core::pack::interaction_graph::NodeBase Class Reference

#include <InteractionGraphBase.hh>

Inheritance diagram for core::pack::interaction_graph::NodeBase:

Collaboration diagram for core::pack::interaction_graph::NodeBase:

List of all members.

Public Member Functions
virtual	~NodeBase ()
	virtual destructor
	NodeBase (InteractionGraphBase *, int node_id, int num_states)
	Main constructor, no default constructor nor copy constructor.
int	get_num_states () const
	returns the number of states for this node
std::list< EdgeBase * >::iterator	add_edge (EdgeBase *edge_ptr)
	adds edge pointer to edge list; returns an iterator to the new list element
void	drop_edge (std::list< EdgeBase * >::iterator edge_iterator)
	removes an edge iterator from the node's edge list
void	drop_all_edges ()
	deletes all edges incident upon this node
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.
virtual void	assign_zero_state ()=0
virtual void	prepare_for_simulated_annealing ()=0
virtual void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b)=0
virtual void	add_to_one_body_energy (int state, core::PackerEnergy energy)=0
virtual void	update_one_body_energy (int state, core::PackerEnergy energy)=0
virtual void	zero_one_body_energies ()=0
virtual void	print () const =0
virtual bool	state_unassigned () const =0
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.
virtual unsigned int	count_static_memory () const =0
virtual unsigned int	count_dynamic_memory () const
	memory accounting scheme
std::list< EdgeBase * > ::const_iterator	edge_list_begin ()
std::list< EdgeBase * > ::const_iterator	edge_list_end ()
Protected Member Functions
void	update_edge_vector ()
	converts edge-list to edge-vector representation
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
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)
bool	get_edge_vector_up_to_date () const
InteractionGraphBase const *	get_owner () const
InteractionGraphBase *	get_owner ()

---

Constructor & Destructor Documentation

core::pack::interaction_graph::NodeBase::~NodeBase

(

)

[virtual]

virtual destructor

NodeBase::~NodeBase

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Authors:

apl

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

Main constructor, no default constructor nor copy constructor.

NodeBase::NodeBase(InteractionGraphBase *, int, int)

Detailed:

Parameters:

owner

- [in] - the owning interaction graph node_id - [in] - the index for this node amongst its owners set num_states - [in] - the number of states for this node

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Authors:

apl

Last Modified:

---

Member Function Documentation

std::list< EdgeBase * >::iterator core::pack::interaction_graph::NodeBase::add_edge

(

EdgeBase *

edge_ptr

)

adds edge pointer to edge list; returns an iterator to the new list element

NodeBase::add_edge

Detailed:

If the other node this node is attached to by edge_ptr has a higher index then the edge is added to the end of its edge list; if the node has a smaller index, the edge pointer is added to the front of the edge list. The presence of a new edge means the edge vector is not up to date.

Parameters:

edge_ptr

- [in] - the new edge

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Authors:

apl

Last Modified:

References core::pack::interaction_graph::EdgeBase::get_other_ind().

virtual void core::pack::interaction_graph::NodeBase::add_to_one_body_energies

(

ObjexxFCL::FArray1< core::PackerEnergy > &

energy1b

)

[pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::OnTheFlyNode, and core::pack::interaction_graph::PDNode.

virtual void core::pack::interaction_graph::NodeBase::add_to_one_body_energy	(	int	state,
		core::PackerEnergy	energy
	)		[pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::OnTheFlyNode, core::pack::interaction_graph::PDNode, and protocols::flexpack::interaction_graph::FlexbbNode.

virtual void core::pack::interaction_graph::NodeBase::assign_zero_state

(

)

[pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::DoubleLazyNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::LazyNode, core::pack::interaction_graph::LinearMemNode, core::pack::interaction_graph::PDNode, and protocols::flexpack::interaction_graph::MinimalistFlexbbNode.

unsigned int core::pack::interaction_graph::NodeBase::count_dynamic_memory

(

)

const [virtual]

memory accounting scheme

Reimplemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::DoubleLazyNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::LazyNode, core::pack::interaction_graph::LinearMemNode, core::pack::interaction_graph::OnTheFlyNode, core::pack::interaction_graph::PDNode, protocols::flexpack::interaction_graph::FlexbbNode, protocols::flexpack::interaction_graph::MinimalistFlexbbNode, and protocols::flexpack::interaction_graph::OTFFlexbbNode.

Referenced by protocols::flexpack::interaction_graph::FlexbbNode::count_dynamic_memory().

virtual unsigned int core::pack::interaction_graph::NodeBase::count_static_memory

(

)

const [pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::DoubleLazyNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::LazyNode, core::pack::interaction_graph::LinearMemNode, core::pack::interaction_graph::OnTheFlyNode, core::pack::interaction_graph::PDNode, and protocols::flexpack::interaction_graph::MinimalistFlexbbNode.

void core::pack::interaction_graph::NodeBase::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.

NodeBase::depth_first_connected_component_counting

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Authors:

apl

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References core::pack::interaction_graph::InteractionGraphBase::note_vertex_reached(), and core::pack::interaction_graph::InteractionGraphBase::vertex_already_reached().

void core::pack::interaction_graph::NodeBase::drop_all_edges

(

)

deletes all edges incident upon this node

NodeBase::drop_all_edges

Detailed:

Parameters:

@par	Global Read:

Global Write:

Remarks:

References:

Authors:

apl

Last Modified:

Referenced by core::pack::interaction_graph::InteractionGraphBase::drop_all_edges_for_node().

void core::pack::interaction_graph::NodeBase::drop_edge

(

std::list< EdgeBase * >::iterator

edge

)

removes an edge iterator from the node's edge list

NodeBase::drop_edge

Detailed:

edges efficiently delete themselves from the edge lists of the nodes they are incident upon by keeping a pair of iterators. Edges request nodes delete them by handing the iterator back to the node.

Parameters:

edge	- [in] - the iterator for this node's edge list that points at the edge which is trying to delete itself

Global Read:

Global Write:

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Authors:

apl

Last Modified:

Referenced by core::pack::interaction_graph::EdgeBase::~EdgeBase().

std::list< EdgeBase * >::const_iterator core::pack::interaction_graph::NodeBase::edge_list_begin

(

)

std::list< EdgeBase * >::const_iterator core::pack::interaction_graph::NodeBase::edge_list_end

(

)

EdgeBase * core::pack::interaction_graph::NodeBase::find_edge

(

int

other_node

)

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.

NodeBase::find_edge

Detailed:

Parameters:

other_node

- [in] - the index of the node that the desired edge connects this node to

Global Read:

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NodeBase const* core::pack::interaction_graph::NodeBase::get_adjacent_node

(

int

index

)

const [inline, protected]

Referenced by core::pack::interaction_graph::FASTERNode::get_adjacent_faster_node(), protocols::flexpack::interaction_graph::FlexbbNode::get_adjacent_flexbb_node(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_adjacent_minimalistflexbb_node(), and protocols::flexpack::interaction_graph::OTFFlexbbNode::get_adjacent_otfflexbb_node().

NodeBase* core::pack::interaction_graph::NodeBase::get_adjacent_node

(

int

index

)

[inline, protected]

bool core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date

(

)

const [inline, protected]

Referenced by core::pack::interaction_graph::FASTERNode::prepare_for_FASTER(), core::pack::interaction_graph::PDNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::LinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::LazyNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::FASTERNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::DoubleLazyNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::DoubleDensePDNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::DensePDNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::PDNode::update_internal_energy_sums(), core::pack::interaction_graph::LinearMemNode::update_internal_energy_sums(), core::pack::interaction_graph::LazyNode::update_internal_energy_sums(), core::pack::interaction_graph::FASTERNode::update_internal_energy_sums(), core::pack::interaction_graph::DoubleLazyNode::update_internal_energy_sums(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_energy_sums(), and core::pack::interaction_graph::DensePDNode::update_internal_energy_sums().

