core::pack::interaction_graph::FASTERNode Class Reference

#include <FASTERInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::FASTERNode:

Public Types
typedef PrecomputedPairEnergiesNode	parent

Public Member Functions
	FASTERNode (InteractionGraphBase *owner, int node_id, int num_states)
	main constructor, no default or copy constructors More...
	~FASTERNode () override
	destructor More...
void	print () const override
	prints a description of the node and all of it's one-body energies More...
void	update_one_body_energy (int state, core::PackerEnergy energy) override
	update energy to the one-body energy for state More...
virtual void	update_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energies)
	set all the one-body energies for this node More...
void	add_to_one_body_energy (int state, core::PackerEnergy energy) override
	adds energy to the one-body energy for state state More...
void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energies) override
	adds all the energies in energies to the one-body energies for this node More...
void	zero_one_body_energies () override
	sets all of the one-body energies for this node to zero More...
core::PackerEnergy	get_one_body_energy (int state) const override
	returns the one body energy for a state More...
void	prepare_for_simulated_annealing () override
	prepares node for simulated annealing More...
void	prepare_for_FASTER ()
void	assign_zero_state () override
	assigns node's state to it's zero, or "unassigned" state. More...
bool	state_unassigned () const override
void	assign_state (int new_state)
	assigns node a new_state More...
int	get_current_state () const
	returns the state the node is currently assigned More...
core::PackerEnergy	get_one_body_energy_current_state () const
	returns the one body energy for the state the node is currently assigned More...
core::PackerEnergy	project_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_node_energy)
	returns the change in energy that would be induced by switching this node from its current state into another state More...
void	commit_considered_substitution ()
	tells the node that it should change its state to the last state it was asked to consider (from a call to project_deltaE_for_substitution) More...
void	acknowledge_neighbors_state_substitution (int edge_to_altered_neighbor, core::PackerEnergy new_edge_energy, int other_node_new_state)
	updates bookkeeping arrays for when a neighbor has changed its state More...
void	print_internal_energies () const
	outputs to standard error the bookkeeping energies for the node in its current state assignment More...
void	update_internal_energy_sums ()
	removes numerical drift long stretches of efficient bookkeeping produces More...
unsigned int	count_static_memory () const override
	If FASTERNode is the most-derived class being used, then this function will be called and will return the amount of memory statically allocated by a single FASTERNode. More...
unsigned int	count_dynamic_memory () const override
	Called either by the IGBase if the FASTERNode is the most-derived class, or called recursively by a derived class. Called to account for the dynamically allocated memory that this node uses. More...
void	get_total_energy_in_curr_state_assignment_for_all_states ()
void	partial_assign_state_with_lowest_one_body_energy ()
void	partial_assign_relaxed_state (Real probability)
void	partial_assign_state (int state)
void	acknowledge_neighbors_partial_state_assignment (int which_neighbor, int neighbors_new_state)
void	complete_partial_state_assignment ()
void	acknowledge_neighbors_perturbed_state (int which_neighbor, int const neighbors_perturbed_state)
void	prepare_for_perturbation ()
void	set_no_longer_perturbed ()
void	set_perturbed_state (int perturbed_state)
void	relax_neighbors ()
void	relax ()
void	reset_relaxed_for_neighbors ()
void	reset_relaxed ()
void	tell_neighbors_to_prep_for_relaxation ()
void	prep_for_neighbors_perturbation ()
void	relax_after_neighbors_perturbation ()
core::PackerEnergy	get_deltaE_for_relaxed_state_following_perturbation ()
core::PackerEnergy	get_one_body_energy_for_relaxed_state () const
int	get_relaxed_state () const
int	get_random_neighbor ()
Public Member Functions inherited from core::pack::interaction_graph::PrecomputedPairEnergiesNode
	~PrecomputedPairEnergiesNode () override
	PrecomputedPairEnergiesNode (InteractionGraphBase *owner, int node_id, int num_states)
Public Member Functions inherited from core::pack::interaction_graph::FixedBBNode
	~FixedBBNode () override
	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
void	update_internal_vectors ()
	updates bookkeeping arrays that correspond to edge-list. More...
FASTEREdge const *	get_incident_faster_edge (int index) const
FASTEREdge *	get_incident_faster_edge (int index)
FASTERNode const *	get_adjacent_faster_node (int index) const
FASTERNode *	get_adjacent_faster_node (int index)
FASTERInteractionGraph const *	get_fasterig_owner () const
FASTERInteractionGraph *	get_fasterig_owner ()
Protected Member Functions inherited from core::pack::interaction_graph::NodeBase
void	update_edge_vector ()
	converts edge-list to edge-vector representation More...
bool	get_edge_vector_up_to_date () const
InteractionGraphBase const *	get_owner () const
InteractionGraphBase *	get_owner ()

Private Member Functions
	FASTERNode ()
	FASTERNode (FASTERNode const &)
FASTERNode &	operator= (FASTERNode const &)

Private Attributes
std::vector< core::PackerEnergy >	one_body_energies_
std::vector< int >	neighbors_curr_state_
std::vector < ObjexxFCL::FArray2A < core::PackerEnergy > >	edge_matrix_ptrs_
int	current_state_
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_
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	have_prepared_once_for_FASTER_
bool	in_FASTER_mode_
bool	perturbed_
bool	have_relaxed_since_neighbors_perturbation_
bool	have_contributed_deltaE_following_perturbation_
int	relaxed_state_
std::vector< core::PackerEnergy >	state_energies_in_current_state_assignment_
std::vector< core::PackerEnergy >	state_energies_in_current_context_
std::vector< bool >	neighbor_relaxed_in_sBR_
std::vector< core::PackerEnergy >	perturbed_two_body_energies_

Friends
class	::FASTERInteractionGraphTests

Member Typedef Documentation

typedef PrecomputedPairEnergiesNode core::pack::interaction_graph::FASTERNode::parent

Constructor & Destructor Documentation

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

main constructor, no default or copy constructors

allocates one-body energy array and initializes it to zero.

core::pack::interaction_graph::FASTERNode::~FASTERNode ( )

overridedefault

destructor

not responsible for any dynamically allocated memory, so node does nothing it's member variables, of course, are implicitly destructed

core::pack::interaction_graph::FASTERNode::FASTERNode ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

void core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_partial_state_assignment	(	int	which_neighbor,
		int	neighbors_new_state
	)

References neighbors_curr_state_.

Referenced by core::pack::interaction_graph::FASTEREdge::acknowledge_partial_state_assignment().

void core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_perturbed_state	(	int	which_neighbor,
		int const	neighbors_perturbed_state
	)

References edge_matrix_ptrs_, core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes(), core::pack::interaction_graph::NodeBase::get_num_states(), have_relaxed_since_neighbors_perturbation_, neighbors_curr_state_, perturbed_, and state_energies_in_current_context_.

Referenced by core::pack::interaction_graph::FASTEREdge::acknowledge_perturbed_state().

void core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_state_substitution ( int  edge_to_altered_neighbor, core::PackerEnergy  new_edge_energy, int  other_node_new_state  )

inline

updates bookkeeping arrays for when a neighbor has changed its state

Parameters

edge_to_altered_neighbor	- [in] - the index for the edge that connects this node to the node that just changed its state
new_edge_energ	- [in] - the pair energy between this node in its current state and the new state of the node that just changed its state
other_node_new_state	- [in] - the state the neighbor just adopted

References curr_state_total_energy_, curr_state_two_body_energies_, and neighbors_curr_state_.

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

void core::pack::interaction_graph::FASTERNode::add_to_one_body_energies ( ObjexxFCL::FArray1< core::PackerEnergy > &  energies )

overridevirtual

adds all the energies in energies to the one-body energies for this node

Parameters

energies

- [in] - the array of energies. Must hold num_states_ entries

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

References core::pack::interaction_graph::NodeBase::get_num_states(), and one_body_energies_.

void core::pack::interaction_graph::FASTERNode::add_to_one_body_energy ( int  state, core::PackerEnergy  energy  )

overridevirtual

adds energy to the one-body energy for state state

Parameters

state	- [in] - one-based index of the state
energy	- [in] - the energy that should be added.

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

References protocols::buns::energy, and one_body_energies_.

void core::pack::interaction_graph::FASTERNode::assign_state

(

int

new_state

)

assigns node a new_state

node updates its curr_state one and two body energies

Parameters

new_state

- [in] - the new state the node should be assigned

References core::pack::interaction_graph::FASTEREdge::acknowledge_state_change(), alternate_state_is_being_considered_, assign_zero_state(), curr_state_one_body_energy_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, get_incident_faster_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(), one_body_energies_, and relaxed_state_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::set_network_state(), and core::pack::interaction_graph::FASTERInteractionGraph::set_state_for_node().

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

overridevirtual

assigns node's state to it's zero, or "unassigned" state.

zeros the edge-energy array, informs neighbors that it's in its unassigned state

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

References core::pack::interaction_graph::FASTEREdge::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_faster_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and relaxed_state_.

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

void core::pack::interaction_graph::FASTERNode::commit_considered_substitution

(

)

tells the node that it should change its state to the last state it was asked to consider (from a call to project_deltaE_for_substitution)

updates edge energy vector, iterates across neighbors having them update their edge energies. Bookkeeping recaptures performance lost by leaving energy2b structure

References core::pack::interaction_graph::FASTEREdge::acknowledge_substitution(), 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_total_energy_, curr_state_two_body_energies_, current_state_, get_incident_faster_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and relaxed_state_.

void core::pack::interaction_graph::FASTERNode::complete_partial_state_assignment

(

)

References curr_state_total_energy_, curr_state_two_body_energies_, core::pack::interaction_graph::FASTEREdge::get_curr_state_energy_following_partial_state_assignment(), get_incident_faster_edge(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), get_total_energy_in_curr_state_assignment_for_all_states(), and in_FASTER_mode_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::assign_BMEC(), core::pack::interaction_graph::FASTERInteractionGraph::commit_relaxation(), and core::pack::interaction_graph::FASTERInteractionGraph::probabilistically_commit_relaxation().

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

overridevirtual

Called either by the IGBase if the FASTERNode is the most-derived class, or called recursively by a derived class. Called to account for the dynamically allocated memory that this node uses.

Reimplemented from core::pack::interaction_graph::NodeBase.

References alternate_state_two_body_energies_, core::pack::interaction_graph::NodeBase::count_dynamic_memory(), curr_state_two_body_energies_, edge_matrix_ptrs_, neighbor_relaxed_in_sBR_, neighbors_curr_state_, one_body_energies_, perturbed_two_body_energies_, state_energies_in_current_context_, and state_energies_in_current_state_assignment_.

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

overridevirtual

If FASTERNode is the most-derived class being used, then this function will be called and will return the amount of memory statically allocated by a single FASTERNode.

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

References FASTERNode().

FASTERNode const * core::pack::interaction_graph::FASTERNode::get_adjacent_faster_node ( int  index ) const

inlineprotected

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

Referenced by relax_neighbors(), reset_relaxed_for_neighbors(), and tell_neighbors_to_prep_for_relaxation().

FASTERNode * core::pack::interaction_graph::FASTERNode::get_adjacent_faster_node ( int  index )

inlineprotected

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

int core::pack::interaction_graph::FASTERNode::get_current_state

(

)

const

returns the state the node is currently assigned

References current_state_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::get_current_network_state(), core::pack::interaction_graph::FASTERInteractionGraph::get_current_state_for_node(), and core::pack::interaction_graph::FASTERInteractionGraph::print_current_state_assignment().

core::PackerEnergy core::pack::interaction_graph::FASTERNode::get_deltaE_for_relaxed_state_following_perturbation

(

)

References curr_state_one_body_energy_, core::pack::interaction_graph::FASTEREdge::get_deltaE_for_perturbation(), get_incident_faster_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), have_contributed_deltaE_following_perturbation_, neighbor_relaxed_in_sBR_, one_body_energies_, perturbed_, and relaxed_state_.

Referenced by core::pack::interaction_graph::FASTEREdge::get_deltaE_for_neighbor_following_perturbation(), core::pack::interaction_graph::FASTERInteractionGraph::perturb_dBR_and_relax(), and core::pack::interaction_graph::FASTERInteractionGraph::perturb_sBR_and_relax().

