Defines a NPDHBond Edge which connects two first-class NPDHBond Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...

#include <NPDHBondInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::NPDHBondEdge< V, E, G >:

[legend]

Public Types
typedef FirstClassEdge< V, E, G >	parent

Public Member Functions
	NPDHBondEdge (G *owner, int node1, int node2)
	main constructor. No default, or copy constructors, no assignment operator More...

	~NPDHBondEdge () override

void	prepare_for_simulated_annealing () override
	drops zero submatrices of the AminoAcidNeighborSparseMatrix and if the two_body_energies_ member then holds nothing, More...

void	acknowledge_state_zeroed (int node_index, Size node_seqpos)
	respond to when one of its vertices enters the "unassigned" state. More...

void	acknowledge_substitution (bool update_hbonds)
	bookkeeping following the decision to substitute a nodes current state with the alternate it was asked to consider. More...

void	declare_energies_final () override
	Reduces memory usage in the two body energy table after the energy calculating function declares that the energies will not change thereafter. More...

virtual unsigned int	getMemoryUsageInBytes () const

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override

void	consider_alternate_state_step1 (int node_index, int state_index, conformation::Residue const &alt_state, utility::vector1< NPDHBondOP > &res_hbonds, utility::vector1< utility::vector1< NPDHBondOP > > &atom_hbonds, utility::vector1< char > &hbonding_to_res)

Real	consider_alternate_state_step2 (utility::vector1< char > const &hbonding_to_res)

Public Member Functions inherited from core::pack::interaction_graph::FirstClassEdge< V, E, G >
	~FirstClassEdge () override
	FirstClassEdge destructor. More...

	FirstClassEdge (G *owner, int first_node_ind, int second_node_ind)
	FirstClassEdge constructor. More...

unsigned int	count_dynamic_memory () const override

Protected Member Functions
NPDHBondNode< V, E, G > const *	get_npd_hbond_node (int index) const

NPDHBondNode< V, E, G > *	get_npd_hbond_node (int index)

NPDHBondInteractionGraph< V, E, G > const *	get_npd_hbond_owner () const

NPDHBondInteractionGraph< V, E, G > *	get_npd_hbond_owner ()

Private Member Functions
void	inform_non_changing_node_of_neighbors_change ()

	NPDHBondEdge ()

	NPDHBondEdge (NPDHBondEdge< V, E, G > const &)

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

Private Attributes
int	node_changing_

int	node_not_changing_

int	nodes_curr_states_ [2]

int	nodes_alt_states_ [2]

Detailed Description

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

Defines a NPDHBond Edge which connects two first-class NPDHBond Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast.

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef FirstClassEdge< V, E, G > core::pack::interaction_graph::NPDHBondEdge< V, E, G >::parent

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

core::pack::interaction_graph::NPDHBondEdge< V, E, G >::NPDHBondEdge	(	G *	owner,
		int	node1,
		int	node2
	)

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

Parameters

owner - [in] - the owning interaction graph object node1 - [in] - the index of the lower-indexed NPDHBondNode node2 - [in] - the index of the higher-indexed NPDHBondNode

References core::pack::interaction_graph::NPDHBondEdge< V, E, G >::nodes_alt_states_, and core::pack::interaction_graph::NPDHBondEdge< V, E, G >::nodes_curr_states_.

template<typename V , typename E , typename G >

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

override

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

core::pack::interaction_graph::NPDHBondEdge< V, E, G >::NPDHBondEdge ( NPDHBondEdge< V, E, G > const & )

private

Member Function Documentation

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondEdge< V, E, G >::acknowledge_state_zeroed	(	int	node_that_changed,
		Size	node_seqpos
	)

respond to when one of its vertices enters the "unassigned" state.

called during the NPDHBIG::blanket_assign_state_0 -> NPDHBondNode::assign_zero_state() cascade of calls.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondEdge< V, E, G >::acknowledge_substitution ( bool update_hbonds )

bookkeeping following the decision to substitute a nodes current state with the alternate it was asked to consider.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondEdge< V, E, G >::consider_alternate_state_step1	(	int	node_index,
		int	state_index,
		conformation::Residue const &	alt_state,
		utility::vector1< NPDHBondOP > &	res_hbonds,
		utility::vector1< utility::vector1< NPDHBondOP > > &	atom_hbonds,
		utility::vector1< char > &	hbonding_to_res
	)

References core::pack::interaction_graph::NPDHBondNode< V, E, G >::alternate_hbs(), core::pack::interaction_graph::NPDHBondNode< V, E, G >::alternate_hbs_for_atoms(), core::pack::interaction_graph::create_hbonds_one_way(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::hbond_database(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::hbond_options(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::npd_hbond_set(), and core::conformation::Residue::seqpos().

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::NPDHBondEdge< V, E, G >::consider_alternate_state_step2 ( utility::vector1< char > const & hbonding_to_res )

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::NPDHBondEdge< V, E, G >::count_dynamic_memory ( ) const

override

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::NPDHBondEdge< V, E, G >::count_static_memory ( ) const

override

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondEdge< V, E, G >::declare_energies_final ( )

override

Reduces memory usage in the two body energy table after the energy calculating function declares that the energies will not change thereafter.

Remarks: (all by apl) In the PDEdge's version of this method, after invoking two_body_energies_.drop_zero_submatrices_where_possible(); the PDEdge checks if the two body energy table it now holds is empty. If the table is empty, the edge deletes itself.

template<typename V, typename E, typename G>

NPDHBondNode< V, E, G > const* core::pack::interaction_graph::NPDHBondEdge< V, E, G >::get_npd_hbond_node ( int index ) const

inlineprotected

template<typename V, typename E, typename G>

NPDHBondNode< V, E, G >* core::pack::interaction_graph::NPDHBondEdge< V, E, G >::get_npd_hbond_node ( int index )

inlineprotected

template<typename V, typename E, typename G>

NPDHBondInteractionGraph< V, E, G > const* core::pack::interaction_graph::NPDHBondEdge< V, E, G >::get_npd_hbond_owner ( ) const

inlineprotected

template<typename V, typename E, typename G>

NPDHBondInteractionGraph< V, E, G >* core::pack::interaction_graph::NPDHBondEdge< V, E, G >::get_npd_hbond_owner ( )

inlineprotected

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::NPDHBondEdge< V, E, G >::getMemoryUsageInBytes ( ) const

virtual

Remarks: Not implemented.

template<typename V, typename E, typename G>

void core::pack::interaction_graph::NPDHBondEdge< V, E, G >::inform_non_changing_node_of_neighbors_change ( )

private

template<typename V, typename E, typename G>

NPDHBondEdge< V, E, G >& core::pack::interaction_graph::NPDHBondEdge< V, E, G >::operator= ( NPDHBondEdge< V, E, G > const & )

private

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondEdge< V, E, G >::prepare_for_simulated_annealing ( )

override

drops zero submatrices of the AminoAcidNeighborSparseMatrix and if the two_body_energies_ member then holds nothing,

Member Data Documentation

template<typename V, typename E, typename G>

int core::pack::interaction_graph::NPDHBondEdge< V, E, G >::node_changing_

private

template<typename V, typename E, typename G>

int core::pack::interaction_graph::NPDHBondEdge< V, E, G >::node_not_changing_

private

template<typename V, typename E, typename G>

int core::pack::interaction_graph::NPDHBondEdge< V, E, G >::nodes_alt_states_[2]

private

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

template<typename V, typename E, typename G>

int core::pack::interaction_graph::NPDHBondEdge< V, E, G >::nodes_curr_states_[2]

private

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

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::NPDHBondEdge< V, E, G >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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