Rosetta 3.4
core::kinematics::tree::BondedAtom Member List
This is the complete list of members for core::kinematics::tree::BondedAtom, including all inherited members.
abort_bad_call() const core::kinematics::tree::Atom_ [protected]
append_atom(Atom *)core::kinematics::tree::Atom_ [virtual]
Atom()core::kinematics::tree::Atom [inline, protected]
Atom(Atom const &)core::kinematics::tree::Atom [inline, protected]
Atom_()core::kinematics::tree::Atom_ [inline, protected]
Atom_(Atom_ const &atom)core::kinematics::tree::Atom_ [inline, protected]
atom_id() const core::kinematics::tree::Atom_ [inline, virtual]
atom_id_core::kinematics::tree::Atom_ [protected]
atom_is_on_path_from_root(Atom const *atm) const core::kinematics::tree::Atom_ [protected, virtual]
AtomID typedefcore::kinematics::tree::Atom
AtomID_Mask typedefcore::kinematics::tree::Atom
Atoms typedefcore::kinematics::tree::Atom
atoms_core::kinematics::tree::Atom_ [protected]
atoms_begin() const core::kinematics::tree::Atom_ [inline, virtual]
atoms_begin()core::kinematics::tree::Atom_ [inline, virtual]
Atoms_ConstIterator typedefcore::kinematics::tree::Atom
atoms_end() const core::kinematics::tree::Atom_ [inline, virtual]
atoms_end()core::kinematics::tree::Atom_ [inline, virtual]
Atoms_Iterator typedefcore::kinematics::tree::Atom
BondedAtom()core::kinematics::tree::BondedAtom [inline]
child(Size const k) const core::kinematics::tree::Atom_ [virtual]
child(Size const k)core::kinematics::tree::Atom_ [virtual]
child_index(Atom const *child) const core::kinematics::tree::Atom_ [virtual]
clone(Atom *parent_in, AtomPointer2D &atom_pointer) const core::kinematics::tree::BondedAtom [virtual]
copy_coords(Atom const &src)core::kinematics::tree::BondedAtom [virtual]
delete_atom(Atom *)core::kinematics::tree::Atom_ [virtual]
dfs(AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const core::kinematics::tree::BondedAtom [virtual]
difference_type typedefcore::kinematics::tree::Atom
dihedral_between_bonded_children(Atom const *child1, Atom const *child2) const core::kinematics::tree::Atom_ [virtual]
distance(Atom const &atom) const core::kinematics::tree::Atom_ [inline, virtual]
core::kinematics::tree::Atom::distance(Atom const &atom1, Atom const &atom2)core::kinematics::tree::Atom [friend]
distance_squared(Atom const &atom) const core::kinematics::tree::Atom_ [inline, virtual]
core::kinematics::tree::Atom::distance_squared(Atom const &atom1, Atom const &atom2)core::kinematics::tree::Atom [friend]
dof(DOF_Type const type) const core::kinematics::tree::BondedAtom [virtual]
DOF_ID typedefcore::kinematics::tree::Atom
DOF_ID_Mask typedefcore::kinematics::tree::Atom
dof_refold_index() const core::kinematics::tree::Atom_ [inline, protected]
DOF_Type typedefcore::kinematics::tree::Atom
downstream(Atom const *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::BondedAtom [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< Atom const * > &path) const core::kinematics::tree::Atom_ [protected, virtual]
get_stub() const core::kinematics::tree::Atom_ [virtual]
id() const core::kinematics::tree::Atom_ [inline, virtual]
id(AtomID const &id_in)core::kinematics::tree::Atom_ [inline, virtual]
input_stub_atom0() const core::kinematics::tree::Atom_ [inline, virtual]
input_stub_atom0_id() const core::kinematics::tree::Atom_ [inline, virtual]
input_stub_atom1() const core::kinematics::tree::Atom_ [inline, virtual]
input_stub_atom1_id() const core::kinematics::tree::Atom_ [inline, virtual]
input_stub_atom2() const core::kinematics::tree::Atom_ [inline, virtual]
input_stub_atom2_id() const core::kinematics::tree::Atom_ [inline, virtual]
input_stub_atom3() const core::kinematics::tree::Atom_ [inline, virtual]
input_stub_atom3_id() const core::kinematics::tree::Atom_ [inline, virtual]
insert_atom(Atom *)core::kinematics::tree::Atom_ [virtual]
insert_atom(Atom *, int const )core::kinematics::tree::Atom_ [virtual]
is_jump() const core::kinematics::tree::BondedAtom [inline, virtual]
iterator_category typedefcore::kinematics::tree::Atom
jump() const core::kinematics::tree::BondedAtom [inline, virtual]
jump(Jump const &)core::kinematics::tree::BondedAtom [inline, virtual]
jump(Jump const &, AtomDOFChangeSet &)core::kinematics::tree::BondedAtom [inline, virtual]
keep_1st_child_pos() const core::kinematics::tree::BondedAtom [inline, virtual]
keep_dof_fixed(DOF_Type const type) const core::kinematics::tree::BondedAtom [virtual]
Matrix typedefcore::kinematics::tree::Atom
n_atom() const core::kinematics::tree::Atom_ [inline, virtual]
n_children() const core::kinematics::tree::Atom_ [virtual]
n_nonjump_children() const core::kinematics::tree::Atom_ [inline, virtual]
next_child(Atom const *child)core::kinematics::tree::Atom_ [virtual]
nonjump_atoms_begin() const core::kinematics::tree::Atom_ [protected, virtual]
nonjump_atoms_begin()core::kinematics::tree::Atom_ [protected, virtual]
note_dof_change(AtomDOFChangeSet &changset)core::kinematics::tree::Atom_ [protected]
note_xyz_uptodate()core::kinematics::tree::Atom_ [inline, protected]
operator=(Atom_ const &atom)core::kinematics::tree::Atom_ [inline, protected]
core::kinematics::tree::Atom::operator=(Atom const &)core::kinematics::tree::Atom [inline, protected]
parent() const core::kinematics::tree::Atom_ [inline, virtual]
parent(Atom *parent_in)core::kinematics::tree::Atom_ [inline, virtual]
parent()core::kinematics::tree::Atom_ [inline, virtual]
parent_core::kinematics::tree::Atom_ [protected]
Position typedefcore::kinematics::tree::Atom
position() const core::kinematics::tree::Atom_ [inline, virtual]
position(Position const &position_a)core::kinematics::tree::Atom_ [inline, virtual]
position_core::kinematics::tree::Atom_ [protected]
previous_child(Atom const *child) const core::kinematics::tree::Atom_ [virtual]
previous_sibling() const core::kinematics::tree::Atom_ [virtual]
replace_atom(Atom *const old_atom, Atom *const new_atom)core::kinematics::tree::Atom_ [virtual]
set_dof(DOF_Type const type, core::Real const value)core::kinematics::tree::BondedAtom [virtual]
set_dof(DOF_Type const type, core::Real const value, AtomDOFChangeSet &changeset)core::kinematics::tree::BondedAtom [virtual]
setup_min_map(DOF_ID &last_torsion, DOF_ID_Mask const &allow_move, MinimizerMapBase &min_map) const core::kinematics::tree::BondedAtom [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::BondedAtom [inline, virtual]
stub_atom1_id() const core::kinematics::tree::Atom_ [inline, virtual]
stub_atom2() const core::kinematics::tree::BondedAtom [inline, virtual]
stub_atom2_id() const core::kinematics::tree::Atom_ [inline, virtual]
stub_atom3() const core::kinematics::tree::BondedAtom [inline, virtual]
stub_atom3_id() const core::kinematics::tree::Atom_ [inline, virtual]
stub_defined() const core::kinematics::tree::Atom_ [virtual]
transform_Ax_plus_b_recursive(Matrix const &A, Vector const &b, ResidueCoordinateChangeList &res_change_list)core::kinematics::tree::Atom_ [protected, virtual]
update_child_torsions(Atom *const child)core::kinematics::tree::Atom_ [protected, virtual]
update_domain_map(int &current_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::BondedAtom [virtual]
core::kinematics::tree::Atom_::update_internal_coords(bool const recursive)core::kinematics::tree::Atom_ [virtual]
update_stub(Stub &stub) const core::kinematics::tree::BondedAtom [virtual]
update_xyz_coords()core::kinematics::tree::BondedAtom [virtual]
update_xyz_coords(Stub &stub)core::kinematics::tree::BondedAtom [virtual]
x() const core::kinematics::tree::Atom_ [inline, virtual]
xyz() const core::kinematics::tree::Atom_ [inline, virtual]
xyz(Position const &position_a)core::kinematics::tree::Atom_ [inline, virtual]
y() const core::kinematics::tree::Atom_ [inline, virtual]
z() const core::kinematics::tree::Atom_ [inline, virtual]
~Atom()core::kinematics::tree::Atom [inline, virtual]
~Atom_()core::kinematics::tree::Atom_ [inline, virtual]
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