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core::scoring::MinimizationNode Class Reference

#include <MinimizationGraph.hh>

Inheritance diagram for core::scoring::MinimizationNode:
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Collaboration diagram for core::scoring::MinimizationNode:
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Public Types

typedef graph::Node parent
 
typedef utility::vector1
< OneBodyEnergyCOP
OneBodyEnergies
 
typedef
OneBodyEnergies::const_iterator 
OneBodyEnergiesIterator
 
typedef utility::vector1
< TwoBodyEnergyCOP
TwoBodyEnergies
 
typedef
TwoBodyEnergies::const_iterator 
TwoBodyEnergiesIterator
 
typedef conformation::Residue Residue
 
typedef pose::Pose Pose
 
- Public Types inherited from core::graph::Node
typedef EdgeListIterator EdgeListIter
 
typedef EdgeListConstIterator EdgeListConstIter
 

Public Member Functions

 MinimizationNode (graph::Graph *owner, Size index)
 
virtual ~MinimizationNode ()
 
virtual void copy_from (parent const *source)
 copy mmember data from source node More...
 
virtual void print () const
 send summaray data about this node to the screen More...
 
virtual Size count_static_memory () const
 memory accounting scheme More...
 
virtual Size count_dynamic_memory () const
 memory accounting scheme More...
 
ResSingleMinimizationData const & res_min_data () const
 
ResSingleMinimizationDatares_min_data ()
 
bool add_onebody_enmeth (OneBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, int domain_map_color)
 
bool add_twobody_enmeth (TwoBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, EnergyMap const &weights, int domain_map_color)
 
void setup_for_minimizing (Residue const &rsd, Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map)
 
void setup_for_scoring (Residue const &rsd, Pose const &pose, ScoreFunction const &sfxn)
 
void setup_for_derivatives (Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn)
 
void update_active_enmeths_for_residue (Residue const &rsd, pose::Pose const &pose, EnergyMap const &weights, int domain_map_color)
 
Real weight () const
 
void weight (Real setting)
 
OneBodyEnergiesIterator active_1benmeths_begin () const
 
OneBodyEnergiesIterator active_1benmeths_end () const
 
OneBodyEnergiesIterator active_1benmeths_std_begin () const
 
OneBodyEnergiesIterator active_1benmeths_std_end () const
 
OneBodyEnergiesIterator active_1benmeths_ext_begin () const
 
OneBodyEnergiesIterator active_1benmeths_ext_end () const
 
OneBodyEnergiesIterator dof_deriv_1benmeths_begin () const
 
OneBodyEnergiesIterator dof_deriv_1benmeths_end () const
 
OneBodyEnergiesIterator sfs_req_1benmeths_begin () const
 
OneBodyEnergiesIterator sfs_req_1benmeths_end () const
 
OneBodyEnergiesIterator sfd_req_1benmeths_begin () const
 
OneBodyEnergiesIterator sfd_req_1benmeths_end () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_begin () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_end () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_std_begin () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_std_end () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_ext_begin () const
 
TwoBodyEnergiesIterator active_intrares2benmeths_ext_end () const
 
TwoBodyEnergiesIterator dof_deriv_2benmeths_begin () const
 
TwoBodyEnergiesIterator dof_deriv_2benmeths_end () const
 
TwoBodyEnergiesIterator sfs_req_2benmeths_begin () const
 
TwoBodyEnergiesIterator sfs_req_2benmeths_end () const
 
TwoBodyEnergiesIterator sfd_req_2benmeths_begin () const
 
TwoBodyEnergiesIterator sfd_req_2benmeths_end () const
 
- Public Member Functions inherited from core::graph::Node
virtual ~Node ()
 virtual destructor More...
 
 Node (Graph *, platform::Size node_id)
 Main constructor, no default constructor nor copy constructor. More...
 
void add_edge (Edge *edge_ptr, EdgeListIter &)
 adds edge pointer to edge list; returns an iterator to the new list element More...
 
void drop_edge (EdgeListIter edge_iterator)
 removes an edge iterator from the node's edge list. Only called by Edge class. More...
 
void drop_all_edges ()
 deletes all edges incident upon this node More...
 
void set_num_neighbors_counting_self_static (platform::Size neighbor)
 
Edge const * find_edge (platform::Size other_node_index) const
 a "slow" (linear) search for an edge. More...
 
Edgefind_edge (platform::Size other_node_index)
 non-const edge finding method; changes no data, but returns a non-const pointer More...
 
EdgeListIter edge_list_begin ()
 returns a non-const iterator to the beginning of its edge list More...
 
EdgeListConstIter const_edge_list_begin () const
 returns a const iterator to the beginning of its edge list More...
 
EdgeListIter edge_list_end ()
 returns a non-const iterator to the end of its edge list More...
 
EdgeListConstIter const_edge_list_end () const
 returns a const iterator to the end of its edge list More...
 
EdgeListIter lower_edge_list_begin ()
 returns a non-const iterator to the beginning of its lower-edge list More...
 
EdgeListConstIter const_lower_edge_list_begin () const
 returns a const iterator to the beginning of its lower-edge list More...
 
EdgeListIter lower_edge_list_end ()
 returns a non-const iterator to the end of its lower-edge list More...
 
EdgeListConstIter const_lower_edge_list_end () const
 returns a const iterator to the end of its lower-edge list More...
 
EdgeListIter upper_edge_list_begin ()
 returns a non-const iterator to the beginning of its upper-edge list More...
 
EdgeListConstIter const_upper_edge_list_begin () const
 returns a const iterator to the beginning of its upper-edge list More...
 
EdgeListIter upper_edge_list_end ()
 returns a non-const iterator to the end of its upper-edge list More...
 
EdgeListConstIter const_upper_edge_list_end () const
 returns a const iterator to the end of its upper-edge list More...
 
platform::Size get_node_index () const
 the index for this node More...
 
platform::Size num_edges () const
 the number of edges incident on this node, which may include a loop edge More...
 
platform::Size num_neighbors_counting_self () const
 the number of neighbors counting "self" as a neighbor. More...
 
platform::Size num_neighbors_counting_self_static () const
 the number of neighbors counting "self" as neighbor. Defaults to num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures. More...
 
platform::Size get_num_edges_to_smaller_indexed_nodes () const
 the number of lower neighbors More...
 
platform::Size get_num_edges_to_larger_indexed_nodes () const
 the number of upper neighbors – which "self" neighborness is counted if a loop edge is present More...
 
bool loop_incident () const
 NOTE TO SELF: remove loop support. More...
 

Public Attributes

 __pad0__:OneBodyEnergyCOP OneBodyEnergyCOP
 
 __pad1__:TwoBodyEnergyCOP TwoBodyEnergyCOP
 

Private Member Functions

void add_active_1benmeth_std (OneBodyEnergyCOP enmeth)
 
void add_active_1benmeth_ext (OneBodyEnergyCOP enmeth)
 
void add_dof_deriv_1benmeth (OneBodyEnergyCOP enmeth)
 
void add_sfs_1benmeth (OneBodyEnergyCOP enmeth)
 
void add_sfd_1benmeth (OneBodyEnergyCOP enmeth)
 
void add_active_2benmeth_std (TwoBodyEnergyCOP enmeth)
 
void add_active_2benmeth_ext (TwoBodyEnergyCOP enmeth)
 
void add_dof_deriv_2benmeth (TwoBodyEnergyCOP enmeth)
 
void add_sfs_2benmeth (TwoBodyEnergyCOP enmeth)
 
void add_sfd_2benmeth (TwoBodyEnergyCOP enmeth)
 
bool classify_onebody_enmeth (OneBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, int domain_map_color)
 
bool classify_twobody_enmeth (TwoBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, EnergyMap const &weights, int domain_map_color)
 

Private Attributes

ResSingleMinimizationData res_min_data_
 
OneBodyEnergies onebody_enmeths_
 
OneBodyEnergies active_1benmeths_
 
OneBodyEnergies active_1benmeths_std_
 
OneBodyEnergies active_1benmeths_ext_
 
OneBodyEnergies dof_deriv_1benmeths_
 
OneBodyEnergies sfs_req_1benmeths_
 
OneBodyEnergies sfd_req_1benmeths_
 
TwoBodyEnergies twobody_enmeths_
 
TwoBodyEnergies active_intrares2benmeths_
 
TwoBodyEnergies active_intrares2benmeths_std_
 
TwoBodyEnergies active_intrares2benmeths_ext_
 
TwoBodyEnergies dof_deriv_2benmeths_
 
TwoBodyEnergies sfs_req_2benmeths_
 
TwoBodyEnergies sfd_req_2benmeths_
 
Real weight_
 

Additional Inherited Members

- Protected Member Functions inherited from core::graph::Node
Graphget_owner () const
 derived class access to the owner More...
 

Detailed Description

Class MinimizationNode holds the ResSingleMinimizationData information for a single residue in a Pose which is being minimized. The data held in this node will be used in both scoring the residue one-body energies and evaluating atom derivatives during minimization.

Member Typedef Documentation

typedef OneBodyEnergies::const_iterator core::scoring::MinimizationNode::OneBodyEnergiesIterator
typedef TwoBodyEnergies::const_iterator core::scoring::MinimizationNode::TwoBodyEnergiesIterator

Constructor & Destructor Documentation

core::scoring::MinimizationNode::MinimizationNode ( graph::Graph owner,
Size  index 
)

Referenced by count_static_memory().

core::scoring::MinimizationNode::~MinimizationNode ( )
virtual

Member Function Documentation

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_begin ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_end ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_ext_begin ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_ext_end ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_std_begin ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_std_end ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_begin ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_end ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_ext_end ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_std_begin ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_std_end ( ) const
void core::scoring::MinimizationNode::add_active_1benmeth_ext ( OneBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_active_1benmeth_std ( OneBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_active_2benmeth_ext ( TwoBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_active_2benmeth_std ( TwoBodyEnergyCOP  enmeth)
private
void core::scoring::MinimizationNode::add_dof_deriv_1benmeth ( OneBodyEnergyCOP  enmeth)
private

References dof_deriv_1benmeths_.

Referenced by classify_onebody_enmeth().

void core::scoring::MinimizationNode::add_dof_deriv_2benmeth ( TwoBodyEnergyCOP  enmeth)
private

References dof_deriv_2benmeths_.

Referenced by classify_twobody_enmeth().

bool core::scoring::MinimizationNode::add_onebody_enmeth ( OneBodyEnergyCOP  enmeth,
Residue const &  rsd,
Pose const &  pose,
int  domain_map_color 
)
void core::scoring::MinimizationNode::add_sfd_1benmeth ( OneBodyEnergyCOP  enmeth)
private

References sfd_req_1benmeths_.

Referenced by classify_onebody_enmeth().

void core::scoring::MinimizationNode::add_sfd_2benmeth ( TwoBodyEnergyCOP  enmeth)
private

References sfd_req_2benmeths_.

Referenced by classify_twobody_enmeth().

void core::scoring::MinimizationNode::add_sfs_1benmeth ( OneBodyEnergyCOP  enmeth)
private

References sfs_req_1benmeths_.

Referenced by classify_onebody_enmeth().

void core::scoring::MinimizationNode::add_sfs_2benmeth ( TwoBodyEnergyCOP  enmeth)
private

References sfs_req_2benmeths_.

Referenced by classify_twobody_enmeth().

bool core::scoring::MinimizationNode::add_twobody_enmeth ( TwoBodyEnergyCOP  enmeth,
Residue const &  rsd,
Pose const &  pose,
EnergyMap const &  weights,
int  domain_map_color 
)

Note that the minimization graph is used both to evaluate the scores for both the "modern" EnergyMethods and the "old" energy methods (those which still define eval_atom_derivative instead of the pairwise-decomposable derivative evaluation methods) so when these older energy methods are added to the minimization graph, they should not simply be rejected.

References classify_twobody_enmeth(), and twobody_enmeths_.

Referenced by core::scoring::ScoreFunction::setup_for_minimizing_for_node().

bool core::scoring::MinimizationNode::classify_onebody_enmeth ( OneBodyEnergyCOP  enmeth,
Residue const &  rsd,
Pose const &  pose,
int  domain_map_color 
)
private
bool core::scoring::MinimizationNode::classify_twobody_enmeth ( TwoBodyEnergyCOP  enmeth,
Residue const &  rsd,
Pose const &  pose,
EnergyMap const &  weights,
int  domain_map_color 
)
private
void core::scoring::MinimizationNode::copy_from ( parent const *  source)
virtual
Size core::scoring::MinimizationNode::count_dynamic_memory ( ) const
virtual

memory accounting scheme

recursively descend through heirarchy accounting for heap memory usage. Each derived class in the heirarchy should recursively add the amount of dynamic memory its parent allocates by calling parent::count_dynamic_memory

Reimplemented from core::graph::Node.

References core::graph::Node::count_dynamic_memory().

Size core::scoring::MinimizationNode::count_static_memory ( ) const
virtual

memory accounting scheme

called on most-derived class. The most-derived class should NOT recursively call this method on its parent class. The sizeof function will handle the whole Node (or DerivedNode).

Reimplemented from core::graph::Node.

References MinimizationNode().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_1benmeths_begin ( ) const
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_1benmeths_end ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_2benmeths_begin ( ) const
MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_2benmeths_end ( ) const
void core::scoring::MinimizationNode::print ( ) const
virtual

send summaray data about this node to the screen

virtual function to print node to standard out

Reimplemented from core::graph::Node.

References core::graph::Node::print().

ResSingleMinimizationData const& core::scoring::MinimizationNode::res_min_data ( ) const
inline
ResSingleMinimizationData& core::scoring::MinimizationNode::res_min_data ( )
inline

References res_min_data_.

void core::scoring::MinimizationNode::setup_for_derivatives ( Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
)
void core::scoring::MinimizationNode::setup_for_minimizing ( Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
kinematics::MinimizerMapBase const &  min_map 
)
void core::scoring::MinimizationNode::setup_for_scoring ( Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
)
MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_1benmeths_begin ( ) const

References sfd_req_1benmeths_.

Referenced by setup_for_derivatives().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_1benmeths_end ( ) const

References sfd_req_1benmeths_.

Referenced by setup_for_derivatives().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_2benmeths_begin ( ) const

References sfd_req_2benmeths_.

Referenced by setup_for_derivatives().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_2benmeths_end ( ) const

References sfd_req_2benmeths_.

Referenced by setup_for_derivatives().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfs_req_1benmeths_begin ( ) const

References sfs_req_1benmeths_.

Referenced by setup_for_scoring().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfs_req_1benmeths_end ( ) const

References sfs_req_1benmeths_.

Referenced by setup_for_scoring().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfs_req_2benmeths_begin ( ) const

References sfs_req_2benmeths_.

Referenced by setup_for_scoring().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfs_req_2benmeths_end ( ) const

References sfs_req_2benmeths_.

Referenced by setup_for_scoring().

void core::scoring::MinimizationNode::update_active_enmeths_for_residue ( Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap const &  weights,
int  domain_map_color 
)
Real core::scoring::MinimizationNode::weight ( ) const
inline
void core::scoring::MinimizationNode::weight ( Real  setting)
inline

References weight_.

Member Data Documentation

core::scoring::MinimizationNode::__pad0__
core::scoring::MinimizationNode::__pad1__
OneBodyEnergies core::scoring::MinimizationNode::active_1benmeths_
private
OneBodyEnergies core::scoring::MinimizationNode::active_1benmeths_ext_
private
OneBodyEnergies core::scoring::MinimizationNode::active_1benmeths_std_
private
TwoBodyEnergies core::scoring::MinimizationNode::active_intrares2benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::active_intrares2benmeths_ext_
private
TwoBodyEnergies core::scoring::MinimizationNode::active_intrares2benmeths_std_
private
OneBodyEnergies core::scoring::MinimizationNode::dof_deriv_1benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::dof_deriv_2benmeths_
private
OneBodyEnergies core::scoring::MinimizationNode::onebody_enmeths_
private
ResSingleMinimizationData core::scoring::MinimizationNode::res_min_data_
private
OneBodyEnergies core::scoring::MinimizationNode::sfd_req_1benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::sfd_req_2benmeths_
private
OneBodyEnergies core::scoring::MinimizationNode::sfs_req_1benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::sfs_req_2benmeths_
private
TwoBodyEnergies core::scoring::MinimizationNode::twobody_enmeths_
private
Real core::scoring::MinimizationNode::weight_
private

Referenced by copy_from(), and weight().


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