core::pack::interaction_graph::DensePDNode Class Reference

#include <DensePDInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::DensePDNode:

Public Member Functions
	DensePDNode (InteractionGraphBase *owner, int node_id, int num_states)
	main constructor, no default or copy constructors More...
	~DensePDNode () 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	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 DensePDNode 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 DensePDNode. More...
unsigned int	count_dynamic_memory () const override
	Called either by the IGBase if the DensePDNode 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...
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...
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::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
DensePDEdge *	get_incident_dpd_edge (int index)
DensePDEdge const *	get_incident_dpd_edge (int index) const
DensePDNode *	get_adjacent_dpd_node (int index)
DensePDNode const *	get_adjacent_dpd_node (int index) const
DensePDInteractionGraph *	get_dpdig_owner ()
DensePDInteractionGraph const *	get_dpdig_owner () const
	DensePDNode ()
	DensePDNode (DensePDNode const &)
DensePDNode &	operator= (DensePDNode 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_

Constructor & Destructor Documentation

core::pack::interaction_graph::DensePDNode::DensePDNode	(	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::DensePDNode::~DensePDNode ( )

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::DensePDNode::DensePDNode ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

void core::pack::interaction_graph::DensePDNode::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::DensePDEdge::acknowledge_state_zeroed().

void core::pack::interaction_graph::DensePDNode::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::DensePDNode::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::DensePDNode::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::DensePDEdge::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_dpd_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(), and one_body_energies_.

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

void core::pack::interaction_graph::DensePDNode::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 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_dpd_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

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

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

protected

References project_deltaE_for_substitution().

void core::pack::interaction_graph::DensePDNode::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::DensePDEdge::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_dpd_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

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

inlineprotected

References alternate_state_is_being_considered_.

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

overridevirtual

Called either by the IGBase if the DensePDNode 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_, neighbors_curr_state_, and one_body_energies_.

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

overridevirtual

If DensePDNode 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 DensePDNode.

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

References DensePDNode().

DensePDNode * core::pack::interaction_graph::DensePDNode::get_adjacent_dpd_node ( int  index )

inlineprivate

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

DensePDNode const * core::pack::interaction_graph::DensePDNode::get_adjacent_dpd_node ( int  index ) const

inlineprivate

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

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

inlineprotected

References alternate_state_total_energy_.

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

inlineprotected

References alternate_state_.

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

inlineprotected

References curr_state_total_energy_.

int core::pack::interaction_graph::DensePDNode::get_current_state

(

)

const

returns the state the node is currently assigned

References current_state_.

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

DensePDInteractionGraph * core::pack::interaction_graph::DensePDNode::get_dpdig_owner ( )

inlineprivate

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

DensePDInteractionGraph const * core::pack::interaction_graph::DensePDNode::get_dpdig_owner ( ) const

inlineprivate

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

DensePDEdge * core::pack::interaction_graph::DensePDNode::get_incident_dpd_edge ( int  index )

inlineprivate

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

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

DensePDEdge const * core::pack::interaction_graph::DensePDNode::get_incident_dpd_edge ( int  index ) const

inlineprivate

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

core::PackerEnergy core::pack::interaction_graph::DensePDNode::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::DensePDInteractionGraph::get_one_body_energy_for_node_state().

core::PackerEnergy core::pack::interaction_graph::DensePDNode::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::DensePDInteractionGraph::get_energy_sum_for_vertex_group().

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

private

void core::pack::interaction_graph::DensePDNode::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(), and update_internal_vectors().

void core::pack::interaction_graph::DensePDNode::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::DensePDNode::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::DensePDInteractionGraph::print_current_state_assignment().

core::PackerEnergy core::pack::interaction_graph::DensePDNode::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::DensePDEdge::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_.

Referenced by calc_deltaEpd().

void core::pack::interaction_graph::DensePDNode::set_alternate_state ( int  alt )

inlineprotected

References alternate_state_.

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

inlineoverridevirtual

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

References current_state_.

void core::pack::interaction_graph::DensePDNode::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::DensePDEdge::get_current_two_body_energy(), core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date(), get_incident_dpd_edge(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

void core::pack::interaction_graph::DensePDNode::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_dpd_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_simulated_annealing().

void core::pack::interaction_graph::DensePDNode::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::DensePDNode::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::DensePDNode::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_.

Member Data Documentation

int core::pack::interaction_graph::DensePDNode::alternate_state_

private

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

bool core::pack::interaction_graph::DensePDNode::alternate_state_is_being_considered_

private

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

core::PackerEnergy core::pack::interaction_graph::DensePDNode::alternate_state_one_body_energy_

private

Referenced by commit_considered_substitution(), and project_deltaE_for_substitution().

core::PackerEnergy core::pack::interaction_graph::DensePDNode::alternate_state_total_energy_

private

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

std::vector< core::PackerEnergy > core::pack::interaction_graph::DensePDNode::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::DensePDNode::curr_state_one_body_energy_

private

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

core::PackerEnergy core::pack::interaction_graph::DensePDNode::curr_state_total_energy_

private

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

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

private

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

int core::pack::interaction_graph::DensePDNode::current_state_

private

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

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

private

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

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

private

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

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

private

Referenced by add_to_one_body_energies(), add_to_one_body_energy(), assign_state(), count_dynamic_memory(), get_one_body_energy(), print(), project_deltaE_for_substitution(), update_one_body_energies(), update_one_body_energy(), and zero_one_body_energies().

---

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

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