core::kinematics::tree::Atom_ Member List

This is the complete list of members for core::kinematics::tree::Atom_, 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 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_	[inline, virtual]
atoms_begin()	core::kinematics::tree::Atom_	[inline, virtual]
Atoms_ConstIterator typedef	core::kinematics::tree::Atom
atoms_end() const	core::kinematics::tree::Atom_	[inline, virtual]
atoms_end()	core::kinematics::tree::Atom_	[inline, virtual]
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(Atom const *child) const	core::kinematics::tree::Atom_	[virtual]
clone(Atom *parent_in, AtomPointer2D &atom_pointer) const =0	core::kinematics::tree::Atom	[pure virtual]
copy_coords(Atom const &src)=0	core::kinematics::tree::Atom	[pure 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::Atom_	[virtual]
difference_type typedef	core::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 =0	core::kinematics::tree::Atom	[pure virtual]
DOF_ID typedef	core::kinematics::tree::Atom
DOF_ID_Mask typedef	core::kinematics::tree::Atom
dof_refold_index() const	core::kinematics::tree::Atom_	[inline, protected]
DOF_Type typedef	core::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 =0	core::kinematics::tree::Atom	[pure 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 =0	core::kinematics::tree::Atom	[pure virtual]
iterator_category typedef	core::kinematics::tree::Atom
jump() const =0	core::kinematics::tree::Atom	[pure virtual]
jump(Jump const &jump_in)=0	core::kinematics::tree::Atom	[pure virtual]
jump(Jump const &jump_in, AtomDOFChangeSet &set)=0	core::kinematics::tree::Atom	[pure virtual]
keep_1st_child_pos() const =0	core::kinematics::tree::Atom	[pure virtual]
keep_dof_fixed(DOF_Type const ) const	core::kinematics::tree::Atom_	[inline, virtual]
Matrix typedef	core::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 typedef	core::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, Real const value)=0	core::kinematics::tree::Atom	[pure virtual]
set_dof(DOF_Type const type, Real const value, AtomDOFChangeSet &set)=0	core::kinematics::tree::Atom	[pure virtual]
setup_min_map(DOF_ID &last_torsion, DOF_ID_Mask const &move_map, MinimizerMapBase &min_map) const =0	core::kinematics::tree::Atom	[pure virtual]
show() const	core::kinematics::tree::Atom_	[virtual]
show(int const &n_level) const	core::kinematics::tree::Atom_	[virtual]
stub_atom1() const =0	core::kinematics::tree::Atom	[pure virtual]
stub_atom1_id() const	core::kinematics::tree::Atom_	[inline, virtual]
stub_atom2() const =0	core::kinematics::tree::Atom	[pure virtual]
stub_atom2_id() const	core::kinematics::tree::Atom_	[inline, virtual]
stub_atom3() const =0	core::kinematics::tree::Atom	[pure 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(bool const recursive)	core::kinematics::tree::Atom_	[virtual]
core::kinematics::tree::Atom::update_internal_coords(Stub &stub, bool const recursive=true)=0	core::kinematics::tree::Atom	[pure virtual]
update_stub(Stub &stub) const =0	core::kinematics::tree::Atom	[pure virtual]
update_xyz_coords()	core::kinematics::tree::Atom_	[virtual]
core::kinematics::tree::Atom::update_xyz_coords(Stub &stub)=0	core::kinematics::tree::Atom	[pure 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]