Defines a FirstClass node which will keep track of the hydrogen bonds coming in to the residue and the hydrogen bond score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...

#include <NPDHBondInteractionGraph.hh>

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

[legend]

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

typedef V	grandparent

Public Types inherited from core::pack::interaction_graph::FirstClassNode< V, E, G >
typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >	BackgroundEdgeList

typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >::iterator	BackgroundEdgeListIter

typedef std::vector < BackgroundNode< V, E, G > * >	BackgroundNodeVector

typedef std::vector < BackgroundToFirstClassEdge < V, E, G > * >	BackgroundEdgeVector

typedef std::vector < BackgroundToFirstClassEdge < V, E, G > * >::iterator	BackgroundEdgeVectorIter

Public Member Functions
	NPDHBondNode (G *owner, int node_index, int num_states)
	NPDHBondNode constructor. More...

	~NPDHBondNode () override

void	set_rotamers (rotamer_set::RotamerSetCOP rotamers)

conformation::Residue const &	get_rotamer (int state) const

conformation::ResidueCOP	get_rotamer_op (int state) const

conformation::Residue const &	curr_state_rotamer () const

conformation::ResidueOP	curr_state_rotamer_op () const

conformation::Residue const &	alt_state_rotamer () const

conformation::ResidueCOP	alt_state_rotamer_op () const

Size	seqpos () const

void	prepare_for_simulated_annealing () override
	invokes V's prep_for_simA method More...

void	assign_zero_state () override

void	acknowledge_neighbors_substitution ()
	bookkeeping to follow a neighbors state substitution. this method gets called when a NPDHBondNode commits a sub and then broadcasts that change to all its neighboring fc nodes via the incident NPDHBondEdges. More...

void	acknowledge_neighbors_state_zeroed (Size seqpos)

core::PackerEnergy	calculate_PD_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_PDenergies_for_node)
	Returns the change in energy induced by changing a node from its current state into some alternate state for the PD energy terms only. More...

core::PackerEnergy	get_pd_energy_delta ()
	Returns the deltaE for just the PD terms. Separate method from the one above because this one can be called from within a commit_sub call that didn't go through consider_sub(). More...

Real	consider_alternate_state ()
	Return the change in energy induced by substituting an alternate rotamer at this position. More...

void	prepare_for_neighbors_substitution (Size nbrs_seqpos)

void	compute_alt_weights_for_hbonds (bool curr_state)

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	commit_considered_substitution ()
	Sets the current state to the alternate state this node was asked to consider. Copies appropriate score information. Notifies all of its neighbors that it is going through with the state substitution it had been considering. More...

void	reset_after_rejected_substitution ()

virtual unsigned int	getMemoryUsageInBytes () const
	Not implemented, but needs to be! More...

unsigned int	count_static_memory () const override
	Returns the amount of static memory used by this Node object. More...

unsigned int	count_dynamic_memory () const override
	Returns the amount of dynamic memory used by this Node object. More...

void	print () const override
	useful for debugging More...

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

	FirstClassNode (G *owner, int node_id, int num_states)
	FirstClassNode constructor. More...

BackgroundEdgeListIter	add_background_edge (BackgroundToFirstClassEdge< V, E, G > *edge)
	Adds a BackgroundToFirstClassEdge to the node's list of such edges and returns an iterator to that list position. More...

void	drop_background_edge (BackgroundEdgeListIter edge)
	Removes an edge from the node's BackgroundToFirstClassEdge list. More...

unsigned int	count_dynamic_memory () const override
	Returns an int representing the amount of memory in bytes used by this node. More...

Protected Member Functions
NPDHBondEdge< V, E, G > const *	get_incident_npd_hbond_edge (int index) const

NPDHBondEdge< V, E, G > *	get_incident_npd_hbond_edge (int index)

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

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

NPDHBondBackgroundEdge< V, E, G > const *	get_edge_to_npd_hbond_bg_node (int index) const

NPDHBondBackgroundEdge< V, E, G > *	get_edge_to_npd_hbond_bg_node (int index)

NPDHBondBackgroundNode< V, E, G > const *	get_adjacent_npd_hbond_bg_node (int index) const

NPDHBondBackgroundNode< V, E, G > *	get_adjacent_npd_hbond_bg_node (int index)

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

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

Protected Member Functions inherited from core::pack::interaction_graph::FirstClassNode< V, E, G >
int	get_num_edges_to_background_nodes () const

BackgroundToFirstClassEdge< V, E, G > const *	get_edge_to_bg_node (int index) const

BackgroundToFirstClassEdge< V, E, G > *	get_edge_to_bg_node (int index)

int	get_index_of_adjacent_background_node (int index) const

BackgroundNode< V, E, G > const *	get_adjacent_background_node (int index) const

BackgroundNode< V, E, G > *	get_adjacent_background_node (int index)

bool	get_bg_edge_vector_up_to_date_ () const

void	update_bg_edge_vector ()
	Syncs the background edge vector with the background edge list. More...

Private Member Functions
	NPDHBondNode ()

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

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

Private Attributes
core::Size	seqpos_

utility::vector1 < conformation::ResidueCOP >	rotamers_vector_

utility::vector1< Size >	restype_group_for_rotamers_

Size	max_natoms_

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_

Detailed Description

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

Defines a FirstClass node which will keep track of the hydrogen bonds coming in to the residue and the hydrogen bond score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph.

Remarks: No public default constructor makes this class uncopyable.

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef V core::pack::interaction_graph::NPDHBondNode< V, E, G >::grandparent

template<typename V, typename E, typename G>

typedef FirstClassNode< V, E, G > core::pack::interaction_graph::NPDHBondNode< V, E, G >::parent

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

core::pack::interaction_graph::NPDHBondNode< V, E, G >::NPDHBondNode	(	G *	owner,
		int	node_index,
		int	num_states
	)

NPDHBondNode constructor.

References core::pack::interaction_graph::NPDHBondNode< V, E, G >::restype_group_for_rotamers_, and core::pack::interaction_graph::NPDHBondNode< V, E, G >::rotamers_vector_.

template<typename V , typename E , typename G >

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

override

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondNode< V, E, G >::acknowledge_neighbors_state_zeroed ( Size seqpos )

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondNode< V, E, G >::acknowledge_neighbors_substitution ( )

bookkeeping to follow a neighbors state substitution. this method gets called when a NPDHBondNode commits a sub and then broadcasts that change to all its neighboring fc nodes via the incident NPDHBondEdges.

template<typename V , typename E , typename G >

conformation::Residue const & core::pack::interaction_graph::NPDHBondNode< V, E, G >::alt_state_rotamer ( ) const

template<typename V , typename E , typename G >

conformation::ResidueCOP core::pack::interaction_graph::NPDHBondNode< V, E, G >::alt_state_rotamer_op ( ) const

template<typename V , typename E , typename G >

utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondNode< V, E, G >::alternate_hbs ( )

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

template<typename V , typename E , typename G >

utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondNode< 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::NPDHBondNode< V, E, G >::alternate_hbs_for_atoms ( )

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondNode< V, E, G >::assign_zero_state ( )

override

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::NPDHBondNode< V, E, G >::calculate_PD_deltaE_for_substitution	(	int	alternate_state,
		core::PackerEnergy &	prev_PDenergies_for_node
	)

Returns the change in energy induced by changing a node from its current state into some alternate state for the PD energy terms only.

This function always gets called for every substitution. Only the consider_alt_state() call can get procrastinated.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondNode< V, E, G >::commit_considered_substitution ( )

Sets the current state to the alternate state this node was asked to consider. Copies appropriate score information. Notifies all of its neighbors that it is going through with the state substitution it had been considering.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondNode< V, E, G >::compute_alt_weights_for_hbonds ( bool curr_state )

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

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::NPDHBondNode< V, E, G >::consider_alternate_state ( )

Return the change in energy induced by substituting an alternate rotamer at this position.

compute the non-pairwise-decomposable portion of the deltaE

This node must have already been informed what the alternate state is.

template<typename V , typename E , typename G >

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

override

Returns the amount of dynamic memory used by this Node object.

template<typename V , typename E , typename G >

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

override

Returns the amount of static memory used by this Node object.

template<typename V , typename E , typename G >

conformation::Residue const & core::pack::interaction_graph::NPDHBondNode< V, E, G >::curr_state_rotamer ( ) const

template<typename V , typename E , typename G >

conformation::ResidueOP core::pack::interaction_graph::NPDHBondNode< V, E, G >::curr_state_rotamer_op ( ) const

template<typename V , typename E , typename G >

utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondNode< V, E, G >::current_hbs ( )

template<typename V, typename E, typename G>

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

inlineprotected

References core::pack::interaction_graph::FirstClassNode< V, E, G >::get_adjacent_background_node().

template<typename V, typename E, typename G>

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

inlineprotected

References core::pack::interaction_graph::FirstClassNode< V, E, G >::get_adjacent_background_node().

template<typename V, typename E, typename G>

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

inlineprotected

template<typename V, typename E, typename G>

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

inlineprotected

template<typename V, typename E, typename G>

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

inlineprotected

References core::pack::interaction_graph::FirstClassNode< V, E, G >::get_edge_to_bg_node().

template<typename V, typename E, typename G>

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

inlineprotected

References core::pack::interaction_graph::FirstClassNode< V, E, G >::get_edge_to_bg_node().

template<typename V, typename E, typename G>

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

inlineprotected

template<typename V, typename E, typename G>

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

inlineprotected

template<typename V, typename E, typename G>

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

inlineprotected

template<typename V, typename E, typename G>

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

inlineprotected

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_pd_energy_delta ( )

Returns the deltaE for just the PD terms. Separate method from the one above because this one can be called from within a commit_sub call that didn't go through consider_sub().

template<typename V , typename E , typename G >

conformation::Residue const & core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_rotamer ( int state ) const

template<typename V , typename E , typename G >

conformation::ResidueCOP core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_rotamer_op ( int state ) const

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_upper_npd_hbond_energy_totals ( ) const

References protocols::mean_field::min().

template<typename V , typename E , typename G >

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

virtual

Not implemented, but needs to be!

template<typename V, typename E, typename G>

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

private

template<typename V , typename E , typename G >

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

template<typename V , typename E , typename G >

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

override

invokes V's prep_for_simA method

template<typename V , typename E , typename G >

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

override

useful for debugging

useful for debugging - writes information about a node to the tracer

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondNode< V, E, G >::reset_after_rejected_substitution ( )

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::NPDHBondNode< V, E, G >::seqpos ( ) const

inline

References core::pack::interaction_graph::NPDHBondNode< V, E, G >::seqpos_.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondNode< V, E, G >::set_rotamers ( rotamer_set::RotamerSetCOP rotamers )

Need to save a reference to the rotamer_set so that we can determine what a particular state change will do to the score

Member Data Documentation

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::NPDHBondNode< V, E, G >::max_natoms_

private

template<typename V, typename E, typename G>

utility::vector1< Size > core::pack::interaction_graph::NPDHBondNode< V, E, G >::restype_group_for_rotamers_

private

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

template<typename V, typename E, typename G>

utility::vector1< conformation::ResidueCOP > core::pack::interaction_graph::NPDHBondNode< V, E, G >::rotamers_vector_

private

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

template<typename V, typename E, typename G>

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

private

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

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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