| add_segment(bool n_terminus) | protocols::sewing::data_storage::SmartAssembly | |
| add_segment(bool n_terminus, core::Size seg_ID_to_add, core::Size res_ID_1, core::Size res_ID_2) | protocols::sewing::data_storage::SmartAssembly | virtual |
| add_segment_and_neighbors_to_local_segments(SmartSegmentCOP ref_seg, core::Size new_id=0) | protocols::sewing::data_storage::SmartAssembly | |
| all_basis_pairs_ | protocols::sewing::data_storage::SmartAssembly | private |
| c_terminal_segment_ | protocols::sewing::data_storage::SmartAssembly | private |
| c_terminal_segments_ | protocols::sewing::data_storage::SmartAssembly | private |
| can_delete() | protocols::sewing::data_storage::SmartAssembly | |
| chimerize(BasisPair basis_pair, bool n_terminus) | protocols::sewing::data_storage::SmartAssembly | |
| clone() const | protocols::sewing::data_storage::SmartAssembly | |
| const_ligands_ | protocols::sewing::data_storage::SmartAssembly | private |
| const_pdb_segments() const | protocols::sewing::data_storage::SmartAssembly | |
| counter_segment_ | protocols::sewing::data_storage::SmartAssembly | private |
| current_basis_pair_ | protocols::sewing::data_storage::SmartAssembly | private |
| delete_segment(bool n_terminus) | protocols::sewing::data_storage::SmartAssembly | |
| dump_side_chains() | protocols::sewing::data_storage::SmartAssembly | |
| first_segment_ | protocols::sewing::data_storage::SmartAssembly | private |
| get_c_terminal_segment() const | protocols::sewing::data_storage::SmartAssembly | |
| get_comprehensive_assembly_string() const | protocols::sewing::data_storage::SmartAssembly | |
| get_comprehensive_forward_assembly() const | protocols::sewing::data_storage::SmartAssembly | |
| get_comprehensive_reverse_assembly() const | protocols::sewing::data_storage::SmartAssembly | |
| get_forward_assembly() const | protocols::sewing::data_storage::SmartAssembly | |
| get_last_change() const | protocols::sewing::data_storage::SmartAssembly | |
| get_last_change_was_n_terminal() const | protocols::sewing::data_storage::SmartAssembly | |
| get_last_chimaera() const | protocols::sewing::data_storage::SmartAssembly | |
| get_last_chimaera_deleted() const | protocols::sewing::data_storage::SmartAssembly | |
| get_length() const | protocols::sewing::data_storage::SmartAssembly | |
| get_local_ligands() | protocols::sewing::data_storage::SmartAssembly | |
| get_local_ligands() const | protocols::sewing::data_storage::SmartAssembly | |
| get_modifiable_terminus(char op) | protocols::sewing::data_storage::SmartAssembly | |
| get_modifiable_terminus() | protocols::sewing::data_storage::SmartAssembly | |
| get_n_terminal_segment() const | protocols::sewing::data_storage::SmartAssembly | |
| get_output_partner() const | protocols::sewing::data_storage::SmartAssembly | |
| get_partner() const | protocols::sewing::data_storage::SmartAssembly | |
| get_partner_ligands() const | protocols::sewing::data_storage::SmartAssembly | |
| get_random_segment_id(bool n_terminus) | protocols::sewing::data_storage::SmartAssembly | |
| get_resID_1() const | protocols::sewing::data_storage::SmartAssembly | protected |
| get_resID_2() const | protocols::sewing::data_storage::SmartAssembly | protected |
| get_reverse_assembly() const | protocols::sewing::data_storage::SmartAssembly | |
| get_segID_1() const | protocols::sewing::data_storage::SmartAssembly | protected |
| get_segID_2() const | protocols::sewing::data_storage::SmartAssembly | protected |
| get_segment(core::Size seg_id) | protocols::sewing::data_storage::SmartAssembly | |
| get_segment_vector() const | protocols::sewing::data_storage::SmartAssembly | |
| get_size() const | protocols::sewing::data_storage::SmartAssembly | |
| get_start_node_vital_segments() | protocols::sewing::data_storage::SmartAssembly | |
| get_window_width() const | protocols::sewing::data_storage::SmartAssembly | |
| has_segment(core::Size seg_id) | protocols::sewing::data_storage::SmartAssembly | |
| is_continuous() const | protocols::sewing::data_storage::SmartAssembly | |
| iterate_over_basis_pairs(SmartSegmentCOP segment_1, SmartSegmentCOP segment_2, bool n_terminus) | protocols::sewing::data_storage::SmartAssembly | |
| last_change_ | protocols::sewing::data_storage::SmartAssembly | private |
| last_change_was_n_terminal_ | protocols::sewing::data_storage::SmartAssembly | private |
| last_chimaera_ | protocols::sewing::data_storage::SmartAssembly | private |
| last_chimaera_deleted_ | protocols::sewing::data_storage::SmartAssembly | private |
| last_reverted_parent_chimaera_ | protocols::sewing::data_storage::SmartAssembly | private |
| last_sampled_ligand_ | protocols::sewing::data_storage::SmartAssembly | private |
| length_ | protocols::sewing::data_storage::SmartAssembly | private |
| ligand_conformers_ | protocols::sewing::data_storage::SmartAssembly | private |
| load_initial_conformers(data_storage::LigandDescription ligdes) | protocols::sewing::data_storage::SmartAssembly | |
| local_ligands_ | protocols::sewing::data_storage::SmartAssembly | private |
| local_segments() | protocols::sewing::data_storage::SmartAssembly | |
| local_segments_ | protocols::sewing::data_storage::SmartAssembly | private |
| modifiable_terminus_ | protocols::sewing::data_storage::SmartAssembly | private |
| n_terminal_segment_ | protocols::sewing::data_storage::SmartAssembly | private |
| n_terminal_segments_ | protocols::sewing::data_storage::SmartAssembly | private |
| output_partner_ | protocols::sewing::data_storage::SmartAssembly | private |
| partner_ | protocols::sewing::data_storage::SmartAssembly | private |
| partner_ligands_ | protocols::sewing::data_storage::SmartAssembly | private |
| pdb_segments(std::map< core::Size, data_storage::SmartSegmentOP >) | protocols::sewing::data_storage::SmartAssembly | |
| pdb_segments() | protocols::sewing::data_storage::SmartAssembly | |
| pdb_segments_ | protocols::sewing::data_storage::SmartAssembly | private |
| pick_random_starting_segment() | protocols::sewing::data_storage::SmartAssembly | |
| reconstitute_assembly_from_string(std::string) | protocols::sewing::data_storage::SmartAssembly | |
| recurse_revert_far_c_terminal_parent(SmartSegmentOP current_segment) | protocols::sewing::data_storage::SmartAssembly | |
| recurse_revert_far_n_terminal_parent(SmartSegmentOP current_segment) | protocols::sewing::data_storage::SmartAssembly | |
| reset_chimaera_contacts(LigandResidueOP ligand, LigandSegmentOP ligand_chimaera, Basis nterm_basis, Basis cterm_basis, bool nterm) | protocols::sewing::data_storage::SmartAssembly | |
| resID_1_ | protocols::sewing::data_storage::SmartAssembly | private |
| resID_2_ | protocols::sewing::data_storage::SmartAssembly | private |
| revert() | protocols::sewing::data_storage::SmartAssembly | |
| sample_ligand() | protocols::sewing::data_storage::SmartAssembly | |
| segID_1_ | protocols::sewing::data_storage::SmartAssembly | private |
| segID_2_ | protocols::sewing::data_storage::SmartAssembly | private |
| segment_vector_ | protocols::sewing::data_storage::SmartAssembly | private |
| set_c_terminal_segment(SmartSegmentOP new_segment) | protocols::sewing::data_storage::SmartAssembly | |
| set_last_change(char) | protocols::sewing::data_storage::SmartAssembly | |
| set_last_change_was_n_terminal(bool) | protocols::sewing::data_storage::SmartAssembly | |
| set_last_chimaera(SmartSegmentOP) | protocols::sewing::data_storage::SmartAssembly | |
| set_last_chimaera_deleted(BasisPair) | protocols::sewing::data_storage::SmartAssembly | |
| set_length(core::Size) | protocols::sewing::data_storage::SmartAssembly | |
| set_modifiable_terminus(char modifiable_terminus) | protocols::sewing::data_storage::SmartAssembly | |
| set_n_terminal_segment(SmartSegmentOP new_segment) | protocols::sewing::data_storage::SmartAssembly | |
| set_output_partner(bool) | protocols::sewing::data_storage::SmartAssembly | |
| set_partner(core::pose::PoseOP partner_pose) | protocols::sewing::data_storage::SmartAssembly | |
| set_partner_ligands(std::map< core::Size, LigandResidueCOP >) | protocols::sewing::data_storage::SmartAssembly | |
| set_resID_1(core::Size) | protocols::sewing::data_storage::SmartAssembly | protected |
| set_resID_2(core::Size) | protocols::sewing::data_storage::SmartAssembly | protected |
| set_segID_1(core::Size) | protocols::sewing::data_storage::SmartAssembly | protected |
| set_segID_2(core::Size) | protocols::sewing::data_storage::SmartAssembly | protected |
| set_segment_vector(hashing::SegmentVectorCOP) | protocols::sewing::data_storage::SmartAssembly | |
| set_size(core::Size) | protocols::sewing::data_storage::SmartAssembly | |
| set_start_node_vital_segments(std::string start_node_vital_segments) | protocols::sewing::data_storage::SmartAssembly | |
| set_starting_segment(SmartSegmentOP start_segment, std::string start_node_vital_segments) | protocols::sewing::data_storage::SmartAssembly | |
| set_window_width(core::Size) | protocols::sewing::data_storage::SmartAssembly | |
| size_ | protocols::sewing::data_storage::SmartAssembly | private |
| SmartAssembly() | protocols::sewing::data_storage::SmartAssembly | |
| SmartAssembly(hashing::SegmentVectorCOP segment_vector, core::Size window_width=1) | protocols::sewing::data_storage::SmartAssembly | |
| SmartAssembly(SmartAssembly const &src) | protocols::sewing::data_storage::SmartAssembly | |
| start_node_vital_segments_ | protocols::sewing::data_storage::SmartAssembly | private |
| switch_segment(bool n_terminus) | protocols::sewing::data_storage::SmartAssembly | |
| to_pose(std::string) | protocols::sewing::data_storage::SmartAssembly | |
| transform_segments(BasisPair basis_pair) | protocols::sewing::data_storage::SmartAssembly | |
| trim_terminal_segments(char, core::Size) | protocols::sewing::data_storage::SmartAssembly | |
| unchimerize_ligand_segment(LigandSegmentOP ligseg) | protocols::sewing::data_storage::SmartAssembly | |
| undelete_segment() | protocols::sewing::data_storage::SmartAssembly | |
| unsample_ligand() | protocols::sewing::data_storage::SmartAssembly | |
| unswitch_segment() | protocols::sewing::data_storage::SmartAssembly | |
| window_width_ | protocols::sewing::data_storage::SmartAssembly | private |
| ~SmartAssembly() override | protocols::sewing::data_storage::SmartAssembly | |
1.8.7