an atom which are bonded to its parent, derived from Atom_ More...

#include <BondedAtom.hh>

Inheritance diagram for core::kinematics::tree::BondedAtom:

Public Member Functions
	BondedAtom ()

void	dfs (AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const override
	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. Will recurse on younger siblings if a phi on this atom has changed. More...

void	update_xyz_coords () override
	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...

void	update_xyz_coords (Stub &stub) override
	update cartesian coordinates for this atom from its input stub and internal cooridnates More...

void	update_internal_coords (std::deque< std::pair< Atom , core::kinematics::Stub > > childlist, std::deque< core::kinematics::Stub > stublist, Stub &stub) override
	update internal coordinates for this atom from its xyz position and input stub More...

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

void	set_dof (DOF_Type const type, core::Real const value) override
	set degrees of freedom (internal coordinates) More...

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

core::Real	dof (DOF_Type const type) const override
	get degrees of freedom More...

Jump const &	jump () const override
	abort if attempt to get jump for a bonded atom More...

void	jump (Jump const &) override
	abort if attempt to set jump for a bonded atom More...

void	jump (Jump const &, AtomDOFChangeSet &) override
	abort if attempt to set jump for a bonded atom More...

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

void	setup_min_map (DOF_ID &last_torsion, DOF_ID_Mask const &allow_move, MinimizerMapBase &min_map) const override
	for minimizing,add DOF(PHI,THETA,D) for a BondedAtom into the MinimizerMap More...

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

bool	is_jump () const override
	bonded atom is a jump? of course not!!! More...

bool	keep_1st_child_pos () const override
	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...

bool	keep_dof_fixed (DOF_Type const type) const override
	whether a DOF for this atom should be fixed? More...

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

AtomCOP	stub_atom1 () const override
	stub_atom1 of a bonded atom More...

AtomCOP	stub_atom2 () const override
	stub_atom2 of a bonded atom More...

AtomCOP	stub_atom3 () const override
	stub_atom3 of a bonded atom More...

void	steal_inversion (AtomOP steal_from) override

bool	get_inversion ()

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

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

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

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

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...

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 ()

Private Types
typedef Atom_	Super

Private Attributes
Real	phi_
	DOF properties of a bonded atom. More...

Real	theta_

Real	d_

bool	dof_change_propagates_to_younger_siblings_
	Track whether a dof change from this node (since the last update_xyz) induces a coordinate change for this node's younger siblings. More...

bool	inverted_frame_
	Stores whether or not this atom is folding in an inverted coordinate system. 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...

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 inherited from core::kinematics::tree::Atom_
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...

Detailed Description

an atom which are bonded to its parent, derived from Atom_

See AtomTree overview and concepts for details.

Member Typedef Documentation

typedef Atom_ core::kinematics::tree::BondedAtom::Super

private

Constructor & Destructor Documentation

core::kinematics::tree::BondedAtom::BondedAtom ( )

inline

Referenced by clone().

Member Function Documentation

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

overridevirtual

copy this atom

Note: This will recursively clone all this atom's offspring atoms; Assumes that atom_pointer has already been properly dimensioned

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

References core::pose::motif::a(), core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), BondedAtom(), core::id::D, dof(), dof_change_propagates_to_younger_siblings_, core::kinematics::tree::Atom_::id(), inverted_frame_, core::chemical::rings::PHI, core::kinematics::tree::Atom_::position(), and core::chemical::rings::THETA.

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

overridevirtual

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_::atom_id(), core::kinematics::tree::Atom::atom_id(), core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), core::kinematics::tree::Atom::child(), core::id::D, d_, core::kinematics::tree::Atom::dof(), core::kinematics::tree::Atom_::n_children(), core::kinematics::tree::Atom::n_children(), core::kinematics::tree::Atom_::operator=(), core::chemical::rings::PHI, phi_, core::chemical::rings::THETA, and theta_.

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

overridevirtual

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. Will recurse on younger siblings if a phi on this atom has changed.

Invokes Atom_ dfs function before, optionally recursing to younger siblings should those younger siblings be effected by a DOF change on this node (e.g. phi_ change).

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

References core::kinematics::tree::Atom_::dfs(), dof_change_propagates_to_younger_siblings_, core::kinematics::tree::Atom_::dof_refold_index(), core::kinematics::tree::Atom_::parent(), and core::kinematics::tree::Atom_::parent_.

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

overridevirtual

get degrees of freedom

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

References core::id::D, d_, core::chemical::rings::PHI, phi_, core::chemical::rings::THETA, and theta_.

Referenced by clone().

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

overridevirtual

get rotation axis and end_pos for a BondedAtom.

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

consider simple case like, A->B->C->D and we want to know the change of D position with respect to the rotation along B->C bond( dr/dphi). In this case, Eab is the unit vector along B->C, end_positon is C, and dr/dphi is given as Eab x (D-C).
For B->C bond rotation is the DOF(PHI) of Atom D, so end_pos is input_stub.v which is the position of Atom C and axis is input_stub.M.col(1) which is the unit vector pointing from B to C.
For DOF(THETA) of Atom D, it is a rotation around a unit vector (ending at C) which is perpendicular to B->C->D plane. So the end_pos is the position of Atom C and the axix is the my_stub.M.col(3). For DOF(D) of Atom D, it is a translation along C->D axis and that is my_stub.M.col(1)

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

References core::id::D, core::kinematics::tree::Atom_::get_input_stub(), core::kinematics::tree::Atom_::get_stub(), inverted_frame_, core::kinematics::Stub::M, core::chemical::rings::PHI, core::chemical::rings::THETA, and core::kinematics::Stub::v.

bool core::kinematics::tree::BondedAtom::get_inversion ( )

inline

References inverted_frame_.

Referenced by steal_inversion().

bool core::kinematics::tree::BondedAtom::is_jump ( ) const

inlineoverridevirtual

bonded atom is a jump? of course not!!!

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

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

inlineoverridevirtual

abort if attempt to get jump for a bonded atom

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

References core::kinematics::tree::Atom_::abort_bad_call(), and core::kinematics::tree::BOGUS_JUMP.

void core::kinematics::tree::BondedAtom::jump ( Jump const & )

inlineoverridevirtual

abort if attempt to set jump for a bonded atom

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

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

void core::kinematics::tree::BondedAtom::jump	(	Jump const &	,
		AtomDOFChangeSet &
	)

inlineoverridevirtual

abort if attempt to set jump for a bonded atom

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

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

bool core::kinematics::tree::BondedAtom::keep_1st_child_pos ( ) const

inlineoverridevirtual

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::BondedAtom::keep_dof_fixed ( DOF_Type const type ) const

overridevirtual

whether a DOF for this atom should be fixed?

bond distance D can always be flexible
bond angle THETA is not meaningful if it is defined by A-B-A in some special cases, for example N-CA-C in which CA is a jump atom, then THETA of the N atom is defined by N-CA-N.
torsion angle PHI is not meaningful if it is defined by A-B-A-D or A-B-D-A or A-D-B-A in some special cases.

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

References core::id::D, core::kinematics::tree::Atom_::id(), core::kinematics::tree::Atom_::parent(), core::kinematics::tree::Atom_::parent_, core::chemical::rings::PHI, core::chemical::rings::THETA, and core::kinematics::tree::TR().

Referenced by setup_min_map(), update_internal_coords(), and update_xyz_coords().

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

overridevirtual

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

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

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

overridevirtual

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

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

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

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

overridevirtual

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

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

References core::kinematics::tree::is_collinear(), core::kinematics::tree::Atom::is_jump(), core::kinematics::tree::Atom_::raw_parent(), core::kinematics::tree::Atom::raw_stub_atom2(), core::kinematics::tree::Atom::raw_stub_atom3(), and core::kinematics::tree::Atom::stub_defined().

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

overridevirtual

set degrees of freedom (internal coordinates)

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

References core::id::D, d_, core::id::PHI, phi_, core::id::THETA, and theta_.

Referenced by set_dof().

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

overridevirtual

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

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

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

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

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

overridevirtual

for minimizing,add DOF(PHI,THETA,D) for a BondedAtom into the MinimizerMap

last torsion is the torsion( Phi for BondedAtom and RB for JumpAtom) of the parent atom or previous bonded sibling. Since BondedAtom's PHI is dependent on its previous sibling BondedAtom,this may modify last_torsion, if our bond torsion angle is changing and this atom has other sibling atoms after itself. 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::D, keep_dof_fixed(), core::chemical::rings::PHI, core::id::phi_torsion(), and core::chemical::rings::THETA.

void core::kinematics::tree::BondedAtom::steal_inversion ( AtomOP steal_from )

overridevirtual

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

References get_inversion(), and inverted_frame_.

