#include <SymmMinimalistInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SymmMinimalistNode:

Public Member Functions
	SymmMinimalistNode (InteractionGraphBase *owner, int node_id, int num_states)
	main constructor, no default ctor, uncopyable More...

	~SymmMinimalistNode () override
	virtual dstor More...

void	prepare_for_simulated_annealing () override
	symmin ig does not have to do anything before sim annealing begins More...

void	print () const override
	write internal energy and bookkeeping data to standard out More...

bool	state_unassigned () const override
	state 0 represents the unasigned state More...

virtual core::PackerEnergy	get_totalE () const
	return the total energy for this node; includes full energies to neighboring residues More...

void	assign_zero_state () override
	set to state 0 More...

void	assign_state (int new_state)
	set to a particular state – updates the energies internally More...

void	partial_assign_state (int new_state)
	first half of an entire-graph state assignment that avoids unnecessary energy updates as produced in assign_state. Adjust all node's states first, then update all energies. More...

void	complete_state_assignment ()
	second half of the entire-graph state assignment. More...

int	get_current_state () const
	return the index of the currently assigned state More...

core::PackerEnergy	get_one_body_energy_current_state () const
	return the one-body energy for the currently assigned state More...

core::PackerEnergy	project_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_node_energy)
	compute the change in energy induced by substituting the currently assigned state with some alternative state More...

void	commit_considered_substitution ()
	proceed to change the currently assigned state to the alternative state considered in the last call to project_deltaE_for_substitution More...

void	acknowledge_last_substititon_not_committed ()
	update bookkeeping info to acknolwedge that the last alternative state considered was not in fact chosen for the currently assigned state. More...

core::PackerEnergy	compute_pair_energy_for_current_state (int edge_making_energy_request)
	comupute the interaction energy between the currently assigned state on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two More...

core::PackerEnergy	compute_pair_energy_for_alternate_state (int edge_making_energy_request)
	comupute the interaction energy between the alternate state being considered on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two More...

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

void	acknowledge_neighbors_partial_state_substitution (int edge_to_altered_neighbor, int other_node_new_state)

void	print_internal_energies () const

void	update_internal_energy_sums ()

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override
	memory accounting scheme More...

SymmMinimalistEdge const *	get_incident_symmin_edge (int index) const

SymmMinimalistEdge *	get_incident_symmin_edge (int index)

SymmMinimalistNode const *	get_adjacent_symmin_node (int index) const

SymmMinimalistNode *	get_adjacent_symmin_node (int index)

SymmMinimalistInteractionGraph const *	get_symmin_ig_owner () const

SymmMinimalistInteractionGraph *	get_symmin_ig_owner ()

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

	~SymmOnTheFlyNode () override

void	set_rotamers (rotamer_set::RotamerSetCOP rotamers)

void	zero_one_body_energies () override

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

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

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

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

virtual void	zero_one_body_energy (int state)

int	get_num_res_types () const
	the number of distinct ResidueType objects pointed to by all of the rotamrs for this node. More...

int	get_num_restype_groups () const
	the number of ResidueType groups, as defined by the RotamerSet's logic for grouping different ResidueType objects which have the same "name3" and the same neighbor radius. More...

utility::vector1< int > &	get_num_states_for_restype_group ()

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

int	get_num_states_for_restype_group (int restype_group)

int	get_state_offset_for_restype_group (int restype_group) const

core::PackerEnergy	get_one_body_energy (int state) const

bool	distinguish_backbone_and_sidechain () const

void	distinguish_backbone_and_sidechain (bool setting)

unsigned int	count_dynamic_memory () const override

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

conformation::Residue const &	get_rotamer (int state, int subunit) const
	Returns a reference to the rotamer object in the requested subunit. This reference is valid only until the next call to get_rotamer, and which point, the coordinates inside the requested rotamer may change. More...

conformation::Residue const &	get_asu_rotamer (int state) const
	Returns a reference to the rotamer object in the asymmetric unit. More...

BoundingSphere	sc_bounding_sphere (int state, int subunit) const
	Returns a bounding sphere for the sidechain of a given state on a particular subunit. More...

BoundingSphere	bb_bounding_sphere (int subunit) const
	Returns a bounding sphere for the backbone on a particular subunit. More...

SymmOnTheFlyEdge *	get_incident_otf_edge (int edge)

SymmOnTheFlyEdge const *	get_incident_otf_edge (int edge) const

SymmOnTheFlyNode *	get_adjacent_otf_node (int index)

SymmOnTheFlyNode const *	get_adjacent_otf_node (int index) const

SymmOnTheFlyInteractionGraph *	get_on_the_fly_owner ()

SymmOnTheFlyInteractionGraph const *	get_on_the_fly_owner () const

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)

Private Member Functions
void	update_internal_vectors ()

Private Attributes
utility::vector1< int >	neighbors_curr_state_
	Data. More...

int	current_state_

core::PackerEnergy	curr_state_one_body_energy_

core::PackerEnergy	curr_state_total_energy_

utility::vector1 < core::PackerEnergy >	curr_state_two_body_energies_

int	alternate_state_

core::PackerEnergy	alternate_state_one_body_energy_

core::PackerEnergy	alternate_state_total_energy_

utility::vector1 < core::PackerEnergy >	alternate_state_two_body_energies_

bool	alternate_state_is_being_considered_

bool	already_prepped_for_simA_

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

typedef numeric::HomogeneousTransform < Real >	HTReal

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 ()

Constructor & Destructor Documentation

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

main constructor, no default ctor, uncopyable

main constructor, no default or copy constructors

Referenced by count_static_memory().

core::pack::interaction_graph::SymmMinimalistNode::~SymmMinimalistNode ( )

overridedefault

virtual dstor

Member Function Documentation

void core::pack::interaction_graph::SymmMinimalistNode::acknowledge_last_substititon_not_committed ( )

update bookkeeping info to acknolwedge that the last alternative state considered was not in fact chosen for the currently assigned state.

References alternate_state_is_being_considered_.

Referenced by core::pack::interaction_graph::SymmMinimalistInteractionGraph::consider_substitution().

void core::pack::interaction_graph::SymmMinimalistNode::acknowledge_neighbors_partial_state_substitution	(	int	edge_to_altered_neighbor,
		int	other_node_new_state
	)

References curr_state_total_energy_, curr_state_two_body_energies_, and neighbors_curr_state_.

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

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

inline

References curr_state_total_energy_, curr_state_two_body_energies_, and neighbors_curr_state_.

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

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

set to a particular state – updates the energies internally

References core::pack::interaction_graph::SymmMinimalistEdge::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_symmin_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 core::pack::interaction_graph::SymmOnTheFlyNode::get_one_body_energy().

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

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

overridevirtual

set to state 0

puts the symminNode in the 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_symmin_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

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

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

proceed to change the currently assigned state to the alternative state considered in the last call to project_deltaE_for_substitution

commits the last substitution that was considered by this Node

References core::pack::interaction_graph::SymmMinimalistEdge::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_symmin_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

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

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

second half of the entire-graph state assignment.

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

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

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistNode::compute_pair_energy_for_alternate_state ( int edge_making_energy_request )

comupute the interaction energy between the alternate state being considered on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

References alternate_state_, core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), and neighbors_curr_state_.

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

comupute the interaction energy between the currently assigned state on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

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

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

overridevirtual

memory accounting scheme

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

References alternate_state_two_body_energies_, core::pack::interaction_graph::SymmOnTheFlyNode::count_dynamic_memory(), curr_state_two_body_energies_, and neighbors_curr_state_.

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

overridevirtual

Implements core::pack::interaction_graph::SymmOnTheFlyNode.

References SymmMinimalistNode().