EdgeBase* core::pack::interaction_graph::NodeBase::get_incident_edge

(

int

index

)

[inline, protected]

EdgeBase const* core::pack::interaction_graph::NodeBase::get_incident_edge

(

int

index

)

const [inline, protected]

Referenced by core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::FASTERNode::get_incident_faster_edge(), protocols::flexpack::interaction_graph::FlexbbNode::get_incident_flexbb_edge(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_incident_minimalistflexbb_edge(), protocols::flexpack::interaction_graph::OTFFlexbbNode::get_incident_otfflexbb_edge(), and core::pack::interaction_graph::PDNode::get_weighted_energy_with_higher_indexed_nodes().

int core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node

(

int

index

)

const [inline, protected]

Referenced by core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), core::pack::interaction_graph::FASTERNode::get_random_neighbor(), protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current_following_flexbb_accept(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::LazyNode::print(), core::pack::interaction_graph::DoubleLazyNode::print(), core::pack::interaction_graph::PDNode::print_internal_energies(), core::pack::interaction_graph::LinearMemNode::print_internal_energies(), core::pack::interaction_graph::FASTERNode::print_internal_energies(), core::pack::interaction_graph::DoubleDensePDNode::print_internal_energies(), core::pack::interaction_graph::DensePDNode::print_internal_energies(), and core::pack::interaction_graph::PDNode::update_internal_vectors().

int core::pack::interaction_graph::NodeBase::get_node_index

(

)

const [inline, protected]

Referenced by core::pack::interaction_graph::PDNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::LazyNode::assign_state(), core::pack::interaction_graph::FASTERNode::assign_state(), core::pack::interaction_graph::DoubleLazyNode::assign_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_state(), core::pack::interaction_graph::DensePDNode::assign_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state(), core::pack::interaction_graph::PDNode::assign_zero_state(), core::pack::interaction_graph::LinearMemNode::assign_zero_state(), core::pack::interaction_graph::LazyNode::assign_zero_state(), core::pack::interaction_graph::FASTERNode::assign_zero_state(), core::pack::interaction_graph::DoubleLazyNode::assign_zero_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_zero_state(), core::pack::interaction_graph::DensePDNode::assign_zero_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution(), core::pack::interaction_graph::PDNode::commit_considered_substitution(), core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), core::pack::interaction_graph::LazyNode::commit_considered_substitution(), core::pack::interaction_graph::FASTERNode::commit_considered_substitution(), core::pack::interaction_graph::DoubleLazyNode::commit_considered_substitution(), core::pack::interaction_graph::DoubleDensePDNode::commit_considered_substitution(), core::pack::interaction_graph::DensePDNode::commit_considered_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::FASTERNode::get_deltaE_for_relaxed_state_following_perturbation(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), core::pack::interaction_graph::PDNode::get_weighted_energy_with_higher_indexed_nodes(), protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current_following_flexbb_accept(), protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump(), protocols::flexpack::interaction_graph::FlexbbNode::inform_incident_edges_about_partial_state_assignment(), core::pack::interaction_graph::LinearMemNode::partial_assign_state(), core::pack::interaction_graph::LazyNode::partial_assign_state(), core::pack::interaction_graph::FASTERNode::partial_assign_state(), core::pack::interaction_graph::DoubleLazyNode::partial_assign_state(), core::pack::interaction_graph::LinearMemNode::prepare_for_simulated_annealing(), protocols::flexpack::interaction_graph::FlexbbNode::print(), core::pack::interaction_graph::PDNode::print(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::LazyNode::print(), core::pack::interaction_graph::FASTERNode::print(), core::pack::interaction_graph::DoubleLazyNode::print(), core::pack::interaction_graph::DoubleDensePDNode::print(), core::pack::interaction_graph::DensePDNode::print(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution(), core::pack::interaction_graph::FASTERNode::relax_neighbors(), protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs(), core::pack::interaction_graph::FASTERNode::set_perturbed_state(), core::pack::interaction_graph::PDNode::update_internal_vectors(), and protocols::flexpack::interaction_graph::FlexbbNode::write_current_state_to_state_array().

