| add_lead_zero_to_tag_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| align_only_over_base_atoms_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| align_to_quick_alignment_pose(core::pose::Pose &pose, std::string const &tag) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| all_pose_to_output_pose_ID_map_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| check_for_closeness(core::pose::PoseOP const &pose_op, std::string const &tag) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| check_for_closeness_without_working_parameters(core::pose::PoseOP const &pose_op) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| cluster() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| cluster_centers_neighbor_list_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| create_large_cluster_centers_member_list() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| create_silent_file_and_tag_list() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| create_tags_map() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| current_tags_map_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| distinguish_pucker_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| do_some_clustering() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| filter_virtual_res_list_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| first_pose_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| full_length_loop_rmsd_clustering_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| get_act_alignment_res() const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| get_act_calc_rms_res() const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| get_act_full_to_sub() const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| get_act_is_prepend_map() const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| get_best_neighboring_shift_RMSD_and_output_silent_file(std::string const &silent_file) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| get_poseOP(core::Size const n) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| ignore_FARFAR_no_auto_bulge_parent_tag_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| ignore_FARFAR_no_auto_bulge_tag_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| ignore_unmatched_virtual_res_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| initialize_max_memory_pose_num() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| initialize_parameters_and_input() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| initialize_quick_alignment_pose() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| initialize_VDW_rep_checker() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| input_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| is_new_cluster_center_with_working_parameters(core::pose::PoseOP const &pose_op, std::string const &tag) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| is_old_individual_suite_cluster(core::pose::Pose const ¤t_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 | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| keep_pose_in_memory_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| keep_pose_in_memory_hydrid_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| large_cluster_pose_list_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| loop_cluster_radius_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| max_decoys_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| max_memory_pose_num_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| min_num_south_sugar_filter_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| optimize_memory_usage_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| output_pdb_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| output_silent_file(std::string const &silent_file) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| parent_tags_map_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| pass_FARFAR_no_auto_bulge_filter(core::io::silent::SilentStructOP const &silent_struct) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| PBP_clustering_at_chain_closure_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| perform_filters_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| perform_score_diff_cut_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| perform_VDW_rep_screen_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| pose_output_list_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| quick_alignment_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| quick_alignment_pose_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| quick_alignment_pose_is_intialized_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| quick_alignment_tag_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| 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) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| rename_tags_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| rsd_set_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| score_diff_cut_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| set_add_lead_zero_to_tag(core::Real const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_align_only_over_base_atoms(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_cluster_radius(core::Real const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_distinguish_pucker(core::Real const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_filter_virtual_res_list(utility::vector1< core::Size > const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_full_length_loop_rmsd_clustering(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_ignore_FARFAR_no_auto_bulge_parent_tag(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_ignore_FARFAR_no_auto_bulge_tag(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_ignore_unmatched_virtual_res(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_keep_pose_in_memory(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_loop_cluster_radius(core::Real const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_max_decoys(core::Size const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_min_num_south_sugar_filter(core::Size const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_optimize_memory_usage(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_output_pdb(bool const setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_PBP_clustering_at_chain_closure(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_perform_filters(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_perform_score_diff_cut(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_perform_VDW_rep_screen(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_quick_alignment(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_rename_tags(core::Real const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_score_diff_cut(core::Real const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_skip_clustering(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_suite_cluster_radius(core::Real const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_two_stage_clustering(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_user_input_VDW_bin_checker(protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_VDW_rep_screen_info(utility::vector1< std::string > const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_verbose(bool const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | inline |
| set_working_parameters(protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &working_parameters) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| set_working_parameters_exist(bool const working_parameters_exist) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| setup_fail_triangle_inequailty_list(core::pose::Pose ¤t_pose, std::string const &tag, utility::vector1< bool > &fail_triangle_inequality_list) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| silent_files_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| silent_struct_output_list_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| skip_clustering_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| sliced_pose_job_params_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| StepWiseRNA_Clusterer(utility::vector1< std::string > const &silent_files_in) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| StepWiseRNA_Clusterer(std::string const &silent_file_in) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| StepWiseRNA_Clusterer(core::io::silent::SilentFileDataOP &sfd) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
| suite_cluster_radius_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| tag_output_list_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| two_stage_clustering() | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| two_stage_clustering_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| use_triangle_inequality_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| user_input_VDW_bin_checker_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| VDW_rep_screen_info_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| verbose_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| whole_struct_cluster_radius_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| working_parameters_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| working_parameters_exist_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | private |
| ~StepWiseRNA_Clusterer() override | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer | |
1.8.7