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core::kinematics::tree::Atom Member List

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

append_atom(AtomOP)=0core::kinematics::tree::Atompure virtual
Atom()core::kinematics::tree::Atominlineprotected
Atom(Atom const &)core::kinematics::tree::Atominlineprotected
atom_id() const =0core::kinematics::tree::Atompure virtual
atom_is_on_path_from_root(AtomCOP atm) const =0core::kinematics::tree::Atompure virtual
AtomID typedefcore::kinematics::tree::Atom
AtomID_Mask typedefcore::kinematics::tree::Atom
Atoms typedefcore::kinematics::tree::Atom
atoms_begin() const =0core::kinematics::tree::Atompure virtual
atoms_begin()=0core::kinematics::tree::Atompure virtual
Atoms_ConstIterator typedefcore::kinematics::tree::Atom
atoms_end() const =0core::kinematics::tree::Atompure virtual
atoms_end()=0core::kinematics::tree::Atompure virtual
Atoms_Iterator typedefcore::kinematics::tree::Atom
child(Size const k) const =0core::kinematics::tree::Atompure virtual
child(Size const k)=0core::kinematics::tree::Atompure virtual
child_index(AtomCOP child) const =0core::kinematics::tree::Atompure virtual
clone(AtomAP parent_in, AtomPointer2D &atom_pointer) const =0core::kinematics::tree::Atompure virtual
copy_coords(Atom const &src)=0core::kinematics::tree::Atompure virtual
delete_atom(AtomOP)=0core::kinematics::tree::Atompure virtual
dfs(AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const =0core::kinematics::tree::Atompure virtual
difference_type typedefcore::kinematics::tree::Atom
dihedral_between_bonded_children(AtomCOP child1, AtomCOP child2) const =0core::kinematics::tree::Atompure virtual
distance(Atom const &atom) const =0core::kinematics::tree::Atompure virtual
distance(Atom const &atom1, Atom const &atom2)core::kinematics::tree::Atomfriend
distance_squared(Atom const &atom) const =0core::kinematics::tree::Atompure virtual
distance_squared(Atom const &atom1, Atom const &atom2)core::kinematics::tree::Atomfriend
dof(DOF_Type const type) const =0core::kinematics::tree::Atompure virtual
DOF_ID typedefcore::kinematics::tree::Atom
DOF_ID_Mask typedefcore::kinematics::tree::Atom
DOF_Type typedefcore::kinematics::tree::Atom
downstream(AtomCOP atom1) const =0core::kinematics::tree::Atompure virtual
get_dof_axis_and_end_pos(Vector &axis, Position &end_pos, DOF_Type const type) const =0core::kinematics::tree::Atompure virtual
get_input_stub() const =0core::kinematics::tree::Atompure virtual
get_nonjump_atom(Size const i) const =0core::kinematics::tree::Atompure virtual
get_path_from_root(utility::vector1< AtomCOP > &path) const =0core::kinematics::tree::Atompure virtual
get_stub() const =0core::kinematics::tree::Atompure virtual
id() const =0core::kinematics::tree::Atompure virtual
id(AtomID const &id_in)=0core::kinematics::tree::Atompure virtual
input_stub_atom0() const =0core::kinematics::tree::Atompure virtual
input_stub_atom0_id() const =0core::kinematics::tree::Atompure virtual
input_stub_atom1() const =0core::kinematics::tree::Atompure virtual
input_stub_atom1_id() const =0core::kinematics::tree::Atompure virtual
input_stub_atom2() const =0core::kinematics::tree::Atompure virtual
input_stub_atom2_id() const =0core::kinematics::tree::Atompure virtual
input_stub_atom3() const =0core::kinematics::tree::Atompure virtual
input_stub_atom3_id() const =0core::kinematics::tree::Atompure virtual
insert_atom(AtomOP)=0core::kinematics::tree::Atompure virtual
insert_atom(AtomOP, int const )=0core::kinematics::tree::Atompure virtual
is_jump() const =0core::kinematics::tree::Atompure virtual
iterator_category typedefcore::kinematics::tree::Atom
jump() const =0core::kinematics::tree::Atompure virtual
jump(Jump const &jump_in)=0core::kinematics::tree::Atompure virtual
jump(Jump const &jump_in, AtomDOFChangeSet &set)=0core::kinematics::tree::Atompure virtual
keep_1st_child_pos() const =0core::kinematics::tree::Atompure virtual
keep_dof_fixed(DOF_Type const ) const core::kinematics::tree::Atominlinevirtual
Matrix typedefcore::kinematics::tree::Atom
n_atom() const =0core::kinematics::tree::Atompure virtual
n_children() const =0core::kinematics::tree::Atompure virtual
n_nonjump_children() const =0core::kinematics::tree::Atompure virtual
next_child(AtomCOP child)=0core::kinematics::tree::Atompure virtual
nonjump_atoms_begin() const =0core::kinematics::tree::Atomprotectedpure virtual
nonjump_atoms_begin()=0core::kinematics::tree::Atomprotectedpure virtual
operator=(Atom const &)core::kinematics::tree::Atominlineprotected
parent() const =0core::kinematics::tree::Atompure virtual
parent(AtomAP parent_in)=0core::kinematics::tree::Atompure virtual
parent()=0core::kinematics::tree::Atompure virtual
Position typedefcore::kinematics::tree::Atom
position() const =0core::kinematics::tree::Atompure virtual
position(Position const &position_a)=0core::kinematics::tree::Atompure virtual
previous_child(AtomCOP child) const =0core::kinematics::tree::Atompure virtual
previous_sibling() const =0core::kinematics::tree::Atompure virtual
replace_atom(AtomOP const old_atom, AtomOP const new_atom)=0core::kinematics::tree::Atompure virtual
set_dof(DOF_Type const type, Real const value)=0core::kinematics::tree::Atompure virtual
set_dof(DOF_Type const type, Real const value, AtomDOFChangeSet &set)=0core::kinematics::tree::Atompure virtual
set_weak_ptr_to_self(AtomAP weak_ptr)=0core::kinematics::tree::Atompure virtual
setup_min_map(DOF_ID &last_torsion, DOF_ID_Mask const &move_map, MinimizerMapBase &min_map) const =0core::kinematics::tree::Atompure virtual
show() const =0core::kinematics::tree::Atompure virtual
show(int const &) const =0core::kinematics::tree::Atompure virtual
stub_atom1() const =0core::kinematics::tree::Atompure virtual
stub_atom1_id() const =0core::kinematics::tree::Atompure virtual
stub_atom2() const =0core::kinematics::tree::Atompure virtual
stub_atom2_id() const =0core::kinematics::tree::Atompure virtual
stub_atom3() const =0core::kinematics::tree::Atompure virtual
stub_atom3_id() const =0core::kinematics::tree::Atompure virtual
stub_defined() const =0core::kinematics::tree::Atompure virtual
transform_Ax_plus_b_recursive(Matrix const &A, Vector const &b, ResidueCoordinateChangeList &res_change_list)=0core::kinematics::tree::Atompure virtual
update_child_torsions(AtomOP const child)=0core::kinematics::tree::Atomprotectedpure virtual
update_domain_map(int &current_color, int &biggest_color, DomainMap &domain_map, AtomID_Mask const &dof_moved, AtomID_Mask const &atom_moved) const =0core::kinematics::tree::Atompure virtual
update_internal_coords(Stub &stub, bool const recursive=true)=0core::kinematics::tree::Atompure virtual
update_internal_coords(bool const recursive)=0core::kinematics::tree::Atompure virtual
update_stub(Stub &stub) const =0core::kinematics::tree::Atompure virtual
update_xyz_coords()=0core::kinematics::tree::Atompure virtual
update_xyz_coords(Stub &stub)=0core::kinematics::tree::Atompure virtual
x() const =0core::kinematics::tree::Atompure virtual
xyz() const =0core::kinematics::tree::Atompure virtual
xyz(Position const &position_a)=0core::kinematics::tree::Atompure virtual
y() const =0core::kinematics::tree::Atompure virtual
z() const =0core::kinematics::tree::Atompure virtual
~Atom()core::kinematics::tree::Atominlinevirtual