| abort_bad_call() const | core::kinematics::tree::Atom_ | protected |
| append_atom(AtomOP) override | core::kinematics::tree::Atom_ | virtual |
| Atom()=default | core::kinematics::tree::Atom | inlineprotected |
| Atom_() | core::kinematics::tree::Atom_ | inlineprotected |
| Atom_(Atom_ const &atom) | core::kinematics::tree::Atom_ | inlineprotected |
| atom_id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| atom_id_ | core::kinematics::tree::Atom_ | protected |
| atom_is_on_path_from_root(AtomCOP atm) const override | 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 override | core::kinematics::tree::Atom_ | inlinevirtual |
| atoms_begin() override | core::kinematics::tree::Atom_ | inlinevirtual |
| Atoms_ConstIterator typedef | core::kinematics::tree::Atom | |
| atoms_end() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| atoms_end() override | core::kinematics::tree::Atom_ | inlinevirtual |
| Atoms_Iterator typedef | core::kinematics::tree::Atom | |
| BondedAtom() | core::kinematics::tree::BondedAtom | inline |
| child(Size const k) const override | core::kinematics::tree::Atom_ | virtual |
| child(Size const k) override | core::kinematics::tree::Atom_ | virtual |
| child_index(AtomCOP child) const override | core::kinematics::tree::Atom_ | virtual |
| clone(AtomAP parent_in, AtomPointer2D &atom_pointer) const override | core::kinematics::tree::BondedAtom | virtual |
| copy_coords(Atom const &src) override | core::kinematics::tree::BondedAtom | virtual |
| d_ | core::kinematics::tree::BondedAtom | private |
| delete_atom(AtomOP) override | core::kinematics::tree::Atom_ | virtual |
| dfs(AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const override | core::kinematics::tree::BondedAtom | virtual |
| difference_type typedef | core::kinematics::tree::Atom | |
| dihedral_between_bonded_children(Atom const &child1, Atom const &child2) const override | core::kinematics::tree::Atom_ | virtual |
| distance(Atom const &atom) const override | core::kinematics::tree::Atom_ | inlinevirtual |
| distance_squared(Atom const &atom) const override | core::kinematics::tree::Atom_ | inlinevirtual |
| dof(DOF_Type const type) const override | core::kinematics::tree::BondedAtom | virtual |
| dof_change_propagates_to_younger_siblings_ | core::kinematics::tree::BondedAtom | private |
| 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 override | core::kinematics::tree::Atom_ | virtual |
| get_dof_axis_and_end_pos(Vector &axis, Position &end_pos, DOF_Type const type) const override | core::kinematics::tree::BondedAtom | virtual |
| get_input_stub() const override | core::kinematics::tree::Atom_ | virtual |
| get_inversion() | core::kinematics::tree::BondedAtom | inline |
| get_nonjump_atom(Size const i) const override | core::kinematics::tree::Atom_ | virtual |
| get_path_from_root(utility::vector1< AtomCAP > &path) const override | core::kinematics::tree::Atom_ | protectedvirtual |
| get_self_ptr() const | core::kinematics::tree::Atom | inline |
| get_self_ptr() | core::kinematics::tree::Atom | inline |
| get_self_weak_ptr() const | core::kinematics::tree::Atom | inline |
| get_self_weak_ptr() | core::kinematics::tree::Atom | inline |
| get_stub() const override | core::kinematics::tree::Atom_ | virtual |
| id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| id(AtomID const &id_in) override | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom0() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom0_id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom1() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom1_id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom2() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom2_id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom3() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| input_stub_atom3_id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| insert_atom(AtomOP) override | core::kinematics::tree::Atom_ | virtual |
| insert_atom(AtomOP, int const ) override | core::kinematics::tree::Atom_ | virtual |
| inverted_frame_ | core::kinematics::tree::BondedAtom | private |
| is_jump() const override | core::kinematics::tree::BondedAtom | inlinevirtual |
| iterator_category typedef | core::kinematics::tree::Atom | |
| jump() const override | core::kinematics::tree::BondedAtom | inlinevirtual |
| jump(Jump const &) override | core::kinematics::tree::BondedAtom | inlinevirtual |
| jump(Jump const &, AtomDOFChangeSet &) override | core::kinematics::tree::BondedAtom | inlinevirtual |
| keep_1st_child_pos() const override | core::kinematics::tree::BondedAtom | inlinevirtual |
| keep_dof_fixed(DOF_Type const type) const override | core::kinematics::tree::BondedAtom | virtual |
| Matrix typedef | core::kinematics::tree::Atom | |
| n_atom() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| n_children() const override | core::kinematics::tree::Atom_ | virtual |
| n_nonjump_children() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| next_child(AtomCOP child) override | core::kinematics::tree::Atom_ | virtual |
