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 >:

[legend]

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

◆ parent

template<typename V , typename E , typename G >

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

Constructor & Destructor Documentation

◆ NPDHBondBackgroundNode() [1/3]

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

◆ ~NPDHBondBackgroundNode()

template<typename V , typename E , typename G >

core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::~NPDHBondBackgroundNode

override

◆ NPDHBondBackgroundNode() [2/3]

template<typename V , typename E , typename G >

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

private

◆ NPDHBondBackgroundNode() [3/3]

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

◆ acknowledge_neighbors_state_zeroed()

template<typename V , typename E , typename G >

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

◆ acknowledge_substitution()

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

◆ alternate_hbs()

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().

◆ alternate_hbs_for_atom()

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 )

◆ alternate_hbs_for_atoms()

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().

◆ compute_alt_weights_for_hbonds()

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().

◆ count_dynamic_memory()

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::count_dynamic_memory

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 >.

◆ count_static_memory()

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::count_static_memory

overridevirtual

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

◆ current_hbs()

template<typename V , typename E , typename G >

utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::current_hbs

◆ get_npd_hbond_bg_edge()

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().

◆ get_npd_hbond_owner()

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().

◆ get_rotamer()

template<typename V , typename E , typename G >

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

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

◆ get_rotamer_op()

template<typename V , typename E , typename G >

conformation::ResidueCOP core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_rotamer_op

◆ get_upper_npd_hbond_energy_totals()

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_upper_npd_hbond_energy_totals

References protocols::mean_field::min().

◆ operator=()

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

◆ prepare_for_neighbors_substitution()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::prepare_for_neighbors_substitution ( Size nbrs_seqpos )

◆ prepare_for_simulated_annealing()

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 >.

◆ print()

template<typename V , typename E , typename G >

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

overridevirtual

used only for debugging

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

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

◆ seqpos()

template<typename V , typename E , typename G >

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

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

◆ set_rotamer()

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

◆ alt_atom_hbonds_

template<typename V , typename E , typename G >

utility::vector1< utility::vector1< NPDHBondOP > > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::alt_atom_hbonds_

private

◆ alt_hbonds_

template<typename V , typename E , typename G >

utility::vector1< NPDHBondOP > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::alt_hbonds_

private

◆ curr_atom_hbonds_

template<typename V , typename E , typename G >

utility::vector1< utility::vector1< NPDHBondOP > > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::curr_atom_hbonds_

private

◆ curr_hbonds_

template<typename V , typename E , typename G >

utility::vector1< NPDHBondOP > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::curr_hbonds_

private

◆ prepared_for_simA_

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::prepared_for_simA_

private

◆ rotamer_

template<typename V , typename E , typename G >

conformation::ResidueOP core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::rotamer_

private

◆ seqpos_

template<typename V , typename E , typename G >

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

private

◆ tmp_energies_

template<typename V , typename E , typename G >

utility::vector1< Real > core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::tmp_energies_

private

◆ tmp_weights_

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

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

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

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ NPDHBondBackgroundNode() [1/3]

◆ ~NPDHBondBackgroundNode()

◆ NPDHBondBackgroundNode() [2/3]

◆ NPDHBondBackgroundNode() [3/3]

Member Function Documentation

◆ acknowledge_neighbors_state_zeroed()

◆ acknowledge_substitution()

◆ alternate_hbs()

◆ alternate_hbs_for_atom()

◆ alternate_hbs_for_atoms()

◆ compute_alt_weights_for_hbonds()

◆ count_dynamic_memory()

◆ count_static_memory()

◆ current_hbs()

◆ get_npd_hbond_bg_edge()

◆ get_npd_hbond_owner()

◆ get_rotamer()

◆ get_rotamer_op()

◆ get_upper_npd_hbond_energy_totals()

◆ operator=()

◆ prepare_for_neighbors_substitution()

◆ prepare_for_simulated_annealing()

◆ print()

◆ seqpos()

◆ set_rotamer()

Member Data Documentation

◆ alt_atom_hbonds_

◆ alt_hbonds_

◆ curr_atom_hbonds_

◆ curr_hbonds_

◆ prepared_for_simA_

◆ rotamer_

◆ seqpos_

◆ tmp_energies_

◆ tmp_weights_

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