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core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > Class Template Reference

Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable. More...

#include <NPDHBondInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >:
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Public Types

typedef BackgroundNode< V, E, Gparent
 
- Public Types inherited from core::pack::interaction_graph::BackgroundNode< V, E, G >
typedef std::list
< BackgroundToFirstClassEdge
< V, E, G > * >::iterator 
BackgroundEdgeListIter
 
typedef std::list
< BackgroundToFirstClassEdge
< V, E, G > * > 
BackgroundEdgeList
 
typedef std::vector
< BackgroundToFirstClassEdge
< V, E, G > * > 
BackgroundEdgeVector
 
typedef std::vector
< BackgroundToFirstClassEdge
< V, E, G > * >::iterator 
BackgroundEdgeVectorIter
 
typedef std::vector
< FirstClassNode< V, E, G > * > 
FirstClassNodeVector
 

Public Member Functions

 NPDHBondBackgroundNode (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int node_index)
 main constructor. No default constructor, copy constructor or assignment operator More...
 
 ~NPDHBondBackgroundNode () override
 
void set_rotamer (conformation::ResidueOP const &rotamer)
 inits the RotamerOP held by a background node. called in the NPDHBondIG::initialize method. More...
 
conformation::Residue const & get_rotamer () const
 
conformation::ResidueCOP get_rotamer_op () const
 
Size seqpos () const
 
void prepare_for_simulated_annealing () override
 
void prepare_for_neighbors_substitution (Size nbrs_seqpos)
 
void compute_alt_weights_for_hbonds ()
 
utility::vector1< NPDHBondOP > & current_hbs ()
 
utility::vector1< NPDHBondOP > & alternate_hbs ()
 
utility::vector1
< utility::vector1< NPDHBondOP > > & 
alternate_hbs_for_atoms ()
 
utility::vector1< NPDHBondOP > & alternate_hbs_for_atom (Size atom_index)
 
Real get_upper_npd_hbond_energy_totals () const
 
void acknowledge_substitution ()
 bookkeeping to reflect a neighboring NPDHBondNode's state substitution More...
 
void acknowledge_neighbors_state_zeroed (Size neighbors_seqpos)
 
unsigned int count_static_memory () const override
 
unsigned int count_dynamic_memory () const override
 Returns an int representing the amount of memory in bytes used by this node. More...
 
void print () const override
 used only for debugging More...
 
- Public Member Functions inherited from core::pack::interaction_graph::BackgroundNode< V, E, G >
virtual ~BackgroundNode ()
 BackgroundNode destructor. More...
 
 BackgroundNode (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int node_index)
 BackgroundNode constructor - no default or copy constructors; no operator =. More...
 
BackgroundEdgeListIter add_edge (BackgroundToFirstClassEdge< V, E, G > *edge_ptr)
 Adds a BackgroundToFirstClassEdge to the edge list for this node. Returns an iterator to the new list element. More...
 
void drop_edge (BackgroundEdgeListIter edge)
 removes an edge from the nodes edge list in constant time More...
 
BackgroundToFirstClassEdge< V,
E, G > * 
find_edge (int fc_node_index)
 Linear time edge lookup function. More...
 

Protected Member Functions

NPDHBondBackgroundEdge< V, E, G > * get_npd_hbond_bg_edge (int index)
 
NPDHBondInteractionGraph< V, E,
G > * 
get_npd_hbond_owner () const
 
- Protected Member Functions inherited from core::pack::interaction_graph::BackgroundNode< V, E, G >
void update_edge_vector ()
 Syncs the edge vector with the edge list. More...
 
int get_node_index () const
 
int get_num_incident_edges () const
 
BackgroundToFirstClassEdge< V,
E, G > * 
get_incident_edge (int index) const
 
int get_index_of_adjacent_first_class_node (int index) const
 
FirstClassNode< V, E, G > * get_adjacent_first_class_node (int index) const
 
bool get_edge_vector_up_to_date () const
 
AdditionalBackgroundNodesInteractionGraph
< V, E, G > * 
get_owner () const
 

Private Member Functions

 NPDHBondBackgroundNode ()
 
 NPDHBondBackgroundNode (NPDHBondBackgroundNode< V, E, G > const &)
 
NPDHBondBackgroundNode< V, E, G > & operator= (NPDHBondBackgroundNode< V, E, G > const &)
 

Private Attributes

conformation::ResidueOP rotamer_
 
Size seqpos_
 
utility::vector1
< utility::vector1< NPDHBondOP > > 
curr_atom_hbonds_
 
utility::vector1
< utility::vector1< NPDHBondOP > > 
alt_atom_hbonds_
 
utility::vector1< NPDHBondOPcurr_hbonds_
 
utility::vector1< NPDHBondOPalt_hbonds_
 
utility::vector1< Realtmp_energies_
 
utility::vector1< Realtmp_weights_
 
bool prepared_for_simA_
 

Detailed Description

template<typename V, typename E, typename G>
class core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >

Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable.

