Kinematics Atom abstract base class. More...

#include <Atom_.hh>

Inheritance diagram for core::kinematics::tree::Atom_:

Public Member Functions
	~Atom_ () override
	Destructor. More...

void	update_xyz_coords () override
	update xyz position of this atom and its offspring atoms More...

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

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

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

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

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

void	show (int const &n_level) const override
	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 override
	update domain map More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Atom const *	raw_previous_sibling () const override
	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...

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

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

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

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

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

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

Public Member Functions inherited from core::kinematics::tree::Atom
AtomCOP	get_self_ptr () const

AtomOP	get_self_ptr ()

AtomCAP	get_self_weak_ptr () const

AtomAP	get_self_weak_ptr ()

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_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 void	steal_inversion (AtomOP)=0

virtual AtomCOP	stub_atom1 () const =0

virtual AtomCOP	stub_atom2 () const =0

virtual AtomCOP	stub_atom3 () const =0

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...

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

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

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

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

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

Atoms_Iterator	nonjump_atoms_begin () override
	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...

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

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

bool	atom_is_on_path_from_root (AtomCOP atm) const override

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
	Default constructor. More...

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

Protected Attributes
AtomID	atom_id_
	Atom ID. More...

AtomAP	parent_
	Associated conformation Atom. More...

Atom *	raw_parent_
	Workaround copy of the parent pointer for use in functions where locking and unlocking the parent_ pointer would be prohibitively slow. 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_.

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

inlineoverride

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

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

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

overridevirtual

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_, core::kinematics::tree::Atom::get_self_weak_ptr(), and nonjump_atoms_begin().

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

inlineoverridevirtual

Atom identifier.

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

References atom_id_.

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

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

overrideprotectedvirtual

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

References parent(), and parent_.

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

inlineoverridevirtual

starting const iterator of the children atom list

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

References atoms_.

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

inlineoverridevirtual

starting iterator of the children atom list

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

References atoms_.

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

inlineoverridevirtual

ending const iterator of the children atom list

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

References atoms_.

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

inlineoverridevirtual

ending iterator of the children atom list

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

References atoms_.

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

overridevirtual

get a child atom by index (const method)

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

References atoms_.

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

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

overridevirtual

get a child atom by index

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

References atoms_.

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

overridevirtual

the atom-index of this child

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

References atoms_.

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

overridevirtual

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_, and child().

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

overridevirtual

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	(	Atom const &	child1,
		Atom const &	child2
	)		const

overridevirtual

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(), core::kinematics::tree::Atom::is_jump(), nonjump_atoms_begin(), core::chemical::rings::PHI, and core::kinematics::tree::Atom::raw_parent().

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

inlineoverridevirtual

Distance to an Atom.

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

References core::kinematics::tree::Atom::position(), and position_.

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

inlineoverridevirtual

Distance squared to an Atom.

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

References 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

overridevirtual

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

overridevirtual

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 atom_id(), core::kinematics::default_stub, input_stub_atom0(), input_stub_atom1(), input_stub_atom1_id(), input_stub_atom2(), input_stub_atom2_id(), input_stub_atom3(), input_stub_atom3_id(), parent_, position(), and core::kinematics::tree::TR().

Referenced by core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos(), show(), 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

overridevirtual

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< AtomCAP > & path ) const

overrideprotectedvirtual

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

References core::kinematics::tree::Atom::get_self_weak_ptr(), parent(), and parent_.

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

overridevirtual

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 atom_id(), input_stub_atom1(), input_stub_atom1_id(), input_stub_atom2(), input_stub_atom2_id(), input_stub_atom3(), input_stub_atom3_id(), position(), core::kinematics::tree::Atom::stub_atom1(), core::kinematics::tree::Atom::stub_atom2(), core::kinematics::tree::Atom::stub_atom3(), and core::kinematics::tree::TR().

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

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

inlineoverridevirtual

Atom identifier.

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

References atom_id_.

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

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

inlineoverridevirtual

AtomID assignment.

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

References atom_id_.

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

inlineoverridevirtual

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().

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

inlineoverridevirtual

input stub atom0's id

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

References core::kinematics::tree::Atom::id(), and raw_input_stub_atom0().

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

inlineoverridevirtual

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 get_stub().

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

inlineoverridevirtual

input stub atom1's id

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

References core::kinematics::tree::Atom::id(), and raw_input_stub_atom1().

Referenced by get_input_stub(), and get_stub().

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

inlineoverridevirtual

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 get_stub().

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

inlineoverridevirtual

input stub atom2's id

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

References core::kinematics::tree::Atom::id(), and raw_input_stub_atom2().

Referenced by get_input_stub(), and get_stub().

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

inlineoverridevirtual

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::is_collinear(), core::kinematics::tree::Atom::is_jump(), parent(), and previous_sibling().

Referenced by get_input_stub(), get_stub(), and input_stub_atom3_id().

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

inlineoverridevirtual

input stub atom3's id

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

References input_stub_atom3().

Referenced by get_input_stub(), and get_stub().

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

overridevirtual

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_, core::kinematics::tree::Atom::get_self_weak_ptr(), and nonjump_atoms_begin().

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

overridevirtual

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_, core::kinematics::tree::Atom::get_self_weak_ptr(), and nonjump_atoms_begin().

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

inlineoverridevirtual

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

inlineoverridevirtual

number of children atoms

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

References atoms_.

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

overridevirtual

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

inlineoverridevirtual

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 )

overridevirtual

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_, and child().

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

overrideprotectedvirtual

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(), n_nonjump_children(), and raw_get_nonjump_atom().

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

overrideprotectedvirtual

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().

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

inlineoverridevirtual

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

inlineoverridevirtual

Parent atom pointer.

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

References parent_.

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

inlineoverridevirtual

parent assignment

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

References parent_, and raw_parent_.

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

inlineoverridevirtual

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 )

inlineoverridevirtual

Position assignment.

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

References position_.

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

overridevirtual

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_, and child().

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

overridevirtual

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 core::kinematics::tree::Atom::get_self_ptr(), and parent().

Referenced by input_stub_atom3().

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

overridevirtual

the atom-index of this child

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

References atoms_, child(), and core::kinematics::tree::Atom::raw_parent().

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

overridevirtual

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

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

References atoms_, and nonjump_atoms_begin().

Referenced by core::kinematics::tree::JumpAtom::raw_stub_atom2(), and core::kinematics::tree::JumpAtom::raw_stub_atom3().

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

overridevirtual

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

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

References raw_parent().

Referenced by input_stub_atom0_id().

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

overridevirtual

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

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

References raw_parent(), and core::kinematics::tree::Atom::raw_stub_atom1().

Referenced by input_stub_atom1_id().

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

overridevirtual

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

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

References raw_parent(), and core::kinematics::tree::Atom::raw_stub_atom2().

Referenced by input_stub_atom2_id().

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

overridevirtual

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

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

References core::kinematics::tree::Atom::id(), core::kinematics::tree::is_collinear(), core::kinematics::tree::Atom::is_jump(), raw_parent(), raw_previous_sibling(), core::kinematics::tree::Atom::raw_stub_atom1(), core::kinematics::tree::Atom::raw_stub_atom2(), core::kinematics::tree::Atom::raw_stub_atom3(), and core::kinematics::tree::Atom::stub_atom2_id().

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

overridevirtual

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

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

References raw_parent_.

Referenced by raw_input_stub_atom0(), raw_input_stub_atom1(), raw_input_stub_atom2(), raw_input_stub_atom3(), core::kinematics::tree::JumpAtom::raw_stub_atom1(), core::kinematics::tree::JumpAtom::raw_stub_atom2(), core::kinematics::tree::BondedAtom::raw_stub_atom2(), core::kinematics::tree::JumpAtom::raw_stub_atom3(), and core::kinematics::tree::BondedAtom::raw_stub_atom3().

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

overridevirtual

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

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

References atoms_, and child().

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

overridevirtual

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.

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

References raw_parent_, and core::kinematics::tree::Atom::raw_previous_child().

Referenced by raw_input_stub_atom3().

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

overridevirtual

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_, core::kinematics::tree::Atom::get_self_weak_ptr(), and core::kinematics::tree::TR().

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

overridevirtual

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

overridevirtual

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_, core::chemical::element::F, get_input_stub(), get_stub(), parent(), core::kinematics::tree::TR(), x(), y(), and z().

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

inlineoverridevirtual

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

inlineoverridevirtual

stub atom2's id

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

References core::kinematics::tree::Atom::id(), and core::kinematics::tree::Atom::raw_stub_atom2().

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

inlineoverridevirtual

stub atom3's id

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

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

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

overridevirtual

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::raw_stub_atom1(), core::kinematics::tree::JumpAtom::raw_stub_atom2(), core::kinematics::tree::JumpAtom::raw_stub_atom3(), core::kinematics::tree::JumpAtom::stub_atom1(), core::kinematics::tree::JumpAtom::stub_atom2(), and core::kinematics::tree::JumpAtom::stub_atom3().

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

overrideprotectedvirtual

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_, protocols::match::upstream::b, core::kinematics::ResidueCoordinateChangeList::mark_residue_moved(), and position_.

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

overrideprotectedvirtual

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_, and get_stub().

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

overridevirtual

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 )

overridevirtual

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().

Referenced by update_internal_coords().