#include <DensePDInteractionGraph.hh>

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

Collaboration 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...

virtual	~DensePDNode ()
	destructor More...

virtual void	print () const
	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)
	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)
	adds energy to the one-body energy for state state More...

virtual void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energies)
	adds all the energies in energies to the one-body energies for this node More...

virtual void	zero_one_body_energies ()
	sets all of the one-body energies for this node to zero More...

core::PackerEnergy	get_one_body_energy (int state)
	returns the one body energy for a state More...

virtual void	prepare_for_simulated_annealing ()
	prepares node for simulated annealing More...

void	assign_zero_state ()
	assigns node's state to it's zero, or "unassigned" state. More...

virtual bool	state_unassigned () const

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 ()
	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...

virtual unsigned int	count_static_memory () const
	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...

virtual unsigned int	count_dynamic_memory () const
	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
virtual	~PrecomputedPairEnergiesNode ()

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

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
void	update_internal_vectors ()
	updates bookkeeping arrays that correspond to edge-list. More...

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_

Detailed Description

Definition at line 51 of file DensePDInteractionGraph.hh.

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.

Definition at line 56 of file DensePDInteractionGraph.cc.

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

virtual

destructor

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

Definition at line 72 of file DensePDInteractionGraph.cc.

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

Definition at line 433 of file DensePDInteractionGraph.hh.

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)

virtual

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.

Definition at line 127 of file DensePDInteractionGraph.cc.

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
	)

virtual

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.

Definition at line 118 of file DensePDInteractionGraph.cc.

References 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

Definition at line 201 of file DensePDInteractionGraph.cc.

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 ( )

virtual

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.

Definition at line 167 of file DensePDInteractionGraph.cc.

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::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

Definition at line 246 of file DensePDInteractionGraph.cc.

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().

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

virtual

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.

Definition at line 346 of file DensePDInteractionGraph.cc.

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

virtual

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.

Definition at line 337 of file DensePDInteractionGraph.cc.

References DensePDNode().

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

inlineprivate

Definition at line 384 of file DensePDInteractionGraph.hh.

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

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

inlineprivate

Definition at line 390 of file DensePDInteractionGraph.hh.

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

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

returns the state the node is currently assigned

Definition at line 230 of file DensePDInteractionGraph.cc.

References current_state_.

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

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

inlineprivate

Definition at line 396 of file DensePDInteractionGraph.hh.

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

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

inlineprivate

Definition at line 402 of file DensePDInteractionGraph.hh.

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

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

inlineprivate

Definition at line 373 of file DensePDInteractionGraph.hh.

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

Definition at line 378 of file DensePDInteractionGraph.hh.

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

core::PackerEnergy core::pack::interaction_graph::DensePDNode::get_one_body_energy ( int state)

returns the one body energy for a state

Parameters

state - [in]

Definition at line 149 of file DensePDInteractionGraph.cc.

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 ( )

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

Definition at line 236 of file DensePDInteractionGraph.cc.

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 ( )

virtual

prepares node for simulated annealing

updates internal edge vector + other vectorized edge information

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

Definition at line 157 of file DensePDInteractionGraph.cc.

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

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

virtual

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

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

Definition at line 76 of file DensePDInteractionGraph.cc.

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

Definition at line 304 of file DensePDInteractionGraph.cc.

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.

Definition at line 518 of file DensePDInteractionGraph.hh.

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_.

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

inlinevirtual

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

Definition at line 69 of file DensePDInteractionGraph.hh.

References current_state_.

void core::pack::interaction_graph::DensePDNode::update_internal_energy_sums ( )

removes numerical drift long stretches of efficient bookkeeping produces

Definition at line 320 of file DensePDInteractionGraph.cc.

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

Definition at line 282 of file DensePDInteractionGraph.cc.

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

Definition at line 104 of file DensePDInteractionGraph.cc.

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
	)

virtual

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.

Definition at line 95 of file DensePDInteractionGraph.cc.

References one_body_energies_.

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

virtual

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

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

Definition at line 138 of file DensePDInteractionGraph.cc.

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

Definition at line 155 of file DensePDInteractionGraph.hh.

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

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

private

Definition at line 170 of file DensePDInteractionGraph.hh.

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

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

private

Definition at line 156 of file DensePDInteractionGraph.hh.

Referenced by commit_considered_substitution(), and project_deltaE_for_substitution().

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

private

Definition at line 157 of file DensePDInteractionGraph.hh.

Referenced by commit_considered_substitution(), and project_deltaE_for_substitution().

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

private

Definition at line 158 of file DensePDInteractionGraph.hh.

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

Definition at line 151 of file DensePDInteractionGraph.hh.

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

Definition at line 152 of file DensePDInteractionGraph.hh.

Referenced by acknowledge_neighbors_state_substitution(), assign_state(), assign_zero_state(), commit_considered_substitution(), 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

Definition at line 153 of file DensePDInteractionGraph.hh.

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

Definition at line 150 of file DensePDInteractionGraph.hh.

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

Definition at line 148 of file DensePDInteractionGraph.hh.

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

Definition at line 147 of file DensePDInteractionGraph.hh.

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

Definition at line 145 of file DensePDInteractionGraph.hh.

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

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation