#include <MinimizerMap.hh>

Public Types
typedef std::list< DOF_NodeOP >	DOF_Nodes

typedef DOF_Nodes::iterator	iterator

typedef DOF_Nodes::const_iterator	const_iterator

typedef id::AtomID	AtomID

typedef id::DOF_ID	DOF_ID

typedef id::DOF_Type	DOF_Type

typedef kinematics::MinimizerMapBase	parent

typedef scoring::DerivVectorPair	DerivVectorPair

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
	MinimizerMap ()

	~MinimizerMap ()

void	setup (pose::Pose &pose, kinematics::MoveMap const &move_map)

virtual void	add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent)
	Allow the AtomTree to communicate to this class that a particular torsion (or angle or distance – a particular DOF) belongs in the minimization task to inform this class the parent DOF for that torsion. More...

virtual void	add_atom (AtomID const &atom_id, DOF_ID const &dof_id)
	Allow the AtomTree to inform this class that a particular atom belongs in the derivative calculation for a certain DOF. That certain DOF must have already been included in the minimization process through a prior invocation of the add_torsion method. More...

const_iterator	begin () const

const_iterator	end () const

iterator	begin ()

iterator	end ()

DOF_Nodes const &	dof_nodes () const

DOF_Nodes &	dof_nodes ()

void	link_torsion_vectors ()
	this will only work if DOF_nodes are sorted! More...

void	zero_torsion_vectors ()

void	reset (pose::Pose const &pose)
	clears old data+dimensions dof_node_pointer using size data from the pose More...

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

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

int	nangles () const

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

Real	torsion_scale_factor (DOF_Node const &tor) const

virtual kinematics::DomainMap const &	domain_map () const

DOF_NodeOP	dof_node_from_id (DOF_ID const &id)
	get a dof_node by its dof_id More...

utility::vector1 < DerivVectorPair > &	atom_derivatives (Size resid)

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

virtual	~MinimizerMapBase ()
	dstor More...

Private Member Functions
void	clear_dof_nodes ()
	deletes and clears dof_nodes_ More...

void	assign_rosetta_torsions (pose::Pose const &pose)

Private Attributes
DOF_Nodes	dof_nodes_
	list of all the moving degrees of freedom More...

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 < DerivVectorPair > >	atom_derivatives_

Member Typedef Documentation

typedef id::AtomID core::optimization::MinimizerMap::AtomID

typedef DOF_Nodes::const_iterator core::optimization::MinimizerMap::const_iterator

typedef scoring::DerivVectorPair core::optimization::MinimizerMap::DerivVectorPair

typedef id::DOF_ID core::optimization::MinimizerMap::DOF_ID

typedef std::list< DOF_NodeOP > core::optimization::MinimizerMap::DOF_Nodes

typedef id::DOF_Type core::optimization::MinimizerMap::DOF_Type

typedef DOF_Nodes::iterator core::optimization::MinimizerMap::iterator

typedef kinematics::MinimizerMapBase core::optimization::MinimizerMap::parent

Constructor & Destructor Documentation

core::optimization::MinimizerMap::MinimizerMap ( )

inline

core::optimization::MinimizerMap::~MinimizerMap ( )

References clear_dof_nodes().

Member Function Documentation

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

virtual

Allow the AtomTree to inform this class that a particular atom belongs in the derivative calculation for a certain DOF. That certain DOF must have already been included in the minimization process through a prior invocation of the add_torsion method.

Implements core::kinematics::MinimizerMapBase.

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

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

virtual

Allow the AtomTree to communicate to this class that a particular torsion (or angle or distance – a particular DOF) belongs in the minimization task to inform this class the parent DOF for that torsion.

Implements core::kinematics::MinimizerMapBase.

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

void core::optimization::MinimizerMap::assign_rosetta_torsions ( pose::Pose const & pose )

private

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 setup().

utility::vector1< DerivVectorPair >& core::optimization::MinimizerMap::atom_derivatives ( Size resid )

inline

References atom_derivatives_.

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

const_iterator core::optimization::MinimizerMap::begin ( ) const

inline