Atom tree multifunction class. More...

#include <SymMinimizerMap.hh>

Inheritance diagram for core::optimization::symmetry::SymMinimizerMap:

Public Types
typedef conformation::symmetry::SymmetryInfoCOP	SymmetryInfoCOP

typedef std::list< DOF_NodeOP >	DOF_Nodes

typedef DOF_Nodes::const_iterator	const_iterator

Public Types inherited from core::kinematics::MinimizerMapBase
typedef id::AtomID	AtomID

typedef id::DOF_ID	DOF_ID

typedef id::DOF_Type	DOF_Type

Public Member Functions
	SymMinimizerMap (pose::Pose const &pose, kinematics::MoveMap const &mm, SymmetryInfoCOP symm_info, bool const new_sym_min=false)

	~SymMinimizerMap () override
	Destructor. More...

void	add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent) override
	The atom tree will report that a new torsion has been identified as free in the traversal of the atom tree. If this is an independent torsion, then the SymMinimizerMap will add a new DOF_Node, but otherwise, will ignore the DOF. The atom tree will traverse through dependent torsions in addition to independent torsions, and it's the job of the SymMinimizerMap to weed out the dependent torsions. More...

void	add_atom (AtomID const &atom_id, DOF_ID const &dof_id) override
	Add an atom to the list of atoms controlled by a given DOF. The SymMinimzierMap will figure out, first, if the dof_id is a dependent or independent dof. If it's a dependent DOF, then it will figure out if the given atom has any interactions with an independent residue. If not, then the atom is ignored. If it does, then the SymMinimizerMap will figure out what independent DOF the given dependent DOF is a a clone of, and add this atom as being controlled by that dependent DOF. More...

kinematics::DomainMap const &	domain_map () const override

void	copy_dofs_from_pose (pose::Pose const &pose, Multivec &dofs) const

void	copy_dofs_to_pose (pose::Pose &pose, Multivec const &dofs) const

DOF_NodeOP	dof_node_from_id (DOF_ID const &id) const

Size	nangles () const

void	zero_torsion_vectors ()

void	link_torsion_vectors ()

Real	torsion_scale_factor (DOF_Node const &dof_node) const

void	reset_jump_rb_deltas (pose::Pose &pose, Multivec &dofs) const

const_iterator	begin () const
	begin iterator for the independent dofs More...

const_iterator	end () const
	End iterator for the independent dofs. More...

const_iterator	dependent_begin () const

const_iterator	dependent_end () const

DOF_Nodes const &	dof_nodes () const

utility::vector1< scoring::DerivVectorPair > &	atom_derivatives (Size resid)
	Retrieve the per-atom derivatives that are accumulated in to. More...

bool	new_sym_min () const

id::DOF_ID	asymmetric_dof (DOF_ID const &cloned_dof) const
	Convert a cloned dof into its equivalent in the asymmetric unit. More...

Public Member Functions inherited from core::kinematics::MinimizerMapBase
	MinimizerMapBase ()
	default ctor; noop More...

	~MinimizerMapBase () override
	dstor More...

Private Member Functions
void	add_new_dof_node (DOF_ID const &new_torsion, DOF_ID const &parent, bool dependent)
	Non-virtual method – not invoked directly by the atom tree. More...

void	assign_rosetta_torsions ()

Private Attributes
pose::Pose const &	pose_

SymmetryInfoCOP	symm_info_

utility::vector1< bool >	res_interacts_with_asymmetric_unit_

DOF_Nodes	dof_nodes_

DOF_Nodes	dependent_dof_nodes_

Size	n_independent_dof_nodes_

id::DOF_ID_Map< DOF_NodeOP >	dof_node_pointer_
	pointer from DOF_ID to the corresponding DOF_NodeOP More...

kinematics::DomainMap	domain_map_

utility::vector1< utility::vector1< scoring::DerivVectorPair > >	atom_derivatives_

id::DOF_ID_Map< id::TorsionID >	dof_id2torsion_id_
	adding this guy so we can tell more accurately which dof's are dependent/independent More...

bool	new_sym_min_

Detailed Description

Atom tree multifunction class.