int core::pack::interaction_graph::NodeBase::get_num_edges_to_larger_indexed_nodes

(

)

const [inline, protected]

Referenced by core::pack::interaction_graph::PDNode::update_internal_vectors().

int core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes

(

)

const [inline, protected]

Referenced by core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_perturbed_state(), protocols::flexpack::interaction_graph::FlexbbNode::count_energy_to_node_in_my_fragtotalE(), core::pack::interaction_graph::FASTERNode::get_total_energy_in_curr_state_assignment_for_all_states(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution(), core::pack::interaction_graph::PDNode::project_deltaE_for_substitution(), core::pack::interaction_graph::FASTERNode::project_deltaE_for_substitution(), core::pack::interaction_graph::DensePDNode::project_deltaE_for_substitution(), and core::pack::interaction_graph::DoubleDensePDNode::update_internal_vectors().

int core::pack::interaction_graph::NodeBase::get_num_incident_edges

(

)

const [inline, protected]

Referenced by core::pack::interaction_graph::PDNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::LazyNode::assign_state(), core::pack::interaction_graph::FASTERNode::assign_state(), core::pack::interaction_graph::DoubleLazyNode::assign_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_state(), core::pack::interaction_graph::DensePDNode::assign_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state(), core::pack::interaction_graph::PDNode::assign_zero_state(), core::pack::interaction_graph::LinearMemNode::assign_zero_state(), core::pack::interaction_graph::LazyNode::assign_zero_state(), core::pack::interaction_graph::FASTERNode::assign_zero_state(), core::pack::interaction_graph::DoubleLazyNode::assign_zero_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_zero_state(), core::pack::interaction_graph::DensePDNode::assign_zero_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution(), core::pack::interaction_graph::PDNode::commit_considered_substitution(), core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), core::pack::interaction_graph::LazyNode::commit_considered_substitution(), core::pack::interaction_graph::FASTERNode::commit_considered_substitution(), core::pack::interaction_graph::DoubleLazyNode::commit_considered_substitution(), core::pack::interaction_graph::DoubleDensePDNode::commit_considered_substitution(), core::pack::interaction_graph::DensePDNode::commit_considered_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment(), core::pack::interaction_graph::FASTERNode::complete_partial_state_assignment(), core::pack::interaction_graph::LinearMemNode::complete_state_assignment(), core::pack::interaction_graph::LazyNode::complete_state_assignment(), core::pack::interaction_graph::DoubleLazyNode::complete_state_assignment(), core::pack::interaction_graph::OnTheFlyNode::distinguish_backbone_and_sidechain(), core::pack::interaction_graph::FASTERNode::get_deltaE_for_relaxed_state_following_perturbation(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), core::pack::interaction_graph::FASTERNode::get_random_neighbor(), core::pack::interaction_graph::FASTERNode::get_total_energy_in_curr_state_assignment_for_all_states(), core::pack::interaction_graph::PDNode::get_weighted_energy_with_higher_indexed_nodes(), protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current(), protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current_following_flexbb_accept(), protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_considered_fixedbb_substition_uncommitted(), protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump(), protocols::flexpack::interaction_graph::FlexbbNode::inform_incident_edges_about_partial_state_assignment(), core::pack::interaction_graph::LinearMemNode::partial_assign_state(), core::pack::interaction_graph::LazyNode::partial_assign_state(), core::pack::interaction_graph::FASTERNode::partial_assign_state(), core::pack::interaction_graph::DoubleLazyNode::partial_assign_state(), core::pack::interaction_graph::FASTERNode::prep_for_neighbors_perturbation(), core::pack::interaction_graph::FASTERNode::prepare_for_FASTER(), core::pack::interaction_graph::LinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::LazyNode::print(), core::pack::interaction_graph::DoubleLazyNode::print(), core::pack::interaction_graph::PDNode::print_internal_energies(), core::pack::interaction_graph::LinearMemNode::print_internal_energies(), core::pack::interaction_graph::LazyNode::print_internal_energies(), core::pack::interaction_graph::FASTERNode::print_internal_energies(), core::pack::interaction_graph::DoubleLazyNode::print_internal_energies(), core::pack::interaction_graph::DoubleDensePDNode::print_internal_energies(), core::pack::interaction_graph::DensePDNode::print_internal_energies(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution(), core::pack::interaction_graph::PDNode::project_deltaE_for_substitution(), core::pack::interaction_graph::FASTERNode::project_deltaE_for_substitution(), core::pack::interaction_graph::DoubleDensePDNode::project_deltaE_for_substitution(), core::pack::interaction_graph::DensePDNode::project_deltaE_for_substitution(), core::pack::interaction_graph::FASTERNode::relax_neighbors(), core::pack::interaction_graph::FASTERNode::reset_relaxed_for_neighbors(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::resolve_uncommitted_substitution(), core::pack::interaction_graph::FASTERNode::set_perturbed_state(), core::pack::interaction_graph::FASTERNode::tell_neighbors_to_prep_for_relaxation(), protocols::flexpack::interaction_graph::FlexbbNode::update_internal_energy_sums(), core::pack::interaction_graph::PDNode::update_internal_energy_sums(), core::pack::interaction_graph::LinearMemNode::update_internal_energy_sums(), core::pack::interaction_graph::LazyNode::update_internal_energy_sums(), core::pack::interaction_graph::FASTERNode::update_internal_energy_sums(), core::pack::interaction_graph::DoubleLazyNode::update_internal_energy_sums(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_energy_sums(), core::pack::interaction_graph::DensePDNode::update_internal_energy_sums(), protocols::flexpack::interaction_graph::FlexbbNode::update_internal_vectors(), core::pack::interaction_graph::PDNode::update_internal_vectors(), core::pack::interaction_graph::FASTERNode::update_internal_vectors(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_vectors(), and core::pack::interaction_graph::DensePDNode::update_internal_vectors().

int core::pack::interaction_graph::NodeBase::get_num_states

(

)

const

returns the number of states for this node

NodeBase::~get_num_states

Detailed:

Global Read:

Global Write:

Remarks:

References:

Authors:

apl

Last Modified:

Referenced by core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_perturbed_state(), protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energies(), core::pack::interaction_graph::PDNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::LazyNode::assign_state(), core::pack::interaction_graph::FASTERNode::assign_state(), core::pack::interaction_graph::DoubleLazyNode::assign_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_state(), core::pack::interaction_graph::DensePDNode::assign_state(), protocols::flexpack::interaction_graph::FlexbbNode::FlexbbNode(), protocols::flexpack::interaction_graph::FlexbbNode::get_all_states(), core::pack::interaction_graph::PDNode::get_sparse_mat_info_for_state(), core::pack::interaction_graph::FASTERNode::get_total_energy_in_curr_state_assignment_for_all_states(), core::pack::interaction_graph::FASTERNode::partial_assign_state_with_lowest_one_body_energy(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_closest_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state(), core::pack::interaction_graph::FASTERNode::prepare_for_FASTER(), core::pack::interaction_graph::LinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::PDNode::print(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::LazyNode::print(), core::pack::interaction_graph::FASTERNode::print(), core::pack::interaction_graph::DoubleLazyNode::print(), core::pack::interaction_graph::DoubleDensePDNode::print(), core::pack::interaction_graph::DensePDNode::print(), core::pack::interaction_graph::FASTERNode::relax(), core::pack::interaction_graph::FASTERNode::relax_after_neighbors_perturbation(), protocols::flexpack::interaction_graph::FlexbbNode::set_amino_acid_types(), core::pack::interaction_graph::PDNode::set_amino_acid_types(), protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs(), protocols::flexpack::interaction_graph::FlexbbNode::set_num_states_per_backbone(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_vectors(), core::pack::interaction_graph::PDNode::update_one_body_energies(), core::pack::interaction_graph::PDNode::zero_one_body_energies(), core::pack::interaction_graph::FASTERNode::zero_one_body_energies(), core::pack::interaction_graph::DoubleDensePDNode::zero_one_body_energies(), and core::pack::interaction_graph::DensePDNode::zero_one_body_energies().

