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core::optimization::MinimizerMap Class Reference

#include <MinimizerMap.hh>

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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_
 

Detailed Description

Definition at line 75 of file MinimizerMap.hh.

Member Typedef Documentation

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

Definition at line 82 of file MinimizerMap.hh.

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

Definition at line 80 of file MinimizerMap.hh.

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

Definition at line 87 of file MinimizerMap.hh.

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

Definition at line 83 of file MinimizerMap.hh.

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

Definition at line 78 of file MinimizerMap.hh.

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

Definition at line 84 of file MinimizerMap.hh.

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

Definition at line 79 of file MinimizerMap.hh.

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

Definition at line 85 of file MinimizerMap.hh.

Constructor & Destructor Documentation

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

Definition at line 92 of file MinimizerMap.hh.

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

Definition at line 62 of file MinimizerMap.cc.

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.

Definition at line 135 of file MinimizerMap.cc.

References dof_node_pointer_, 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.

Definition at line 106 of file MinimizerMap.cc.

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

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

Definition at line 332 of file MinimizerMap.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 setup().

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

Definition at line 237 of file MinimizerMap.hh.

References atom_derivatives_.

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

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

Definition at line 126 of file MinimizerMap.hh.

References dof_nodes_.

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::atom_tree_get_atompairE_deriv(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), and core::optimization::numerical_derivative_check().

iterator core::optimization::MinimizerMap::begin ( )
inline

Definition at line 140 of file MinimizerMap.hh.

References dof_nodes_.

void core::optimization::MinimizerMap::clear_dof_nodes ( )
private

deletes and clears dof_nodes_

Definition at line 190 of file MinimizerMap.cc.

References dof_node_pointer_, and dof_nodes_.

Referenced by reset(), and ~MinimizerMap().

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

Definition at line 219 of file MinimizerMap.cc.

References core::pose::Pose::dof(), core::optimization::DOF_Node::dof_id(), dof_nodes_, and torsion_scale_factor().

Referenced by core::optimization::AtomTreeMinimizer::run().

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

Definition at line 236 of file MinimizerMap.cc.

References core::optimization::DOF_Node::dof_id(), dof_nodes_, core::pose::Pose::set_dof(), and torsion_scale_factor().

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::AtomTreeMultifunc::operator()(), and core::optimization::SingleResidueMultifunc::operator()().

DOF_NodeOP core::optimization::MinimizerMap::dof_node_from_id ( DOF_ID const &  id)
inline

get a dof_node by its dof_id

Definition at line 223 of file MinimizerMap.hh.

References dof_node_pointer_.

DOF_Nodes const& core::optimization::MinimizerMap::dof_nodes ( ) const
inline

Definition at line 154 of file MinimizerMap.hh.

References dof_nodes_.

DOF_Nodes& core::optimization::MinimizerMap::dof_nodes ( )
inline

Definition at line 161 of file MinimizerMap.hh.

References dof_nodes_.

virtual kinematics::DomainMap const& core::optimization::MinimizerMap::domain_map ( ) const
inlinevirtual

Implements core::kinematics::MinimizerMapBase.

Definition at line 216 of file MinimizerMap.hh.

References domain_map_.

Referenced by core::optimization::atom_tree_get_atompairE_deriv(), protocols::cartesian::MolecularDynamics::createCartesianDerivatives(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), protocols::cartesian::MolecularDynamics::MolecularDynamics(), and core::optimization::AtomTreeMinimizer::run().

const_iterator core::optimization::MinimizerMap::end ( ) const
inline

Definition at line 133 of file MinimizerMap.hh.

References dof_nodes_.

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::atom_tree_get_atompairE_deriv(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), and core::optimization::numerical_derivative_check().

iterator core::optimization::MinimizerMap::end ( )
inline

Definition at line 147 of file MinimizerMap.hh.

References dof_nodes_.

void core::optimization::MinimizerMap::link_torsion_vectors ( )

this will only work if DOF_nodes are sorted!

Definition at line 72 of file MinimizerMap.cc.

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

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

int core::optimization::MinimizerMap::nangles ( ) const
inline

Definition at line 195 of file MinimizerMap.hh.

References dof_nodes_.

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::numerical_derivative_check(), and core::optimization::AtomTreeMinimizer::run().

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

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

Definition at line 204 of file MinimizerMap.cc.

References atom_derivatives_, clear_dof_nodes(), dof_node_pointer_, 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

Definition at line 253 of file MinimizerMap.cc.

References core::optimization::DOF_Node::atom_id(), dof_nodes_, core::id::DOF_type_is_rb(), core::kinematics::Jump::fold_in_rb_deltas(), core::pose::Pose::jump(), core::pose::Pose::set_jump(), and core::optimization::DOF_Node::type().

Referenced by core::optimization::AtomTreeMinimizer::run().

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

Definition at line 283 of file MinimizerMap.cc.

References assign_rosetta_torsions(), core::conformation::Conformation::atom_tree(), core::pose::Pose::atom_tree(), core::id::BOGUS_DOF_ID, core::pose::Pose::conformation(), core::optimization::DOF_Node_sorter(), dof_nodes_, domain_map_, core::pose::initialize_atomid_map(), reset(), core::kinematics::AtomTree::root(), core::pose::setup_dof_mask_from_move_map(), core::pose::Pose::total_residue(), and core::kinematics::AtomTree::update_domain_map().

Referenced by protocols::cartesian::MolecularDynamics::MolecularDynamics(), and core::optimization::AtomTreeMinimizer::run().

Real core::optimization::MinimizerMap::torsion_scale_factor ( DOF_Node const &  tor) const

Definition at line 158 of file MinimizerMap.cc.

References core::id::D, core::id::PHI, core::id::RB1, core::id::RB2, core::id::RB3, core::id::RB4, core::id::RB5, core::id::RB6, core::id::THETA, and core::optimization::DOF_Node::type().

Referenced by core::optimization::atom_tree_dfunc(), copy_dofs_from_pose(), and copy_dofs_to_pose().

void core::optimization::MinimizerMap::zero_torsion_vectors ( )

Definition at line 86 of file MinimizerMap.cc.

References atom_derivatives_, and dof_nodes_.

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

Member Data Documentation

utility::vector1< utility::vector1< DerivVectorPair > > core::optimization::MinimizerMap::atom_derivatives_
private

Definition at line 261 of file MinimizerMap.hh.

Referenced by atom_derivatives(), reset(), and zero_torsion_vectors().

id::DOF_ID_Map< DOF_NodeOP > core::optimization::MinimizerMap::dof_node_pointer_
private

pointer from DOF_ID to the corresponding DOF_NodeOP

Definition at line 256 of file MinimizerMap.hh.

Referenced by add_atom(), add_torsion(), clear_dof_nodes(), dof_node_from_id(), and reset().

DOF_Nodes core::optimization::MinimizerMap::dof_nodes_
private

list of all the moving degrees of freedom

Definition at line 253 of file MinimizerMap.hh.

Referenced by add_torsion(), assign_rosetta_torsions(), begin(), clear_dof_nodes(), copy_dofs_from_pose(), copy_dofs_to_pose(), dof_nodes(), end(), link_torsion_vectors(), nangles(), reset_jump_rb_deltas(), setup(), and zero_torsion_vectors().

kinematics::DomainMap core::optimization::MinimizerMap::domain_map_
private

Definition at line 259 of file MinimizerMap.hh.

Referenced by domain_map(), and setup().

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