Member Typedef Documentation

template<typename V, typename E, typename G>
typedef BackgroundNode< V, E, G > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::parent

Constructor & Destructor Documentation

template<typename V , typename E , typename G >
core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::NPDHBondBackgroundNode ( AdditionalBackgroundNodesInteractionGraph< V, E, G > *  owner,
int  node_index 
)

main constructor. No default constructor, copy constructor or assignment operator

template<typename V , typename E , typename G >
core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::~NPDHBondBackgroundNode ( )
override
template<typename V, typename E, typename G>
core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::NPDHBondBackgroundNode ( )
private
template<typename V, typename E, typename G>
core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::NPDHBondBackgroundNode ( NPDHBondBackgroundNode< V, E, G > const &  )
private

Member Function Documentation

template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::acknowledge_neighbors_state_zeroed ( Size  neighbors_seqpos)
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::acknowledge_substitution ( )

bookkeeping to reflect a neighboring NPDHBondNode's state substitution

template<typename V , typename E , typename G >
utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::alternate_hbs ( )
template<typename V , typename E , typename G >
utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::alternate_hbs_for_atom ( Size  atom_index)
template<typename V , typename E , typename G >
utility::vector1< utility::vector1< NPDHBondOP > > & core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::alternate_hbs_for_atoms ( )
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::compute_alt_weights_for_hbonds ( )
template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::count_dynamic_memory ( ) const
overridevirtual

Returns an int representing the amount of memory in bytes used by this node.

Remarks
ronj lists consume more memory because they maintain pointers to the previous and next nodes ronj current calculation uses 4 * # elements in list * sizeof(pointer), but I think this is wrong ronj isn't it only 3 * # elements in list * sizeof(pointer)?
Parameters
total_memory- [out] - the amount of memory used by this node

Reimplemented from core::pack::interaction_graph::BackgroundNode< V, E, G >.

template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::count_static_memory ( ) const
overridevirtual
template<typename V , typename E , typename G >
utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::current_hbs ( )
template<typename V, typename E, typename G>
NPDHBondBackgroundEdge< V, E, G >* core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_npd_hbond_bg_edge ( int  index)
inlineprotected
template<typename V, typename E, typename G>
NPDHBondInteractionGraph< V, E, G >* core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_npd_hbond_owner ( ) const
inlineprotected
template<typename V , typename E , typename G >
conformation::Residue const & core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_rotamer ( ) const
template<typename V , typename E , typename G >
conformation::ResidueCOP core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_rotamer_op ( ) const
template<typename V , typename E , typename G >
Real core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_upper_npd_hbond_energy_totals ( ) const
template<typename V, typename E, typename G>
NPDHBondBackgroundNode< V, E, G >& core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::operator= ( NPDHBondBackgroundNode< V, E, G > const &  )
private
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::prepare_for_neighbors_substitution ( Size  nbrs_seqpos)
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::prepare_for_simulated_annealing ( )
overridevirtual
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::print ( ) const
overridevirtual
template<typename V , typename E , typename G >
Size core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::seqpos ( ) const
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::set_rotamer ( conformation::ResidueOP const &  rotamer)

inits the RotamerOP held by a background node. called in the NPDHBondIG::initialize method.

Member Data Documentation

template<typename V, typename E, typename G>
utility::vector1< utility::vector1< NPDHBondOP > > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::alt_atom_hbonds_
private
template<typename V, typename E, typename G>
utility::vector1< NPDHBondOP > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::alt_hbonds_
private
template<typename V, typename E, typename G>
utility::vector1< utility::vector1< NPDHBondOP > > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::curr_atom_hbonds_
private
template<typename V, typename E, typename G>
utility::vector1< NPDHBondOP > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::curr_hbonds_
private
template<typename V, typename E, typename G>
bool core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::prepared_for_simA_
private
template<typename V, typename E, typename G>
conformation::ResidueOP core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::rotamer_
private
template<typename V, typename E, typename G>
Size core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::seqpos_
private
template<typename V, typename E, typename G>
utility::vector1< Real > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::tmp_energies_
private
template<typename V, typename E, typename G>
utility::vector1< Real > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::tmp_weights_
private

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