This is the complete list of members for protocols::swa::rna::StepWiseRNA_Clusterer, including all inherited members.

add_lead_zero_to_tag_	protocols::swa::rna::StepWiseRNA_Clusterer	private
align_only_over_base_atoms_	protocols::swa::rna::StepWiseRNA_Clusterer	private
align_to_quick_alignment_pose(core::pose::Pose &pose, std::string const &tag) const	protocols::swa::rna::StepWiseRNA_Clusterer	private
all_pose_to_output_pose_ID_map_	protocols::swa::rna::StepWiseRNA_Clusterer	private
check_for_closeness(core::pose::PoseOP const &pose_op, std::string const &tag)	protocols::swa::rna::StepWiseRNA_Clusterer	private
check_for_closeness_without_job_parameters(core::pose::PoseOP const &pose_op)	protocols::swa::rna::StepWiseRNA_Clusterer	private
cluster()	protocols::swa::rna::StepWiseRNA_Clusterer
cluster_centers_neighbor_list_	protocols::swa::rna::StepWiseRNA_Clusterer	private
create_large_cluster_centers_member_list()	protocols::swa::rna::StepWiseRNA_Clusterer	private
create_silent_file_and_tag_list()	protocols::swa::rna::StepWiseRNA_Clusterer	private
create_tags_map()	protocols::swa::rna::StepWiseRNA_Clusterer	private
current_tags_map_	protocols::swa::rna::StepWiseRNA_Clusterer	private
distinguish_pucker_	protocols::swa::rna::StepWiseRNA_Clusterer	private
do_some_clustering()	protocols::swa::rna::StepWiseRNA_Clusterer	private
filter_virtual_res_list_	protocols::swa::rna::StepWiseRNA_Clusterer	private
first_pose_	protocols::swa::rna::StepWiseRNA_Clusterer	private
full_length_loop_rmsd_clustering_	protocols::swa::rna::StepWiseRNA_Clusterer	private
get_act_alignment_res() const	protocols::swa::rna::StepWiseRNA_Clusterer	private
get_act_full_to_sub() const	protocols::swa::rna::StepWiseRNA_Clusterer	private
get_act_Is_prepend_map() const	protocols::swa::rna::StepWiseRNA_Clusterer	private
get_act_rmsd_res_list() const	protocols::swa::rna::StepWiseRNA_Clusterer	private
get_best_neighboring_shift_RMSD_and_output_silent_file(std::string const &silent_file)	protocols::swa::rna::StepWiseRNA_Clusterer
get_poseOP(Size const n)	protocols::swa::rna::StepWiseRNA_Clusterer	private
ignore_FARFAR_no_auto_bulge_parent_tag_	protocols::swa::rna::StepWiseRNA_Clusterer	private
ignore_FARFAR_no_auto_bulge_tag_	protocols::swa::rna::StepWiseRNA_Clusterer	private
ignore_unmatched_virtual_res_	protocols::swa::rna::StepWiseRNA_Clusterer	private
initialize_max_memory_pose_num()	protocols::swa::rna::StepWiseRNA_Clusterer	private
initialize_parameters_and_input()	protocols::swa::rna::StepWiseRNA_Clusterer	private
initialize_quick_alignment_pose()	protocols::swa::rna::StepWiseRNA_Clusterer	private
initialize_VDW_rep_screener()	protocols::swa::rna::StepWiseRNA_Clusterer	private
input_	protocols::swa::rna::StepWiseRNA_Clusterer	private
Is_new_cluster_center_with_job_parameters(core::pose::PoseOP const &pose_op, std::string const &tag)	protocols::swa::rna::StepWiseRNA_Clusterer	private
Is_old_individual_suite_cluster(core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, utility::vector1< core::Size > const &rmsd_res_list, 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	protocols::swa::rna::StepWiseRNA_Clusterer	private
job_parameters_	protocols::swa::rna::StepWiseRNA_Clusterer	private
job_parameters_exist_	protocols::swa::rna::StepWiseRNA_Clusterer	private
keep_pose_in_memory_	protocols::swa::rna::StepWiseRNA_Clusterer	private
keep_pose_in_memory_hydrid_	protocols::swa::rna::StepWiseRNA_Clusterer	private
large_cluster_pose_list_	protocols::swa::rna::StepWiseRNA_Clusterer	private
loop_cluster_radius_	protocols::swa::rna::StepWiseRNA_Clusterer	private
max_decoys_	protocols::swa::rna::StepWiseRNA_Clusterer	private
max_memory_pose_num_	protocols::swa::rna::StepWiseRNA_Clusterer	private
min_num_south_ribose_filter_	protocols::swa::rna::StepWiseRNA_Clusterer	private
optimize_memory_usage_	protocols::swa::rna::StepWiseRNA_Clusterer	private
output_pdb_	protocols::swa::rna::StepWiseRNA_Clusterer	private
output_silent_file(std::string const &silent_file)	protocols::swa::rna::StepWiseRNA_Clusterer
parent_tags_map_	protocols::swa::rna::StepWiseRNA_Clusterer	private
pass_FARFAR_no_auto_bulge_filter(core::io::silent::SilentStructOP const &silent_struct) const	protocols::swa::rna::StepWiseRNA_Clusterer	private
PBP_clustering_at_chain_closure_	protocols::swa::rna::StepWiseRNA_Clusterer	private
perform_filters_	protocols::swa::rna::StepWiseRNA_Clusterer	private
perform_score_diff_cut_	protocols::swa::rna::StepWiseRNA_Clusterer	private
perform_VDW_rep_screen_	protocols::swa::rna::StepWiseRNA_Clusterer	private
pose_output_list_	protocols::swa::rna::StepWiseRNA_Clusterer	private
quick_alignment_	protocols::swa::rna::StepWiseRNA_Clusterer	private
quick_alignment_pose_	protocols::swa::rna::StepWiseRNA_Clusterer	private
