Kinematics Atom abstract base class. More...

#include <Atom_.hh>

Public Member Functions
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_xyz_coords ()
	update xyz position of this atom and its offspring atoms More...

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

bool	keep_dof_fixed (DOF_Type const ) const
	for DOFs which must be kept fixed due to topology of tree 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...

virtual void	dfs (AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const
	base class implementation that traverses the subtree routed at this node in the depth-first traversal of the atoms requiring coordinate updates. More...

Public Member Functions inherited from core::kinematics::tree::Atom
virtual	~Atom ()
	Destructor. 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_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 AtomCOP	stub_atom1 () const =0

virtual AtomCOP	stub_atom2 () const =0

virtual AtomCOP	stub_atom3 () const =0

Protected Member Functions
	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
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...

Private Types
typedef Atom	Super

Private Attributes
Size	dof_refold_index_
	Track my position in my owner's list of Atoms with modified DOFs. 0 when my dofs have not changed since the last update_coords. 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

Detailed Description

Kinematics Atom abstract base class.

Member Typedef Documentation

typedef Atom core::kinematics::tree::Atom_::Super

private

Constructor & Destructor Documentation

core::kinematics::tree::Atom_::Atom_ ( )

inlineprotected

Default constructor.

References atoms_.

core::kinematics::tree::Atom_::Atom_ ( Atom_ const & atom )

inlineprotected

Copy constructor.

Note: Copies value and type state but not context state

References atoms_.

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

inlinevirtual

Destructor.

Member Function Documentation

void core::kinematics::tree::Atom_::abort_bad_call ( ) const

protected

helper function to abort if something is wrong in atom tree

References utility_exit.

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

void core::kinematics::tree::Atom_::append_atom ( AtomOP atom )

virtual

append an atom as this atom's child

if the child atom is a jump atom, put it before all the non-jump children atoms but after all the children jump atoms. Otherwise, put it at the end of the children atom list.

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

References atoms_, nonjump_atoms_begin(), and this_weak_ptr_.

AtomID const& core::kinematics::tree::Atom_::atom_id ( ) const

inlinevirtual

Atom identifier.

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

References atom_id_.

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

bool core::kinematics::tree::Atom_::atom_is_on_path_from_root ( AtomCOP atm ) const

protectedvirtual

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

References parent_.

Atoms_ConstIterator core::kinematics::tree::Atom_::atoms_begin ( ) const

inlinevirtual

starting const iterator of the children atom list

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

References atoms_.

Atoms_Iterator core::kinematics::tree::Atom_::atoms_begin ( )

inlinevirtual

starting iterator of the children atom list

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

References atoms_.

Atoms_ConstIterator core::kinematics::tree::Atom_::atoms_end ( ) const

inlinevirtual

ending const iterator of the children atom list

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

References atoms_.

Atoms_Iterator core::kinematics::tree::Atom_::atoms_end ( )

inlinevirtual

ending iterator of the children atom list

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

References atoms_.

AtomCOP core::kinematics::tree::Atom_::child ( Size const k ) const

virtual

get a child atom by index (const method)

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

References atoms_.

Referenced by delete_atom(), downstream(), next_child(), and previous_child().

AtomOP core::kinematics::tree::Atom_::child ( Size const k )

virtual

get a child atom by index

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

References atoms_.

Size core::kinematics::tree::Atom_::child_index ( AtomCOP child ) const

virtual

the atom-index of this child

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

References atoms_, and utility_exit_with_message.

void core::kinematics::tree::Atom_::delete_atom ( AtomOP child )

virtual

remove an atom from this atom's children

only unlink the child atom from this atom (parent). No recursive operation or freeing memory( use Atom_::erase() to free up memory for an atom and all its children

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

References atoms_, child(), and utility_exit.

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

virtual

base class implementation that traverses the subtree routed at this node in the depth-first traversal of the atoms requiring coordinate updates.

the "start atom index" is used to determine which subtrees have already been examined. The atom tree guarantees that the dfs's occur in increasing order by dof refold indices. If this atom has a dof refold index less than the start atom index, then a dfs has previously been launched from this node and the recursion must stop: subtrees must be visited at most once, or running time grows quadratically in the number of atoms in the tree. The atom is responsible for handing the start atom index down to its children in the recursion (if it continues recursing).

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

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

References atom_id_, atoms_, atoms_begin(), atoms_end(), dof_refold_index_, and core::kinematics::ResidueCoordinateChangeList::mark_residue_moved().

Referenced by core::kinematics::tree::JumpAtom::dfs(), and core::kinematics::tree::BondedAtom::dfs().