SymmMinimalistNode const * core::pack::interaction_graph::SymmMinimalistNode::get_adjacent_symmin_node ( int index ) const

inline

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

SymmMinimalistNode * core::pack::interaction_graph::SymmMinimalistNode::get_adjacent_symmin_node ( int index )

inline

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

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

inline

return the index of the currently assigned state

References current_state_.

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

SymmMinimalistEdge const * core::pack::interaction_graph::SymmMinimalistNode::get_incident_symmin_edge ( int index ) const

inline

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

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

SymmMinimalistEdge * core::pack::interaction_graph::SymmMinimalistNode::get_incident_symmin_edge ( int index )

inline

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

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

inline

return the one-body energy for the currently assigned state

References curr_state_one_body_energy_.

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

SymmMinimalistInteractionGraph const * core::pack::interaction_graph::SymmMinimalistNode::get_symmin_ig_owner ( ) const

inline

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

SymmMinimalistInteractionGraph * core::pack::interaction_graph::SymmMinimalistNode::get_symmin_ig_owner ( )

inline

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

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

inlinevirtual

return the total energy for this node; includes full energies to neighboring residues

References curr_state_total_energy_.

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

first half of an entire-graph state assignment that avoids unnecessary energy updates as produced in assign_state. Adjust all node's states first, then update all energies.

References core::pack::interaction_graph::SymmMinimalistEdge::acknowledge_partial_state_change(), alternate_state_is_being_considered_, assign_zero_state(), current_state_, get_incident_symmin_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

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

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

overridevirtual

symmin ig does not have to do anything before sim annealing begins

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

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

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

overridevirtual

write internal energy and bookkeeping data to standard out

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

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

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

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

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(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and core::pack::interaction_graph::T().

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

compute the change in energy induced by substituting the currently assigned state with some alternative state

Referenced by core::pack::interaction_graph::SymmMinimalistInteractionGraph::consider_substitution().

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

inlineoverridevirtual

state 0 represents the unasigned state

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

References current_state_.

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

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

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

private

References alternate_state_two_body_energies_, curr_state_two_body_energies_, 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().

Member Data Documentation

bool core::pack::interaction_graph::SymmMinimalistNode::already_prepped_for_simA_

private

Referenced by prepare_for_simulated_annealing().

int core::pack::interaction_graph::SymmMinimalistNode::alternate_state_

private

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

bool core::pack::interaction_graph::SymmMinimalistNode::alternate_state_is_being_considered_

private

Referenced by acknowledge_last_substititon_not_committed(), assign_state(), assign_zero_state(), commit_considered_substitution(), partial_assign_state(), and print().

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistNode::alternate_state_one_body_energy_

private

Referenced by commit_considered_substitution(), and print().

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistNode::alternate_state_total_energy_

private

Referenced by commit_considered_substitution().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmMinimalistNode::alternate_state_two_body_energies_

private

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

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistNode::curr_state_one_body_energy_

private

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

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistNode::curr_state_total_energy_

private

Referenced by acknowledge_neighbors_partial_state_substitution(), acknowledge_neighbors_state_substitution(), assign_state(), assign_zero_state(), commit_considered_substitution(), complete_state_assignment(), get_totalE(), print_internal_energies(), and update_internal_energy_sums().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmMinimalistNode::curr_state_two_body_energies_

private

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

int core::pack::interaction_graph::SymmMinimalistNode::current_state_

private

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), complete_state_assignment(), compute_pair_energy_for_current_state(), get_current_state(), partial_assign_state(), print(), print_internal_energies(), and state_unassigned().

utility::vector1< int > core::pack::interaction_graph::SymmMinimalistNode::neighbors_curr_state_

private

Data.

Referenced by acknowledge_neighbors_partial_state_substitution(), acknowledge_neighbors_state_substitution(), compute_pair_energy_for_alternate_state(), compute_pair_energy_for_current_state(), count_dynamic_memory(), and update_internal_vectors().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation