#include <DoubleDensePDInteractionGraph.hh>

Public Member Functions
	DoubleDensePDInteractionGraph (int num_nodes)
	main constructor: no default nor copy constructors provided. More...

virtual void	initialize (rotamer_set::RotamerSetsBase const &rot_sets)
	The DoubleDensePDIG only needs to know how many states each node has. This function causes the downstream instantiation of the DoubleDensePDNodes. More...

virtual core::PackerEnergy	get_one_body_energy_for_node_state (int node, int state)
	returns the one body energy for a particular state on a node More...

virtual int	get_num_aatypes () const

virtual void	blanket_assign_state_0 ()
	assigns the state of all nodes in the interaction graph to their unassigned or zero states. More...

virtual core::PackerEnergy	set_state_for_node (int node_ind, int new_state)
	sets the state on node node_ind to new_state More...

virtual core::PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states)
	takes in a vector of states, one state per node, and sets the state for each of the nodes to the specified state. More...

virtual void	consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node)
	considers altering the state of a particular node; returns the change in energy that the state substitution would produce More...

virtual core::PackerEnergy	commit_considered_substitution ()
	Accepts (commits) the state change previously considered in a call to consider_substitution and returns the energy of the entire graph. More...

virtual core::PackerEnergy	get_energy_current_state_assignment ()
	removes all accumulated numerical drift and returns the energy for the current state assignment. More...

virtual int	get_edge_memory_usage () const
	returns the number of floats used in all edge two-body energy tables More...

virtual void	print_current_state_assignment () const
	outputs the current state for each node, useful for debugging More...

virtual void	set_errorfull_deltaE_threshold (core::PackerEnergy)

virtual core::PackerEnergy	get_energy_sum_for_vertex_group (int group_id)
	a user may define subsets of the vertex set for which they would like to know the internal energy sum. More...

virtual unsigned int	count_static_memory () const
	returns the amount of static memory allocated for a single DoubleDensePDInteractionGraph. Does not account for any of the edges or nodes that the graph contains: that part of the algorithm is implemented by the InteractionGraphBase class. More...

virtual unsigned int	count_dynamic_memory () const
	returns the amount of dynamic memory allocated for a single DoubleDensePDInteractionGraph and recurses on the parent class. Does not account for any of the edges or nodes that the graph contains: that part of the algorithm is implemented by the InteractionGraphBase class. More...

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

	PrecomputedPairEnergiesInteractionGraph (int num_nodes)

void	add_to_two_body_energies_for_edge (int node1, int node2, ObjexxFCL::FArray2< core::PackerEnergy > const &res_res_energy_array)
	interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies More...

void	add_to_two_body_energies_for_edge (int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy)
	interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies More...

void	set_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy)
	interface to PDEdge::set_two_body_energy More...

void	clear_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2)
	interface to PDEdge::clear_two_body_energy More...

virtual void	declare_edge_energies_final (int node1, int node2)
	call this if you're done storing energies in an edge - it will reduce the memory usage for that edge if possible More...

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

	FixedBBInteractionGraph (int num_nodes)

virtual bool	aa_submatrix_energies_retrievable () const

virtual int	aatype_for_node_state (int node_ind, int node_state) const

virtual ObjexxFCL::FArray2D < core::PackerEnergy >	get_aa_submatrix_energies_for_edge (int node1, int node2, int node1aa, int node2aa) const

void	set_sparse_aa_info_for_edge (int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info)
	interface to PDEdge::set_sparse_aa_info More...

bool	get_sparse_aa_info_for_edge (int node1, int node2, int node1aa, int node2aa)
	returns true if node1aa and node2aa are amino acid neighbors More...

void	force_aa_neighbors_for_edge (int node1, int node2, int node1aa, int node2aa)
	interface to FixedBBEdge::force_aa_neighbors More...

void	force_all_aa_neighbors_for_edge (int node1, int node2)
	interface to PDEdge::force_aa_neighbors More...

virtual core::PackerEnergy	get_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2) const
	interface to FixedBBEdge::get_two_body_energy More...

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

	InteractionGraphBase (int num_nodes)
	main constructor More...

virtual int	get_num_nodes_v () const

int	get_num_nodes () const

void	set_num_states_for_node (int node, int num_states)
	sets the number of states for a node of a particular index NEW REQUIREMENT: Nodes must have their num-states set in ascending order by node index; that is, node 1 must go first, node 2 next, and so on. More...

int	get_num_states_for_node (int node) const
	returns the number of states for a particular node More...

int	get_num_total_states () const

void	add_edge (int node1, int node2)
	creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order More...

bool	get_edge_exists (int node1, int node2)
	returns true if an edge between node1 and node2 exists More...

void	drop_all_edges_for_node (int node)
	deletes all edges adjacent to the node specified More...

void	print_vertices () const
	calls print() on each of the nodes in the graph More...

virtual void	print () const

void	output_connectivity (std::ostream &os) const
	writes out a list of all the edges in the graph More...

void	output_dimacs (std::ostream &os) const
	writes out a connectivity description of the graph in the famous dimacs format. (where the first column "DIMACS:" should be sed'ed out) More...

virtual void	prepare_for_simulated_annealing ()
	iterate across edges and nodes and allow them to prepare for simulated annealing More...

void	set_edge_weight (int node1, int node2, Real edge_weight)

Real	get_edge_weight (int node1, int node2) const

bool	any_vertex_state_unassigned () const
	Returns true if any node in the graph is in state 0, the unassigned state. More...

void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &one_body_energies)
	takes one FArray of energies – one energy for each state for each node More...

void	update_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &old_energy1b, ObjexxFCL::FArray1< core::PackerEnergy > &new_energy1b)
	decrements the one body energies by the values held in old_energy1b, increments the one body energies by the values held in new_energy1b, and copies new_energy1b into old_energy1b. More...

void	zero_one_body_energies_for_node (int node)

void	add_to_nodes_one_body_energy (int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies)

void	add_to_nodes_one_body_energy (int node_ind, ObjexxFCL::FArray1< core::PackerEnergy > const &one_body_energies)

void	add_to_nodes_one_body_energy (int node_ind, int state_id, core::PackerEnergy const one_body_energy)
	interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy More...

void	set_number_of_energy_sum_vertex_groups (int num_groups)
	a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More...

void	set_vertex_member_of_group (int vertex, int group)
	a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More...

void	print_vertex_groups ()

int	count_connected_components_and_initialize_vertex_groups ()
	makes a depth first traversal of the graph, counting the number of connected components, and initializes the vertex group memberships to reflect the connected components. Returns the number of connected components in the graph. More...

void	note_vertex_reached (int node_index)
	marks a vertex as belonging to the connected component currently being traversed in the depth first traversal. More...

bool	vertex_already_reached (int node_index)
	used by class NodeBase during the depth-first traversal to determine the number of connected components in the graph. returns true if the dft has already reached the node. More...

bool	get_vertex_member_of_energy_sum_group (int node_index, int group_id)

virtual unsigned int	getTotalMemoryUsage () const

void	reset_edge_list_iterator_for_node (int node_index) const
	set the Graph's (single) edge list iterator to the beginning of the edge list for a particular node More...

void	increment_edge_list_iterator () const
	increment the (single) edge list iterator to the next element More...

bool	edge_list_iterator_at_end () const
	test: have we arrived at the edge list end? More...

EdgeBase const &	get_edge () const
	return a const reference to an edge pointed at by the list iterator More...

EdgeBase const *	find_edge (int node1, int node2) const
	returns the edge connecting node1 and node2 More...

EdgeBase *	find_edge (int node1, int node2)

NodeBase *	get_node (int index) const

int	get_num_edges () const

std::list< EdgeBase * >::iterator	get_edge_list_begin ()

std::list< EdgeBase * > ::const_iterator	get_edge_list_begin () const

std::list< EdgeBase * > ::const_iterator	get_edge_list_end () const

Protected Member Functions
virtual NodeBase *	create_new_node (int node_index, int num_states)
	factory method that instantiates a DoubleDensePDNode. More...

virtual EdgeBase *	create_new_edge (int index1, int index2)
	factory method that instantiates a DoubleDensePDEdge More...

void	update_internal_energy_totals ()
	removes numerical drift that can accumulate over the course of many state assignment changes within simulated annealing More...

DoubleDensePDNode *	get_dpd_node (int index) const

Protected Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph
FixedBBNode const *	get_fixedbb_node (int node_index) const
	Downcasts. More...

FixedBBNode *	get_fixedbb_node (int node_index)

FixedBBEdge const *	get_fixedbb_edge (int node1, int node2) const

FixedBBEdge *	get_fixedbb_edge (int node1, int node2)

Protected Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase
void	drop_edge (std::list< EdgeBase * >::iterator edge)
	removes edge from edge list at iterator iter More...

int	get_node_state_offset (int index) const

bool	mine (EdgeBase const *edge) const

Private Member Functions
	DoubleDensePDInteractionGraph ()

	DoubleDensePDInteractionGraph (DoubleDensePDInteractionGraph const &)

DoubleDensePDInteractionGraph &	operator= (DoubleDensePDInteractionGraph const &)

Private Attributes
int	num_commits_since_last_update_

core::PackerEnergy	total_energy_current_state_assignment_

core::PackerEnergy	total_energy_alternate_state_assignment_

int	node_considering_alt_state_

Static Private Attributes
static const int	COMMIT_LIMIT_BETWEEN_UPDATES = 1024

Constructor & Destructor Documentation

core::pack::interaction_graph::DoubleDensePDInteractionGraph::DoubleDensePDInteractionGraph ( int num_nodes )

main constructor: no default nor copy constructors provided.

Parameters

num_nodes - [in] - the number of nodes in this graph

core::pack::interaction_graph::DoubleDensePDInteractionGraph::DoubleDensePDInteractionGraph ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

void core::pack::interaction_graph::DoubleDensePDInteractionGraph::blanket_assign_state_0 ( )

virtual

assigns the state of all nodes in the interaction graph to their unassigned or zero states.

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleDensePDNode::assign_zero_state(), get_dpd_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), and total_energy_current_state_assignment_.

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDInteractionGraph::commit_considered_substitution ( )

virtual

Accepts (commits) the state change previously considered in a call to consider_substitution and returns the energy of the entire graph.

to avoid too much numerical drift from accumulating, the bookkeeping arrays are updated once every 2^10 state commits

Implements core::pack::interaction_graph::InteractionGraphBase.

References COMMIT_LIMIT_BETWEEN_UPDATES, get_dpd_node(), node_considering_alt_state_, num_commits_since_last_update_, total_energy_alternate_state_assignment_, total_energy_current_state_assignment_, and update_internal_energy_totals().

void core::pack::interaction_graph::DoubleDensePDInteractionGraph::consider_substitution	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_energy_for_node
	)

virtual

considers altering the state of a particular node; returns the change in energy that the state substitution would produce

to avoid too much numerical drift from accumulating, the bookkeeping arrays are updated once every 2^10 state commits

Parameters

node_ind	- [in] - the index of the node considering a state change
new_state	- [in] - the new state that node is considering
alt_total_energy	- [out] - the total network energy produced under the new state
delta_energy	- [out] - the change in energy produced under the substitution
prev_energy_for_node	- [out] - the sum of the one and two body energies for this node under the current state assignment

Implements core::pack::interaction_graph::InteractionGraphBase.

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

virtual

returns the amount of dynamic memory allocated for a single DoubleDensePDInteractionGraph and recurses on the parent class. Does not account for any of the edges or nodes that the graph contains: that part of the algorithm is implemented by the InteractionGraphBase class.

Reimplemented from core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::InteractionGraphBase::count_dynamic_memory().

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

virtual

returns the amount of static memory allocated for a single DoubleDensePDInteractionGraph. Does not account for any of the edges or nodes that the graph contains: that part of the algorithm is implemented by the InteractionGraphBase class.

Implements core::pack::interaction_graph::InteractionGraphBase.

References DoubleDensePDInteractionGraph().

EdgeBase * core::pack::interaction_graph::DoubleDensePDInteractionGraph::create_new_edge	(	int	index1,
		int	index2
	)

protectedvirtual

factory method that instantiates a DoubleDensePDEdge

Parameters

index1	- [in] - the smaller-indexed node this edge is incident upon
index2	- [in] - the larger-indexed node this edge is incident upon

Implements core::pack::interaction_graph::InteractionGraphBase.

NodeBase * core::pack::interaction_graph::DoubleDensePDInteractionGraph::create_new_node	(	int	node_index,
		int	num_states
	)

protectedvirtual

factory method that instantiates a DoubleDensePDNode.

Parameters

node_index	- [in] - the index of the node being created
num_states	- [in] - the total number of states for the new node

Implements core::pack::interaction_graph::InteractionGraphBase.

DoubleDensePDNode* core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_dpd_node ( int index ) const

inlineprotected

References core::pack::interaction_graph::InteractionGraphBase::get_node().

Referenced by blanket_assign_state_0(), commit_considered_substitution(), get_energy_sum_for_vertex_group(), get_one_body_energy_for_node_state(), print_current_state_assignment(), set_network_state(), set_state_for_node(), and update_internal_energy_totals().

int core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_edge_memory_usage ( ) const

virtual

returns the number of floats used in all edge two-body energy tables

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), and sum().

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_energy_current_state_assignment ( )

virtual

removes all accumulated numerical drift and returns the energy for the current state assignment.

Implements core::pack::interaction_graph::InteractionGraphBase.

References total_energy_current_state_assignment_, and update_internal_energy_totals().

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_energy_sum_for_vertex_group ( int group_id )

virtual

a user may define subsets of the vertex set for which they would like to know the internal energy sum.

For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) ask the graph for the energies of the induced subgraph defined by a particular group.

Parameters

group_id - [in] - the groups for which you're interested in retrieving energies of the induced subgraph

Implements core::pack::interaction_graph::InteractionGraphBase.

References get_dpd_node(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), core::pack::interaction_graph::DoubleDensePDNode::get_one_body_energy_current_state(), and core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group().

virtual int core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_num_aatypes ( ) const

inlinevirtual

Implements core::pack::interaction_graph::FixedBBInteractionGraph.

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_one_body_energy_for_node_state	(	int	node,
		int	state
	)

virtual

returns the one body energy for a particular state on a node

Implements core::pack::interaction_graph::InteractionGraphBase.

References get_dpd_node(), and core::pack::interaction_graph::DoubleDensePDNode::get_one_body_energy().

void core::pack::interaction_graph::DoubleDensePDInteractionGraph::initialize ( rotamer_set::RotamerSetsBase const & rot_sets )

virtual

The DoubleDensePDIG only needs to know how many states each node has. This function causes the downstream instantiation of the DoubleDensePDNodes.

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::rotamer_set::RotamerSets::nmoltenres(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_moltenresidue(), and core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node().

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

private

void core::pack::interaction_graph::DoubleDensePDInteractionGraph::print_current_state_assignment ( ) const

virtual

outputs the current state for each node, useful for debugging

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleDensePDNode::get_current_state(), get_dpd_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), and core::pack::interaction_graph::DoubleDensePDNode::print_internal_energies().

virtual void core::pack::interaction_graph::DoubleDensePDInteractionGraph::set_errorfull_deltaE_threshold ( core::PackerEnergy )

inlinevirtual

Implements core::pack::interaction_graph::InteractionGraphBase.

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDInteractionGraph::set_network_state ( ObjexxFCL::FArray1_int & node_states )

virtual

takes in a vector of states, one state per node, and sets the state for each of the nodes to the specified state.

also calls "update internal energy totals" to undo any numerical noise accumulated during the transition.

Parameters

node_states - [in] - array of states, one for each node.

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleDensePDNode::assign_state(), get_dpd_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), total_energy_current_state_assignment_, and update_internal_energy_totals().

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDInteractionGraph::set_state_for_node	(	int	node_ind,
		int	new_state
	)

virtual

sets the state on node node_ind to new_state

Parameters

node_ind	- [in] - the index of the node in question
new_state	- [in] - the new state the node is being assigned to

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleDensePDNode::assign_state(), get_dpd_node(), total_energy_current_state_assignment_, and update_internal_energy_totals().

void core::pack::interaction_graph::DoubleDensePDInteractionGraph::update_internal_energy_totals ( )

protected

removes numerical drift that can accumulate over the course of many state assignment changes within simulated annealing

Iterates across nodes and then edges to look-up the energies for the current state assignmnet removing any numerical drift which accumulated in the member variable total_energy_current_state_assignment_.

References get_dpd_node(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), num_commits_since_last_update_, and total_energy_current_state_assignment_.

Referenced by commit_considered_substitution(), get_energy_current_state_assignment(), set_network_state(), and set_state_for_node().

Member Data Documentation

const int core::pack::interaction_graph::DoubleDensePDInteractionGraph::COMMIT_LIMIT_BETWEEN_UPDATES = 1024

staticprivate

Referenced by commit_considered_substitution().

int core::pack::interaction_graph::DoubleDensePDInteractionGraph::node_considering_alt_state_

private

Referenced by commit_considered_substitution().

int core::pack::interaction_graph::DoubleDensePDInteractionGraph::num_commits_since_last_update_

private

Referenced by commit_considered_substitution(), and update_internal_energy_totals().

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDInteractionGraph::total_energy_alternate_state_assignment_

private

Referenced by commit_considered_substitution().

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDInteractionGraph::total_energy_current_state_assignment_

private

Referenced by blanket_assign_state_0(), commit_considered_substitution(), get_energy_current_state_assignment(), set_network_state(), set_state_for_node(), and update_internal_energy_totals().

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

src/core/pack/interaction_graph/DoubleDensePDInteractionGraph.hh
src/core/pack/interaction_graph/DoubleDensePDInteractionGraph.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation