add_edge(int const start, int const stop, int const label) | core::kinematics::FoldTree | |
add_edge(int const start, int const stop, std::string const &start_atom, std::string const &stop_atom) | core::kinematics::FoldTree | |
add_edge(Edge const &new_edge) | core::kinematics::FoldTree | |
add_vertex(int const v) | core::kinematics::FoldTree | private |
append_residue(bool const attach_by_jump=false, int 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(int 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 |
begin() | core::kinematics::FoldTree | inlineprivate |
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(int const cut_point) | core::kinematics::FoldTree | |
cut_random_edge(ObjexxFCL::FArray1D_float const &cut_bias_sum, int const nres_in) | core::kinematics::FoldTree | private |
cutpoint(int const cut) const | core::kinematics::FoldTree | inline |
cutpoint_ | core::kinematics::FoldTree | mutableprivate |
cutpoint_by_jump(int const jump_number) const | core::kinematics::FoldTree | |
cutpoint_map(int 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(int jump_begin, int jump_end, Size cut=0) | core::kinematics::FoldTree | |
delete_jump_and_intervening_cutpoint(int const jump_number) | core::kinematics::FoldTree | |
delete_jump_seqpos(int const seqpos) | core::kinematics::FoldTree | private |
delete_segment(int const seg_begin, int const seg_end) | core::kinematics::FoldTree | |
delete_self_edges() | core::kinematics::FoldTree | |
delete_seqpos(int const seqpos) | core::kinematics::FoldTree | |
delete_seqpos_simple(int const seqpos) | core::kinematics::FoldTree | private |
delete_unordered_edge(int const start, int const stop, int const label) | core::kinematics::FoldTree | |
downstream_atom(int const jump_number) const | core::kinematics::FoldTree | |
downstream_jump_residue(int const jump_number) const | core::kinematics::FoldTree | |
edge_count | core::kinematics::FoldTree | mutableprivate |
edge_label(int const start, int 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 |
end() | core::kinematics::FoldTree | inlineprivate |
FoldTree() | core::kinematics::FoldTree | inline |
FoldTree(int const nres_in) | core::kinematics::FoldTree | inline |
get_chemical_edges() const | core::kinematics::FoldTree | |
get_jump_edges() const | core::kinematics::FoldTree | |
get_jump_that_builds_residue(int const seqpos) const | core::kinematics::FoldTree | |
get_outgoing_edges(int const seqpos) const | core::kinematics::FoldTree | |
get_parent_residue(int const seqpos, bool &connected_by_jump) const | core::kinematics::FoldTree | |
get_parent_residue(int const seqpos) const | core::kinematics::FoldTree | |
get_polymer_residue_direction(int const seqpos) const | core::kinematics::FoldTree | |
get_residue_edge(int 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, int const insert_seqpos, int const insert_jumppos, int const anchor_pos, int anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="") | core::kinematics::FoldTree | |
insert_polymer_residue(int const seqpos, bool const join_lower, bool const join_upper) | core::kinematics::FoldTree | |
insert_residue_by_chemical_bond(int const seqpos, int const anchor_residue, std::string const &anchor_atom, std::string const &root_atom) | core::kinematics::FoldTree | |
insert_residue_by_jump(int const seqpos, int anchor_pos, std::string const &anchor_atom="", std::string const &root_atomno="") | core::kinematics::FoldTree | |
is_cutpoint(int const seqpos) const | core::kinematics::FoldTree | inline |
is_cutpoint_ | core::kinematics::FoldTree | mutableprivate |
is_jump_point(int const seqpos) const | core::kinematics::FoldTree | inline |
is_jump_point_ | core::kinematics::FoldTree | mutableprivate |
is_root(int const seqpos) const | core::kinematics::FoldTree | inline |
is_simple_tree() const | core::kinematics::FoldTree | |
iterator typedef | core::kinematics::FoldTree | |
jump_edge(int const jump_number) const | core::kinematics::FoldTree | |
jump_edge(int const jump_number) | core::kinematics::FoldTree | |
jump_edge_ | core::kinematics::FoldTree | mutableprivate |
jump_edge_count | core::kinematics::FoldTree | mutableprivate |
jump_exists(int const pos1, int const pos2) const | core::kinematics::FoldTree | inline |
jump_nr(core::Size upstream_res, core::Size downstream_res) const | core::kinematics::FoldTree | inline |
jump_point(int const lower_higher, int const jump_number) const | core::kinematics::FoldTree | |
jump_point_ | core::kinematics::FoldTree | mutableprivate |
min_edge_count | core::kinematics::FoldTree | mutableprivate |
new_chemical_bond(int const anchor_pos, int const root_pos, std::string const &anchor_atom, std::string const &root_atom, int const new_cutpoint) | core::kinematics::FoldTree | |
new_jump(int const jump_pos1, int const jump_pos2, int 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(int const jump_number, FoldTree &f1, FoldTree &f2) const | core::kinematics::FoldTree | |
partition_by_jump(int 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(int 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(int const nres_in, int const num_jump_in, ObjexxFCL::FArray2D_int const &jump_point, ObjexxFCL::FArray1D_float const &cut_bias, int const root_in=1, bool const allow_jump_at_1_or_NRES=false) | core::kinematics::FoldTree | |
random_tree_from_jump_points(int const nres_in, int const num_jump_in, ObjexxFCL::FArray2D_int const &jump_point, std::vector< int > const &obligate_cut_points, ObjexxFCL::FArray1D_float const &cut_bias, int 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(int 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 | |
root() const | core::kinematics::FoldTree | inline |
set_jump_atoms(int const jump_number, std::string const &upstream_atom, std::string const &downstream_atom, bool bKeepStubInResidue=false) | core::kinematics::FoldTree | |
set_jump_atoms(int 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(int 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(int const resNo) | core::kinematics::FoldTree | |
to_string() const | core::kinematics::FoldTree | |
tree_from_jumps_and_cuts(int const nres_in, int const num_jump_in, ObjexxFCL::FArray2D_int const &jump_point, ObjexxFCL::FArray1D_int const &cuts, int const root_in=1, bool const verbose=false) | core::kinematics::FoldTree | |
update_cutpoints() const | core::kinematics::FoldTree | private |
update_edge_label(int const start, int 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(int const jump_number) const | core::kinematics::FoldTree | |
upstream_jump_residue(int const jump_number) const | core::kinematics::FoldTree | |
~FoldTree() override | core::kinematics::FoldTree | |