an atom who are connected to its parent via rigid-body transformation "Jump" More...

#include <JumpAtom.hh>

Public Member Functions
virtual void	dfs (AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const
	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 ()
	The atom must retrieve an appropriate stub from its parent; it is the root of the subtree being refolded. Valid only if this atom is the maximal root of a subtree requiring coordinate updates – if any ancestor of this atom requires a coordinate update, then the Stub this atom generates for itself will be invalid. More...

virtual void	update_xyz_coords (Stub &stub)
	update this atom's xyz position More...

virtual void	update_internal_coords (Stub &stub, bool const recursive=true)
	update the jump info More...

virtual void	set_dof (DOF_Type const type, Real const value)
	set a degree of freedom for jump More...

virtual void	set_dof (DOF_Type const type, core::Real const value, AtomDOFChangeSet &changeset)
	set degrees of freedom (internal coordinates). For use in output-sensitive refold subroutine. More...

virtual Real	dof (DOF_Type const type) const
	get a degree of freedom from jump More...

virtual Jump const &	jump () const
	access the jump More...

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

virtual void	jump (Jump const &jump_in, AtomDOFChangeSet &changeset)
	set the jump. For use with output-sensitive refold subroutine. More...

virtual AtomOP	clone (AtomAP parent_in, AtomPointer2D &atom_pointer) const
	copy this atom More...

virtual void	setup_min_map (DOF_ID &last_torsion, DOF_ID_Mask const &allow_move, MinimizerMapBase &min_map) const
	for minimizing, add DOF(RB) for a JumpAtom into the MinimizerMap More...

virtual void	get_dof_axis_and_end_pos (Vector &axis, Position &end_pos, DOF_Type const type) const
	get rotation axis and end_pos for a JumpAtom. More...

virtual bool	is_jump () const
	a jump atom is a jump? of course yes!!! More...

virtual bool	keep_1st_child_pos () const
	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 type) const
	whether a jump should be fixed in some special cases More...

virtual void	copy_coords (Atom const &src)
	copy DOFs, xyz's More...

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

AtomCOP	stub_atom1 () const
	stub_atom1 of a jump-atom More...

AtomCOP	stub_atom2 () const
	stub_atom2 of a jump-atom More...

AtomCOP	stub_atom3 () const
	stub_atom3 of a jump atom More...

Public Member Functions inherited from core::kinematics::tree::Atom_
virtual	~Atom_ ()
	Destructor. More...

virtual void	set_weak_ptr_to_self (AtomAP weak_ptr)
	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...

void	update_internal_coords (bool const recursive)
	update internal coords of this atom and its offspring atoms (if recursive) More...

Real	dihedral_between_bonded_children (AtomCOP child1, AtomCOP child2) const
	dihedral angle between two bonded children to this atom More...

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

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

void	update_domain_map (int &current_color, int &biggest_color, DomainMap &domain_map, AtomID_Mask const &dof_moved, AtomID_Mask const &atom_moved) const
	update domain map More...

Atoms_ConstIterator	atoms_begin () const
	starting const iterator of the children atom list More...

Atoms_ConstIterator	atoms_end () const
	ending const iterator of the children atom list More...

Atoms_Iterator	atoms_begin ()
	starting iterator of the children atom list More...

Atoms_Iterator	atoms_end ()
	ending iterator of the children atom list More...

Size	n_atom () const
	number of children atoms More...

void	append_atom (AtomOP)
	append an atom as this atom's child More...

void	delete_atom (AtomOP)
	remove an atom from this atom's children More...

void	insert_atom (AtomOP)
	insert an atom as this atom's child More...

void	insert_atom (AtomOP, int const )
	tries to insert at the position specified by the second argument More...

void	replace_atom (AtomOP const old_atom, AtomOP const new_atom)
	replace the old atom by the new atom in the child atom list More...

AtomCOP	get_nonjump_atom (Size const i) const
	get non-jump atom by its index from the children atoms list More...

Size	n_children () const
	number of the child atoms More...

Size	n_nonjump_children () const
	number of the non-jump child atoms More...

AtomCOP	child (Size const k) const
	get a child atom by index (const method) More...

AtomOP	child (Size const k)
	get a child atom by index More...

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

bool	downstream (AtomCOP atom1) const
	whether atom1 is downstream of this atom. More...

AtomID const &	id () const
	Atom identifier. More...

void	id (AtomID const &id_in)
	AtomID assignment. More...

AtomID const &	atom_id () const
	Atom identifier. More...

Position const &	position () const
	Position. More...

void	position (Position const &position_a)
	Position assignment. More...

Position const &	xyz () const
	Position. More...

void	xyz (Position const &position_a)
	Position assignment. More...

Length const &	x () const
	x coordinate More...

Length const &	y () const
	y coordinate More...

Length const &	z () const
	z coordinate More...

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

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

AtomCOP	parent () const
	Parent atom pointer. More...

void	parent (AtomAP parent_in)
	parent assignment More...

AtomOP	parent ()
	Parent atom pointer. More...

Stub	get_stub () const
	stub centerd at this atom More...

Stub	get_input_stub () const
	stub used to build this atom More...

AtomID const &	stub_atom1_id () const
	stub atom1 's id More...

AtomID const &	stub_atom2_id () const
	stub atom2's id More...

AtomID const &	stub_atom3_id () const
	stub atom3's id More...

AtomCOP	input_stub_atom0 () const
	the center of the input stub for refolding this atom More...

AtomCOP	input_stub_atom1 () const
	the first atom to construct the input stub for refolding this atom More...

AtomCOP	input_stub_atom2 () const
	the second atom to construct the input stub for refolding this atom More...

AtomCOP	input_stub_atom3 () const
	the third atom to construct the input stub for refolding this atom More...

AtomID const &	input_stub_atom0_id () const
	input stub atom0's id More...

AtomID const &	input_stub_atom1_id () const
	input stub atom1's id More...

AtomID const &	input_stub_atom2_id () const
	input stub atom2's id More...

AtomID const &	input_stub_atom3_id () const
	input stub atom3's id More...

AtomCOP	previous_sibling () const
	routines for navigating the tree find the sibling atom before itself More...

AtomCOP	previous_child (AtomCOP child) const
	find the child atom before this child in the list More...

AtomOP	next_child (AtomCOP child)
	find the child atom after this child in the list More...

bool	stub_defined () const
	whether a Stub can be defined for this atom More...

Public Member Functions inherited from core::kinematics::tree::Atom
virtual	~Atom ()
	Destructor. More...

Private Types
typedef Atom_	Super

Private Attributes
Jump	jump_
	Jump. More...

Additional Inherited Members
Public Types inherited from core::kinematics::tree::Atom
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

Protected Member Functions inherited from core::kinematics::tree::Atom_
	Atom_ ()
	Default constructor. More...

	Atom_ (Atom_ const &atom)
	Copy constructor. More...

Atom_ &	operator= (Atom_ const &atom)
	Copy assignment. More...

AtomAP	this_weak_ptr ()
	Read access to the replacement "this" pointer. More...

AtomCAP	this_weak_ptr () const
	Read access to the replacement "this" pointer. More...

void	update_child_torsions (AtomOP const child)
	when subtrees have changed their coordinates More...

Atoms_ConstIterator	nonjump_atoms_begin () const
	constant iterator of the first non-jump (bonded) atom in the vector of children atoms. More...

Atoms_Iterator	nonjump_atoms_begin ()
	iterator of the first non-jump (bonded) atom in the vector of children atoms. More...

void	abort_bad_call () const
	helper function to abort if something is wrong in atom tree More...

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

void	get_path_from_root (utility::vector1< AtomCOP > &path) const

bool	atom_is_on_path_from_root (AtomCOP atm) const

void	note_dof_change (AtomDOFChangeSet &changset)
	Records this atom as having a changed DOF in the input list of Atoms with changed DOFs. For use in output-sensitive refold subroutine. More...

void	note_xyz_uptodate ()
	To ensure proper function of the output-senstive refold subroutine, derived classes must invoke this function during their update_xyz_coord subroutines. More...

Size	dof_refold_index () const
	read access for derived classes More...

Protected Member Functions inherited from core::kinematics::tree::Atom
	Atom ()
	Default constructor. More...

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

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

Protected Attributes inherited from core::kinematics::tree::Atom_
AtomAP	this_weak_ptr_
	Each atom must hold a weak pointer to itself, and this weak pointer must be given to the atom at its construction. More...

AtomID	atom_id_
	Atom ID. More...

AtomAP	parent_
	Associated conformation Atom. More...

PointPosition	position_
	xyz More...

Atoms	atoms_
	Children atom pointers. More...

Detailed Description

an atom who are connected to its parent via rigid-body transformation "Jump"

See AtomTree overview and concepts for details.

Member Typedef Documentation

typedef Atom_ core::kinematics::tree::JumpAtom::Super

private

Member Function Documentation

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

virtual

copy this atom

Note: this will recursively clone all this atom's offspring atoms

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), core::kinematics::tree::Atom_::id(), jump_, and core::kinematics::tree::Atom_::position().

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

virtual

copy DOFs, xyz's

copy DOFs, xyz's. this asserts equal topology. do recursively to copy for all its children

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), core::kinematics::tree::Atom::child(), core::kinematics::tree::Atom_::id(), core::kinematics::tree::Atom::id(), core::kinematics::tree::Atom::jump(), jump_, core::kinematics::tree::Atom_::n_children(), core::kinematics::tree::Atom::n_children(), core::kinematics::tree::Atom_::operator=(), and utility_exit.

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

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.

Invokes Atom_ dfs function (which visits the subtree routed at this node). No younger siblings are effected by a DOF change at a JumpAtom.

Reimplemented from core::kinematics::tree::Atom_.

References core::kinematics::tree::Atom_::dfs().

Real core::kinematics::tree::JumpAtom::dof ( DOF_Type const type ) const

virtual

get a degree of freedom from jump

Note: along n2c direction

Implements core::kinematics::tree::Atom.

References core::kinematics::Jump::get_rb_delta(), core::id::get_rb_number(), jump_, and utility_exit.

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

virtual

get rotation axis and end_pos for a JumpAtom.

axis is the unit vector along the rotation axis for that DOF(Eab). 2li end_pos is the ending point of this unit vector(Vb).

RB1, RB2 and RB3 are translation along x, y and z axis in the jump_start (input_stub) frame, which are input_stub.col(1), input_stub.col(2) and input_stub.col(3).
RB4, RB5 and RB6 are rotations along x, y and z axis in the input_stub frame, and the rotation is applied around the point of "rb_center" written in the jump_end (my_stub) frame. So "end_pos"for these 3 DOFs is the rb_center rewritten in xyz frame, which is my_stub.V+my_stub.M*rb_center. The axis is not simply x, y and z in the input_stub because these 3 DOFs are not independently applied. Here are how they are derived (by me and there might be other smarter way to think of it):

the jump rotation matrix is R = Rz(RB6) * Ry(RB5) * Rx(RB4) * rt.rotation.

if RB6 is perturbed by "d", the new rotation matrix is R' = Rz(d+RB6) * Ry(RB5) * Rx(RB4) * rt.rotation = Rz(d) * Rz(RB6) * Ry(RB5) * Rx(RB4) * rt.rotation = Rz(d) * R. This is to say perturbing RB6 by d is equivalent to making an extra rotation around Z axis in the input_stub frame and therefore the axis is just input_stub.col(3).

if RB5 is perturbed by "d", the new rotation matrix is R' = Rz(RB6) * Ry(d+RB5) * Rx(RB4) * rt.rotation = Rz(RB6) * Ry(d) * Ry(RB5) * Rx(RB4) * rt.rotation = Rz(RB6) * Ry(d) * Rz(RB6)^ * R. This is to say perturbing RB5 by d is equivalent to making an extra rotation Rz(RB6) * Ry(d) * Rz(RB6)^ in the input_stub frame and the axis of rotation is the one we try to get. what is it? Remember this rotation matrix is in the context of the input_stub frame M, so rewritting it in the xyz lab frame results in M * Rz(RB6) * Ry(d) * Rz(RB6)^ * M^. Since for matrices (A*B)^ = B^ * A^, we get (M *Rz(RB6)) * Ry(d) * (M * Rz(RB6))^ and this is eqivanelent to making a rotation around y axis in the frame of (M *Rz(RB6)) and therefore the axis is (input_stub.M * Z_rotation ).col(2)

similarly, one can the axis for a perturbation to RB4 DOF.

Implements core::kinematics::tree::Atom.

References numeric::xyzMatrix< class >::col(), core::kinematics::tree::Atom_::get_input_stub(), core::kinematics::Jump::get_rb_center(), core::kinematics::Jump::get_rb_delta(), core::id::get_rb_number(), core::kinematics::tree::Atom_::get_stub(), jump_, core::kinematics::Stub::M, core::id::RB4, core::id::RB5, core::id::RB6, utility_exit, core::kinematics::Stub::v, numeric::y_rotation_matrix_degrees(), y_rotation_matrix_degrees(), numeric::z_rotation_matrix_degrees(), and z_rotation_matrix_degrees().

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

inlinevirtual

a jump atom is a jump? of course yes!!!

Implements core::kinematics::tree::Atom.

Jump const & core::kinematics::tree::JumpAtom::jump ( ) const

virtual

access the jump

Implements core::kinematics::tree::Atom.

References jump_.

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

virtual

set the jump

Implements core::kinematics::tree::Atom.

References jump_.

void core::kinematics::tree::JumpAtom::jump	(	Jump const &	jump_in,
		AtomDOFChangeSet &	changeset
	)

virtual

set the jump. For use with output-sensitive refold subroutine.

Implements core::kinematics::tree::Atom.

References jump_, and core::kinematics::tree::Atom_::note_dof_change().

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

inlinevirtual

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

Implements core::kinematics::tree::Atom.

bool core::kinematics::tree::JumpAtom::keep_dof_fixed ( DOF_Type const type ) const

virtual

whether a jump should be fixed in some special cases

the root jump is not flexible (currently)

Reimplemented from core::kinematics::tree::Atom_.

References core::kinematics::tree::Atom_::parent().

Referenced by setup_min_map().

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

virtual

set a degree of freedom for jump

Note: along n2c direction

Implements core::kinematics::tree::Atom.

References core::id::get_rb_number(), jump_, core::kinematics::tree::Atom_::parent(), core::kinematics::Jump::set_rb_delta(), and utility_exit.

Referenced by set_dof().

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

virtual

set degrees of freedom (internal coordinates). For use in output-sensitive refold subroutine.

calls set_dof non-polymorphically: assumption is that JumpAtom is not subclassed, or, that if it is, that the derived class implements this overloaded set_dof function.

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::note_dof_change(), and set_dof().

void core::kinematics::tree::JumpAtom::setup_min_map	(	DOF_ID &	last_torsion,
		DOF_ID_Mask const &	allow_move,
		MinimizerMapBase &	min_map
	)		const

virtual

for minimizing, add DOF(RB) for a JumpAtom into the MinimizerMap

last torsion is the torsion( Phi for BondedAtom and RB for JumpAtom) of the parent atom or the previous bonded sibling. Since unlike BondedAtom, JumpAtom's RB is independent from other sibling atoms, this will not modify last_torsion, unlike Atom::setup_min_map. recursively done all its offspring

Implements core::kinematics::tree::Atom.

References core::kinematics::MinimizerMapBase::add_atom(), core::kinematics::MinimizerMapBase::add_torsion(), core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), core::id::get_rb_type(), keep_dof_fixed(), core::kinematics::tree::Atom_::parent(), and type.

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

inlinevirtual

stub_atom1 of a jump-atom

it is itself if a stub can be defined for it. Otherwise it is parent

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::parent(), and core::kinematics::tree::Atom_::stub_defined().

AtomCOP core::kinematics::tree::JumpAtom::stub_atom2 ( ) const

inlinevirtual

stub_atom2 of a jump-atom

it is its first bonded child if a stub can be defined for it. Otherwise it is parent's stub_atom2.

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::get_nonjump_atom(), core::kinematics::tree::Atom_::parent(), and core::kinematics::tree::Atom_::stub_defined().

AtomCOP core::kinematics::tree::JumpAtom::stub_atom3 ( ) const

inlinevirtual

stub_atom3 of a jump atom

it is its child's child or its second child if a stub can be defined for it, otherwise it is its parent's stub_atom3

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::get_nonjump_atom(), core::kinematics::tree::Atom_::parent(), and core::kinematics::tree::Atom_::stub_defined().

void core::kinematics::tree::JumpAtom::update_internal_coords	(	Stub &	stub,
		bool const	recursive = `true`
	)

virtual

update the jump info

update the jump from the input stub and this atom's own stub. If defined, will recursively update internal coords for all its offspring atoms.

Note: The input stub is not changed.

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), core::kinematics::Jump::from_stubs(), core::kinematics::tree::Atom_::get_stub(), core::kinematics::Stub::is_orthogonal(), and jump_.

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

inlinevirtual

update the stub without actually updating coordinates

since for a jump atom, update internal coords or xyz dont change input jump, so we do not do anything here

Implements core::kinematics::tree::Atom.

void core::kinematics::tree::JumpAtom::update_xyz_coords ( )

virtual

The atom must retrieve an appropriate stub from its parent; it is the root of the subtree being refolded. Valid only if this atom is the maximal root of a subtree requiring coordinate updates – if any ancestor of this atom requires a coordinate update, then the Stub this atom generates for itself will be invalid.

Relies on get_input_stub, which will use the coordinates of this atom's ancestors to build a stub. If this function has been invoked by AtomTree update_xyz_coords(), then these coordinates are guaranteed correct, since this atom is the root of a tree which needs to be refolded. Ergo, nothing in the tree above this atom needs to be refolded.

Reimplemented from core::kinematics::tree::Atom_.

References core::kinematics::tree::Atom_::get_input_stub().

void core::kinematics::tree::JumpAtom::update_xyz_coords ( Stub & stub )

virtual

update this atom's xyz position

call make_jump to "jump" from parent to this atom. Will recursively update xyz positions for all its offspring atoms.

Note: the input stub is not changed

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), core::kinematics::Stub::is_orthogonal(), jump_, core::kinematics::Jump::make_jump(), core::kinematics::tree::Atom_::note_xyz_uptodate(), and core::kinematics::tree::Atom_::position().

Member Data Documentation

Jump core::kinematics::tree::JumpAtom::jump_

private

Jump.

A jump atom is connected to its parent via rigid-body transformation("jump"). It requires two stubs to define a jump, one is the parent atoms's stub and the other is the stub centered at this jump atom, which requires at least three atoms on the jump atom's side (including itself). For example, a stub is defined from B-A-C or A-B-C (A is the jump atom, B and C are its offspring). If less than 3 atoms on the jump atom's side, i.e., stub_defined() == False, this atom will just use its parent stub.

Referenced by clone(), copy_coords(), dof(), get_dof_axis_and_end_pos(), jump(), set_dof(), update_internal_coords(), and update_xyz_coords().

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

symlinks/rosetta/src/core/kinematics/tree/JumpAtom.hh
symlinks/rosetta/src/core/kinematics/tree/JumpAtom.cc

Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Member Function Documentation

Member Data Documentation