Kinematics Atom interface class. More...

#include <Atom.hh>

Inheritance diagram for core::kinematics::tree::Atom:

Public Types
typedef PointPosition	Position

typedef utility::vector0< AtomOP >	Atoms

typedef Atoms::ConstIterator	Atoms_ConstIterator

typedef Atoms::Iterator	Atoms_Iterator

typedef numeric::xyzMatrix< Real >	Matrix

typedef id::DOF_Type	DOF_Type

typedef id::DOF_ID	DOF_ID

typedef id::AtomID	AtomID

typedef id::AtomID_Mask	AtomID_Mask

typedef id::DOF_ID_Mask	DOF_ID_Mask

typedef void	iterator_category

typedef void	difference_type

Public Member Functions
AtomCOP	get_self_ptr () const

AtomOP	get_self_ptr ()

AtomCAP	get_self_weak_ptr () const

AtomAP	get_self_weak_ptr ()

virtual void	dfs (AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const =0
	Perform a depth-first traversal of the tree that would be effected by a DOF change from this atom. Stop at atoms that have already been traversed. More...

virtual void	update_xyz_coords ()=0
	The atom must retrieve an appropriate stub from its parent; it is the root of the subtree being refolded. More...

virtual void	update_xyz_coords (Stub &stub)=0
	update xyz coords from stub and internal coords and More...

virtual void	update_internal_coords (std::deque< std::pair< Atom , core::kinematics::Stub > > childlist, std::deque< core::kinematics::Stub > stublist, Stub &stub)=0
	update internal coords from stub and xyz coords. More...

virtual void	update_internal_coords (Stub &stub, bool const recursive=true)=0
	Update internal coordinates for this atom and possibly all children. More...

virtual void	update_internal_coords (bool const recursive)=0
	calculate my input_stub from the current xyz's and use that input_stub to update my torsions More...

virtual void	update_stub (Stub &stub) const =0
	update the stub without actually updating coordinates More...

virtual void	copy_coords (Atom const &src)=0
	copy DOFs and xyz coords from src Atom More...

virtual Real	dof (DOF_Type const type) const =0
	get dof More...

virtual void	set_dof (DOF_Type const type, Real const value)=0
	set dof, use "set_" syntax since we have multiple dof's More...

virtual void	set_dof (DOF_Type const type, Real const value, AtomDOFChangeSet &set)=0
	set dof, use "set_" syntax since we have multiple dof's – for use in output-sensitive refold routine More...

virtual Jump const &	jump () const =0
	get Jump More...

virtual void	jump (Jump const &jump_in)=0
	set Jump More...

virtual void	jump (Jump const &jump_in, AtomDOFChangeSet &set)=0
	set Jump – for use in output-sensitive refolding More...

virtual AtomOP	clone (AtomAP parent_in, AtomPointer2D &atom_pointer) const =0
	copy atom with new memory allocation More...

virtual void	setup_min_map (DOF_ID &last_torsion, DOF_ID_Mask const &move_map, MinimizerMapBase &min_map) const =0

virtual void	get_dof_axis_and_end_pos (Vector &axis, Position &end_pos, DOF_Type const type) const =0

virtual bool	is_jump () const =0
	atom is a jump atom? More...

virtual bool	keep_1st_child_pos () const =0
	when other atoms are inserted insert after 1st child if available. –> this enables us to keep a stub of Downstream Jump atoms inside a single residue More...

virtual bool	keep_dof_fixed (DOF_Type const ) const
	DoF should be fixed for this atom? More...

virtual void	show () const =0
	dump out AtomID for this atom, its parent and all its offspring More...

virtual void	show (int const &) const =0
	dump out AtomID for this atom, its parent and all its offspring up to n_level More...

virtual Real	dihedral_between_bonded_children (Atom const &child1, Atom const &child2) const =0
	dihedral angle between two bonded children to this atom More...

virtual void	update_domain_map (int &current_color, int &biggest_color, DomainMap &domain_map, AtomID_Mask const &dof_moved, AtomID_Mask const &atom_moved) const =0

virtual Atoms_ConstIterator	atoms_begin () const =0

virtual Atoms_ConstIterator	atoms_end () const =0

virtual Atoms_Iterator	atoms_begin ()=0

virtual Atoms_Iterator	atoms_end ()=0

virtual Size	n_atom () const =0

virtual void	append_atom (AtomOP)=0

virtual void	delete_atom (AtomOP)=0

virtual void	insert_atom (AtomOP)=0

virtual void	insert_atom (AtomOP, int const )=0

virtual void	replace_atom (AtomOP const old_atom, AtomOP const new_atom)=0

virtual AtomCOP	get_nonjump_atom (Size const i) const =0

virtual Size	n_children () const =0

virtual Size	n_nonjump_children () const =0

virtual AtomCOP	child (Size const k) const =0

virtual AtomOP	child (Size const k)=0

virtual Size	child_index (AtomCOP child) const =0
	the atom-index of this child More...

virtual Size	raw_child_index (Atom const *child) const =0
	the atom-index of this child More...

virtual bool	downstream (AtomCOP atom1) const =0

virtual void	steal_inversion (AtomOP)=0

virtual AtomID const &	id () const =0
	Atom identifier. More...

virtual void	id (AtomID const &id_in)=0
	AtomID assignment. More...

virtual AtomID const &	atom_id () const =0
	Atom identifier. More...

virtual Position const &	position () const =0
	Position. More...

virtual void	position (Position const &position_a)=0
	Position assignment. More...

virtual Position const &	xyz () const =0
	Position. More...

virtual void	xyz (Position const &position_a)=0
	Position assignment. More...

virtual Length const &	x () const =0
	x coordinate More...

virtual Length const &	y () const =0
	y coordinate More...

virtual Length const &	z () const =0
	z coordinate More...

virtual Length	distance (Atom const &atom) const =0
	Distance to an Atom. More...

virtual Length	distance_squared (Atom const &atom) const =0
	Distance squared to an Atom. More...

virtual void	transform_Ax_plus_b_recursive (Matrix const &A, Vector const &b, ResidueCoordinateChangeList &res_change_list)=0
	Transform atom and children by linear transformation. More...

virtual AtomCOP	parent () const =0
	Parent atom pointer, NULL for root atom. More...

virtual void	get_path_from_root (utility::vector1< AtomCAP > &path) const =0

virtual bool	atom_is_on_path_from_root (AtomCOP atm) const =0

virtual void	parent (AtomAP parent_in)=0
	parent assignment More...

virtual AtomOP	parent ()=0
	Parent atom pointer, NULL for root atom. More...

virtual Stub	get_stub () const =0
	Get stub information. More...

virtual Stub	get_input_stub () const =0

virtual AtomCOP	stub_atom1 () const =0

virtual AtomCOP	stub_atom2 () const =0

virtual AtomCOP	stub_atom3 () const =0

virtual AtomID const &	stub_atom1_id () const =0

virtual AtomID const &	stub_atom2_id () const =0

virtual AtomID const &	stub_atom3_id () const =0

virtual AtomCOP	input_stub_atom0 () const =0

virtual AtomCOP	input_stub_atom1 () const =0

virtual AtomCOP	input_stub_atom2 () const =0

virtual AtomCOP	input_stub_atom3 () const =0

virtual AtomID const &	input_stub_atom0_id () const =0

virtual AtomID const &	input_stub_atom1_id () const =0

virtual AtomID const &	input_stub_atom2_id () const =0

virtual AtomID const &	input_stub_atom3_id () const =0

virtual AtomCOP	previous_sibling () const =0

virtual AtomCOP	previous_child (AtomCOP child) const =0

virtual AtomOP	next_child (AtomCOP child)=0

virtual Atom const *	raw_parent () const =0
	Rapid (increment-of-reference-count-avoiding) access to the parent atom pointer. More...

virtual Atom const *	raw_previous_sibling () const =0
	Rapid (increment-of-reference-count-avoiding) access to the previous sibling pointer, i.e. the first child in the parent's children list to precede this atom. More...

virtual Atom const *	raw_previous_child (Atom const *child) const =0
	Rapid (increment-of-reference-count-avoiding) access to the previous child pointer;. More...

virtual Atom const *	raw_stub_atom1 () const =0
	Rapid (increment-of-reference-count-avoiding) access to the fist stub atom. More...

virtual Atom const *	raw_stub_atom2 () const =0
	Rapid (increment-of-reference-count-avoiding) access to the second stub atom. More...

virtual Atom const *	raw_stub_atom3 () const =0
	Rapid (increment-of-reference-count-avoiding) access to the third stub atom. More...

virtual Atom const *	raw_input_stub_atom0 () const =0
	Rapid (increment-of-reference-count-avoiding) access to the 0th input stub atom;. More...

virtual Atom const *	raw_input_stub_atom1 () const =0
	Rapid (increment-of-reference-count-avoiding) access to the 1st input stub atom;. More...

virtual Atom const *	raw_input_stub_atom2 () const =0
	Rapid (increment-of-reference-count-avoiding) access to the 2nd input stub atom;. More...

virtual Atom const *	raw_input_stub_atom3 () const =0
	Rapid (increment-of-reference-count-avoiding) access to the 3rd input stub atom;. More...

virtual Atom const *	raw_get_nonjump_atom (Size const i) const =0
	Rapid (increment-of-reference-count-avoiding) access to the ith non-jump atom in this atom's list of children. More...

virtual bool	stub_defined () const =0

Protected Member Functions
	Atom ()=default
	Default constructor. More...

Atom &	operator= (Atom const &)=default
	Copy assignment. More...

virtual void	update_child_torsions (AtomOP const child)=0

virtual Atoms_ConstIterator	nonjump_atoms_begin () const =0

virtual Atoms_Iterator	nonjump_atoms_begin ()=0

Friends
Length	distance (Atom const &atom1, Atom const &atom2)
	Distance between two Atoms. More...

Length	distance_squared (Atom const &atom1, Atom const &atom2)
	Distance squared between two Atoms. More...

Detailed Description

Kinematics Atom interface class.

Member Typedef Documentation

typedef id::AtomID core::kinematics::tree::Atom::AtomID

typedef id::AtomID_Mask core::kinematics::tree::Atom::AtomID_Mask

typedef utility::vector0< AtomOP > core::kinematics::tree::Atom::Atoms

typedef Atoms::ConstIterator core::kinematics::tree::Atom::Atoms_ConstIterator

typedef Atoms::Iterator core::kinematics::tree::Atom::Atoms_Iterator

typedef void core::kinematics::tree::Atom::difference_type

typedef id::DOF_ID core::kinematics::tree::Atom::DOF_ID

typedef id::DOF_ID_Mask core::kinematics::tree::Atom::DOF_ID_Mask

typedef id::DOF_Type core::kinematics::tree::Atom::DOF_Type

typedef void core::kinematics::tree::Atom::iterator_category

typedef numeric::xyzMatrix< Real > core::kinematics::tree::Atom::Matrix

typedef PointPosition core::kinematics::tree::Atom::Position

Constructor & Destructor Documentation

core::kinematics::tree::Atom::Atom ( )

inlineprotecteddefault

Default constructor.

Member Function Documentation

virtual void core::kinematics::tree::Atom::append_atom ( AtomOP )

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomID const& core::kinematics::tree::Atom::atom_id ( ) const

pure virtual

Atom identifier.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::BondedAtom::copy_coords(), and protocols::viewer::visit_atomtree_node().

virtual bool core::kinematics::tree::Atom::atom_is_on_path_from_root ( AtomCOP atm ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual Atoms_ConstIterator core::kinematics::tree::Atom::atoms_begin ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by protocols::viewer::visit_atomtree_node().

virtual Atoms_Iterator core::kinematics::tree::Atom::atoms_begin ( )

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual Atoms_ConstIterator core::kinematics::tree::Atom::atoms_end ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by protocols::viewer::visit_atomtree_node().

virtual Atoms_Iterator core::kinematics::tree::Atom::atoms_end ( )

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::child ( Size const k ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by protocols::environment::bond_angles(), protocols::environment::bond_lengths(), core::kinematics::tree::JumpAtom::copy_coords(), core::kinematics::tree::BondedAtom::copy_coords(), protocols::environment::jump_dofs(), and core::conformation::show_atom_tree().

virtual AtomOP core::kinematics::tree::Atom::child ( Size const k )

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual Size core::kinematics::tree::Atom::child_index ( AtomCOP child ) const

pure virtual

the atom-index of this child

Implemented in core::kinematics::tree::Atom_.

virtual AtomOP core::kinematics::tree::Atom::clone	(	AtomAP	parent_in,
		AtomPointer2D &	atom_pointer
	)		const

pure virtual

copy atom with new memory allocation

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::copy_coords ( Atom const & src )

pure virtual

copy DOFs and xyz coords from src Atom

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::delete_atom ( AtomOP )

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::dfs	(	AtomDOFChangeSet &	changeset,
		ResidueCoordinateChangeList &	res_change_list,
		Size const	start_atom_index
	)		const

pure virtual

Perform a depth-first traversal of the tree that would be effected by a DOF change from this atom. Stop at atoms that have already been traversed.

Implemented in core::kinematics::tree::Atom_, core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual Real core::kinematics::tree::Atom::dihedral_between_bonded_children	(	Atom const &	child1,
		Atom const &	child2
	)		const

pure virtual

dihedral angle between two bonded children to this atom

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Length core::kinematics::tree::Atom::distance ( Atom const & atom ) const

pure virtual

Distance to an Atom.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::distance(), and protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::store_target_icoors().

virtual Length core::kinematics::tree::Atom::distance_squared ( Atom const & atom ) const

pure virtual

Distance squared to an Atom.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::distance_squared().

virtual Real core::kinematics::tree::Atom::dof ( DOF_Type const type ) const

pure virtual

get dof

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::BondedAtom::copy_coords(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::store_target_icoors(), core::kinematics::AtomTree::torsion_angle_dof_id(), and core::optimization::torsional_derivative_from_cartesian_derivatives().

virtual bool core::kinematics::tree::Atom::downstream ( AtomCOP atom1 ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::get_dof_axis_and_end_pos	(	Vector &	axis,
		Position &	end_pos,
		DOF_Type const	type
	)		const

pure virtual

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), and core::optimization::torsional_derivative_from_cartesian_derivatives().

virtual Stub core::kinematics::tree::Atom::get_input_stub ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::get_nonjump_atom ( Size const i ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::get_path_from_root ( utility::vector1< AtomCAP > & path ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

AtomCOP core::kinematics::tree::Atom::get_self_ptr ( ) const

inline

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::simple_moves::ConstrainToIdealMover::check_if_really_connected(), protocols::backrub::BackrubSegment::end_atoms1(), core::pose::copydofs::CopyDofs::figure_out_dofs(), core::pose::rna::fix_sugar_coords(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map(), core::pose::rna::initialize_atoms_for_which_we_need_new_dofs(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), core::kinematics::tree::Atom_::previous_sibling(), protocols::rna::denovo::print_internal_coords(), protocols::backrub::BackrubSegment::start_atoms1(), protocols::backrub::BackrubSegment::start_atoms2(), core::kinematics::tree::JumpAtom::stub_atom1(), core::kinematics::tree::BondedAtom::stub_atom1(), core::kinematics::tree::BondedAtom::stub_atom3(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), and protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry().

