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core::pack::interaction_graph::NodeBase Class Referenceabstract

#include <InteractionGraphBase.hh>

Inheritance diagram for core::pack::interaction_graph::NodeBase:
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Collaboration diagram for core::pack::interaction_graph::NodeBase:
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Public Member Functions

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...
 
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. More...
 
virtual unsigned int count_static_memory () const =0
 
virtual unsigned int count_dynamic_memory () const
 memory accounting scheme 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_edge_vector ()
 converts edge-list to edge-vector representation More...
 
bool get_edge_vector_up_to_date () const
 
InteractionGraphBase const * get_owner () const
 
InteractionGraphBase * get_owner ()
 

Private Member Functions

 NodeBase ()
 
 NodeBase (NodeBase const &)
 
NodeBase & operator= (NodeBase &)
 

Private Attributes

int node_index_
 
int num_states_
 
int num_incident_edges_
 
int num_edges_to_smaller_indexed_nodes_
 
int num_edges_to_larger_indexed_nodes_
 
std::list< EdgeBase * > incident_edge_list_
 
std::vector< EdgeBase * > incident_edge_vector_
 
std::vector< int > adjacent_node_ind_
 
std::vector< NodeBase * > adjacent_node_
 
bool edge_vector_up_to_date_
 
InteractionGraphBase * owner_
 

Detailed Description

Definition at line 48 of file InteractionGraphBase.hh.

Constructor & Destructor Documentation

core::pack::interaction_graph::NodeBase::~NodeBase ( )
virtual

virtual destructor

NodeBase::~NodeBase

Detailed:
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

Definition at line 63 of file InteractionGraphBase.cc.

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
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

Definition at line 91 of file InteractionGraphBase.cc.

core::pack::interaction_graph::NodeBase::NodeBase ( )
private
core::pack::interaction_graph::NodeBase::NodeBase ( NodeBase const &  )
private

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
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

Definition at line 148 of file InteractionGraphBase.cc.

References edge_vector_up_to_date_, core::pack::interaction_graph::EdgeBase::get_other_ind(), incident_edge_list_, node_index_, num_edges_to_larger_indexed_nodes_, num_edges_to_smaller_indexed_nodes_, and num_incident_edges_.

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

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

virtual void core::pack::interaction_graph::NodeBase::assign_zero_state ( )
pure virtual

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

Definition at line 372 of file InteractionGraphBase.cc.

References adjacent_node_, adjacent_node_ind_, incident_edge_list_, and incident_edge_vector_.

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

virtual unsigned int core::pack::interaction_graph::NodeBase::count_static_memory ( ) const
pure virtual

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

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

Detailed:
Parameters
@parGlobal Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

Definition at line 292 of file InteractionGraphBase.cc.

References incident_edge_list_, node_index_, core::pack::interaction_graph::InteractionGraphBase::note_vertex_reached(), owner_, 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
@parGlobal Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

Definition at line 223 of file InteractionGraphBase.cc.

References edge_vector_up_to_date_, and incident_edge_list_.

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:
Remarks
References:
Authors
apl
Last Modified:

Definition at line 188 of file InteractionGraphBase.cc.

References edge_vector_up_to_date_, incident_edge_list_, node_index_, num_edges_to_larger_indexed_nodes_, num_edges_to_smaller_indexed_nodes_, and num_incident_edges_.

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

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

Definition at line 309 of file InteractionGraphBase.cc.

References incident_edge_list_.

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

Definition at line 315 of file InteractionGraphBase.cc.

References incident_edge_list_.

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:
Global Write:
Remarks
References:
Authors
Last Modified:

Definition at line 259 of file InteractionGraphBase.cc.

References incident_edge_list_, and node_index_.

NodeBase const* core::pack::interaction_graph::NodeBase::get_adjacent_node ( int  index) const
inline

Definition at line 133 of file InteractionGraphBase.hh.

References adjacent_node_, and edge_vector_up_to_date_.

Referenced by core::pack::interaction_graph::DoubleLazyNode::get_adjacent_dlazy_node(), core::pack::interaction_graph::DoubleDensePDNode::get_adjacent_dpd_node(), core::pack::interaction_graph::DensePDNode::get_adjacent_dpd_node(), core::pack::interaction_graph::FASTERNode::get_adjacent_faster_node(), protocols::flexpack::interaction_graph::FlexbbNode::get_adjacent_flexbb_node(), core::pack::interaction_graph::LazyNode::get_adjacent_lazy_node(), core::pack::interaction_graph::LinearMemNode::get_adjacent_linmem_node(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_adjacent_minimalistflexbb_node(), protocols::flexpack::interaction_graph::OTFFlexbbNode::get_adjacent_otfflexbb_node(), core::pack::interaction_graph::SymmMinimalistNode::get_adjacent_symmin_node(), and core::pack::interaction_graph::SymmLinearMemNode::get_adjacent_symmlinmem_node().

NodeBase* core::pack::interaction_graph::NodeBase::get_adjacent_node ( int  index)
inline

Definition at line 141 of file InteractionGraphBase.hh.

References adjacent_node_, and edge_vector_up_to_date_.

bool core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date ( ) const
inlineprotected

Definition at line 149 of file InteractionGraphBase.hh.

References edge_vector_up_to_date_.

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

EdgeBase const* core::pack::interaction_graph::NodeBase::get_incident_edge ( int  index) const
inline

These functions are public for the sake of writing good unit tests.

Definition at line 112 of file InteractionGraphBase.hh.

References edge_vector_up_to_date_, and incident_edge_vector_.

Referenced by core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::DoubleLazyNode::get_incident_dlazy_edge(), core::pack::interaction_graph::DoubleDensePDNode::get_incident_dpd_edge(), core::pack::interaction_graph::DensePDNode::get_incident_dpd_edge(), core::pack::interaction_graph::FASTERNode::get_incident_faster_edge(), protocols::flexpack::interaction_graph::FlexbbNode::get_incident_flexbb_edge(), core::pack::interaction_graph::LazyNode::get_incident_lazy_edge(), core::pack::interaction_graph::LinearMemNode::get_incident_linmem_edge(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_incident_minimalistflexbb_edge(), protocols::flexpack::interaction_graph::OTFFlexbbNode::get_incident_otfflexbb_edge(), core::pack::interaction_graph::PDNode::get_incident_pd_edge(), core::pack::interaction_graph::SymmMinimalistNode::get_incident_symmin_edge(), core::pack::interaction_graph::SymmLinearMemNode::get_incident_symmlinmem_edge(), and core::pack::interaction_graph::PDNode::get_weighted_energy_with_higher_indexed_nodes().

EdgeBase* core::pack::interaction_graph::NodeBase::get_incident_edge ( int  index)
inline

Definition at line 119 of file InteractionGraphBase.hh.

References edge_vector_up_to_date_, and incident_edge_vector_.

int core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node ( int  index) const
inline

Definition at line 126 of file InteractionGraphBase.hh.

References adjacent_node_ind_, and edge_vector_up_to_date_.

Referenced by core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::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::SymmMinimalistNode::print(), core::pack::interaction_graph::SymmLinearMemNode::print(), core::pack::interaction_graph::LazyNode::print(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::DoubleLazyNode::print(), core::pack::interaction_graph::FASTERNode::print_internal_energies(), core::pack::interaction_graph::DoubleDensePDNode::print_internal_energies(), core::pack::interaction_graph::DensePDNode::print_internal_energies(), core::pack::interaction_graph::SymmMinimalistNode::print_internal_energies(), core::pack::interaction_graph::SymmLinearMemNode::print_internal_energies(), core::pack::interaction_graph::PDNode::print_internal_energies(), core::pack::interaction_graph::LinearMemNode::print_internal_energies(), core::pack::interaction_graph::LazyNode::update_internal_vectors(), core::pack::interaction_graph::PDNode::update_internal_vectors(), and core::pack::interaction_graph::LinearMemNode::update_internal_vectors().

int core::pack::interaction_graph::NodeBase::get_node_index ( ) const
inline

Definition at line 84 of file InteractionGraphBase.hh.

References node_index_.

