#include <LazyInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::LazyNode:

Collaboration diagram for core::pack::interaction_graph::LazyNode:

Public Member Functions
	LazyNode (InteractionGraphBase *owner, int node_id, int num_states)
	main constructor, no default or copy constructors More...

virtual	~LazyNode ()

virtual void	prepare_for_simulated_annealing ()

virtual void	print () const

virtual bool	state_unassigned () const

virtual core::PackerEnergy	get_totalE () const

void	assign_zero_state ()

void	assign_state (int new_state)

void	partial_assign_state (int new_state)

void	complete_state_assignment ()

int	get_current_state () const

core::PackerEnergy	get_one_body_energy_current_state () const

core::PackerEnergy	project_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_node_energy)

void	commit_considered_substitution ()

core::PackerEnergy	compute_pair_energy_for_current_state (int edge_making_energy_request)

void	acknowledge_neighbors_state_substitution (int edge_to_altered_neighbor, core::PackerEnergy new_edge_energy, int other_node_new_state, SparseMatrixIndex const &other_node_new_state_sparse_info)

void	acknowledge_neighbors_partial_state_substitution (int edge_to_altered_neighbor, int other_node_new_, SparseMatrixIndex const &other_node_new_state_sparse_info)

SparseMatrixIndex const &	get_sparse_mat_info_for_curr_state () const

void	print_internal_energies () const

void	update_internal_energy_sums ()

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

virtual int	aatype_for_state (int state) const

Public Member Functions inherited from core::pack::interaction_graph::OnTheFlyNode
	OnTheFlyNode (InteractionGraphBase *owner, int node_id, int num_states)
	main constructor, no default or copy constructors More...

virtual	~OnTheFlyNode ()

void	set_rotamers (rotamer_set::RotamerSetCOP rotamers)

virtual void	zero_one_body_energies ()

virtual void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b)

virtual void	update_one_body_energy (int state, core::PackerEnergy energy)

virtual void	set_one_body_energy (int state, core::PackerEnergy energy)

virtual void	add_to_one_body_energy (int state, core::PackerEnergy energy)

virtual void	zero_one_body_energy (int state)

int	get_num_aa_types () const

utility::vector1< int > &	get_num_states_for_aa_types ()

utility::vector1< int > const &	get_num_states_for_aa_types () const

int	get_num_states_for_aa_type (int aa_type)

SparseMatrixIndex const &	get_sparse_mat_info_for_state (int state) const

int	get_state_offset_for_aatype (int aatype) const

core::PackerEnergy	get_one_body_energy (int state) const

bool	distinguish_backbone_and_sidechain () const

void	distinguish_backbone_and_sidechain (bool setting)

core::PackerEnergy	compute_rotamer_pair_energy (int edge_making_energy_request, int state_this, int state_other) const

Public Member Functions inherited from core::pack::interaction_graph::FixedBBNode
virtual	~FixedBBNode ()

	FixedBBNode (InteractionGraphBase *owner, int node_id, int num_states)

Public Member Functions inherited from core::pack::interaction_graph::NodeBase
virtual	~NodeBase ()
	virtual destructor More...

	NodeBase (InteractionGraphBase *, int node_id, int num_states)
	Main constructor, no default constructor nor copy constructor. More...

int	get_num_states () const
	returns the number of states for this node More...

std::list< EdgeBase * >::iterator	add_edge (EdgeBase *edge_ptr)
	adds edge pointer to edge list; returns an iterator to the new list element More...

void	drop_edge (std::list< EdgeBase * >::iterator edge_iterator)
	removes an edge iterator from the node's edge list More...

void	drop_all_edges ()
	deletes all edges incident upon this node More...

