| absolute_vec(numeric::xyzVector< core::Real > vector) | protocols::features::strand_assembly::SandwichFeatures | |
| add_AA_to_terminal_loops(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_by_components_PK_id_counter, core::Size sw_can_by_sh_id, std::string tag, bool starting_loop, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| add_dssp_ratio_in_sw(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| add_ending_loop(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_by_components_PK_id_counter, core::Size sw_can_by_sh_id, std::string tag) | protocols::features::strand_assembly::SandwichFeatures | |
| add_num_edge_strands_in_each_sw(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| add_num_strands_in_each_sw(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| add_number_of_inward_pointing_LWY_in_core_strands_in_sw(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| add_number_of_inward_pointing_W_in_sw(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| add_starting_loop(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_by_components_PK_id_counter, core::Size sw_can_by_sh_id, std::string tag) | protocols::features::strand_assembly::SandwichFeatures | |
| add_sw_res_size(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| allowed_deviation_for_turn_type_id_ | protocols::features::strand_assembly::SandwichFeatures | private |
| cal_dis_angle_to_find_sheet(core::pose::Pose const &pose, core::Size res_i_0, core::Size res_i_1, core::Size res_i_2, core::Size res_j_0, core::Size res_j_1, core::Size res_j_2) | protocols::features::strand_assembly::SandwichFeatures | |
| cal_min_dis_between_sheets_by_cen_res(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sheet_id_1, core::Size sheet_id_2) | protocols::features::strand_assembly::SandwichFeatures | |
| cal_num_of_sheets_that_surround_this_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, utility::vector1< core::Size > all_distinct_sheet_ids, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| calculate_dihedral_w_4_resnums(core::pose::Pose const &pose, core::Size res1_sheet_i, core::Size res2_sheet_i, core::Size res1_sheet_j, core::Size res2_sheet_j) | protocols::features::strand_assembly::SandwichFeatures | |
| CB_b_factor_cutoff_for_electrostatic_interactions_ | protocols::features::strand_assembly::SandwichFeatures | private |
| change_sheet_id_if_possible(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose) | protocols::features::strand_assembly::SandwichFeatures | |
| check_canonicalness_cutoff_ | protocols::features::strand_assembly::SandwichFeatures | private |
| check_canonicalness_of_LR(core::Size loop_size, bool intra_sheet, std::string LR) | protocols::features::strand_assembly::SandwichFeatures | |
| check_canonicalness_of_PA(core::Size loop_size, bool intra_sheet, std::string PA_by_preceding_E, std::string PA_by_following_E, core::Real check_canonicalness_cutoff_) | protocols::features::strand_assembly::SandwichFeatures | |
| check_canonicalness_of_parallel_EE(core::Size loop_size, bool intra_sheet, std::string parallel_EE) | protocols::features::strand_assembly::SandwichFeatures | |
| check_heading_direction(core::pose::Pose &dssp_pose, core::Size preceding_E, core::Size following_E, std::string check_heading_direction_by_) | protocols::features::strand_assembly::SandwichFeatures | |
| check_helix_existence(core::pose::Pose const &pose) | protocols::features::strand_assembly::SandwichFeatures | |
| check_LR(core::pose::Pose &dssp_pose, core::Size preceding_E, core::Size following_E) | protocols::features::strand_assembly::SandwichFeatures | |
| check_N_to_C_direction_by_ | protocols::features::strand_assembly::SandwichFeatures | private |
| check_PA(core::pose::Pose &dssp_pose, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| check_relevant_residues(utility::vector1< bool > const &relevant_residues, core::Size res1) const | protocols::features::FeaturesReporter | |
| check_relevant_residues(utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const | protocols::features::FeaturesReporter | |
| check_relevant_residues(utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const | protocols::features::FeaturesReporter | |
| check_relevant_residues_range(utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const | protocols::features::FeaturesReporter | |
| check_strand_too_closeness(core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j) | protocols::features::strand_assembly::SandwichFeatures | |
| check_sw_by_dis(core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, bool antiparalell) | protocols::features::strand_assembly::SandwichFeatures | |
| check_whether_hairpin_connects_short_strand(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size start_res, core::Size next_start_res) | protocols::features::strand_assembly::SandwichFeatures | |
| check_whether_same_direction_strands_connect_two_sheets_or_a_loop(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size start_res, core::Size next_start_res) | protocols::features::strand_assembly::SandwichFeatures | |
| check_whether_sheets_are_connected_with_near_bb_atoms(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| check_whether_strand_i_is_in_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size segment_id) | protocols::features::strand_assembly::SandwichFeatures | |
| check_whether_sw_by_sh_id_still_alive(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| check_whether_sw_is_not_connected_with_continuous_atoms(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| check_whether_this_pdb_should_be_excluded(std::string tag) | protocols::features::strand_assembly::SandwichFeatures | |
| check_whether_this_sheet_is_too_short(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_i) | protocols::features::strand_assembly::SandwichFeatures | |
| count_AA(core::pose::Pose const &pose, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| count_AA_w_direction(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::pose::Pose const &pose_w_center_000, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| count_AA_with_direction_ | protocols::features::strand_assembly::SandwichFeatures | private |
| delete_record(StructureID, utility::sql_database::sessionOP) | protocols::features::FeaturesReporter | inlinevirtual |
| delete_records_from_table(std::string const &table_name, StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::FeaturesReporter | protected |
| delete_this_sw_can_by_sh_id_from_sw_by_comp(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| determine_core_heading_surface_heading_by_distance(core::pose::Pose const &pose_w_center_000, core::Size residue_num) | protocols::features::strand_assembly::SandwichFeatures | |
| determine_heading_direction_by_vector(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end, core::Size ii) | protocols::features::strand_assembly::SandwichFeatures | |
| distance_cutoff_for_electrostatic_interactions_ | protocols::features::strand_assembly::SandwichFeatures | private |
| do_not_connect_sheets_by_loops_ | protocols::features::strand_assembly::SandwichFeatures | private |
| exclude_desinated_pdbs_ | protocols::features::strand_assembly::SandwichFeatures | private |
| exclude_sandwich_that_has_near_backbone_atoms_between_sheets_ | protocols::features::strand_assembly::SandwichFeatures | private |
| exclude_sandwich_that_is_linked_w_same_direction_strand_ | protocols::features::strand_assembly::SandwichFeatures | private |
| extract_sandwich_ | protocols::features::strand_assembly::SandwichFeatures | private |
| features_reporter_dependencies() const | protocols::features::strand_assembly::SandwichFeatures | virtual |
| FeaturesReporter() | protocols::features::FeaturesReporter | inline |
| fill_sw_by_components(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_by_components_PK_id_counter, std::string tag, core::Size sw_can_by_sh_id, core::Size sheet_id, std::string sheet_antiparellel, core::Size sw_by_components_bs_id, std::string strand_is_at_edge, core::Size component_size, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| find_sheet(core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, bool antiparalell) | protocols::features::strand_assembly::SandwichFeatures | |
| find_tag(core::pose::Pose const &pose) const | protocols::features::FeaturesReporter | protected |
| generate_scorefxn(bool fullatom=false) | protocols::features::strand_assembly::SandwichFeatures | private |
| get_all_strands_in_sheet_i(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_avg_dis_CA_CA(core::pose::Pose const &pose, core::Size i_resnum, core::Size i_resnum_1, core::Size i_resnum_2, core::Size i_resnum_3, core::Size j_resnum, core::Size j_resnum_1, core::Size j_resnum_2, core::Size j_resnum_3) | protocols::features::strand_assembly::SandwichFeatures | |
| get_avg_dis_strands(core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j) | protocols::features::strand_assembly::SandwichFeatures | |
| get_cen_res_in_other_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_cen_residues_in_this_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_central_residues_in_each_of_two_edge_strands(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sheet_i) | protocols::features::strand_assembly::SandwichFeatures | |
| get_chain_B_resNum(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_closest_distance_between_strands(core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j) | protocols::features::strand_assembly::SandwichFeatures | |
| get_current_bs_id_and_closest_edge_bs_id_in_different_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| get_current_strands_in_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| get_distinct_sheet_id_from_sheet_table(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| get_distinct_sw_id_from_sw_by_components_table(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| get_full_strands(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| get_full_strands_from_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_list_of_residues_in_sheet_i(utility::vector1< SandwichFragment > all_strands_in_sheet_i) | protocols::features::strand_assembly::SandwichFeatures | |
| get_max_sheet_id(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| get_next_starting_res_for_connecting_strands(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size former_ending_res) | protocols::features::strand_assembly::SandwichFeatures | |
| get_num_of_distinct_sheet_id(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| get_num_of_sheets_that_surround_this_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_num_strands_in_this_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_relevant_residues_mode() const | protocols::features::FeaturesReporter | |
| get_segment_id(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size all_strands_index) | protocols::features::strand_assembly::SandwichFeatures | |
| get_sheet_antiparallel_info(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_shortest_among_4_vals(core::Real arr_dis_inter_sheet[]) | protocols::features::strand_assembly::SandwichFeatures | |
| get_size_sw_by_components_PK_id(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_start_end_res_num_in_the_longest_strand(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_starting_res_for_connecting_strands(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size former_res_end) | protocols::features::strand_assembly::SandwichFeatures | |
| get_tag(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| get_vec_AA_kind(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_vec_distinct_sheet_id(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| get_vec_sw_can_by_sh_id(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| get_vector_AA_distribution_w_direction(StructureID struct_id, utility::sql_database::sessionOP db_session, std::string heading_direction, std::string strand_location) | protocols::features::strand_assembly::SandwichFeatures | |
| get_vector_AA_distribution_wo_direction(StructureID struct_id, utility::sql_database::sessionOP db_session, std::string loop_kind) | protocols::features::strand_assembly::SandwichFeatures | |
| identify_sheet_id_by_residue_end(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_ | protocols::features::strand_assembly::SandwichFeatures | private |
| is_this_strand_at_edge(core::pose::Pose const &pose, StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| is_this_strand_at_edge_by_looking_db(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_begin) | protocols::features::strand_assembly::SandwichFeatures | |
| judge_facing(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sheet_i, core::Size sheet_j) | protocols::features::strand_assembly::SandwichFeatures | |
| load_into_pose(utility::sql_database::sessionOP, StructureID, core::pose::Pose &) | protocols::features::FeaturesReporter | inlinevirtual |
| mark_sw_which_is_not_connected_with_continuous_atoms(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, std::string sw_is_not_connected_with_continuous_atoms) | protocols::features::strand_assembly::SandwichFeatures | |
| max_abs_inter_strand_dihedral_to_not_be_same_direction_strands_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_CA_CA_dis_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_E_in_extracted_sw_loop_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_ending_loop_size_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_H_in_extracted_sw_loop_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_inter_sheet_dis_CA_CA_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_inter_strand_angle_to_not_be_same_direction_strands_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_num_strands_to_deal_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_num_sw_per_pdb_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_O_N_dis_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_sheet_angle_by_four_term_cen_res_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_sheet_angle_with_cen_res_in_smaller_sheet_and_two_terminal_res_in_larger_sheet_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_sheet_dis_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_sheet_torsion_cen_res_ | protocols::features::strand_assembly::SandwichFeatures | private |
| max_starting_loop_size_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_C_O_N_angle_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_CA_CA_dis_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_inter_sheet_dis_CA_CA_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_N_H_O_angle_between_two_sheets_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_N_O_dis_between_two_sheets_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_num_strands_in_sheet_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_num_strands_to_deal_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_O_N_dis_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_res_in_strand_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_sheet_angle_by_four_term_cen_res_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_sheet_dis_ | protocols::features::strand_assembly::SandwichFeatures | private |
| min_sheet_torsion_cen_res_ | protocols::features::strand_assembly::SandwichFeatures | private |
| no_helix_in_pdb_ | protocols::features::strand_assembly::SandwichFeatures | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) | protocols::features::strand_assembly::SandwichFeatures | virtual |
| prepare_to_fill_sw_by_components(StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| primary_seq_distance_cutoff_for_beta_sheet_capping_after_C_term_capping_ | protocols::features::strand_assembly::SandwichFeatures | private |
| primary_seq_distance_cutoff_for_beta_sheet_capping_after_N_term_capping_ | protocols::features::strand_assembly::SandwichFeatures | private |
| primary_seq_distance_cutoff_for_beta_sheet_capping_before_C_term_capping_ | protocols::features::strand_assembly::SandwichFeatures | private |
| primary_seq_distance_cutoff_for_beta_sheet_capping_before_N_term_capping_ | protocols::features::strand_assembly::SandwichFeatures | private |
| primary_seq_distance_cutoff_for_electrostatic_interactions_ | protocols::features::strand_assembly::SandwichFeatures | private |
| process_decoy(core::pose::Pose &dssp_pose, core::scoring::ScoreFunction const &) const | protocols::features::strand_assembly::SandwichFeatures | |
| relevant_residues_mode_ | protocols::features::FeaturesReporter | protected |
| report_avg_b_factor_CB_at_each_component(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| report_dihedral_angle_between_core_strands_across_facing_sheets(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| report_features(core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | virtual |
| protocols::features::FeaturesReporter::report_features(core::pose::Pose const &, StructureID, utility::sql_database::sessionOP) | protocols::features::FeaturesReporter | |
| report_heading_directions_of_all_AA_in_a_strand(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| report_hydrophobic_ratio_net_charge(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| report_number_of_electrostatic_interactions_of_residues(std::string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, std::string dssp_code, std::string heading_direction) | protocols::features::strand_assembly::SandwichFeatures | |
| report_number_of_inward_pointing_aro_AAs_in_a_pair_of_edge_strands(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size current_bs_id, core::Size closest_bs_id) | protocols::features::strand_assembly::SandwichFeatures | |
| report_number_of_inward_pointing_charged_AAs_in_a_pair_of_edge_strands(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size current_bs_id, core::Size closest_bs_id) | protocols::features::strand_assembly::SandwichFeatures | |
| report_topology_candidate(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id) | protocols::features::strand_assembly::SandwichFeatures | |
| report_turn_AA(core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size i, StructureID struct_id, utility::sql_database::sessionOP db_session, std::string turn_type) | protocols::features::strand_assembly::SandwichFeatures | |
| report_turn_type(core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size start_res, core::Size end_res, StructureID struct_id, utility::sql_database::sessionOP db_session) | protocols::features::strand_assembly::SandwichFeatures | |
| retrieve_residue_num_of_rkde(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, std::string dssp_code, std::string heading_direction) | protocols::features::strand_assembly::SandwichFeatures | |
| round_to_float(float x) | protocols::features::strand_assembly::SandwichFeatures | |
| round_to_Real(core::Real x) | protocols::features::strand_assembly::SandwichFeatures | |
| round_to_Size(core::Real x) | protocols::features::strand_assembly::SandwichFeatures | |
| SandwichFeatures() | protocols::features::strand_assembly::SandwichFeatures | |
| schema() const | protocols::features::FeaturesReporter | inlinevirtual |
| see_edge_or_core(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_num) | protocols::features::strand_assembly::SandwichFeatures | |
| see_whether_sheet_is_antiparallel(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size i_sheet) | protocols::features::strand_assembly::SandwichFeatures | |
| see_whether_sheets_can_be_combined(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size i_sheet, core::Size j_sheet) | protocols::features::strand_assembly::SandwichFeatures | |
| set_relevant_residues_mode(RelevantResiduesMode::T setting) | protocols::features::FeaturesReporter | |
| type_name() const | protocols::features::strand_assembly::SandwichFeatures | inlinevirtual |
| update_num_of_sheets_that_surround_this_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id, core::Size num_of_sheets_that_surround_this_sheet) | protocols::features::strand_assembly::SandwichFeatures | |
| update_rkde(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size RKDE_PK_id_counter, std::string tag, core::Size residue_number, std::string residue_type) | protocols::features::strand_assembly::SandwichFeatures | |
| update_rkde_in_strands(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size RKDE_in_strands_PK_id_counter, std::string tag, core::Size sw_can_by_sh_id, core::Size residue_number, std::string residue_type, std::string heading_direction) | protocols::features::strand_assembly::SandwichFeatures | |
| update_sheet_antiparallel(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id, std::string antiparallel) | protocols::features::strand_assembly::SandwichFeatures | |
| update_sheet_connectivity(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_by_components_PK_id_counter, std::string tag, core::Size sw_can_by_sh_id, std::string loop_kind, core::Size intra_sheet_con_id, core::Size inter_sheet_con_id, std::string LR, std::string cano_LR, std::string PA_by_preceding_E, std::string PA_by_following_E, std::string cano_PA, std::string heading_direction, std::string heading_parallel, std::string cano_parallel_EE, core::Size loop_size, core::Size start_res, core::Size end_res) | protocols::features::strand_assembly::SandwichFeatures | |
| update_sheet_id(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size new_sheet_id, core::Size old_sheet_id) | protocols::features::strand_assembly::SandwichFeatures | |
| update_sw_by_components_by_AA_w_direction(StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::pose::Pose const &pose_w_center_000, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end) | protocols::features::strand_assembly::SandwichFeatures | |
| write_AA_distribution_files_w_direction_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_AA_distribution_files_wo_direction_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_AA_kind_files_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_all_info_files_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_beta_sheet_capping_info_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_chain_B_resnum_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_electrostatic_interactions_of_all_residues_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_electrostatic_interactions_of_all_residues_in_a_strand_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_electrostatic_interactions_of_surface_residues_in_a_strand_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_heading_directions_of_all_AA_in_a_strand_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_p_aa_pp_files_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_phi_psi_of_all_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_phi_psi_of_E_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_rama_at_AA_to_files_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_resfile_ | protocols::features::strand_assembly::SandwichFeatures | private |
| write_schema_to_db(utility::sql_database::sessionOP db_session) const | protocols::features::strand_assembly::SandwichFeatures | virtual |
| write_to_sheet(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_PK_id_counter, core::Size sheet_id, core::Size segment_id) | protocols::features::strand_assembly::SandwichFeatures | |
| write_to_sw_can_by_sh(StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_PK_id_counter, std::string tag, core::Size sw_can_by_sh_id_counter, core::Size sheet_id, core::Size num_strands_from_sheet) | protocols::features::strand_assembly::SandwichFeatures | |
| ~FeaturesReporter() | protocols::features::FeaturesReporter | virtual |
| ~SandwichFeatures() | protocols::features::strand_assembly::SandwichFeatures | |
1.8.7