| add_edge(core::Size const start, core::Size const stop, int const label) | core::kinematics::FoldTree | |
| add_edge(Size const start, Size const stop, std::string const &start_atom, std::string const &stop_atom) | core::kinematics::FoldTree | |
| add_edge(Size const start, Size const stop, int const label, std::string const &start_atom, std::string const &stop_atom) | core::kinematics::FoldTree | |
| add_edge(Edge const &new_edge) | core::kinematics::FoldTree | |
| add_vertex(Size const v) | core::kinematics::FoldTree | private |
| append_residue(bool const attach_by_jump=false, core::Size const jump_anchor_residue=0, std::string const &jump_upstream_atom="", std::string const &jump_downstream_atom="") | core::kinematics::FoldTree | |
| append_residue_by_chemical_bond(core::Size const anchor_residue, std::string const &anchor_atom, std::string const &root_atom) | core::kinematics::FoldTree | |
| apply_sequence_mapping(id::SequenceMapping const &old2new) | core::kinematics::FoldTree | |
| begin() const | core::kinematics::FoldTree | inline |
| boundary_left(Size res) const | core::kinematics::FoldTree | inline |
| boundary_right(Size res) const | core::kinematics::FoldTree | inline |
| check_edges_for_atom_info() const | core::kinematics::FoldTree | |
| check_fold_tree() const | core::kinematics::FoldTree | |
| check_order() const | core::kinematics::FoldTree | inlineprivate |
| check_topology() const | core::kinematics::FoldTree | inlineprivate |
| clear() | core::kinematics::FoldTree | inline |
| clone() | core::kinematics::FoldTree | inline |
| connected() const | core::kinematics::FoldTree | |
| const_iterator typedef | core::kinematics::FoldTree | |
| count_fixed_residues(Size const begin_res, Size const size, Size &min_edge_count_out) const | core::kinematics::FoldTree | |
| cut_edge(Size const cut_point) | core::kinematics::FoldTree | |
| cut_random_edge(ObjexxFCL::FArray1D_float const &cut_bias_sum, Size const nres_in) | core::kinematics::FoldTree | private |
| cutpoint(Size const cut) const | core::kinematics::FoldTree | inline |
| cutpoint_ | core::kinematics::FoldTree | mutableprivate |
| cutpoint_by_jump(Size const jump_number) const | core::kinematics::FoldTree | |
| cutpoint_map(Size const seqpos) const | core::kinematics::FoldTree | inline |
| cutpoint_map_ | core::kinematics::FoldTree | mutableprivate |
| cutpoints() const | core::kinematics::FoldTree | |
| delete_edge(iterator edge) | core::kinematics::FoldTree | |
| delete_edge(Edge const &edge) | core::kinematics::FoldTree | |
| delete_extra_vertices() | core::kinematics::FoldTree | |
| delete_jump_and_intervening_cutpoint(Size jump_begin, Size jump_end, Size cut=0) | core::kinematics::FoldTree | |
| delete_jump_and_intervening_cutpoint(Size const jump_number) | core::kinematics::FoldTree | |
| delete_jump_seqpos(Size const seqpos) | core::kinematics::FoldTree | private |
| delete_segment(Size const seg_begin, Size const seg_end) | core::kinematics::FoldTree | |
| delete_self_edges() | core::kinematics::FoldTree | |
| delete_seqpos(Size const seqpos) | core::kinematics::FoldTree | |
| delete_seqpos_simple(Size const seqpos) | core::kinematics::FoldTree | private |
| delete_unordered_edge(Size const start, Size const stop, int const label) | core::kinematics::FoldTree | |
| downstream_atom(Size const jump_number) const | core::kinematics::FoldTree | |
| downstream_jump_residue(Size const jump_number) const | core::kinematics::FoldTree | |
| edge_count | core::kinematics::FoldTree | mutableprivate |
| edge_label(Size const start, Size const stop) | core::kinematics::FoldTree | |
| edge_list_ | core::kinematics::FoldTree | private |
| EdgeList typedef | core::kinematics::FoldTree | |
| empty() const | core::kinematics::FoldTree | inline |
| end() const | core::kinematics::FoldTree | inline |
| FoldTree() | core::kinematics::FoldTree | inline |
| FoldTree(int const nres_in) | core::kinematics::FoldTree | inline |
| FoldTree(FoldTree const &)=default | core::kinematics::FoldTree | |
| get_chemical_edges() const | core::kinematics::FoldTree | |
| get_jump_edges() const | core::kinematics::FoldTree | |
| get_jump_that_builds_residue(Size const seqpos) const | core::kinematics::FoldTree | |
| get_outgoing_edges(Size const seqpos) const | core::kinematics::FoldTree | |
| get_parent_residue(Size const seqpos, bool &connected_by_jump) const | core::kinematics::FoldTree | |
| get_parent_residue(Size const seqpos) const | core::kinematics::FoldTree | |
| get_polymer_residue_direction(Size const seqpos) const | core::kinematics::FoldTree | |
| get_residue_edge(Size const seqpos) const | core::kinematics::FoldTree | |
| hash_value() const | core::kinematics::FoldTree | |
| hasher | core::kinematics::FoldTree | private |
| insert_fold_tree_by_jump(FoldTree const &subtree, Size const insert_seqpos, Size const insert_jumppos, Size const anchor_pos, Size anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="") | core::kinematics::FoldTree | |
| insert_polymer_residue(Size const seqpos, bool const join_lower, bool const join_upper) | core::kinematics::FoldTree | |
| insert_residue_by_chemical_bond(Size const seqpos, Size const anchor_residue, std::string const &anchor_atom, std::string const &root_atom) | core::kinematics::FoldTree | |
| insert_residue_by_jump(Size const seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atomno="") | core::kinematics::FoldTree | |
| is_cutpoint(Size const seqpos) const | core::kinematics::FoldTree | inline |
| is_cutpoint_ | core::kinematics::FoldTree | mutableprivate |
| is_equivalent(FoldTree const &b) const | core::kinematics::FoldTree | |
| is_jump_point(Size const seqpos) const | core::kinematics::FoldTree | inline |
| is_jump_point_ | core::kinematics::FoldTree | mutableprivate |
| is_root(Size const seqpos) const | core::kinematics::FoldTree | inline |
| is_simple_tree() const | core::kinematics::FoldTree | |
| iterator typedef | core::kinematics::FoldTree | |
| jump_edge(Size const jump_number) const | core::kinematics::FoldTree | |
| jump_edge(Size const jump_number) | core::kinematics::FoldTree | |
| jump_edge_ | core::kinematics::FoldTree | mutableprivate |
| jump_edge_count | core::kinematics::FoldTree | mutableprivate |
| jump_exists(Size const pos1, Size const pos2) const | core::kinematics::FoldTree | inline |
| jump_nr(core::Size upstream_res, core::Size downstream_res) const | core::kinematics::FoldTree | inline |
| jump_point(Size const lower_higher, Size const jump_number) const | core::kinematics::FoldTree | |
| jump_point_ | core::kinematics::FoldTree | mutableprivate |
| linked_ | core::kinematics::FoldTree | mutableprivate |
| min_edge_count | core::kinematics::FoldTree | mutableprivate |
| nc_begin() | core::kinematics::FoldTree | inlineprivate |
| nc_end() | core::kinematics::FoldTree | inlineprivate |
| new_chemical_bond(Size const anchor_pos, Size const root_pos, std::string const &anchor_atom, std::string const &root_atom, Size const new_cutpoint) | core::kinematics::FoldTree | |
| new_jump(Size const jump_pos1, Size const jump_pos2, Size const cutpoint) | core::kinematics::FoldTree | |
| new_order | core::kinematics::FoldTree | mutableprivate |
| new_topology | core::kinematics::FoldTree | mutableprivate |
| nres() const | core::kinematics::FoldTree | inline |
| nres_ | core::kinematics::FoldTree | mutableprivate |
| num_cutpoint() const | core::kinematics::FoldTree | inline |
| num_cutpoint_ | core::kinematics::FoldTree | mutableprivate |
| num_jump() const | core::kinematics::FoldTree | inline |
| num_jump_ | core::kinematics::FoldTree | mutableprivate |
| operator!=(FoldTree const &a, FoldTree const &b) | core::kinematics::FoldTree | friend |
| operator<<(std::ostream &os, FoldTree const &t) | core::kinematics::FoldTree | friend |
| operator=(FoldTree const &src) | core::kinematics::FoldTree | inline |
| operator==(FoldTree const &a, FoldTree const &b) | core::kinematics::FoldTree | friend |
| operator>>(std::istream &is, FoldTree &t) | core::kinematics::FoldTree | friend |
| partition_by_jump(Size const jump_number, FoldTree &f1, FoldTree &f2) const | core::kinematics::FoldTree | |
| partition_by_jump(Size const jump_number, ObjexxFCL::FArray1D_bool &partner1) const | core::kinematics::FoldTree | |
| partition_by_jump(Size const jump_nr) const | core::kinematics::FoldTree | |
| partition_by_residue(Size const seqpos, ObjexxFCL::FArray1D_bool &partner1) const | core::kinematics::FoldTree | |
| partition_coloring(utility::vector1< Size > const &jump_numbers) const | core::kinematics::FoldTree | |
| possible_root(Size const &seqpos) const | core::kinematics::FoldTree | inline |
| prepend_edge(Edge const &new_edge) | core::kinematics::FoldTree | |
| put_jump_stubs_intra_residue() | core::kinematics::FoldTree | |
| random_tree_from_jump_points(Size const nres_in, Size const num_jump_in, ObjexxFCL::FArray2D< Size > const &jump_point, ObjexxFCL::FArray1D_float const &cut_bias, Size const root_in=1, bool const allow_jump_at_1_or_NRES=false) | core::kinematics::FoldTree | |
| random_tree_from_jump_points(Size const nres_in, Size const num_jump_in, ObjexxFCL::FArray2D< Size > const &jump_point, std::vector< Size > const &obligate_cut_points, ObjexxFCL::FArray1D_float const &cut_bias, Size const root_in=1, bool const allow_jump_at_1_or_NRES=false) | core::kinematics::FoldTree | |
| reassign_atoms_for_intra_residue_stubs() | core::kinematics::FoldTree | |
| renumber_jumps() | core::kinematics::FoldTree | |
| renumber_jumps_ordered() | core::kinematics::FoldTree | |
| reorder(Size const start_residue, bool const verbose_if_fail=true) | core::kinematics::FoldTree | |
| replace_edge(Edge const &old_edge, Edge const &replacement_edge) | core::kinematics::FoldTree | |
| residue_is_in_fold_tree(Size seqpos) const | core::kinematics::FoldTree | |
| root() const | core::kinematics::FoldTree | inline |
| seen_ | core::kinematics::FoldTree | mutableprivate |
| set_jump_atoms(Size const jump_number, std::string const &upstream_atom, std::string const &downstream_atom, bool bKeepStubInResidue=false) | core::kinematics::FoldTree | |
| set_jump_atoms(Size const jump_number, core::Size res1, std::string const &atom1, core::Size res2, std::string const &atom2, bool bKeepStubInResidue=false) | core::kinematics::FoldTree | |
| setup_edge_counts() const | core::kinematics::FoldTree | private |
| show(std::ostream &out) const | core::kinematics::FoldTree | |
| simple_tree(Size const nres_in) | core::kinematics::FoldTree | |
| size() const | core::kinematics::FoldTree | inline |
| slide_cutpoint(Size const current_cut, Size const target_cut) | core::kinematics::FoldTree | |
| slide_jump(Size const jump_number, Size const new_res1, Size const new_res2) | core::kinematics::FoldTree | |
| split_existing_edge_at_residue(Size const resNo) | core::kinematics::FoldTree | |
| to_string() const | core::kinematics::FoldTree | |
| tree_from_jumps_and_cuts(Size const nres_in, Size const num_jump_in, ObjexxFCL::FArray2D< Size > const &jump_point, ObjexxFCL::FArray1D< Size > const &cuts, Size const root_in=1, bool const verbose=false) | core::kinematics::FoldTree | |
| update_cutpoints() const | core::kinematics::FoldTree | private |
| update_edge_label(Size const start, Size const stop, int const old_label, int const new_label) | core::kinematics::FoldTree | |
| update_edge_labels() | core::kinematics::FoldTree | private |
| update_jump_edge() const | core::kinematics::FoldTree | private |
| update_jump_points() const | core::kinematics::FoldTree | private |
| update_nres() const | core::kinematics::FoldTree | private |
| update_num_jump() const | core::kinematics::FoldTree | private |
| upstream_atom(Size const jump_number) const | core::kinematics::FoldTree | |
| upstream_jump_residue(Size const jump_number) const | core::kinematics::FoldTree | |
| ~FoldTree() override | core::kinematics::FoldTree | |
1.8.7