EdgeBase *	find_edge (int other_node_index) const
	a slow (linear) search for an edge. The edge is identified by the index of the node to which the edge connects this node. Returns NULL when there is no such connecting edge. More...

void	depth_first_connected_component_counting ()
	performs a depth first traversal of the graph. Each node informs the graph that the traversal resulted in arriving at the node. More...

std::list< EdgeBase * > ::const_iterator	edge_list_begin ()

std::list< EdgeBase * > ::const_iterator	edge_list_end ()

int	get_node_index () const

int	get_num_incident_edges () const

int	get_num_edges_to_smaller_indexed_nodes () const

int	get_num_edges_to_larger_indexed_nodes () const

EdgeBase const *	get_incident_edge (int index) const
	These functions are public for the sake of writing good unit tests. More...

EdgeBase *	get_incident_edge (int index)

int	get_index_of_adjacent_node (int index) const

NodeBase const *	get_adjacent_node (int index) const

NodeBase *	get_adjacent_node (int index)

Protected Member Functions
core::PackerEnergy	get_curr_pd_energy_total () const

core::PackerEnergy	get_alt_pd_energy_total () const

void	set_alternate_state (int alt)

int	get_alternate_state () const

void	calc_deltaEpd (int alternate_state)

bool	considering_alternate_state () const

Protected Member Functions inherited from core::pack::interaction_graph::OnTheFlyNode
OnTheFlyEdge *	get_incident_otf_edge (int edge)

OnTheFlyEdge const *	get_incident_otf_edge (int edge) const

OnTheFlyNode *	get_adjacent_otf_node (int index)

OnTheFlyNode const *	get_adjacent_otf_node (int index) const

OnTheFlyInteractionGraph *	get_on_the_fly_owner ()

OnTheFlyInteractionGraph const *	get_on_the_fly_owner () const

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

BoundingSphere const &	sc_bounding_sphere (int state) const

BoundingSphere const &	bb_bounding_sphere () const

Private Member Functions
void	update_internal_vectors ()

LazyEdge const *	get_incident_lazy_edge (int index) const
	Pointer Downcasts. More...

LazyEdge *	get_incident_lazy_edge (int index)

LazyNode const *	get_adjacent_lazy_node (int index) const

LazyNode *	get_adjacent_lazy_node (int index)

LazyInteractionGraph const *	get_lazy_ig_owner () const

LazyInteractionGraph *	get_lazy_ig_owner ()

	LazyNode ()

	LazyNode (LazyNode const &)

LazyNode &	operator= (LazyNode const &)

Private Attributes
FArray3D_int	aa_offsets_for_edges_

FArray2D_int	num_states_for_aa_type_for_higher_indexed_neighbor_

std::vector< FArray1A < core::PackerEnergy > >	edge_matrix_ptrs_

std::vector< int >	neighbors_curr_state_

std::vector< SparseMatrixIndex >	neighbors_curr_state_sparse_info_

int	current_state_

SparseMatrixIndex	curr_state_sparse_mat_info_

core::PackerEnergy	curr_state_one_body_energy_

core::PackerEnergy	curr_state_total_energy_

std::vector< core::PackerEnergy >	curr_state_two_body_energies_

int	alternate_state_

SparseMatrixIndex	alt_state_sparse_mat_info_

core::PackerEnergy	alternate_state_one_body_energy_

core::PackerEnergy	alternate_state_total_energy_

std::vector< core::PackerEnergy >	alternate_state_two_body_energies_

bool	alternate_state_is_being_considered_

bool	procrastinated_

Additional Inherited Members
Public Types inherited from core::pack::interaction_graph::OnTheFlyNode
typedef std::pair< Vector, Real >	BoundingSphere

Detailed Description

Definition at line 38 of file LazyInteractionGraph.hh.

Constructor & Destructor Documentation

core::pack::interaction_graph::LazyNode::LazyNode	(	InteractionGraphBase *	owner,
		int	node_id,
		int	num_states
	)

main constructor, no default or copy constructors

LazyNode::(InteractionGraphBase *, int, int)

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@par	Global Read:

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Remarks

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Authors: apl

Last Modified:

Definition at line 50 of file LazyInteractionGraph.cc.

core::pack::interaction_graph::LazyNode::~LazyNode ( )

virtual

LazyNode::~LazyNode()

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@par	Global Read:

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Authors: apl

Last Modified:

Definition at line 88 of file LazyInteractionGraph.cc.

core::pack::interaction_graph::LazyNode::LazyNode ( )

private

Referenced by count_static_memory().

core::pack::interaction_graph::LazyNode::LazyNode ( LazyNode const & )

private

Member Function Documentation

int core::pack::interaction_graph::LazyNode::aatype_for_state ( int state) const

virtual

Definition at line 218 of file LazyInteractionGraph.cc.

