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 >:

Public Types
typedef BackgroundNode< V, E, G >	parent
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< NPDHBondOP >	curr_hbonds_
utility::vector1< NPDHBondOP >	alt_hbonds_
utility::vector1< Real >	tmp_energies_
utility::vector1< Real >	tmp_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

(

)

Referenced by core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1().

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

(

)

Referenced by core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::compute_alt_weights_for_hbonds

(

)

References core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds().

Referenced by core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1().

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

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

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

References core::pack::interaction_graph::BackgroundNode< V, E, G >::get_incident_edge().

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

References core::pack::interaction_graph::BackgroundNode< V, E, G >::get_owner().

template<typename V , typename E , typename G >

conformation::Residue const & core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_rotamer

(

)

const

Referenced by core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1().

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

References protocols::mean_field::min().

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

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::print ( ) const

overridevirtual

used only for debugging

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

References core::pack::interaction_graph::TR().

template<typename V , typename E , typename G >

Size core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::seqpos

(

)

const

Referenced by core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1().

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:

• src/core/pack/interaction_graph/NPDHBondInteractionGraph.hh