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

inlineoverridevirtual

stub_atom1 of a bonded atom

it is itself

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

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

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

inlineoverridevirtual

stub_atom2 of a bonded atom

it is its parent

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

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

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

inlineoverridevirtual

stub_atom3 of a bonded atom

if this atom's parent is a bonded_atom it is this atom's parent's parent.
if this atom's parent is a jump atom, it is this atom's first non-jump sibling or its second non-jump sibling (if it itself is the first) or its first non-jump child (if it does not have any sibling)

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

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

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

overridevirtual

update internal coordinates for this atom from its xyz position and input stub

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

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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

References core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), d_, inverted_frame_, core::kinematics::Stub::is_orthogonal(), keep_dof_fixed(), core::kinematics::Stub::M, phi_, core::kinematics::tree::Atom_::position(), core::chemical::rings::THETA, theta_, core::id::to_string(), core::kinematics::Stub::v, core::kinematics::tree::Atom_::x(), core::kinematics::tree::Atom_::y(), and core::kinematics::tree::Atom_::z().

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

overridevirtual

update the stub without actually updating coordinates

pass out the stub we would pass out if we were actually updating coords or DOFs, which is rotate the stub around its x axis by phi_.

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

References core::kinematics::Stub::M, and phi_.

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

overridevirtual

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 dof_change_propagates_to_younger_siblings_, core::kinematics::tree::Atom_::get_input_stub(), inverted_frame_, core::kinematics::Stub::M, core::kinematics::Jump::mirror_z_transform, core::kinematics::tree::Atom_::parent(), and core::kinematics::tree::Atom_::parent_.

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

overridevirtual

update cartesian coordinates for this atom from its input stub and internal cooridnates

starting from the input stub, calculate xyz position of this atom from its internal coordinates d_, theta_ and phi_. If recursive is true, obtain the new stub centered at this atom and pass the new stub to all its children atoms to update their xyz positions recursively.

Note: stub passed in is modified by rotating phi_ around x in the stub frame

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

References core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), d_, dof_change_propagates_to_younger_siblings_, inverted_frame_, core::kinematics::Stub::is_orthogonal(), keep_dof_fixed(), core::kinematics::Stub::M, core::kinematics::tree::Atom_::note_xyz_uptodate(), phi_, core::kinematics::tree::Atom_::position(), core::chemical::rings::THETA, theta_, and core::kinematics::Stub::v.

Member Data Documentation

Real core::kinematics::tree::BondedAtom::d_

private

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

bool core::kinematics::tree::BondedAtom::dof_change_propagates_to_younger_siblings_

private

Track whether a dof change from this node (since the last update_xyz) induces a coordinate change for this node's younger siblings.

Referenced by clone(), dfs(), set_dof(), and update_xyz_coords().

bool core::kinematics::tree::BondedAtom::inverted_frame_

private

Stores whether or not this atom is folding in an inverted coordinate system.

Referenced by clone(), get_dof_axis_and_end_pos(), get_inversion(), steal_inversion(), update_internal_coords(), and update_xyz_coords().

Real core::kinematics::tree::BondedAtom::phi_

private

DOF properties of a bonded atom.

a bonded atom is an atom who connects to its parent by a "bond" (covalent or virtual) and therefore its position is defined by three internal coordinates: d_, theta_, and phi_.
d_ is the bond distance between this atom and its parent.
theta_ is the bond angle between this atom(A), its parent's stub_atom1(B) and its parent's stub_atom2(C), i.e., angle in between B->A ^ C->B.
phi_ is either the torsion angle defined by A, B, C and D (C's parents), or the improper angle defined by A, B, C and D (B's child and A's previous sibling).

Referenced by copy_coords(), dof(), set_dof(), update_internal_coords(), update_stub(), and update_xyz_coords().

Real core::kinematics::tree::BondedAtom::theta_

private

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

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

src/core/kinematics/tree/BondedAtom.hh
src/core/kinematics/tree/BondedAtom.cc

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