quick_alignment_pose_is_intialized_	protocols::swa::rna::StepWiseRNA_Clusterer	private
quick_alignment_tag_	protocols::swa::rna::StepWiseRNA_Clusterer	private
recalculate_rmsd_and_output_silent_file(std::string const &silent_file, protocols::swa::rna::StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup, bool const write_score_only)	protocols::swa::rna::StepWiseRNA_Clusterer
rename_tags_	protocols::swa::rna::StepWiseRNA_Clusterer	private
rsd_set_	protocols::swa::rna::StepWiseRNA_Clusterer	private
score_diff_cut_	protocols::swa::rna::StepWiseRNA_Clusterer	private
set_add_lead_zero_to_tag(core::Real const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_align_only_over_base_atoms(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_cluster_radius(core::Real const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_distinguish_pucker(core::Real const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_filter_virtual_res_list(utility::vector1< core::Size > const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_full_length_loop_rmsd_clustering(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_ignore_FARFAR_no_auto_bulge_parent_tag(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_ignore_FARFAR_no_auto_bulge_tag(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_ignore_unmatched_virtual_res(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_job_parameters(protocols::swa::rna::StepWiseRNA_JobParametersCOP &job_parameters)	protocols::swa::rna::StepWiseRNA_Clusterer
set_job_parameters_exist(bool const job_parameters_exist)	protocols::swa::rna::StepWiseRNA_Clusterer
set_keep_pose_in_memory(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_loop_cluster_radius(core::Real const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_max_decoys(core::Size const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_min_num_south_ribose_filter(Size const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_optimize_memory_usage(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_output_pdb(bool const setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_PBP_clustering_at_chain_closure(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_perform_filters(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_perform_score_diff_cut(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_perform_VDW_rep_screen(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_quick_alignment(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_rename_tags(core::Real const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_score_diff_cut(core::Real const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_skip_clustering(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_suite_cluster_radius(core::Real const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_two_stage_clustering(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_user_input_VDW_bin_screener(protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_VDW_rep_screen_info(utility::vector1< std::string > const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
set_verbose(bool const &setting)	protocols::swa::rna::StepWiseRNA_Clusterer	inline
setup_fail_triangle_inequailty_list(core::pose::Pose &current_pose, std::string const &tag, utility::vector1< bool > &fail_triangle_inequality_list)	protocols::swa::rna::StepWiseRNA_Clusterer	private
silent_files_	protocols::swa::rna::StepWiseRNA_Clusterer	private
silent_struct_output_list_	protocols::swa::rna::StepWiseRNA_Clusterer	private
skip_clustering_	protocols::swa::rna::StepWiseRNA_Clusterer	private
sliced_pose_job_params_	protocols::swa::rna::StepWiseRNA_Clusterer	private
StepWiseRNA_Clusterer(utility::vector1< std::string > const &silent_files_in)	protocols::swa::rna::StepWiseRNA_Clusterer
StepWiseRNA_Clusterer(std::string const &silent_file_in)	protocols::swa::rna::StepWiseRNA_Clusterer
StepWiseRNA_Clusterer(core::io::silent::SilentFileDataOP &sfd)	protocols::swa::rna::StepWiseRNA_Clusterer
suite_cluster_radius_	protocols::swa::rna::StepWiseRNA_Clusterer	private
tag_output_list_	protocols::swa::rna::StepWiseRNA_Clusterer	private
two_stage_clustering()	protocols::swa::rna::StepWiseRNA_Clusterer	private
two_stage_clustering_	protocols::swa::rna::StepWiseRNA_Clusterer	private
use_triangle_inequality_	protocols::swa::rna::StepWiseRNA_Clusterer	private
user_input_VDW_bin_screener_	protocols::swa::rna::StepWiseRNA_Clusterer	private
VDW_rep_screen_info_	protocols::swa::rna::StepWiseRNA_Clusterer	private
verbose_	protocols::swa::rna::StepWiseRNA_Clusterer	private
whole_struct_cluster_radius_	protocols::swa::rna::StepWiseRNA_Clusterer	private
~StepWiseRNA_Clusterer()	protocols::swa::rna::StepWiseRNA_Clusterer	virtual