References core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), and core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state().

Referenced by core::pack::interaction_graph::LazyInteractionGraph::aatype_for_node_state().

void core::pack::interaction_graph::LazyNode::acknowledge_neighbors_partial_state_substitution	(	int	edge_to_altered_neighbor,
		int	other_node_new_state,
		SparseMatrixIndex const &	other_node_new_state_sparse_info
	)

LazyNode::acknowledge_neighbors_partial_state_substitution

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@par	Global Read:

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Authors: apl

Last Modified:

Definition at line 520 of file LazyInteractionGraph.cc.

References curr_state_total_energy_, curr_state_two_body_energies_, neighbors_curr_state_, and neighbors_curr_state_sparse_info_.

Referenced by core::pack::interaction_graph::LazyEdge::acknowledge_partial_state_change().

void core::pack::interaction_graph::LazyNode::acknowledge_neighbors_state_substitution	(	int	edge_to_altered_neighbor,
		core::PackerEnergy	new_edge_energy,
		int	other_node_new_state,
		SparseMatrixIndex const &	other_node_new_state_sparse_info
	)

inline

LazyNode::acknowledge_neighbors_state_substitution

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@par	Global Read:

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Authors: apl

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Definition at line 572 of file LazyInteractionGraph.hh.

References curr_state_total_energy_, curr_state_two_body_energies_, neighbors_curr_state_, and neighbors_curr_state_sparse_info_.

Referenced by core::pack::interaction_graph::LazyEdge::acknowledge_state_change(), core::pack::interaction_graph::LazyEdge::acknowledge_state_zeroed(), and core::pack::interaction_graph::LazyEdge::acknowledge_substitution().

void core::pack::interaction_graph::LazyNode::assign_state ( int new_state)

LazyNode::assign_state

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@par	Global Read:

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Authors: apl

Last Modified:

Definition at line 287 of file LazyInteractionGraph.cc.

References core::pack::interaction_graph::LazyEdge::acknowledge_state_change(), alternate_state_is_being_considered_, assign_zero_state(), curr_state_one_body_energy_, curr_state_sparse_mat_info_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, get_incident_lazy_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::NodeBase::get_num_states(), core::pack::interaction_graph::OnTheFlyNode::get_one_body_energy(), and core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state().

Referenced by core::pack::interaction_graph::LazyInteractionGraph::set_state_for_node().

void core::pack::interaction_graph::LazyNode::assign_zero_state ( )

virtual

LazyNode::assign_zero_state

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@par	Global Read:

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Remarks

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Authors: apl

Last Modified:

Implements core::pack::interaction_graph::NodeBase.

Definition at line 245 of file LazyInteractionGraph.cc.

References core::pack::interaction_graph::LazyEdge::acknowledge_state_zeroed(), alternate_state_, alternate_state_is_being_considered_, curr_state_one_body_energy_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, get_incident_lazy_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

Referenced by assign_state(), core::pack::interaction_graph::LazyInteractionGraph::blanket_assign_state_0(), and partial_assign_state().

void core::pack::interaction_graph::LazyNode::calc_deltaEpd ( int alternate_state)

protected

Definition at line 688 of file LazyInteractionGraph.cc.

References project_deltaE_for_substitution().

void core::pack::interaction_graph::LazyNode::commit_considered_substitution ( )

LazyNode::commit_considered_substitution

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@par	Global Read:

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Authors: apl

Last Modified:

Definition at line 417 of file LazyInteractionGraph.cc.

References core::pack::interaction_graph::LazyEdge::acknowledge_substitution(), alt_state_sparse_mat_info_, alternate_state_, alternate_state_is_being_considered_, alternate_state_one_body_energy_, alternate_state_total_energy_, alternate_state_two_body_energies_, curr_state_one_body_energy_, curr_state_sparse_mat_info_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, get_incident_lazy_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

Referenced by core::pack::interaction_graph::LazyInteractionGraph::commit_considered_substitution().

void core::pack::interaction_graph::LazyNode::complete_state_assignment ( )

LazyNode::complete_state_assignment

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@par	Global Read:

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Authors: apl

Last Modified:

Definition at line 379 of file LazyInteractionGraph.cc.

References curr_state_one_body_energy_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, get_incident_lazy_edge(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and core::pack::interaction_graph::OnTheFlyNode::get_one_body_energy().

Referenced by core::pack::interaction_graph::LazyInteractionGraph::set_network_state().

core::PackerEnergy core::pack::interaction_graph::LazyNode::compute_pair_energy_for_current_state ( int edge_making_energy_request)

LazyNode::compute_pair_energy_for_current_state

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@par	Global Read:

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Authors: apl

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Definition at line 487 of file LazyInteractionGraph.cc.

References core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), current_state_, and neighbors_curr_state_.

bool core::pack::interaction_graph::LazyNode::considering_alternate_state ( ) const

inlineprotected

Definition at line 127 of file LazyInteractionGraph.hh.

References alternate_state_is_being_considered_.

unsigned int core::pack::interaction_graph::LazyNode::count_dynamic_memory ( ) const

virtual

reports the amount of dynamic memory this node allocates recursing to its base class

Reimplemented from core::pack::interaction_graph::OnTheFlyNode.

Definition at line 199 of file LazyInteractionGraph.cc.

References aa_offsets_for_edges_, alternate_state_two_body_energies_, core::pack::interaction_graph::OnTheFlyNode::count_dynamic_memory(), curr_state_two_body_energies_, edge_matrix_ptrs_, neighbors_curr_state_, neighbors_curr_state_sparse_info_, and num_states_for_aa_type_for_higher_indexed_neighbor_.

unsigned int core::pack::interaction_graph::LazyNode::count_static_memory ( ) const

virtual

LazyNode::getMemoryUsageInBytes

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@par	Global Read:

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Authors: apl

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Implements core::pack::interaction_graph::OnTheFlyNode.

Definition at line 193 of file LazyInteractionGraph.cc.

References LazyNode().

LazyNode const * core::pack::interaction_graph::LazyNode::get_adjacent_lazy_node ( int index) const

inlineprivate

Definition at line 456 of file LazyInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_adjacent_node().

LazyNode * core::pack::interaction_graph::LazyNode::get_adjacent_lazy_node ( int index)

inlineprivate

Definition at line 462 of file LazyInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_adjacent_node().

core::PackerEnergy core::pack::interaction_graph::LazyNode::get_alt_pd_energy_total ( ) const

inlineprotected

Definition at line 123 of file LazyInteractionGraph.hh.

References alternate_state_total_energy_.

int core::pack::interaction_graph::LazyNode::get_alternate_state ( ) const

inlineprotected

Definition at line 125 of file LazyInteractionGraph.hh.

References alternate_state_.

core::PackerEnergy core::pack::interaction_graph::LazyNode::get_curr_pd_energy_total ( ) const

inlineprotected

Definition at line 122 of file LazyInteractionGraph.hh.

References curr_state_total_energy_.

int core::pack::interaction_graph::LazyNode::get_current_state ( ) const

inline

Definition at line 61 of file LazyInteractionGraph.hh.

References current_state_.

Referenced by core::pack::interaction_graph::LazyEdge::acknowledge_state_change(), core::pack::interaction_graph::LazyEdge::get_energy_following_partial_state_assignment(), and core::pack::interaction_graph::LazyInteractionGraph::print_current_state_assignment().

LazyEdge const * core::pack::interaction_graph::LazyNode::get_incident_lazy_edge ( int index) const

inlineprivate

Pointer Downcasts.

Definition at line 444 of file LazyInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_incident_edge().

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), complete_state_assignment(), partial_assign_state(), update_internal_energy_sums(), and update_internal_vectors().

LazyEdge * core::pack::interaction_graph::LazyNode::get_incident_lazy_edge ( int index)

inlineprivate

Definition at line 450 of file LazyInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_incident_edge().

LazyInteractionGraph const * core::pack::interaction_graph::LazyNode::get_lazy_ig_owner ( ) const

inlineprivate

Definition at line 468 of file LazyInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_owner().

LazyInteractionGraph * core::pack::interaction_graph::LazyNode::get_lazy_ig_owner ( )

inlineprivate

Definition at line 474 of file LazyInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_owner().

core::PackerEnergy core::pack::interaction_graph::LazyNode::get_one_body_energy_current_state ( ) const

inline

Definition at line 64 of file LazyInteractionGraph.hh.

References curr_state_one_body_energy_.

Referenced by core::pack::interaction_graph::LazyInteractionGraph::get_energy_sum_for_vertex_group().

SparseMatrixIndex const & core::pack::interaction_graph::LazyNode::get_sparse_mat_info_for_curr_state ( ) const

inline

LazyNode::get_sparse_mat_info_for_curr_state

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@par	Global Read:

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References:

Authors: apl

Last Modified:

Definition at line 949 of file LazyInteractionGraph.hh.

References current_state_, and core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state().

Referenced by core::pack::interaction_graph::LazyEdge::get_energy_following_partial_state_assignment().

virtual core::PackerEnergy core::pack::interaction_graph::LazyNode::get_totalE ( ) const

inlinevirtual

Definition at line 53 of file LazyInteractionGraph.hh.

References curr_state_total_energy_.

LazyNode& core::pack::interaction_graph::LazyNode::operator= ( LazyNode const & )

private

void core::pack::interaction_graph::LazyNode::partial_assign_state ( int new_state)

LazyNode::partial_assign_state

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@par	Global Read:

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Authors: apl

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Definition at line 338 of file LazyInteractionGraph.cc.

References core::pack::interaction_graph::LazyEdge::acknowledge_partial_state_change(), alternate_state_is_being_considered_, assign_zero_state(), curr_state_sparse_mat_info_, current_state_, get_incident_lazy_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state().

Referenced by core::pack::interaction_graph::LazyInteractionGraph::set_network_state().

void core::pack::interaction_graph::LazyNode::prepare_for_simulated_annealing ( )

virtual

LazyNode::prepare_for_simulated_annealing

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@par	Global Read:

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Remarks

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Authors: apl

Last Modified:

Implements core::pack::interaction_graph::NodeBase.

Definition at line 113 of file LazyInteractionGraph.cc.

References core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date(), and update_internal_vectors().

void core::pack::interaction_graph::LazyNode::print ( ) const

virtual

LazyNode::print

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@par	Global Read:

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Authors: apl

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Implements core::pack::interaction_graph::NodeBase.

Definition at line 144 of file LazyInteractionGraph.cc.

References alternate_state_is_being_considered_, alternate_state_one_body_energy_, alternate_state_two_body_energies_, curr_state_one_body_energy_, curr_state_sparse_mat_info_, curr_state_two_body_energies_, current_state_, core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::NodeBase::get_num_states(), and core::pack::interaction_graph::SparseMatrixIndex::get_state_ind_for_this_aa_type().

Referenced by core::pack::interaction_graph::LazyInteractionGraph::print_current_state_assignment().

void core::pack::interaction_graph::LazyNode::print_internal_energies ( ) const

LazyNode::print_internal_energies

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@par	Global Read:

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Authors: apl

Last Modified:

Definition at line 556 of file LazyInteractionGraph.cc.

References curr_state_one_body_energy_, curr_state_sparse_mat_info_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and core::pack::interaction_graph::SparseMatrixIndex::get_state_ind_for_this_aa_type().

core::PackerEnergy core::pack::interaction_graph::LazyNode::project_deltaE_for_substitution	(	int	alternate_state,
		core::PackerEnergy &	prev_node_energy
	)