InteractionGraphBase const* core::pack::interaction_graph::NodeBase::get_owner

(

)

const [inline, protected]

Referenced by core::pack::interaction_graph::FASTERNode::get_fasterig_owner(), protocols::flexpack::interaction_graph::FlexbbNode::get_flexbbig_owner(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_minimalistflexbbig_owner(), and protocols::flexpack::interaction_graph::OTFFlexbbNode::get_otfflexbbig_owner().

InteractionGraphBase* core::pack::interaction_graph::NodeBase::get_owner

(

)

[inline, protected]

virtual void core::pack::interaction_graph::NodeBase::prepare_for_simulated_annealing

(

)

[pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::DoubleLazyNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::LazyNode, core::pack::interaction_graph::LinearMemNode, core::pack::interaction_graph::PDNode, protocols::flexpack::interaction_graph::FlexbbNode, and protocols::flexpack::interaction_graph::MinimalistFlexbbNode.

Referenced by core::pack::interaction_graph::InteractionGraphBase::prepare_for_simulated_annealing().

virtual void core::pack::interaction_graph::NodeBase::print

(

)

const [pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::DoubleLazyNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::LazyNode, core::pack::interaction_graph::LinearMemNode, core::pack::interaction_graph::PDNode, protocols::flexpack::interaction_graph::FlexbbNode, protocols::flexpack::interaction_graph::MinimalistFlexbbNode, and protocols::flexpack::interaction_graph::OTFFlexbbNode.

virtual bool core::pack::interaction_graph::NodeBase::state_unassigned

(

)

const [pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::DoubleLazyNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::LazyNode, core::pack::interaction_graph::LinearMemNode, core::pack::interaction_graph::PDNode, and protocols::flexpack::interaction_graph::FlexbbNode.

Referenced by core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned().

void core::pack::interaction_graph::NodeBase::update_edge_vector

(

)

[protected]

converts edge-list to edge-vector representation

NodeBase::update_edge_vector

Detailed:

Parameters:

Global Read:

Global Write:

Remarks:

References:

Authors:

apl

Last Modified:

Referenced by protocols::flexpack::interaction_graph::FlexbbNode::update_internal_vectors(), core::pack::interaction_graph::PDNode::update_internal_vectors(), core::pack::interaction_graph::FASTERNode::update_internal_vectors(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_vectors(), and core::pack::interaction_graph::DensePDNode::update_internal_vectors().

virtual void core::pack::interaction_graph::NodeBase::update_one_body_energy	(	int	state,
		core::PackerEnergy	energy
	)		[pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::OnTheFlyNode, core::pack::interaction_graph::PDNode, and protocols::flexpack::interaction_graph::FlexbbNode.

virtual void core::pack::interaction_graph::NodeBase::zero_one_body_energies

(

)

[pure virtual]

Implemented in core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, core::pack::interaction_graph::FASTERNode, core::pack::interaction_graph::OnTheFlyNode, core::pack::interaction_graph::PDNode, and protocols::flexpack::interaction_graph::FlexbbNode.

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

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