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core::pack::interaction_graph::SimpleNode Class Reference

#include <SimpleInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SimpleNode:
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Collaboration diagram for core::pack::interaction_graph::SimpleNode:
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Public Member Functions

 SimpleNode (graph::Graph *owner, Size resnum)
 
virtual ~SimpleNode ()
 
virtual void copy_from (graph::Node const *)
 invoked during graph assignment operators to copy any node data from one graph to another graph. The source node must be the same type as this node. More...
 
virtual void print () const
 send summaray data about this node to the screen More...
 
virtual platform::Size count_static_memory () const
 memory accounting scheme More...
 
virtual platform::Size count_dynamic_memory () const
 memory accounting scheme More...
 
Real one_body_energy () const
 
Real proposed_one_body_energy () const
 
Real current_one_body_energy () const
 
bool moved () const
 Is this node considering a state substitution? More...
 
void commit_change ()
 Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges. More...
 
void commit_change_no_res_pointer_update ()
 Copy the alternate energies to the current energies for this node and its incident edges. More...
 
void reject_change ()
 Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation. More...
 
void set_current (conformation::ResidueCOP res)
 Set the current residue COP, and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "current" energies. More...
 
void set_alternate (conformation::ResidueCOP res)
 Set the alternate residue COP and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "proposed" energies. More...
 
void set_current_no_E_update (conformation::ResidueCOP res)
 Passive mode behavior: set the current residue pointer without updating the current one body or two body energies. More...
 
void set_alternate_no_E_update (conformation::ResidueCOP res)
 Passive mode behavior: set the current residue pointer without updating the alternate one body or proposed two body energies. More...
 
void update_energies_after_passive_change ()
 
conformation::ResidueCOP get_current () const
 return the pointer to the current state (might be 0) More...
 
conformation::ResidueCOP get_alternate () const
 return the pointer to the alternate state (might be 0) More...
 
Vector const & bb_centroid () const
 
Real bb_radius () const
 
Vector const & curr_sc_centroid () const
 
Real curr_sc_radius () const
 
Vector const & alt_sc_centroid () const
 
Real alt_sc_radius () 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...
 

Private Member Functions

void update_current_one_body_energy ()
 
void update_alternate_one_body_energy ()
 
void initialize ()
 

Private Attributes

bool moved_
 
Size resnum_
 
Real current_one_body_energy_
 
Real alternate_one_body_energy_
 
conformation::ResidueCOP current_residue_
 
conformation::ResidueCOP alternate_residue_
 
Vector bb_centroid_
 
Real bb_radius_
 
Vector curr_sc_centroid_
 
Real curr_sc_radius_
 
Vector alt_sc_centroid_
 
Real alt_sc_radius_
 

Additional Inherited Members

- Public Types inherited from core::graph::Node
typedef EdgeListIterator EdgeListIter
 
typedef EdgeListConstIterator EdgeListConstIter
 
- Protected Member Functions inherited from core::graph::Node
Graphget_owner () const
 derived class access to the owner More...
 

Constructor & Destructor Documentation

core::pack::interaction_graph::SimpleNode::SimpleNode ( graph::Graph owner,
Size  resnum 
)

References initialize().

core::pack::interaction_graph::SimpleNode::~SimpleNode ( )
virtual

Member Function Documentation

Vector const & core::pack::interaction_graph::SimpleNode::alt_sc_centroid ( ) const
Real core::pack::interaction_graph::SimpleNode::alt_sc_radius ( ) const
Vector const & core::pack::interaction_graph::SimpleNode::bb_centroid ( ) const
Real core::pack::interaction_graph::SimpleNode::bb_radius ( ) const
void core::pack::interaction_graph::SimpleNode::commit_change ( )

Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges.

References alternate_residue_, commit_change_no_res_pointer_update(), and current_residue_.

void core::pack::interaction_graph::SimpleNode::commit_change_no_res_pointer_update ( )

Copy the alternate energies to the current energies for this node and its incident edges.

References alternate_one_body_energy_, core::pack::interaction_graph::SimpleEdge::commit_change(), current_one_body_energy_, core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), and moved_.

Referenced by commit_change().

virtual void core::pack::interaction_graph::SimpleNode::copy_from ( graph::Node const *  source)
inlinevirtual

invoked during graph assignment operators to copy any node data from one graph to another graph. The source node must be the same type as this node.

copy-from for use in Graph::operator= and copy ctors; derived classes must define their own version of this function

Reimplemented from core::graph::Node.

virtual platform::Size core::pack::interaction_graph::SimpleNode::count_dynamic_memory ( ) const
inlinevirtual

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.

virtual platform::Size core::pack::interaction_graph::SimpleNode::count_static_memory ( ) const
inlinevirtual

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.

Vector const & core::pack::interaction_graph::SimpleNode::curr_sc_centroid ( ) const
Real core::pack::interaction_graph::SimpleNode::curr_sc_radius ( ) const
Real core::pack::interaction_graph::SimpleNode::current_one_body_energy ( ) const
conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::get_alternate ( ) const

return the pointer to the alternate state (might be 0)

References alternate_residue_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::get_current ( ) const

return the pointer to the current state (might be 0)

References current_residue_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

void core::pack::interaction_graph::SimpleNode::initialize ( )
private

Referenced by SimpleNode().

bool core::pack::interaction_graph::SimpleNode::moved ( ) const

Is this node considering a state substitution?

References moved_.

Referenced by core::pack::interaction_graph::SimpleEdge::update_proposed_energy().

Real core::pack::interaction_graph::SimpleNode::one_body_energy ( ) const
virtual void core::pack::interaction_graph::SimpleNode::print ( ) const
inlinevirtual

send summaray data about this node to the screen

virtual function to print node to standard out

Reimplemented from core::graph::Node.

Real core::pack::interaction_graph::SimpleNode::proposed_one_body_energy ( ) const
void core::pack::interaction_graph::SimpleNode::reject_change ( )

Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation.

References moved_.

void core::pack::interaction_graph::SimpleNode::set_alternate ( conformation::ResidueCOP  res)
void core::pack::interaction_graph::SimpleNode::set_alternate_no_E_update ( conformation::ResidueCOP  res)

Passive mode behavior: set the current residue pointer without updating the alternate one body or proposed two body energies.

References alternate_residue_, and moved_.

void core::pack::interaction_graph::SimpleNode::set_current ( conformation::ResidueCOP  res)
void core::pack::interaction_graph::SimpleNode::set_current_no_E_update ( conformation::ResidueCOP  res)

Passive mode behavior: set the current residue pointer without updating the current one body or two body energies.

References current_residue_.

void core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy ( )
private
void core::pack::interaction_graph::SimpleNode::update_current_one_body_energy ( )
private
void core::pack::interaction_graph::SimpleNode::update_energies_after_passive_change ( )

Member Data Documentation

Vector core::pack::interaction_graph::SimpleNode::alt_sc_centroid_
private

Referenced by alt_sc_centroid(), and set_alternate().

Real core::pack::interaction_graph::SimpleNode::alt_sc_radius_
private

Referenced by alt_sc_radius(), and set_alternate().

Real core::pack::interaction_graph::SimpleNode::alternate_one_body_energy_
private
conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::alternate_residue_
private
Vector core::pack::interaction_graph::SimpleNode::bb_centroid_
private

Referenced by bb_centroid(), and set_current().

Real core::pack::interaction_graph::SimpleNode::bb_radius_
private

Referenced by bb_radius(), and set_current().

Vector core::pack::interaction_graph::SimpleNode::curr_sc_centroid_
private

Referenced by curr_sc_centroid(), and set_current().

Real core::pack::interaction_graph::SimpleNode::curr_sc_radius_
private

Referenced by curr_sc_radius(), and set_current().

Real core::pack::interaction_graph::SimpleNode::current_one_body_energy_
private
conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::current_residue_
private
bool core::pack::interaction_graph::SimpleNode::moved_
private
Size core::pack::interaction_graph::SimpleNode::resnum_
private

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