Atom tree multifunction class. More...

#include <SymMinimizerMap.hh>

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

Collaboration 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)

virtual	~SymMinimizerMap ()
	Destructor. More...

virtual void	add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent)
	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...

virtual void	add_atom (AtomID const &atom_id, DOF_ID const &dof_id)
	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...

virtual kinematics::DomainMap const &	domain_map () const

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...

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

virtual	~MinimizerMapBase ()
	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...

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

void	assign_rosetta_torsions (pose::Pose const &pose)

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_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_

Detailed Description

Atom tree multifunction class.

Definition at line 52 of file SymMinimizerMap.hh.

Member Typedef Documentation

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

Definition at line 56 of file SymMinimizerMap.hh.

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

Definition at line 55 of file SymMinimizerMap.hh.

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

Definition at line 54 of file SymMinimizerMap.hh.

Constructor & Destructor Documentation

core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap	(	pose::Pose const &	pose,
		kinematics::MoveMap const &	mm,
		SymmetryInfoCOP	symm_info
	)

Definition at line 59 of file SymMinimizerMap.cc.

References assign_rosetta_torsions(), atom_derivatives_, core::conformation::Conformation::atom_tree(), core::pose::Pose::atom_tree(), core::id::BOGUS_DOF_ID, core::pose::Pose::conformation(), core::graph::Node::const_edge_list_begin(), core::graph::Node::const_edge_list_end(), dof_node_pointer_, core::optimization::symmetry::DOF_Node_sorter(), dof_nodes_, domain_map_, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::graph::Graph::get_node(), core::pose::initialize_atomid_map(), core::pose::initialize_dof_id_map(), core::conformation::Residue::natoms(), res_interacts_with_asymmetric_unit_, core::pose::Pose::residue(), core::kinematics::AtomTree::root(), core::pose::setup_dof_mask_from_move_map(), symm_info_, core::pose::Pose::total_residue(), and core::kinematics::AtomTree::update_domain_map().

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

virtual

Destructor.

Definition at line 130 of file SymMinimizerMap.cc.

Member Function Documentation

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

virtual

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.

Definition at line 160 of file SymMinimizerMap.cc.

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

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.

Definition at line 322 of file SymMinimizerMap.cc.

References dependent_dof_nodes_, dof_node_pointer_, dof_nodes_, n_dof_nodes_, n_independent_dof_nodes_, core::id::DOF_ID::rsd(), symm_info_, and core::id::DOF_ID::valid().

Referenced by add_torsion().

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

virtual

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.

Definition at line 133 of file SymMinimizerMap.cc.

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

void core::optimization::symmetry::SymMinimizerMap::assign_rosetta_torsions ( pose::Pose const & pose)

private

Definition at line 372 of file SymMinimizerMap.cc.

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

Referenced by SymMinimizerMap().

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

private

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

Definition at line 353 of file SymMinimizerMap.cc.

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::DOF_ID::rsd(), core::kinematics::Edge::stop(), symm_info_, and core::id::DOF_ID::type().

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

inline

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

Definition at line 177 of file SymMinimizerMap.hh.

References atom_derivatives_.

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

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.

Definition at line 141 of file SymMinimizerMap.hh.

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().