FASTERInteractionGraph const * core::pack::interaction_graph::FASTERNode::get_fasterig_owner ( ) const

inlineprotected

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

FASTERInteractionGraph * core::pack::interaction_graph::FASTERNode::get_fasterig_owner ( )

inlineprotected

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

FASTEREdge const * core::pack::interaction_graph::FASTERNode::get_incident_faster_edge ( int  index ) const

inlineprotected

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

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), complete_partial_state_assignment(), get_deltaE_for_relaxed_state_following_perturbation(), partial_assign_state(), prep_for_neighbors_perturbation(), relax_neighbors(), set_perturbed_state(), update_internal_energy_sums(), and update_internal_vectors().

FASTEREdge * core::pack::interaction_graph::FASTERNode::get_incident_faster_edge ( int  index )

inlineprotected

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

core::PackerEnergy core::pack::interaction_graph::FASTERNode::get_one_body_energy ( int  state ) const

overridevirtual

returns the one body energy for a state

Parameters

state

- [in]

Implements core::pack::interaction_graph::PrecomputedPairEnergiesNode.

References one_body_energies_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::get_one_body_energy_for_node_state().

core::PackerEnergy core::pack::interaction_graph::FASTERNode::get_one_body_energy_current_state

(

)

const

returns the one body energy for the state the node is currently assigned

References curr_state_one_body_energy_.

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

core::PackerEnergy core::pack::interaction_graph::FASTERNode::get_one_body_energy_for_relaxed_state

(

)

const

References one_body_energies_, and relaxed_state_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::get_energy_following_relaxation().

int core::pack::interaction_graph::FASTERNode::get_random_neighbor

(

)

References core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and core::scoring::rg.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::get_random_neighbor_for_node().

int core::pack::interaction_graph::FASTERNode::get_relaxed_state

(

)

const

References relaxed_state_.

void core::pack::interaction_graph::FASTERNode::get_total_energy_in_curr_state_assignment_for_all_states

(

)

References edge_matrix_ptrs_, core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::NodeBase::get_num_states(), neighbors_curr_state_, one_body_energies_, and state_energies_in_current_state_assignment_.

Referenced by complete_partial_state_assignment(), and prepare_for_FASTER().

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

private

void core::pack::interaction_graph::FASTERNode::partial_assign_relaxed_state

(

Real

probability

)

References protocols::hotspot_hashing::accept, current_state_, partial_assign_state(), relaxed_state_, and core::scoring::rg.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::commit_relaxation(), and core::pack::interaction_graph::FASTERInteractionGraph::probabilistically_commit_relaxation().

void core::pack::interaction_graph::FASTERNode::partial_assign_state

(

int

state

)

References core::pack::interaction_graph::FASTEREdge::acknowledge_partial_state_assignment(), curr_state_one_body_energy_, curr_state_total_energy_, current_state_, get_incident_faster_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), one_body_energies_, and relaxed_state_.

Referenced by partial_assign_relaxed_state(), and partial_assign_state_with_lowest_one_body_energy().

void core::pack::interaction_graph::FASTERNode::partial_assign_state_with_lowest_one_body_energy

(

)

References core::pack::interaction_graph::NodeBase::get_num_states(), one_body_energies_, and partial_assign_state().

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::assign_BMEC().

void core::pack::interaction_graph::FASTERNode::prep_for_neighbors_perturbation

(

)

References core::pack::interaction_graph::FASTEREdge::acknowledge_participation_in_perturbation(), get_incident_faster_edge(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), have_contributed_deltaE_following_perturbation_, perturbed_, state_energies_in_current_context_, and state_energies_in_current_state_assignment_.

Referenced by tell_neighbors_to_prep_for_relaxation().

void core::pack::interaction_graph::FASTERNode::prepare_for_FASTER

(

)

References core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::NodeBase::get_num_states(), get_total_energy_in_curr_state_assignment_for_all_states(), have_prepared_once_for_FASTER_, in_FASTER_mode_, neighbor_relaxed_in_sBR_, perturbed_two_body_energies_, state_energies_in_current_context_, state_energies_in_current_state_assignment_, and update_internal_vectors().

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::prepare_for_FASTER().

void core::pack::interaction_graph::FASTERNode::prepare_for_perturbation

(

)

References have_contributed_deltaE_following_perturbation_, and perturbed_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::perturb_dBR_and_relax(), and core::pack::interaction_graph::FASTERInteractionGraph::perturb_sBR_and_relax().

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

overridevirtual

prepares node for simulated annealing

updates internal edge vector + other vectorized edge information

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

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

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

overridevirtual

prints a description of the node and all of it's one-body energies

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

References core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_states(), and one_body_energies_.

void core::pack::interaction_graph::FASTERNode::print_internal_energies

(

)

const

outputs to standard error the bookkeeping energies for the node in its current state assignment

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

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

core::PackerEnergy core::pack::interaction_graph::FASTERNode::project_deltaE_for_substitution ( int  alternate_state, core::PackerEnergy &  prev_energy_for_node  )

inline

returns the change in energy that would be induced by switching this node from its current state into another state

iterates across the incident edges for a node in two phases: in the first phase, it examines edges leading to higher-indexed nodes in the second phase, it examines edges leading to smaller-indexed nodes. for cache efficiency, all of the amino-acid-neighbor-offset information that each edge calculates is stored on the nodes themselves. The edges are never touched; rather, their private information is stored on the nodes and handed to static member functions of the DensePDEdge class. This "store edge information on the nodes" strategy gives me performance equivalent to the previous energy2b lookup tables.

Parameters

alternate_state	- [in] - the alternate state to consider
previous_energy_for_node	- [out] - the old energy1b/energy2b sum for this node; used by simulate annealing.

References alternate_state_, alternate_state_is_being_considered_, alternate_state_one_body_energy_, alternate_state_total_energy_, alternate_state_two_body_energies_, curr_state_total_energy_, edge_matrix_ptrs_, core::pack::interaction_graph::FASTEREdge::get_alternate_state_energy(), core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), neighbors_curr_state_, and one_body_energies_.

void core::pack::interaction_graph::FASTERNode::relax

(

)

References core::pack::interaction_graph::NodeBase::get_num_states(), relaxed_state_, and state_energies_in_current_context_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::relax_in_current_context().

void core::pack::interaction_graph::FASTERNode::relax_after_neighbors_perturbation

(

)

References core::pack::interaction_graph::NodeBase::get_num_states(), have_relaxed_since_neighbors_perturbation_, perturbed_, relaxed_state_, and state_energies_in_current_context_.

Referenced by relax_neighbors().

void core::pack::interaction_graph::FASTERNode::relax_neighbors

(

)

References core::pack::interaction_graph::FASTEREdge::acknowledge_perturbed_state(), get_adjacent_faster_node(), get_incident_faster_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), neighbor_relaxed_in_sBR_, relax_after_neighbors_perturbation(), and relaxed_state_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::perturb_dBR_and_relax(), and core::pack::interaction_graph::FASTERInteractionGraph::perturb_sBR_and_relax().

void core::pack::interaction_graph::FASTERNode::reset_relaxed

(

)

References current_state_, and relaxed_state_.

Referenced by reset_relaxed_for_neighbors().

void core::pack::interaction_graph::FASTERNode::reset_relaxed_for_neighbors

(

)

References get_adjacent_faster_node(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and reset_relaxed().

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::reject_perturbation().

void core::pack::interaction_graph::FASTERNode::set_no_longer_perturbed

(

)

References perturbed_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::perturb_dBR_and_relax(), and core::pack::interaction_graph::FASTERInteractionGraph::perturb_sBR_and_relax().

void core::pack::interaction_graph::FASTERNode::set_perturbed_state

(

int

perturbed_state

)

References core::pack::interaction_graph::FASTEREdge::acknowledge_participation_in_perturbation(), get_incident_faster_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), perturbed_two_body_energies_, and relaxed_state_.

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::perturb_dBR_and_relax(), and core::pack::interaction_graph::FASTERInteractionGraph::perturb_sBR_and_relax().

bool core::pack::interaction_graph::FASTERNode::state_unassigned ( ) const

inlineoverridevirtual

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

References current_state_.

void core::pack::interaction_graph::FASTERNode::tell_neighbors_to_prep_for_relaxation

(

)

References get_adjacent_faster_node(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), neighbor_relaxed_in_sBR_, perturbed_two_body_energies_, and prep_for_neighbors_perturbation().

Referenced by core::pack::interaction_graph::FASTERInteractionGraph::perturb_dBR_and_relax(), and core::pack::interaction_graph::FASTERInteractionGraph::perturb_sBR_and_relax().

void core::pack::interaction_graph::FASTERNode::update_internal_energy_sums

(

)

removes numerical drift long stretches of efficient bookkeeping produces

References curr_state_one_body_energy_, curr_state_total_energy_, core::pack::interaction_graph::FASTEREdge::get_current_two_body_energy(), core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date(), get_incident_faster_edge(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

void core::pack::interaction_graph::FASTERNode::update_internal_vectors ( )

protected

updates bookkeeping arrays that correspond to edge-list.

calls base class update_edge_vector function, and then proceeds to create appropriate bookkeeping arrays used in simulated annealing

References alternate_state_two_body_energies_, curr_state_two_body_energies_, edge_matrix_ptrs_, get_incident_faster_edge(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), neighbors_curr_state_, and core::pack::interaction_graph::NodeBase::update_edge_vector().

Referenced by prepare_for_FASTER(), and prepare_for_simulated_annealing().

void core::pack::interaction_graph::FASTERNode::update_one_body_energies ( ObjexxFCL::FArray1< core::PackerEnergy > &  energies )

virtual

set all the one-body energies for this node

Parameters

energies

- [in] - the array of energies. Must hold num_states_ entries

References core::pack::interaction_graph::NodeBase::get_num_states(), and one_body_energies_.

void core::pack::interaction_graph::FASTERNode::update_one_body_energy ( int  state, core::PackerEnergy  energy  )

overridevirtual

update energy to the one-body energy for state

Parameters

state	- [in] - one-based index of the state
energy	- [in] - the energy that should be set.

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

References protocols::buns::energy, and one_body_energies_.

void core::pack::interaction_graph::FASTERNode::zero_one_body_energies ( )

overridevirtual

sets all of the one-body energies for this node to zero

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

References core::pack::interaction_graph::NodeBase::get_num_states(), and one_body_energies_.

Friends And Related Function Documentation

friend class ::FASTERInteractionGraphTests

friend

Member Data Documentation

int core::pack::interaction_graph::FASTERNode::alternate_state_

private

Referenced by assign_zero_state(), commit_considered_substitution(), and project_deltaE_for_substitution().

bool core::pack::interaction_graph::FASTERNode::alternate_state_is_being_considered_

private

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), and project_deltaE_for_substitution().

core::PackerEnergy core::pack::interaction_graph::FASTERNode::alternate_state_one_body_energy_

private

Referenced by commit_considered_substitution(), and project_deltaE_for_substitution().

core::PackerEnergy core::pack::interaction_graph::FASTERNode::alternate_state_total_energy_

private

Referenced by commit_considered_substitution(), and project_deltaE_for_substitution().

std::vector< core::PackerEnergy > core::pack::interaction_graph::FASTERNode::alternate_state_two_body_energies_

private

Referenced by commit_considered_substitution(), count_dynamic_memory(), project_deltaE_for_substitution(), and update_internal_vectors().

core::PackerEnergy core::pack::interaction_graph::FASTERNode::curr_state_one_body_energy_

private

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), get_deltaE_for_relaxed_state_following_perturbation(), get_one_body_energy_current_state(), partial_assign_state(), print_internal_energies(), and update_internal_energy_sums().

core::PackerEnergy core::pack::interaction_graph::FASTERNode::curr_state_total_energy_

private

Referenced by acknowledge_neighbors_state_substitution(), assign_state(), assign_zero_state(), commit_considered_substitution(), complete_partial_state_assignment(), partial_assign_state(), print_internal_energies(), project_deltaE_for_substitution(), and update_internal_energy_sums().

std::vector< core::PackerEnergy > core::pack::interaction_graph::FASTERNode::curr_state_two_body_energies_

private

Referenced by acknowledge_neighbors_state_substitution(), assign_state(), assign_zero_state(), commit_considered_substitution(), complete_partial_state_assignment(), count_dynamic_memory(), print_internal_energies(), and update_internal_vectors().

int core::pack::interaction_graph::FASTERNode::current_state_

private

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), get_current_state(), partial_assign_relaxed_state(), partial_assign_state(), print_internal_energies(), reset_relaxed(), and state_unassigned().

std::vector< ObjexxFCL::FArray2A< core::PackerEnergy > > core::pack::interaction_graph::FASTERNode::edge_matrix_ptrs_

private

Referenced by acknowledge_neighbors_perturbed_state(), count_dynamic_memory(), get_total_energy_in_curr_state_assignment_for_all_states(), project_deltaE_for_substitution(), and update_internal_vectors().

bool core::pack::interaction_graph::FASTERNode::have_contributed_deltaE_following_perturbation_

private

Referenced by get_deltaE_for_relaxed_state_following_perturbation(), prep_for_neighbors_perturbation(), and prepare_for_perturbation().

bool core::pack::interaction_graph::FASTERNode::have_prepared_once_for_FASTER_

private

Referenced by prepare_for_FASTER().

bool core::pack::interaction_graph::FASTERNode::have_relaxed_since_neighbors_perturbation_

private

Referenced by acknowledge_neighbors_perturbed_state(), and relax_after_neighbors_perturbation().

bool core::pack::interaction_graph::FASTERNode::in_FASTER_mode_

private

Referenced by complete_partial_state_assignment(), prepare_for_FASTER(), and prepare_for_simulated_annealing().

std::vector< bool > core::pack::interaction_graph::FASTERNode::neighbor_relaxed_in_sBR_

private

Referenced by count_dynamic_memory(), get_deltaE_for_relaxed_state_following_perturbation(), prepare_for_FASTER(), relax_neighbors(), and tell_neighbors_to_prep_for_relaxation().

std::vector< int > core::pack::interaction_graph::FASTERNode::neighbors_curr_state_

private

Referenced by acknowledge_neighbors_partial_state_assignment(), acknowledge_neighbors_perturbed_state(), acknowledge_neighbors_state_substitution(), count_dynamic_memory(), get_total_energy_in_curr_state_assignment_for_all_states(), project_deltaE_for_substitution(), and update_internal_vectors().

std::vector< core::PackerEnergy > core::pack::interaction_graph::FASTERNode::one_body_energies_

private

Referenced by add_to_one_body_energies(), add_to_one_body_energy(), assign_state(), count_dynamic_memory(), get_deltaE_for_relaxed_state_following_perturbation(), get_one_body_energy(), get_one_body_energy_for_relaxed_state(), get_total_energy_in_curr_state_assignment_for_all_states(), partial_assign_state(), partial_assign_state_with_lowest_one_body_energy(), print(), project_deltaE_for_substitution(), update_one_body_energies(), update_one_body_energy(), and zero_one_body_energies().

bool core::pack::interaction_graph::FASTERNode::perturbed_

private

Referenced by acknowledge_neighbors_perturbed_state(), get_deltaE_for_relaxed_state_following_perturbation(), prep_for_neighbors_perturbation(), prepare_for_perturbation(), relax_after_neighbors_perturbation(), and set_no_longer_perturbed().

std::vector< core::PackerEnergy > core::pack::interaction_graph::FASTERNode::perturbed_two_body_energies_

private

Referenced by count_dynamic_memory(), prepare_for_FASTER(), set_perturbed_state(), and tell_neighbors_to_prep_for_relaxation().

int core::pack::interaction_graph::FASTERNode::relaxed_state_

private

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), get_deltaE_for_relaxed_state_following_perturbation(), get_one_body_energy_for_relaxed_state(), get_relaxed_state(), partial_assign_relaxed_state(), partial_assign_state(), relax(), relax_after_neighbors_perturbation(), relax_neighbors(), reset_relaxed(), and set_perturbed_state().

std::vector< core::PackerEnergy > core::pack::interaction_graph::FASTERNode::state_energies_in_current_context_

private

Referenced by acknowledge_neighbors_perturbed_state(), count_dynamic_memory(), prep_for_neighbors_perturbation(), prepare_for_FASTER(), relax(), and relax_after_neighbors_perturbation().

std::vector< core::PackerEnergy > core::pack::interaction_graph::FASTERNode::state_energies_in_current_state_assignment_

private

Referenced by count_dynamic_memory(), get_total_energy_in_curr_state_assignment_for_all_states(), prep_for_neighbors_perturbation(), and prepare_for_FASTER().

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The documentation for this class was generated from the following files:

• src/core/pack/interaction_graph/FASTERInteractionGraph.hh
• src/core/pack/interaction_graph/FASTERInteractionGraph.cc