AtomOP core::kinematics::tree::Atom::get_self_ptr ( )

inline

AtomCAP core::kinematics::tree::Atom::get_self_weak_ptr ( ) const

inline

Referenced by core::kinematics::tree::Atom_::append_atom(), core::kinematics::tree::Atom_::get_path_from_root(), core::kinematics::tree::Atom_::insert_atom(), and core::kinematics::tree::Atom_::replace_atom().

AtomAP core::kinematics::tree::Atom::get_self_weak_ptr ( )

inline

virtual Stub core::kinematics::tree::Atom::get_stub ( ) const

pure virtual

Get stub information.

Implemented in core::kinematics::tree::Atom_.

Referenced by protocols::simple_filters::JumpEvaluator::apply(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::update_current(), core::kinematics::jacobian::ModuleType1::update_screw_vectors(), and protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::update_target().

virtual AtomID const& core::kinematics::tree::Atom::id ( ) const

pure virtual

Atom identifier.

Implemented in core::kinematics::tree::Atom_.

Referenced by protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::backtrack(), protocols::environment::bond_angles(), protocols::environment::bond_lengths(), core::kinematics::tree::JumpAtom::copy_coords(), core::kinematics::tree::Atom_::input_stub_atom0_id(), core::kinematics::tree::Atom_::input_stub_atom1_id(), core::kinematics::tree::Atom_::input_stub_atom2_id(), protocols::environment::jump_dofs(), core::kinematics::tree::Atom_::raw_input_stub_atom3(), core::conformation::show_atom_tree(), core::kinematics::tree::Atom_::stub_atom2_id(), and core::kinematics::AtomTree::torsion_angle_dof_id().

virtual void core::kinematics::tree::Atom::id ( AtomID const & id_in )

pure virtual

AtomID assignment.

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::input_stub_atom0 ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomID const& core::kinematics::tree::Atom::input_stub_atom0_id ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::input_stub_atom1 ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomID const& core::kinematics::tree::Atom::input_stub_atom1_id ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by core::conformation::Conformation::fill_missing_atoms().

virtual AtomCOP core::kinematics::tree::Atom::input_stub_atom2 ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomID const& core::kinematics::tree::Atom::input_stub_atom2_id ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by core::conformation::Conformation::fill_missing_atoms().

virtual AtomCOP core::kinematics::tree::Atom::input_stub_atom3 ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomID const& core::kinematics::tree::Atom::input_stub_atom3_id ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by core::conformation::Conformation::fill_missing_atoms().

virtual void core::kinematics::tree::Atom::insert_atom ( AtomOP )

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::insert_atom	(	AtomOP	,
		int	const
	)

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual bool core::kinematics::tree::Atom::is_jump ( ) const

pure virtual

atom is a jump atom?

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by protocols::environment::bond_angles(), protocols::environment::bond_lengths(), protocols::environment::collect_dofs(), core::kinematics::tree::Atom_::dihedral_between_bonded_children(), core::kinematics::tree::Atom_::input_stub_atom3(), protocols::environment::jump_dofs(), core::kinematics::tree::Atom_::raw_input_stub_atom3(), core::kinematics::tree::BondedAtom::raw_stub_atom3(), core::kinematics::tree::Atom_::stub_defined(), core::kinematics::AtomTree::torsion_angle_dof_id(), core::kinematics::tree::Atom_::update_domain_map(), protocols::viewer::visit_atomtree_node(), and protocols::environment::claims::XYZClaim::yield_elements().

virtual Jump const& core::kinematics::tree::Atom::jump ( ) const

pure virtual

get Jump

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::JumpAtom::copy_coords().

virtual void core::kinematics::tree::Atom::jump ( Jump const & jump_in )

pure virtual

set Jump

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::jump	(	Jump const &	jump_in,
		AtomDOFChangeSet &	set
	)

pure virtual

set Jump – for use in output-sensitive refolding

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual bool core::kinematics::tree::Atom::keep_1st_child_pos ( ) const

pure virtual

when other atoms are inserted insert after 1st child if available. –> this enables us to keep a stub of Downstream Jump atoms inside a single residue

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual bool core::kinematics::tree::Atom::keep_dof_fixed ( DOF_Type const ) const

inlinevirtual

DoF should be fixed for this atom?

for DoFs that must be kept fixed due to topology of tree e.g., phi of stub_atoms for jump_atoms

Reimplemented in core::kinematics::tree::BondedAtom, core::kinematics::tree::JumpAtom, and core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Size core::kinematics::tree::Atom::n_atom ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual Size core::kinematics::tree::Atom::n_children ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by protocols::environment::bond_angles(), protocols::environment::bond_lengths(), core::kinematics::tree::JumpAtom::copy_coords(), core::kinematics::tree::BondedAtom::copy_coords(), protocols::environment::jump_dofs(), and core::conformation::show_atom_tree().

virtual Size core::kinematics::tree::Atom::n_nonjump_children ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomOP core::kinematics::tree::Atom::next_child ( AtomCOP child )

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual Atoms_ConstIterator core::kinematics::tree::Atom::nonjump_atoms_begin ( ) const

protectedpure virtual

Implemented in core::kinematics::tree::Atom_.

virtual Atoms_Iterator core::kinematics::tree::Atom::nonjump_atoms_begin ( )

protectedpure virtual

Implemented in core::kinematics::tree::Atom_.

Atom& core::kinematics::tree::Atom::operator= ( Atom const & )

inlineprotecteddefault

Copy assignment.

virtual AtomCOP core::kinematics::tree::Atom::parent ( ) const

pure virtual

Parent atom pointer, NULL for root atom.

Implemented in core::kinematics::tree::Atom_.

Referenced by protocols::backrub::BackrubMover::add_segment(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::backtrack(), protocols::environment::bond_angles(), protocols::environment::bond_lengths(), core::kinematics::AtomTree::delete_seqpos(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), protocols::backrub::tree_distance(), protocols::viewer::visit_atomtree_node(), and protocols::environment::claims::XYZClaim::yield_elements().

virtual void core::kinematics::tree::Atom::parent ( AtomAP parent_in )

pure virtual

parent assignment

Implemented in core::kinematics::tree::Atom_.

virtual AtomOP core::kinematics::tree::Atom::parent ( )

pure virtual

Parent atom pointer, NULL for root atom.

Implemented in core::kinematics::tree::Atom_.

virtual Position const& core::kinematics::tree::Atom::position ( ) const

pure virtual

Position.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::Atom_::distance(), and core::kinematics::tree::Atom_::distance_squared().

virtual void core::kinematics::tree::Atom::position ( Position const & position_a )

pure virtual

Position assignment.

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::previous_child ( AtomCOP child ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::previous_sibling ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual Size core::kinematics::tree::Atom::raw_child_index ( Atom const * child ) const

pure virtual

the atom-index of this child

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_get_nonjump_atom ( Size const i ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the ith non-jump atom in this atom's list of children.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::JumpAtom::raw_stub_atom3(), and core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_input_stub_atom0 ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the 0th input stub atom;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_input_stub_atom1 ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the 1st input stub atom;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_input_stub_atom2 ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the 2nd input stub atom;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_input_stub_atom3 ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the 3rd input stub atom;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_parent ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the parent atom pointer.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::Atom_::dihedral_between_bonded_children(), core::kinematics::tree::Atom_::raw_child_index(), and core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_previous_child ( Atom const * child ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the previous child pointer;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::Atom_::raw_previous_sibling().

virtual Atom const* core::kinematics::tree::Atom::raw_previous_sibling ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the previous sibling pointer, i.e. the first child in the parent's children list to precede this atom.

Implemented in core::kinematics::tree::Atom_.

virtual Atom const* core::kinematics::tree::Atom::raw_stub_atom1 ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the fist stub atom.

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::Atom_::raw_input_stub_atom1(), and core::kinematics::tree::Atom_::raw_input_stub_atom3().

virtual Atom const* core::kinematics::tree::Atom::raw_stub_atom2 ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the second stub atom.

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::Atom_::raw_input_stub_atom2(), core::kinematics::tree::Atom_::raw_input_stub_atom3(), core::kinematics::tree::JumpAtom::raw_stub_atom2(), core::kinematics::tree::BondedAtom::raw_stub_atom3(), and core::kinematics::tree::Atom_::stub_atom2_id().

virtual Atom const* core::kinematics::tree::Atom::raw_stub_atom3 ( ) const

pure virtual

Rapid (increment-of-reference-count-avoiding) access to the third stub atom.

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::Atom_::raw_input_stub_atom3(), core::kinematics::tree::JumpAtom::raw_stub_atom3(), and core::kinematics::tree::BondedAtom::raw_stub_atom3().

virtual void core::kinematics::tree::Atom::replace_atom	(	AtomOP const	old_atom,
		AtomOP const	new_atom
	)

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::set_dof	(	DOF_Type const	type,
		Real const	value
	)

pure virtual

set dof, use "set_" syntax since we have multiple dof's

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::set_dof	(	DOF_Type const	type,
		Real const	value,
		AtomDOFChangeSet &	set
	)

pure virtual

set dof, use "set_" syntax since we have multiple dof's – for use in output-sensitive refold routine

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::setup_min_map	(	DOF_ID &	last_torsion,
		DOF_ID_Mask const &	move_map,
		MinimizerMapBase &	min_map
	)		const

pure virtual

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::show ( ) const

pure virtual

dump out AtomID for this atom, its parent and all its offspring

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::show ( int const & ) const

pure virtual

dump out AtomID for this atom, its parent and all its offspring up to n_level

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::steal_inversion ( AtomOP )

pure virtual

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual AtomCOP core::kinematics::tree::Atom::stub_atom1 ( ) const

pure virtual

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::Atom_::get_stub(), and core::kinematics::tree::Atom_::stub_atom1_id().

virtual AtomID const& core::kinematics::tree::Atom::stub_atom1_id ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::stub_atom2 ( ) const

pure virtual

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::Atom_::get_stub().

virtual AtomID const& core::kinematics::tree::Atom::stub_atom2_id ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::Atom_::raw_input_stub_atom3().

virtual AtomCOP core::kinematics::tree::Atom::stub_atom3 ( ) const

pure virtual

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::Atom_::get_stub(), and core::kinematics::tree::Atom_::stub_atom3_id().

virtual AtomID const& core::kinematics::tree::Atom::stub_atom3_id ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual bool core::kinematics::tree::Atom::stub_defined ( ) const

pure virtual

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::BondedAtom::raw_stub_atom3().

virtual void core::kinematics::tree::Atom::transform_Ax_plus_b_recursive	(	Matrix const &	A,
		Vector const &	b,
		ResidueCoordinateChangeList &	res_change_list
	)

pure virtual

Transform atom and children by linear transformation.

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::update_child_torsions ( AtomOP const child )

protectedpure virtual

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::update_domain_map	(	int &	current_color,
		int &	biggest_color,
		DomainMap &	domain_map,
		AtomID_Mask const &	dof_moved,
		AtomID_Mask const &	atom_moved
	)		const

pure virtual

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::update_internal_coords	(	std::deque< std::pair< Atom , core::kinematics::Stub > > *	childlist,
		std::deque< core::kinematics::Stub > *	stublist,
		Stub &	stub
	)

pure virtual

update internal coords from stub and xyz coords.

If childlist and stublist are not nullptr, childlist has pairs of (child atom, this stub), and stublist stores unique stubs. (Multiple pointers in childlist can point to the same stub, since that stub ultimately gets updated during the update of the coordinate.) appended so that children may subsequently be updated.