Kinematics Atom interface class. More...

#include <Atom.hh>

Public Member Functions
virtual	~Atom ()
	Destructor. More...

virtual void	set_weak_ptr_to_self (AtomAP weak_ptr)=0
	Set the weak-pointer-to-self for this atom. Must be called after the Atom is created and put inside of an owning_ptr. Required for atoms to be able to hold pointers to their parents: parents must give child atoms weak pointers to themselves. More...

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 (Stub &stub, bool const recursive=true)=0
	update internal coords from stub and xyz coords 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 (AtomCOP child1, AtomCOP 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 bool	downstream (AtomCOP atom1) const =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< AtomCOP > &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 bool	stub_defined () const =0

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

	Atom (Atom const &)
	Copy constructor. More...

Atom &	operator= (Atom const &)
	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 ( )

inlineprotected

Default constructor.

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

inlineprotected

Copy constructor.

virtual core::kinematics::tree::Atom::~Atom ( )

inlinevirtual

Destructor.

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().

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_.

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_.

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 core::kinematics::tree::JumpAtom::copy_coords(), core::kinematics::tree::BondedAtom::copy_coords(), 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	(	AtomCOP	child1,
		AtomCOP	child2
	)		const

pure virtual

dihedral angle between two bonded children to this atom

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

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().

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(), 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 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< AtomCOP > & path ) const

pure virtual

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

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

pure virtual

Get stub information.

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

Referenced by core::scoring::methods::LinearChainbreakEnergy::do_score_ovp().

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

pure virtual

Atom identifier.

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

Referenced by core::kinematics::tree::JumpAtom::copy_coords(), and core::conformation::show_atom_tree().

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 core::kinematics::tree::Atom_::input_stub_atom3(), core::kinematics::tree::Atom_::stub_defined(), and core::kinematics::tree::Atom_::update_domain_map().

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_.

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 core::kinematics::tree::JumpAtom::copy_coords(), core::kinematics::tree::BondedAtom::copy_coords(), 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 & )

inlineprotected

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_.

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 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::set_weak_ptr_to_self ( AtomAP weak_ptr )

pure virtual

Set the weak-pointer-to-self for this atom. Must be called after the Atom is created and put inside of an owning_ptr. Required for atoms to be able to hold pointers to their parents: parents must give child atoms weak pointers to themselves.

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

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

pure virtual

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

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

Referenced by core::kinematics::tree::Atom_::get_stub(), and core::kinematics::tree::Atom_::stub_atom2_id().

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

pure virtual

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

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

pure virtual

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

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_.

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	(	Stub &	stub,
		bool const	recursive = `true`
	)

pure virtual

update internal coords from stub and xyz coords

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

virtual void core::kinematics::tree::Atom::update_internal_coords ( bool const recursive )

pure virtual

calculate my input_stub from the current xyz's and use that input_stub to update my torsions

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

virtual void core::kinematics::tree::Atom::update_stub ( Stub & stub ) const

pure virtual

update the stub without actually updating coordinates

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

virtual void core::kinematics::tree::Atom::update_xyz_coords ( )

pure virtual

The atom must retrieve an appropriate stub from its parent; it is the root of the subtree being refolded.

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

virtual void core::kinematics::tree::Atom::update_xyz_coords ( Stub & stub )

pure virtual

update xyz coords from stub and internal coords and

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

virtual Length const& core::kinematics::tree::Atom::x ( ) const

pure virtual

x coordinate

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

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

pure virtual

Position.

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

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

pure virtual

Position assignment.

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

virtual Length const& core::kinematics::tree::Atom::y ( ) const

pure virtual

y coordinate

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

virtual Length const& core::kinematics::tree::Atom::z ( ) const

pure virtual

z coordinate

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

Friends And Related Function Documentation

Length distance	(	Atom const &	atom1,
		Atom const &	atom2
	)

friend

Distance between two Atoms.

Length distance_squared	(	Atom const &	atom1,
		Atom const &	atom2
	)

friend

Distance squared between two Atoms.

The documentation for this class was generated from the following file:

symlinks/rosetta/src/core/kinematics/tree/Atom.hh

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 Types

Public Member Functions

Protected Member Functions

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation