Rosetta 3.4
Public Types | Public Member Functions
core::optimization::MinimizerMap Class Reference

#include <MinimizerMap.hh>

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List of all members.

Public Types

typedef std::list< DOF_NodeOPDOF_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 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.
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.
const_iterator begin () const
const_iterator end () const
iterator begin ()
iterator end ()
DOF_Nodes const & dof_nodes () const
DOF_Nodesdof_nodes ()
void link_torsion_vectors ()
 this will only work if DOF_nodes are sorted!
void zero_torsion_vectors ()
void reset (pose::Pose const &pose)
 clears old data+dimensions dof_node_pointer using size data from the pose
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
utility::vector1
< DerivVectorPair > & 
atom_derivatives (Size resid)

Member Typedef Documentation

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

Constructor & Destructor Documentation

core::optimization::MinimizerMap::MinimizerMap ( ) [inline]
core::optimization::MinimizerMap::~MinimizerMap ( )

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 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 core::id::DOF_ID::valid().

utility::vector1< DerivVectorPair >& core::optimization::MinimizerMap::atom_derivatives ( Size  resid) [inline]
const_iterator core::optimization::MinimizerMap::begin ( ) const [inline]
iterator core::optimization::MinimizerMap::begin ( ) [inline]
void core::optimization::MinimizerMap::copy_dofs_from_pose ( pose::Pose const &  pose,
Multivec dofs 
) const
void core::optimization::MinimizerMap::copy_dofs_to_pose ( pose::Pose pose,
Multivec const &  dofs 
) const
DOF_NodeOP core::optimization::MinimizerMap::dof_node_from_id ( DOF_ID const &  id) [inline]

get a dof_node by its dof_id

DOF_Nodes const& core::optimization::MinimizerMap::dof_nodes ( ) const [inline]
DOF_Nodes& core::optimization::MinimizerMap::dof_nodes ( ) [inline]
virtual kinematics::DomainMap const& core::optimization::MinimizerMap::domain_map ( ) const [inline, virtual]
const_iterator core::optimization::MinimizerMap::end ( ) const [inline]
iterator core::optimization::MinimizerMap::end ( ) [inline]
void core::optimization::MinimizerMap::link_torsion_vectors ( )

this will only work if DOF_nodes are sorted!

References core::optimization::DOF_Node::depth(), and core::optimization::DOF_Node::link_vectors().

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

int core::optimization::MinimizerMap::nangles ( ) const [inline]
void core::optimization::MinimizerMap::reset ( pose::Pose const &  pose)

clears old data+dimensions dof_node_pointer using size data from the pose

References core::pose::initialize_dof_id_map(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by setup().

void core::optimization::MinimizerMap::reset_jump_rb_deltas ( pose::Pose pose,
Multivec dofs 
) const
void core::optimization::MinimizerMap::setup ( pose::Pose pose,
kinematics::MoveMap const &  move_map 
)
Real core::optimization::MinimizerMap::torsion_scale_factor ( DOF_Node const &  tor) const
void core::optimization::MinimizerMap::zero_torsion_vectors ( )

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