core::kinematics::FoldTree Member List

This is the complete list of members for core::kinematics::FoldTree, including all inherited members.

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
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	private
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(int const desired_root=0)	core::kinematics::FoldTree
delete_jump_and_intervening_cutpoint(int jump_begin, int jump_end)	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_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_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!=(const FoldTree &a, const FoldTree &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_residue(int const seqpos, ObjexxFCL::FArray1D_bool &partner1) const	core::kinematics::FoldTree
possible_root(Size const &seqpos) const	core::kinematics::FoldTree	inline
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
reorder(int const start_residue)	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
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()	core::kinematics::FoldTree	virtual