| abort_bad_call() const | core::kinematics::tree::Atom_ | protected |
| append_atom(AtomOP) | core::kinematics::tree::Atom_ | virtual |
| Atom() | core::kinematics::tree::Atom | inlineprotected |
| Atom(Atom const &) | core::kinematics::tree::Atom | inlineprotected |
| Atom_() | core::kinematics::tree::Atom_ | inlineprotected |
| Atom_(Atom_ const &atom) | core::kinematics::tree::Atom_ | inlineprotected |
| atom_id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| atom_id_ | core::kinematics::tree::Atom_ | protected |
| atom_is_on_path_from_root(AtomCOP atm) const | core::kinematics::tree::Atom_ | protectedvirtual |
| AtomID typedef | core::kinematics::tree::Atom | |
| AtomID_Mask typedef | core::kinematics::tree::Atom | |
| Atoms typedef | core::kinematics::tree::Atom | |
| atoms_ | core::kinematics::tree::Atom_ | protected |
| atoms_begin() const | core::kinematics::tree::Atom_ | inlinevirtual |
| atoms_begin() | core::kinematics::tree::Atom_ | inlinevirtual |
| Atoms_ConstIterator typedef | core::kinematics::tree::Atom | |
| atoms_end() const | core::kinematics::tree::Atom_ | inlinevirtual |
| atoms_end() | core::kinematics::tree::Atom_ | inlinevirtual |
| Atoms_Iterator typedef | core::kinematics::tree::Atom | |
| child(Size const k) const | core::kinematics::tree::Atom_ | virtual |
| child(Size const k) | core::kinematics::tree::Atom_ | virtual |
| child_index(AtomCOP child) const | core::kinematics::tree::Atom_ | virtual |
| clone(AtomAP parent_in, AtomPointer2D &atom_pointer) const | core::kinematics::tree::JumpAtom | virtual |
| copy_coords(Atom const &src) | core::kinematics::tree::JumpAtom | virtual |
| delete_atom(AtomOP) | core::kinematics::tree::Atom_ | virtual |
| dfs(AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const | core::kinematics::tree::JumpAtom | virtual |
| difference_type typedef | core::kinematics::tree::Atom | |
| dihedral_between_bonded_children(AtomCOP child1, AtomCOP child2) const | core::kinematics::tree::Atom_ | virtual |
| distance(Atom const &atom) const | core::kinematics::tree::Atom_ | inlinevirtual |
| distance_squared(Atom const &atom) const | core::kinematics::tree::Atom_ | inlinevirtual |
| dof(DOF_Type const type) const | core::kinematics::tree::JumpAtom | virtual |
| DOF_ID typedef | core::kinematics::tree::Atom | |
| DOF_ID_Mask typedef | core::kinematics::tree::Atom | |
| dof_refold_index() const | core::kinematics::tree::Atom_ | inlineprotected |
| DOF_Type typedef | core::kinematics::tree::Atom | |
| downstream(AtomCOP atom1) const | core::kinematics::tree::Atom_ | virtual |
| get_dof_axis_and_end_pos(Vector &axis, Position &end_pos, DOF_Type const type) const | core::kinematics::tree::JumpAtom | virtual |
| get_input_stub() const | core::kinematics::tree::Atom_ | virtual |
| get_nonjump_atom(Size const i) const | core::kinematics::tree::Atom_ | virtual |
| get_path_from_root(utility::vector1< AtomCOP > &path) const | core::kinematics::tree::Atom_ | protectedvirtual |
| get_stub() const | core::kinematics::tree::Atom_ | virtual |
| id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| id(AtomID const &id_in) | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom0() const | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom0_id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom1() const | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom1_id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom2() const | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom2_id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom3() const | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom3_id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| insert_atom(AtomOP) | core::kinematics::tree::Atom_ | virtual |
| insert_atom(AtomOP, int const ) | core::kinematics::tree::Atom_ | virtual |
| is_jump() const | core::kinematics::tree::JumpAtom | inlinevirtual |
| iterator_category typedef | core::kinematics::tree::Atom | |
| jump() const | core::kinematics::tree::JumpAtom | virtual |
| jump(Jump const &jump_in) | core::kinematics::tree::JumpAtom | virtual |
| jump(Jump const &jump_in, AtomDOFChangeSet &changeset) | core::kinematics::tree::JumpAtom | virtual |
| jump_ | core::kinematics::tree::JumpAtom | private |
| keep_1st_child_pos() const | core::kinematics::tree::JumpAtom | inlinevirtual |
| keep_dof_fixed(DOF_Type const type) const | core::kinematics::tree::JumpAtom | virtual |
| Matrix typedef | core::kinematics::tree::Atom | |
| n_atom() const | core::kinematics::tree::Atom_ | inlinevirtual |
| n_children() const | core::kinematics::tree::Atom_ | virtual |
| n_nonjump_children() const | core::kinematics::tree::Atom_ | inlinevirtual |
| next_child(AtomCOP child) | core::kinematics::tree::Atom_ | virtual |
| nonjump_atoms_begin() const | core::kinematics::tree::Atom_ | protectedvirtual |
| nonjump_atoms_begin() | core::kinematics::tree::Atom_ | protectedvirtual |
| note_dof_change(AtomDOFChangeSet &changset) | core::kinematics::tree::Atom_ | protected |
| note_xyz_uptodate() | core::kinematics::tree::Atom_ | inlineprotected |
| operator=(Atom_ const &atom) | core::kinematics::tree::Atom_ | inlineprotected |
| core::kinematics::tree::Atom::operator=(Atom const &) | core::kinematics::tree::Atom | inlineprotected |
| parent() const | core::kinematics::tree::Atom_ | inlinevirtual |
| parent(AtomAP parent_in) | core::kinematics::tree::Atom_ | inlinevirtual |
| parent() | core::kinematics::tree::Atom_ | inlinevirtual |
| parent_ | core::kinematics::tree::Atom_ | protected |
| position() const | core::kinematics::tree::Atom_ | inlinevirtual |
| position(Position const &position_a) | core::kinematics::tree::Atom_ | inlinevirtual |
| Position typedef | core::kinematics::tree::Atom | |
| position_ | core::kinematics::tree::Atom_ | protected |
| previous_child(AtomCOP child) const | core::kinematics::tree::Atom_ | virtual |
| previous_sibling() const | core::kinematics::tree::Atom_ | virtual |
| replace_atom(AtomOP const old_atom, AtomOP const new_atom) | core::kinematics::tree::Atom_ | virtual |
| set_dof(DOF_Type const type, Real const value) | core::kinematics::tree::JumpAtom | virtual |
| set_dof(DOF_Type const type, core::Real const value, AtomDOFChangeSet &changeset) | core::kinematics::tree::JumpAtom | virtual |
| set_weak_ptr_to_self(AtomAP weak_ptr) | core::kinematics::tree::Atom_ | virtual |
| setup_min_map(DOF_ID &last_torsion, DOF_ID_Mask const &allow_move, MinimizerMapBase &min_map) const | core::kinematics::tree::JumpAtom | virtual |
| show() const | core::kinematics::tree::Atom_ | virtual |
| show(int const &n_level) const | core::kinematics::tree::Atom_ | virtual |
| stub_atom1() const | core::kinematics::tree::JumpAtom | inlinevirtual |
| stub_atom1_id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| stub_atom2() const | core::kinematics::tree::JumpAtom | inlinevirtual |
| stub_atom2_id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| stub_atom3() const | core::kinematics::tree::JumpAtom | inlinevirtual |
| stub_atom3_id() const | core::kinematics::tree::Atom_ | inlinevirtual |
| stub_defined() const | core::kinematics::tree::Atom_ | virtual |
| Super typedef | core::kinematics::tree::JumpAtom | private |
| this_weak_ptr() | core::kinematics::tree::Atom_ | inlineprotected |
| this_weak_ptr() const | core::kinematics::tree::Atom_ | inlineprotected |
| this_weak_ptr_ | core::kinematics::tree::Atom_ | protected |
| transform_Ax_plus_b_recursive(Matrix const &A, Vector const &b, ResidueCoordinateChangeList &res_change_list) | core::kinematics::tree::Atom_ | protectedvirtual |
| update_child_torsions(AtomOP const child) | core::kinematics::tree::Atom_ | protectedvirtual |
| update_domain_map(int ¤t_color, int &biggest_color, DomainMap &domain_map, AtomID_Mask const &dof_moved, AtomID_Mask const &atom_moved) const | core::kinematics::tree::Atom_ | virtual |
| update_internal_coords(Stub &stub, bool const recursive=true) | core::kinematics::tree::JumpAtom | virtual |
| core::kinematics::tree::Atom_::update_internal_coords(bool const recursive) | core::kinematics::tree::Atom_ | virtual |
| update_stub(Stub &) const | core::kinematics::tree::JumpAtom | inlinevirtual |
| update_xyz_coords() | core::kinematics::tree::JumpAtom | virtual |
| update_xyz_coords(Stub &stub) | core::kinematics::tree::JumpAtom | virtual |
| x() const | core::kinematics::tree::Atom_ | inlinevirtual |
| xyz() const | core::kinematics::tree::Atom_ | inlinevirtual |
| xyz(Position const &position_a) | core::kinematics::tree::Atom_ | inlinevirtual |
| y() const | core::kinematics::tree::Atom_ | inlinevirtual |
| z() const | core::kinematics::tree::Atom_ | inlinevirtual |
| ~Atom() | core::kinematics::tree::Atom | inlinevirtual |
| ~Atom_() | core::kinematics::tree::Atom_ | inlinevirtual |
1.8.7