Referenced by core::pack::interaction_graph::LazyNode::assign_state(), core::pack::interaction_graph::SymmMinimalistNode::assign_state(), core::pack::interaction_graph::SymmLinearMemNode::assign_state(), core::pack::interaction_graph::FASTERNode::assign_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_state(), core::pack::interaction_graph::DoubleLazyNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::DensePDNode::assign_state(), core::pack::interaction_graph::PDNode::assign_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state(), core::pack::interaction_graph::LazyNode::assign_zero_state(), core::pack::interaction_graph::SymmMinimalistNode::assign_zero_state(), core::pack::interaction_graph::SymmLinearMemNode::assign_zero_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_zero_state(), core::pack::interaction_graph::FASTERNode::assign_zero_state(), core::pack::interaction_graph::DoubleLazyNode::assign_zero_state(), core::pack::interaction_graph::LinearMemNode::assign_zero_state(), core::pack::interaction_graph::DensePDNode::assign_zero_state(), core::pack::interaction_graph::PDNode::assign_zero_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution(), core::pack::interaction_graph::FASTERNode::commit_considered_substitution(), core::pack::interaction_graph::DoubleDensePDNode::commit_considered_substitution(), core::pack::interaction_graph::LazyNode::commit_considered_substitution(), core::pack::interaction_graph::DensePDNode::commit_considered_substitution(), core::pack::interaction_graph::DoubleLazyNode::commit_considered_substitution(), core::pack::interaction_graph::SymmMinimalistNode::commit_considered_substitution(), core::pack::interaction_graph::SymmLinearMemNode::commit_considered_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(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::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::LazyNode::partial_assign_state(), core::pack::interaction_graph::SymmMinimalistNode::partial_assign_state(), core::pack::interaction_graph::SymmLinearMemNode::partial_assign_state(), core::pack::interaction_graph::DoubleLazyNode::partial_assign_state(), core::pack::interaction_graph::LinearMemNode::partial_assign_state(), core::pack::interaction_graph::FASTERNode::partial_assign_state(), core::pack::interaction_graph::SymmLinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::LinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::SymmMinimalistNode::print(), core::pack::interaction_graph::FASTERNode::print(), core::pack::interaction_graph::SymmLinearMemNode::print(), core::pack::interaction_graph::LazyNode::print(), core::pack::interaction_graph::DoubleDensePDNode::print(), protocols::flexpack::interaction_graph::FlexbbNode::print(), core::pack::interaction_graph::DensePDNode::print(), core::pack::interaction_graph::PDNode::print(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::DoubleLazyNode::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::LazyNode::update_internal_vectors(), core::pack::interaction_graph::PDNode::update_internal_vectors(), core::pack::interaction_graph::LinearMemNode::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

Definition at line 102 of file InteractionGraphBase.hh.

References num_edges_to_larger_indexed_nodes_.

Referenced by core::pack::interaction_graph::LazyNode::update_internal_vectors(), and core::pack::interaction_graph::PDNode::update_internal_vectors().

int core::pack::interaction_graph::NodeBase::get_num_edges_to_smaller_indexed_nodes ( ) const
inline

Definition at line 96 of file InteractionGraphBase.hh.

References num_edges_to_smaller_indexed_nodes_.

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::FASTERNode::project_deltaE_for_substitution(), core::pack::interaction_graph::DensePDNode::project_deltaE_for_substitution(), core::pack::interaction_graph::PDNode::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

Definition at line 90 of file InteractionGraphBase.hh.

References num_incident_edges_.

