| abego() const | protocols::denovo_design::components::StructureData | |
| abego(core::Size const resid) const | protocols::denovo_design::components::StructureData | |
| abego_ | protocols::denovo_design::components::StructureData | private |
| add_covalent_bond(core::Size const res1, std::string const &atom1, core::Size const res2, std::string const &atom2) | protocols::denovo_design::components::StructureData | |
| add_covalent_bond(std::string const &seg1, core::Size const res1, std::string const &atom1, std::string const &seg2, core::Size const res2, std::string const &atom2) | protocols::denovo_design::components::StructureData | protected |
| add_covalent_bond(BondInfo const &bi) | protocols::denovo_design::components::StructureData | protected |
| add_pairing(SegmentPairing const &pairing) | protocols::denovo_design::components::StructureData | |
| add_prefix_to_segments(std::string const &prefix) | protocols::denovo_design::components::StructureData | |
| add_prefix_to_segments(std::string const &prefix, char const delimeter) | protocols::denovo_design::components::StructureData | protected |
| add_segment(Segment const &resis) | protocols::denovo_design::components::StructureData | |
| add_segment(Segment const &resis, std::string const &insert_before_segment) | protocols::denovo_design::components::StructureData | |
| add_segment(Segment const &resis, SegmentNameList::iterator insert_pos) | protocols::denovo_design::components::StructureData | |
| alias(std::string const &alias) const | protocols::denovo_design::components::StructureData | |
| aliases() const | protocols::denovo_design::components::StructureData | inline |
| aliases_ | protocols::denovo_design::components::StructureData | private |
| available_lower_termini() const | protocols::denovo_design::components::StructureData | |
| available_upper_termini() const | protocols::denovo_design::components::StructureData | |
| block_signals() | protocols::denovo_design::components::StructureData | private |
| block_signals_ | protocols::denovo_design::components::StructureData | private |
| CacheableDataOP typedef | protocols::denovo_design::components::StructureData | private |
| changed() | protocols::denovo_design::components::StructureData | private |
| check_chains(core::pose::Pose const &pose) const | protocols::denovo_design::components::StructureData | private |
| check_consistency() const | protocols::denovo_design::components::StructureData | |
| check_improper_termini(core::pose::Pose const &pose) const | protocols::denovo_design::components::StructureData | private |
| check_movable_groups() const | protocols::denovo_design::components::StructureData | private |
| check_pose(core::pose::Pose const &pose) const | protocols::denovo_design::components::StructureData | private |
| check_pose_consistency(core::pose::Pose const &pose) const | protocols::denovo_design::components::StructureData | |
| check_residues() const | protocols::denovo_design::components::StructureData | private |
| choose_new_movable_group() const | protocols::denovo_design::components::StructureData | |
| class_name() | protocols::denovo_design::components::StructureData | static |
| clear_pairings() | protocols::denovo_design::components::StructureData | |
| clone() const override | protocols::denovo_design::components::StructureData | |
| connect_segments(std::string const &segment1, std::string const &segment2) | protocols::denovo_design::components::StructureData | |
| connected_segments(std::string const &seg, bool const stop_at_cutpoint) const | protocols::denovo_design::components::StructureData | |
| copy_data(StructureData const &perm) | protocols::denovo_design::components::StructureData | |
| copy_data(StructureData const &perm, bool const overwrite) | protocols::denovo_design::components::StructureData | private |
| covalent_bonds_ | protocols::denovo_design::components::StructureData | private |
| covalent_bonds_begin() const | protocols::denovo_design::components::StructureData | |
| covalent_bonds_end() const | protocols::denovo_design::components::StructureData | |
| cutpoints() const | protocols::denovo_design::components::StructureData | |
| DATA_DELIMETER | protocols::denovo_design::components::StructureData | static |
| data_int() const | protocols::denovo_design::components::StructureData | inline |
| data_int_ | protocols::denovo_design::components::StructureData | private |
| data_real() const | protocols::denovo_design::components::StructureData | inline |
| data_real_ | protocols::denovo_design::components::StructureData | private |
| data_str() const | protocols::denovo_design::components::StructureData | inline |
| data_str_ | protocols::denovo_design::components::StructureData | private |
| datatype() const override | protocols::denovo_design::components::StructureData | |
| declare_covalent_bond(std::string const &seg1, core::Size const res1, std::string const &atom1, std::string const &seg2, core::Size const res2, std::string const &atom2) | protocols::denovo_design::components::StructureData | |
| declare_covalent_bond(core::Size const res1, std::string const &atom1, core::Size const res2, std::string const &atom2) | protocols::denovo_design::components::StructureData | |
| delete_jump_and_intervening_cutpoint(std::string const &segment1, std::string const &segment2) | protocols::denovo_design::components::StructureData | |
| delete_leading_residues(std::string const &seg) | protocols::denovo_design::components::StructureData | |
| delete_residue(core::Size const pose_resid) | protocols::denovo_design::components::StructureData | |
| delete_segment(std::string const &segment) | protocols::denovo_design::components::StructureData | |
| delete_trailing_residues(std::string const &seg) | protocols::denovo_design::components::StructureData | |
| disconnect_segments(std::string const &segment1, std::string const &segment2) | protocols::denovo_design::components::StructureData | |
| find_lower_terminus(std::set< std::string > &visited, std::string const &seg) const | protocols::denovo_design::components::StructureData | protected |
| find_non_polymer_bond(std::string const &seg1, std::string const &seg2) const | protocols::denovo_design::components::StructureData | |
| find_segment(std::string const &segname) const | protocols::denovo_design::components::StructureData | |
| find_segment(std::string const &segname) | protocols::denovo_design::components::StructureData | protected |
| find_segment_name(std::string const &segname) const | protocols::denovo_design::components::StructureData | |
| find_segment_name(std::string const &segname) | protocols::denovo_design::components::StructureData | protected |
| find_upper_terminus(std::set< std::string > &visited, std::string const &seg) const | protocols::denovo_design::components::StructureData | protected |
| generic_enzdes_header(std::string const &remark_str) const | protocols::denovo_design::components::StructureData | private |
| get_data_int(std::string const &segment_id, std::string const &data_name) const | protocols::denovo_design::components::StructureData | |
| get_data_int(std::string const &data_name) const | protocols::denovo_design::components::StructureData | protected |
| get_data_real(std::string const &segment_id, std::string const &data_name) const | protocols::denovo_design::components::StructureData | |
| get_data_real(std::string const &data_name) const | protocols::denovo_design::components::StructureData | protected |
| get_data_str(std::string const &segment_id, std::string const &data_name) const | protocols::denovo_design::components::StructureData | |
| get_data_str(std::string const &data_name) const | protocols::denovo_design::components::StructureData | protected |
| has_alias(std::string const &alias) const | protocols::denovo_design::components::StructureData | inline |
| has_data_int(std::string const &segment_id, std::string const &data_name) const | protocols::denovo_design::components::StructureData | |
| has_data_int(std::string const &data_name) const | protocols::denovo_design::components::StructureData | inlineprotected |
| has_data_real(std::string const &segment_id, std::string const &data_name) const | protocols::denovo_design::components::StructureData | |
| has_data_real(std::string const &data_name) const | protocols::denovo_design::components::StructureData | inlineprotected |
| has_data_str(std::string const &segment_id, std::string const &data_name) const | protocols::denovo_design::components::StructureData | |
| has_data_str(std::string const &data_name) const | protocols::denovo_design::components::StructureData | inlineprotected |
| has_free_lower_terminus(std::string const &id_val) const | protocols::denovo_design::components::StructureData | |
| has_free_upper_terminus(std::string const &id_val) const | protocols::denovo_design::components::StructureData | |
| has_segment(std::string const &seg) const | protocols::denovo_design::components::StructureData | |
| has_segment_group(std::string const &sname) const | protocols::denovo_design::components::StructureData | |
| id() const | protocols::denovo_design::components::StructureData | |
| id_ | protocols::denovo_design::components::StructureData | private |
| length() const | protocols::denovo_design::components::StructureData | |
| length_ | protocols::denovo_design::components::StructureData | private |
| lower_anchor(std::string const &id_val) const | protocols::denovo_design::components::StructureData | |
| mark_connected(std::string const &lower_seg, std::string const &upper_seg) | protocols::denovo_design::components::StructureData | |
| mark_disconnected(std::string const &seg1, std::string const &seg2) | protocols::denovo_design::components::StructureData | |
| merge(StructureData const &other) | protocols::denovo_design::components::StructureData | |
| merge(StructureData const &other, SegmentNames const &segments) | protocols::denovo_design::components::StructureData | |
| merge_before(StructureData const &other, std::string const &position) | protocols::denovo_design::components::StructureData | |
| merge_before(StructureData const &other, std::string const &position, SegmentNames const &segments) | protocols::denovo_design::components::StructureData | |
| merge_segments(std::string const &segment1, std::string const &segment2, std::string const &new_name) | protocols::denovo_design::components::StructureData | |
| movable_group(core::Size const resid) const | protocols::denovo_design::components::StructureData | |
| movable_groups() const | protocols::denovo_design::components::StructureData | |
| movable_groups_ | protocols::denovo_design::components::StructureData | private |
| move_segment(std::string const &segment1, std::string const &segment2) | protocols::denovo_design::components::StructureData | |
| move_segments(std::string const &segment1, std::string const &segment2_lower, std::string const &segment2_upper) | protocols::denovo_design::components::StructureData | protected |
| non_polymer_bond(std::string const &seg1, std::string const &seg2) const | protocols::denovo_design::components::StructureData | |
| non_polymer_bond_exists(std::string const &seg1, std::string const &seg2) const | protocols::denovo_design::components::StructureData | |
| num_chains() const | protocols::denovo_design::components::StructureData | |
| on_change() | protocols::denovo_design::components::StructureData | protected |
| operator<<(std::ostream &os, StructureData const &perm) | protocols::denovo_design::components::StructureData | friend |
| pairing(SegmentNames const &segments) const | protocols::denovo_design::components::StructureData | |
| pairings_ | protocols::denovo_design::components::StructureData | private |
| pairings_begin() const | protocols::denovo_design::components::StructureData | |
| pairings_end() const | protocols::denovo_design::components::StructureData | |
| parse_subtag(utility::tag::TagCOP tag) | protocols::denovo_design::components::StructureData | |
| parse_tag(utility::tag::TagCOP tag) | protocols::denovo_design::components::StructureData | |
| pose_length() const | protocols::denovo_design::components::StructureData | |
| pose_length_ | protocols::denovo_design::components::StructureData | private |
| pose_residue(std::string const &segment_name, core::Size const local_res) const | protocols::denovo_design::components::StructureData | |
| rename_segment(std::string const &old_name, std::string const &new_name) | protocols::denovo_design::components::StructureData | |
| renumber_movable_group(core::Size const oldg, core::Size const newg) | protocols::denovo_design::components::StructureData | |
| replace_segment(SegmentName const &seg_name, Segment const &segment) | protocols::denovo_design::components::StructureData | |
| retrieve_remarks(core::pose::Pose const &pose) const | protocols::denovo_design::components::StructureData | |
| save_remarks(core::io::Remarks const &remarks) | protocols::denovo_design::components::StructureData | |
| segment(std::string const &id_val) const | protocols::denovo_design::components::StructureData | |
| segment_group(std::string const &sname) const | protocols::denovo_design::components::StructureData | |
| segment_name(core::Size const res) const | protocols::denovo_design::components::StructureData | |
| segment_nonconst(std::string const &id_val) | protocols::denovo_design::components::StructureData | protected |
| segment_order_ | protocols::denovo_design::components::StructureData | private |
| SegmentName typedef | protocols::denovo_design::components::StructureData | private |
| SegmentNameSet typedef | protocols::denovo_design::components::StructureData | private |
| segments() const | protocols::denovo_design::components::StructureData | inlineprotected |
| segments_ | protocols::denovo_design::components::StructureData | private |
| segments_begin() const | protocols::denovo_design::components::StructureData | |
| segments_end() const | protocols::denovo_design::components::StructureData | |
| segments_end_nonconst() | protocols::denovo_design::components::StructureData | protected |
| segments_in_movable_group(core::Size const group) const | protocols::denovo_design::components::StructureData | |
| set_abego(std::string const &abego) | protocols::denovo_design::components::StructureData | |
| set_abego(utility::vector1< std::string > const &abego) | protocols::denovo_design::components::StructureData | |
| set_abego(std::string const &segment, std::string const &abego) | protocols::denovo_design::components::StructureData | |
| set_abego(std::string const &segment, utility::vector1< std::string > const &abego) | protocols::denovo_design::components::StructureData | |
| set_alias(std::string const &alias_name, std::string const &segment_name, core::Size const resi) | protocols::denovo_design::components::StructureData | |
| set_alias(std::string const &alias_name, core::Size const resi) | protocols::denovo_design::components::StructureData | |
| set_cutpoint(core::Size const resid) | protocols::denovo_design::components::StructureData | |
| set_cutpoint(std::string const &seg, SegmentResid const resi) | protocols::denovo_design::components::StructureData | |
| set_data_int(std::string const &segment_id, std::string const &data_name, int const val) | protocols::denovo_design::components::StructureData | |
| set_data_int(std::string const &data_name, int const val) | protocols::denovo_design::components::StructureData | protected |
| set_data_real(std::string const &segment_id, std::string const &data_name, core::Real const val) | protocols::denovo_design::components::StructureData | |
| set_data_real(std::string const &data_name, core::Real const val) | protocols::denovo_design::components::StructureData | protected |
| set_data_str(std::string const &segment_id, std::string const &data_name, std::string const &val) | protocols::denovo_design::components::StructureData | |
| set_data_str(std::string const &data_name, std::string const &val) | protocols::denovo_design::components::StructureData | protected |
| set_id(std::string const &id_str) | protocols::denovo_design::components::StructureData | |
| set_movable_group(std::string const &id, core::Size const mg) | protocols::denovo_design::components::StructureData | |
| set_ss(core::Size const resid, char const ss_type) | protocols::denovo_design::components::StructureData | |
| set_template_pose(std::string const &segment, core::pose::Pose const &template_pose, core::Size const start_resid, core::Size const stop_resid) | protocols::denovo_design::components::StructureData | |
| slice(SegmentNameSet const &segments, bool const force_padding) const | protocols::denovo_design::components::StructureData | |
| slide_jump(core::kinematics::FoldTree const &ft_orig, core::Size const jump_idx, core::Size const new_start, core::Size const new_stop) const | protocols::denovo_design::components::StructureData | protected |
| specific_enzdes_header(core::pose::Pose const &pose, std::string const &generic_remark_str) const | protocols::denovo_design::components::StructureData | private |
| ss() const | protocols::denovo_design::components::StructureData | |
| ss(core::Size const resid) const | protocols::denovo_design::components::StructureData | |
| ss_ | protocols::denovo_design::components::StructureData | private |
| StructureData() | protocols::denovo_design::components::StructureData | |
| StructureData(std::string const &id_val) | protocols::denovo_design::components::StructureData | |
| substitute_variables(std::istream &input) const | protocols::denovo_design::components::StructureData | |
| termini(std::string const &seg) const | protocols::denovo_design::components::StructureData | |
| unblock_signals() | protocols::denovo_design::components::StructureData | private |
| update_numbering() | protocols::denovo_design::components::StructureData | |
| upper_anchor(std::string const &id_val) const | protocols::denovo_design::components::StructureData | |
| write(std::ostream &os) const override | protocols::denovo_design::components::StructureData | |
| ~StructureData() override | protocols::denovo_design::components::StructureData | |
1.8.7