Member Typedef Documentation

◆ const_iterator

typedef DOF_Nodes::const_iterator core::optimization::symmetry::SymMinimizerMap::const_iterator

◆ DOF_Nodes

typedef std::list< DOF_NodeOP > core::optimization::symmetry::SymMinimizerMap::DOF_Nodes

◆ SymmetryInfoCOP

typedef conformation::symmetry::SymmetryInfoCOP core::optimization::symmetry::SymMinimizerMap::SymmetryInfoCOP

Constructor & Destructor Documentation

◆ SymMinimizerMap()

core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap	(	pose::Pose const &	pose,
		kinematics::MoveMap const &	mm,
		SymmetryInfoCOP	symm_info,
		bool const	new_sym_min = `false`
	)

◆ ~SymMinimizerMap()

core::optimization::symmetry::SymMinimizerMap::~SymMinimizerMap ( )

overridedefault

Destructor.

Member Function Documentation

◆ add_atom()

void core::optimization::symmetry::SymMinimizerMap::add_atom	(	AtomID const &	atom_id,
		DOF_ID const &	dof_id
	)

overridevirtual

Add an atom to the list of atoms controlled by a given DOF. The SymMinimzierMap will figure out, first, if the dof_id is a dependent or independent dof. If it's a dependent DOF, then it will figure out if the given atom has any interactions with an independent residue. If not, then the atom is ignored. If it does, then the SymMinimizerMap will figure out what independent DOF the given dependent DOF is a a clone of, and add this atom as being controlled by that dependent DOF.

Implements core::kinematics::MinimizerMapBase.

References dof_node_pointer_, and core::id::DOF_ID::valid().

◆ add_new_dof_node()

void core::optimization::symmetry::SymMinimizerMap::add_new_dof_node	(	DOF_ID const &	new_torsion,
		DOF_ID const &	parent,
		bool	dependent
	)

private

Non-virtual method – not invoked directly by the atom tree.

References dependent_dof_nodes_, dof_node_pointer_, dof_nodes_, n_independent_dof_nodes_, and new_sym_min_.

Referenced by add_torsion().

◆ add_torsion()

void core::optimization::symmetry::SymMinimizerMap::add_torsion	(	DOF_ID const &	new_torsion,
		DOF_ID const &	parent
	)

overridevirtual

The atom tree will report that a new torsion has been identified as free in the traversal of the atom tree. If this is an independent torsion, then the SymMinimizerMap will add a new DOF_Node, but otherwise, will ignore the DOF. The atom tree will traverse through dependent torsions in addition to independent torsions, and it's the job of the SymMinimizerMap to weed out the dependent torsions.

Implements core::kinematics::MinimizerMapBase.

References add_new_dof_node(), core::id::DOF_ID::BOGUS_DOF_ID(), core::pose::Pose::conformation(), dof_id2torsion_id_, core::conformation::symmetry::is_symmetric(), new_sym_min_, pose_, core::id::RB1, symm_info_, core::id::DOF_ID::type(), and core::id::TorsionID::valid().

◆ assign_rosetta_torsions()

void core::optimization::symmetry::SymMinimizerMap::assign_rosetta_torsions ( )

private

References core::optimization::DOF_Node::dof_id(), dof_id2torsion_id_, dof_nodes_, core::id::PHI, core::optimization::DOF_Node::torsion_id(), and core::optimization::DOF_Node::type().

Referenced by SymMinimizerMap().

◆ asymmetric_dof()

id::DOF_ID core::optimization::symmetry::SymMinimizerMap::asymmetric_dof ( DOF_ID const & cloned_dof ) const

Convert a cloned dof into its equivalent in the asymmetric unit.

use the bb_follows mapping to find the residue in the asymmetric unit that this cloned atom corresponds to

References core::id::DOF_ID::atomno(), core::pose::Pose::conformation(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::kinematics::FoldTree::jump_edge(), pose_, core::id::RB1, core::id::RB6, core::id::DOF_ID::rsd(), core::kinematics::Edge::stop(), symm_info_, and core::id::DOF_ID::type().

Referenced by core::optimization::symmetry::atom_tree_dfunc().

◆ atom_derivatives()

utility::vector1< scoring::DerivVectorPair >& core::optimization::symmetry::SymMinimizerMap::atom_derivatives ( Size resid )

inline

Retrieve the per-atom derivatives that are accumulated in to.

References atom_derivatives_.

Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv().

◆ begin()

const_iterator core::optimization::symmetry::SymMinimizerMap::begin ( ) const

inline

begin iterator for the independent dofs

Allow read/write access to the DOF_Nodes themselves, but do not allow anyone to change the DOF_Nodes list. Elements cannot be dropped from the list, nor should the list be clearable. Of course: if you have a const iterator to a list element containing a pointer, then it is entirely possible to perform non-const operations on the thing being pointed at. HOWEVER, neither the pointer nor the list element can be changed.

References dof_nodes_.

Referenced by core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), and core::optimization::symmetry::numerical_derivative_check().