::ignore_unmatched_virtual_res_

private

Referenced by set_ignore_unmatched_virtual_res().

core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::input_

private

protocols::stepwise::sampling::rna::StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::job_parameters_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::job_parameters_exist_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::keep_pose_in_memory_

private

Referenced by set_keep_pose_in_memory().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::keep_pose_in_memory_hydrid_

private

utility::vector1< core::pose::PoseOP > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::large_cluster_pose_list_

private

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::loop_cluster_radius_

private

Referenced by set_loop_cluster_radius().

Size protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::max_decoys_

private

Referenced by set_max_decoys().

Size protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::max_memory_pose_num_

private

Size protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::min_num_south_sugar_filter_

private

Referenced by set_min_num_south_sugar_filter().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::optimize_memory_usage_

private

Referenced by set_optimize_memory_usage().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::output_pdb_

private

Referenced by set_output_pdb().

std::map< std::string, bool > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::parent_tags_map_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::PBP_clustering_at_chain_closure_

private

Referenced by set_PBP_clustering_at_chain_closure().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::perform_filters_

private

Referenced by set_perform_filters().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::perform_score_diff_cut_

private

Referenced by set_perform_score_diff_cut().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::perform_VDW_rep_screen_

private

Referenced by set_perform_VDW_rep_screen().

utility::vector1< core::pose::PoseOP > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::pose_output_list_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::quick_alignment_

private

Referenced by set_quick_alignment().

core::pose::Pose protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::quick_alignment_pose_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::quick_alignment_pose_is_intialized_

private

std::string protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::quick_alignment_tag_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::rename_tags_

private

Referenced by set_rename_tags().

core::chemical::ResidueTypeSetCAP protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::rsd_set_

private

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::score_diff_cut_

private

Referenced by set_score_diff_cut().

utility::vector1< std::string > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::silent_files_

private

utility::vector1< core::io::silent::SilentStructOP > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::silent_struct_output_list_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::skip_clustering_

private

Referenced by set_skip_clustering().

SlicedPoseJobParameters protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::sliced_pose_job_params_

private

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::suite_cluster_radius_

private

Referenced by set_suite_cluster_radius().

utility::vector1< std::string > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::tag_output_list_

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::two_stage_clustering_

private

Referenced by set_two_stage_clustering().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::use_triangle_inequality_

private

protocols::stepwise::sampling::rna::checker::RNA_VDW_BinCheckerOP protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::user_input_VDW_bin_checker_

private

Referenced by set_user_input_VDW_bin_checker().

utility::vector1< std::string > protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::VDW_rep_screen_info_

private

Referenced by set_VDW_rep_screen_info().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::verbose_

private

Referenced by set_verbose().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::whole_struct_cluster_radius_

private

Referenced by set_cluster_radius().

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

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_Clusterer.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_Clusterer.cc