| add_loop_segment(core::pose::Pose const &pose, protocols::loops::Loop loop, core::Size segment) | protocols::legacy_sewing::Assembly | |
| add_model(SewGraphCOP graph, Model const &model, bool available=true) | protocols::legacy_sewing::Assembly | |
| align_model(Model &mobile_model, AtomMap const &atom_alignments, int reference_model_id) const | protocols::legacy_sewing::Assembly | |
| all_segments() const | protocols::legacy_sewing::Assembly | |
| all_segments_ | protocols::legacy_sewing::Assembly | protected |
| append_model(Model const &model, ScoreResult const &edge_score)=0 | protocols::legacy_sewing::Assembly | pure virtual |
| append_segments(utility::vector1< SewSegment > const &segments) | protocols::legacy_sewing::Assembly | |
| Assembly() | protocols::legacy_sewing::Assembly | |
| assembly_begin() const | protocols::legacy_sewing::Assembly | |
| assembly_begin() | protocols::legacy_sewing::Assembly | |
| assembly_end() const | protocols::legacy_sewing::Assembly | |
| assembly_end() | protocols::legacy_sewing::Assembly | |
| atom_map_from_score_result(ScoreResult const &alignment_scores) const | protocols::legacy_sewing::Assembly | |
| available_nodes_ | protocols::legacy_sewing::Assembly | protected |
| blosum_history_ | protocols::legacy_sewing::Assembly | |
| clone()=0 | protocols::legacy_sewing::Assembly | pure virtual |
| create_chimera_segment(SewSegment const &reference_segment, SewSegment const &mobile_segment, AtomMap const &atom_map, bool reference_is_nter) const | protocols::legacy_sewing::Assembly | |
| delete_segments(core::Size seg_index) | protocols::legacy_sewing::Assembly | |
| disconnected_segments() const | protocols::legacy_sewing::Assembly | |
| edge_path_ | protocols::legacy_sewing::Assembly | protected |
| edges() const | protocols::legacy_sewing::Assembly | |
| ending_node() const | protocols::legacy_sewing::Assembly | |
| find_possible_orders(core::Real max_loop_distance) const | protocols::legacy_sewing::Assembly | |
| follow_edge(SewGraphCOP graph, HashEdge const *const edge, core::Size source_index) | protocols::legacy_sewing::Assembly | |
| generate_native_rotamers_map() const | protocols::legacy_sewing::Assembly | |
| get_chimera_segments(std::map< SewSegment, SewSegment > const &matching_segments, std::map< SegmentPair, AtomMap > const &segment_matches, Model const &mobile_model) | protocols::legacy_sewing::Assembly | |
| get_matching_model_segments(Model const &model, ScoreResult const &edge_score) const | protocols::legacy_sewing::Assembly | |
| get_model_segments(int model_id) const | protocols::legacy_sewing::Assembly | |
| get_next_reference_node(SewGraphOP graph) const | protocols::legacy_sewing::Assembly | |
| get_partner() const | protocols::legacy_sewing::Assembly | |
| get_score_result(ModelNode const *model_1_node, HashEdge const *const cur_edge, SewGraphCOP graph) const | protocols::legacy_sewing::Assembly | |
| map_residues(int reference_model_id, Model mobile_model, AtomMap const &atom_alignments) | protocols::legacy_sewing::Assembly | |
| model_ids() const | protocols::legacy_sewing::Assembly | |
| native_positions(core::pose::Pose const &pose) const | protocols::legacy_sewing::Assembly | |
| natives_select(core::pose::Pose const &pose, std::string object_name="") const | protocols::legacy_sewing::Assembly | |
| operator<<(std::ostream &out, Assembly const &atom) | protocols::legacy_sewing::Assembly | friend |
| partner_pose_ | protocols::legacy_sewing::Assembly | protected |
| path() const | protocols::legacy_sewing::Assembly | |
| path_ | protocols::legacy_sewing::Assembly | protected |
| percent_native(core::pose::Pose const &pose) const | protocols::legacy_sewing::Assembly | |
| pose_loop_anchors() const | protocols::legacy_sewing::Assembly | |
| pose_num(int model_id, core::Size resnum) const | protocols::legacy_sewing::Assembly | |
| prepare_for_packing(core::pose::Pose &pose, core::pack::task::TaskFactoryOP task_factory, core::Real base_native_bonus, core::Size neighbor_cutoff) const | protocols::legacy_sewing::Assembly | |
| regenerate_model(int model_id) const | protocols::legacy_sewing::Assembly | |
| reorder(utility::vector1< core::Size > new_order) | protocols::legacy_sewing::Assembly | |
| reorder_randomly(core::Real max_loop_distance) | protocols::legacy_sewing::Assembly | |
| segments() const | protocols::legacy_sewing::Assembly | |
| segments_ | protocols::legacy_sewing::Assembly | protected |
| set_partner(core::pose::PoseOP partner_pose) | protocols::legacy_sewing::Assembly | |
| starting_node() const | protocols::legacy_sewing::Assembly | |
| string_blosum(utility::vector1< std::pair< core::Real, core::Size > > blosum_history) const | protocols::legacy_sewing::Assembly | |
| string_path() const | protocols::legacy_sewing::Assembly | |
| to_multichain_pose(std::string residue_type_set) const | protocols::legacy_sewing::Assembly | |
| to_pose(std::string residue_type_set, bool create_cuts=true) const | protocols::legacy_sewing::Assembly | |
| total_residue() const | protocols::legacy_sewing::Assembly | |
| update_coords_from_pose(core::pose::Pose const &pose) | protocols::legacy_sewing::Assembly | |
1.8.7