| nonjump_atoms_begin() const override | core::kinematics::tree::Atom_ | protectedvirtual |
| nonjump_atoms_begin() override | 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 &)=default | core::kinematics::tree::Atom | inlineprotected |
| parent() override | core::kinematics::tree::Atom_ | inlinevirtual |
| parent() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| parent(AtomAP parent_in) override | core::kinematics::tree::Atom_ | inlinevirtual |
| parent_ | core::kinematics::tree::Atom_ | protected |
| phi_ | core::kinematics::tree::BondedAtom | private |
| Position typedef | core::kinematics::tree::Atom | |
| position() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| position(Position const &position_a) override | core::kinematics::tree::Atom_ | inlinevirtual |
| position_ | core::kinematics::tree::Atom_ | protected |
| previous_child(AtomCOP child) const override | core::kinematics::tree::Atom_ | virtual |
| previous_sibling() const override | core::kinematics::tree::Atom_ | virtual |
| raw_child_index(Atom const *child) const override | core::kinematics::tree::Atom_ | virtual |
| raw_get_nonjump_atom(Size const i) const override | core::kinematics::tree::Atom_ | virtual |
| raw_input_stub_atom0() const override | core::kinematics::tree::Atom_ | virtual |
| raw_input_stub_atom1() const override | core::kinematics::tree::Atom_ | virtual |
| raw_input_stub_atom2() const override | core::kinematics::tree::Atom_ | virtual |
| raw_input_stub_atom3() const override | core::kinematics::tree::Atom_ | virtual |
| raw_parent() const override | core::kinematics::tree::Atom_ | virtual |
| raw_parent_ | core::kinematics::tree::Atom_ | protected |
| raw_previous_child(Atom const *child) const override | core::kinematics::tree::Atom_ | virtual |
| raw_previous_sibling() const override | core::kinematics::tree::Atom_ | virtual |
| raw_stub_atom1() const override | core::kinematics::tree::BondedAtom | virtual |
| raw_stub_atom2() const override | core::kinematics::tree::BondedAtom | virtual |
| raw_stub_atom3() const override | core::kinematics::tree::BondedAtom | virtual |
| replace_atom(AtomOP const old_atom, AtomOP const new_atom) override | core::kinematics::tree::Atom_ | virtual |
| set_dof(DOF_Type const type, core::Real const value) override | core::kinematics::tree::BondedAtom | virtual |
| set_dof(DOF_Type const type, core::Real const value, AtomDOFChangeSet &changeset) override | core::kinematics::tree::BondedAtom | virtual |
| setup_min_map(DOF_ID &last_torsion, DOF_ID_Mask const &allow_move, MinimizerMapBase &min_map) const override | core::kinematics::tree::BondedAtom | virtual |
| show() const override | core::kinematics::tree::Atom_ | virtual |
| show(int const &n_level) const override | core::kinematics::tree::Atom_ | virtual |
| steal_inversion(AtomOP steal_from) override | core::kinematics::tree::BondedAtom | virtual |
| stub_atom1() const override | core::kinematics::tree::BondedAtom | inlinevirtual |
| stub_atom1_id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| stub_atom2() const override | core::kinematics::tree::BondedAtom | inlinevirtual |
| stub_atom2_id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| stub_atom3() const override | core::kinematics::tree::BondedAtom | inlinevirtual |
| stub_atom3_id() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| stub_defined() const override | core::kinematics::tree::Atom_ | virtual |
| Super typedef | core::kinematics::tree::BondedAtom | private |
| theta_ | core::kinematics::tree::BondedAtom | private |
| transform_Ax_plus_b_recursive(Matrix const &A, Vector const &b, ResidueCoordinateChangeList &res_change_list) override | core::kinematics::tree::Atom_ | protectedvirtual |
| update_child_torsions(AtomOP const child) override | 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 override | core::kinematics::tree::Atom_ | virtual |
| update_internal_coords(std::deque< std::pair< Atom *, core::kinematics::Stub * > > *childlist, std::deque< core::kinematics::Stub > *stublist, Stub &stub) override | core::kinematics::tree::BondedAtom | virtual |
| core::kinematics::tree::Atom_::update_internal_coords(bool const recursive) override | core::kinematics::tree::Atom_ | virtual |
| core::kinematics::tree::Atom_::update_internal_coords(Stub &stub, bool const recursive=true) override | core::kinematics::tree::Atom_ | virtual |
| update_stub(Stub &stub) const override | core::kinematics::tree::BondedAtom | virtual |
| update_xyz_coords() override | core::kinematics::tree::BondedAtom | virtual |
| update_xyz_coords(Stub &stub) override | core::kinematics::tree::BondedAtom | virtual |
| x() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| xyz() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| xyz(Position const &position_a) override | core::kinematics::tree::Atom_ | inlinevirtual |
| y() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| z() const override | core::kinematics::tree::Atom_ | inlinevirtual |
| ~Atom_() override | core::kinematics::tree::Atom_ | inline |
1.8.7