Real core::kinematics::tree::Atom_::dihedral_between_bonded_children	(	AtomCOP	child1,
		AtomCOP	child2
	)		const

virtual

dihedral angle between two bonded children to this atom

the improper dihedral from child1 to child2 about my x-axis (ie, axis defined by me and my parent for nonjump atoms). Since phi_ for a non-first branched atom is defined as the improper angle offset with respect to its previous sibling, we just need to add up all the offsets between them.

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

References atoms_end(), nonjump_atoms_begin(), core::chemical::PHI, and utility_exit_with_message.

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

inlinevirtual

Distance to an Atom.

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

References numeric::xyzVector< class >::distance(), core::kinematics::tree::Atom::position(), and position_.

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

inlinevirtual

Distance squared to an Atom.

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

References numeric::xyzVector< class >::distance_squared(), core::kinematics::tree::Atom::position(), and position_.

Size core::kinematics::tree::Atom_::dof_refold_index ( ) const

inlineprotected

read access for derived classes

References dof_refold_index_.

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

bool core::kinematics::tree::Atom_::downstream ( AtomCOP atom1 ) const

virtual

whether atom1 is downstream of this atom.

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

References child(), and n_children().

Stub core::kinematics::tree::Atom_::get_input_stub ( ) const

virtual

stub used to build this atom

the stub that is passed to me during folding, which is normally the stub centered at the parent atom.

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

References core::kinematics::default_stub, input_stub_atom0(), input_stub_atom1(), input_stub_atom2(), input_stub_atom3(), parent_, and position().

Referenced by core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos(), update_internal_coords(), core::kinematics::tree::JumpAtom::update_xyz_coords(), core::kinematics::tree::BondedAtom::update_xyz_coords(), and update_xyz_coords().

AtomCOP core::kinematics::tree::Atom_::get_nonjump_atom ( Size const index ) const

virtual

get non-jump atom by its index from the children atoms list

returns 0 if atom doesnt exist

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

References atoms_, and nonjump_atoms_begin().

Referenced by core::kinematics::tree::JumpAtom::stub_atom2(), core::kinematics::tree::JumpAtom::stub_atom3(), and stub_defined().

void core::kinematics::tree::Atom_::get_path_from_root ( utility::vector1< AtomCOP > & path ) const

protectedvirtual

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

References parent_.

Stub core::kinematics::tree::Atom_::get_stub ( ) const

virtual

stub centerd at this atom

my stub is center at myself. Normally for bonded atom, X direction is from my parent to me; Z direction is perpendicular to the plane defined by myself, my parent and my parent's parent

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

References position(), core::kinematics::tree::Atom::stub_atom1(), core::kinematics::tree::Atom::stub_atom2(), and core::kinematics::tree::Atom::stub_atom3().

Referenced by core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos(), update_child_torsions(), and core::kinematics::tree::JumpAtom::update_internal_coords().

AtomID const& core::kinematics::tree::Atom_::id ( ) const

inlinevirtual

Atom identifier.

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

References atom_id_.

Referenced by core::kinematics::tree::JumpAtom::clone(), core::kinematics::tree::BondedAtom::clone(), and core::kinematics::tree::JumpAtom::copy_coords().

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

inlinevirtual

AtomID assignment.

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

References atom_id_.

AtomCOP core::kinematics::tree::Atom_::input_stub_atom0 ( ) const

inlinevirtual

the center of the input stub for refolding this atom

it is its parent

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

References parent_.

Referenced by get_input_stub(), and input_stub_atom0_id().

AtomID const& core::kinematics::tree::Atom_::input_stub_atom0_id ( ) const

inlinevirtual

input stub atom0's id

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

References input_stub_atom0().

AtomCOP core::kinematics::tree::Atom_::input_stub_atom1 ( ) const

inlinevirtual

the first atom to construct the input stub for refolding this atom

it is its parent's stub_atom1, which normally the parent itself

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

References parent_.

Referenced by get_input_stub(), and input_stub_atom1_id().

AtomID const& core::kinematics::tree::Atom_::input_stub_atom1_id ( ) const

inlinevirtual

input stub atom1's id

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

References input_stub_atom1().

AtomCOP core::kinematics::tree::Atom_::input_stub_atom2 ( ) const

inlinevirtual

the second atom to construct the input stub for refolding this atom

it is its parent's stub_atom2, which normally the parent's parent

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

References parent_.

Referenced by get_input_stub(), and input_stub_atom2_id().

AtomID const& core::kinematics::tree::Atom_::input_stub_atom2_id ( ) const

inlinevirtual

input stub atom2's id

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

References input_stub_atom2().

AtomCOP core::kinematics::tree::Atom_::input_stub_atom3 ( ) const

inlinevirtual

the third atom to construct the input stub for refolding this atom

it is either its previous sibling or its parent's stub_atom3,

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

References core::kinematics::tree::Atom::is_jump(), parent_, and previous_sibling().

Referenced by get_input_stub(), and input_stub_atom3_id().

AtomID const& core::kinematics::tree::Atom_::input_stub_atom3_id ( ) const

inlinevirtual

input stub atom3's id

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

References input_stub_atom3().

void core::kinematics::tree::Atom_::insert_atom ( AtomOP atom )

virtual

insert an atom as this atom's child

if the child atom is a jump atom, put it before all jump children atoms; otherwise, put it before all non-jump children atoms; Different from Atom_::append_atom in that it put the new child atom before instead after the other existing child atoms.

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

References atoms_, nonjump_atoms_begin(), and this_weak_ptr_.

void core::kinematics::tree::Atom_::insert_atom	(	AtomOP	atom,
		int const	index
	)

virtual

tries to insert at the position specified by the second argument

insert the child atom in a specified position. If the specified postion is out of range, put it either at the beginning or the end of the child atom list. note that jump child atoms are always listed before non-jump atoms and the index must be a non-negative integer.

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

References atoms_, nonjump_atoms_begin(), and this_weak_ptr_.

bool core::kinematics::tree::Atom_::keep_dof_fixed ( DOF_Type const ) const

inlinevirtual

for DOFs which must be kept fixed due to topology of tree

eg, phi of stub_atoms for jump_atoms

Reimplemented from core::kinematics::tree::Atom.

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

Size core::kinematics::tree::Atom_::n_atom ( ) const

inlinevirtual

number of children atoms

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

References atoms_.

Size core::kinematics::tree::Atom_::n_children ( ) const

virtual

number of the child atoms

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

References atoms_.

Referenced by core::kinematics::tree::JumpAtom::copy_coords(), core::kinematics::tree::BondedAtom::copy_coords(), and downstream().

Size core::kinematics::tree::Atom_::n_nonjump_children ( ) const

inlinevirtual

number of the non-jump child atoms

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

References atoms_end(), and nonjump_atoms_begin().

AtomOP core::kinematics::tree::Atom_::next_child ( AtomCOP child )

virtual

find the child atom after this child in the list

return 0 if the input child is the last child in the list

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

References atoms_, child(), and utility_exit.

Atom_::Atoms_ConstIterator core::kinematics::tree::Atom_::nonjump_atoms_begin ( ) const

protectedvirtual

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

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

References atoms_.

Referenced by append_atom(), dihedral_between_bonded_children(), get_nonjump_atom(), insert_atom(), and n_nonjump_children().

Atom_::Atoms_Iterator core::kinematics::tree::Atom_::nonjump_atoms_begin ( )

protectedvirtual

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

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

References atoms_.

void core::kinematics::tree::Atom_::note_dof_change ( AtomDOFChangeSet & changset )

protected

Records this atom as having a changed DOF in the input list of Atoms with changed DOFs. For use in output-sensitive refold subroutine.

Records this atom as an atom with one-or-more changed dofs in the input AtomDOFChangeSet if this is first DOF on this atom to change; if it is not the first DOF on this atom that has changed, then this atom is already in set and this atom is recorded at position dof_refold_index_.

References atom_id_, and dof_refold_index_.

Referenced by core::kinematics::tree::JumpAtom::jump(), core::kinematics::tree::JumpAtom::set_dof(), and core::kinematics::tree::BondedAtom::set_dof().

void core::kinematics::tree::Atom_::note_xyz_uptodate ( )

inlineprotected

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

References dof_refold_index_.

Referenced by core::kinematics::tree::JumpAtom::update_xyz_coords(), and core::kinematics::tree::BondedAtom::update_xyz_coords().

Atom_& core::kinematics::tree::Atom_::operator= ( Atom_ const & atom )

inlineprotected

Copy assignment.

Note: Copies value and type state but not context state

References dof_refold_index_, and position_.

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

AtomCOP core::kinematics::tree::Atom_::parent ( ) const

inlinevirtual

Parent atom pointer.

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

References parent_.

void core::kinematics::tree::Atom_::parent ( AtomAP parent_in )

inlinevirtual

parent assignment

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

References parent_.

AtomOP core::kinematics::tree::Atom_::parent ( )

inlinevirtual

Parent atom pointer.

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

References parent_.

Position const& core::kinematics::tree::Atom_::position ( ) const

inlinevirtual

Position.

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

References position_.

Referenced by core::kinematics::tree::JumpAtom::clone(), core::kinematics::tree::BondedAtom::clone(), get_input_stub(), get_stub(), core::kinematics::tree::BondedAtom::update_internal_coords(), core::kinematics::tree::JumpAtom::update_xyz_coords(), and core::kinematics::tree::BondedAtom::update_xyz_coords().

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

inlinevirtual

Position assignment.

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

References position_.

AtomCOP core::kinematics::tree::Atom_::previous_child ( AtomCOP child ) const

virtual

find the child atom before this child in the list

return 0 if the input child is the first child in the list

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

References atoms_, child(), and utility_exit.

AtomCOP core::kinematics::tree::Atom_::previous_sibling ( ) const

virtual

routines for navigating the tree find the sibling atom before itself

call parent's previous_child method to get its previous sibling; return 0 if no parent is present.

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

References parent_, and this_weak_ptr_.

Referenced by input_stub_atom3().

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

virtual

replace the old atom by the new atom in the child atom list

old atom and new atom need to belong to the same type ( either both jump atoms or both non-jump atoms. New atom is inserted at the position of old atom.

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

References atoms_, this_weak_ptr_, and utility_exit.

void core::kinematics::tree::Atom_::set_weak_ptr_to_self ( AtomAP weak_ptr )

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.

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

References this_weak_ptr_.

void core::kinematics::tree::Atom_::show ( ) const

virtual

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

first this atom, then its parent and then recursively all its children

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

References atom_id_, atoms_, and parent_.

void core::kinematics::tree::Atom_::show ( int const & n_level ) const

virtual

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

first this atom, then its parent and then recursively all its children up to n_level

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

References atom_id_, atoms_, parent_, core::kinematics::tree::TR, x(), y(), and z().

AtomID const& core::kinematics::tree::Atom_::stub_atom1_id ( ) const

inlinevirtual

stub atom1 's id

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

References core::kinematics::tree::Atom::stub_atom1().

AtomID const& core::kinematics::tree::Atom_::stub_atom2_id ( ) const

inlinevirtual

stub atom2's id

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

References core::kinematics::tree::Atom::stub_atom2().

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

AtomID const& core::kinematics::tree::Atom_::stub_atom3_id ( ) const

inlinevirtual

stub atom3's id

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

References core::kinematics::tree::Atom::stub_atom3().

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

bool core::kinematics::tree::Atom_::stub_defined ( ) const

virtual

whether a Stub can be defined for this atom

bonded-atom always has its stub defined (from its parent)
jump-atom needs to have at least three atoms (including itself) at its end to define a stub, such as three linearly bonded atoms or two children atoms bonded to itself.

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

References get_nonjump_atom(), and core::kinematics::tree::Atom::is_jump().

Referenced by core::kinematics::tree::JumpAtom::stub_atom1(), core::kinematics::tree::JumpAtom::stub_atom2(), core::kinematics::tree::BondedAtom::stub_atom3(), and core::kinematics::tree::JumpAtom::stub_atom3().

AtomAP core::kinematics::tree::Atom_::this_weak_ptr ( )

inlineprotected

Read access to the replacement "this" pointer.

References this_weak_ptr_.

AtomCAP core::kinematics::tree::Atom_::this_weak_ptr ( ) const

inlineprotected

Read access to the replacement "this" pointer.

References this_weak_ptr_.

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

protectedvirtual

Transform atom and children by linear transformation.

Keep track of any residue that moves so that the Conformation object may be correctly updated.

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

References atom_id_, atoms_, core::kinematics::ResidueCoordinateChangeList::mark_residue_moved(), and position_.

void core::kinematics::tree::Atom_::update_child_torsions ( AtomOP const child )

protectedvirtual

when subtrees have changed their coordinates

the coordinates of the atom "*child" – one of my children – have changed. This routine updates the torsions to reflect this. Useful if we have just repacked or rotamer-trialed, ie sidechain atoms_ have moved but the backbone is still the same, more efficient than calling update_internal_coords on the entire tree...

Note: update_internal_coords is called recursively on all of *child's children.

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

References atom_id_, atoms_, get_stub(), and utility_exit.

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

virtual

update domain map

update domain map for this atom and all its offspring consider this like a graph coloring problem. we are recursively (depth-first) assigning a color to each atom.

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

References atom_id_, atoms_, and core::kinematics::tree::Atom::is_jump().

void core::kinematics::tree::Atom_::update_internal_coords ( bool const recursive )

virtual

update internal coords of this atom and its offspring atoms (if recursive)

get the input stub for building this atom first

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

References get_input_stub().

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

virtual

update xyz position of this atom and its offspring atoms

get the input stub for building this atom first