Referenced by core::pack::interaction_graph::LazyNode::assign_state(), core::pack::interaction_graph::SymmMinimalistNode::assign_state(), core::pack::interaction_graph::SymmLinearMemNode::assign_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_state(), core::pack::interaction_graph::FASTERNode::assign_state(), core::pack::interaction_graph::DoubleLazyNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::DensePDNode::assign_state(), core::pack::interaction_graph::PDNode::assign_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state(), core::pack::interaction_graph::LazyNode::assign_zero_state(), core::pack::interaction_graph::SymmMinimalistNode::assign_zero_state(), core::pack::interaction_graph::SymmLinearMemNode::assign_zero_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_zero_state(), core::pack::interaction_graph::FASTERNode::assign_zero_state(), core::pack::interaction_graph::DoubleLazyNode::assign_zero_state(), core::pack::interaction_graph::LinearMemNode::assign_zero_state(), core::pack::interaction_graph::DensePDNode::assign_zero_state(), core::pack::interaction_graph::PDNode::assign_zero_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution(), core::pack::interaction_graph::DoubleDensePDNode::commit_considered_substitution(), core::pack::interaction_graph::FASTERNode::commit_considered_substitution(), core::pack::interaction_graph::LazyNode::commit_considered_substitution(), core::pack::interaction_graph::DensePDNode::commit_considered_substitution(), core::pack::interaction_graph::DoubleLazyNode::commit_considered_substitution(), core::pack::interaction_graph::SymmMinimalistNode::commit_considered_substitution(), core::pack::interaction_graph::SymmLinearMemNode::commit_considered_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(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment(), core::pack::interaction_graph::FASTERNode::complete_partial_state_assignment(), core::pack::interaction_graph::LazyNode::complete_state_assignment(), core::pack::interaction_graph::SymmMinimalistNode::complete_state_assignment(), core::pack::interaction_graph::SymmLinearMemNode::complete_state_assignment(), core::pack::interaction_graph::DoubleLazyNode::complete_state_assignment(), core::pack::interaction_graph::LinearMemNode::complete_state_assignment(), core::pack::interaction_graph::OnTheFlyNode::distinguish_backbone_and_sidechain(), core::pack::interaction_graph::SymmOnTheFlyNode::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::LazyNode::partial_assign_state(), core::pack::interaction_graph::SymmMinimalistNode::partial_assign_state(), core::pack::interaction_graph::SymmLinearMemNode::partial_assign_state(), core::pack::interaction_graph::DoubleLazyNode::partial_assign_state(), core::pack::interaction_graph::LinearMemNode::partial_assign_state(), core::pack::interaction_graph::FASTERNode::partial_assign_state(), core::pack::interaction_graph::FASTERNode::prep_for_neighbors_perturbation(), core::pack::interaction_graph::FASTERNode::prepare_for_FASTER(), core::pack::interaction_graph::SymmLinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::LinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::SymmMinimalistNode::print(), core::pack::interaction_graph::SymmLinearMemNode::print(), core::pack::interaction_graph::LazyNode::print(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::DoubleLazyNode::print(), core::pack::interaction_graph::FASTERNode::print_internal_energies(), core::pack::interaction_graph::DoubleDensePDNode::print_internal_energies(), core::pack::interaction_graph::LazyNode::print_internal_energies(), core::pack::interaction_graph::DensePDNode::print_internal_energies(), core::pack::interaction_graph::DoubleLazyNode::print_internal_energies(), core::pack::interaction_graph::SymmMinimalistNode::print_internal_energies(), core::pack::interaction_graph::SymmLinearMemNode::print_internal_energies(), core::pack::interaction_graph::PDNode::print_internal_energies(), core::pack::interaction_graph::LinearMemNode::print_internal_energies(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::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::PDNode::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(), core::pack::interaction_graph::FASTERNode::update_internal_energy_sums(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_energy_sums(), core::pack::interaction_graph::LazyNode::update_internal_energy_sums(), core::pack::interaction_graph::DensePDNode::update_internal_energy_sums(), core::pack::interaction_graph::DoubleLazyNode::update_internal_energy_sums(), core::pack::interaction_graph::SymmMinimalistNode::update_internal_energy_sums(), core::pack::interaction_graph::SymmLinearMemNode::update_internal_energy_sums(), core::pack::interaction_graph::PDNode::update_internal_energy_sums(), core::pack::interaction_graph::LinearMemNode::update_internal_energy_sums(), protocols::flexpack::interaction_graph::FlexbbNode::update_internal_energy_sums(), core::pack::interaction_graph::FASTERNode::update_internal_vectors(), core::pack::interaction_graph::SymmMinimalistNode::update_internal_vectors(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_vectors(), core::pack::interaction_graph::DensePDNode::update_internal_vectors(), core::pack::interaction_graph::SymmLinearMemNode::update_internal_vectors(), core::pack::interaction_graph::LazyNode::update_internal_vectors(), core::pack::interaction_graph::DoubleLazyNode::update_internal_vectors(), core::pack::interaction_graph::PDNode::update_internal_vectors(), core::pack::interaction_graph::LinearMemNode::update_internal_vectors(), and protocols::flexpack::interaction_graph::FlexbbNode::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:

Definition at line 119 of file InteractionGraphBase.cc.

References num_states_.

Referenced by core::pack::interaction_graph::FASTERNode::acknowledge_neighbors_perturbed_state(), core::pack::interaction_graph::FASTERNode::add_to_one_body_energies(), core::pack::interaction_graph::DoubleDensePDNode::add_to_one_body_energies(), core::pack::interaction_graph::DensePDNode::add_to_one_body_energies(), core::pack::interaction_graph::PDNode::add_to_one_body_energies(), core::pack::interaction_graph::LazyNode::assign_state(), core::pack::interaction_graph::SymmMinimalistNode::assign_state(), core::pack::interaction_graph::SymmLinearMemNode::assign_state(), core::pack::interaction_graph::FASTERNode::assign_state(), core::pack::interaction_graph::DoubleDensePDNode::assign_state(), core::pack::interaction_graph::DoubleLazyNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::DensePDNode::assign_state(), core::pack::interaction_graph::PDNode::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::SymmLinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::LinearMemNode::prepare_for_simulated_annealing(), core::pack::interaction_graph::SymmMinimalistNode::print(), core::pack::interaction_graph::SymmLinearMemNode::print(), core::pack::interaction_graph::FASTERNode::print(), core::pack::interaction_graph::LazyNode::print(), core::pack::interaction_graph::DoubleDensePDNode::print(), core::pack::interaction_graph::DensePDNode::print(), core::pack::interaction_graph::PDNode::print(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::DoubleLazyNode::print(), core::pack::interaction_graph::FASTERNode::relax(), core::pack::interaction_graph::FASTERNode::relax_after_neighbors_perturbation(), core::pack::interaction_graph::PDNode::set_amino_acid_types(), protocols::flexpack::interaction_graph::FlexbbNode::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::SymmOnTheFlyNode::set_rotamers(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_vectors(), core::pack::interaction_graph::FASTERNode::update_one_body_energies(), core::pack::interaction_graph::DoubleDensePDNode::update_one_body_energies(), core::pack::interaction_graph::DensePDNode::update_one_body_energies(), core::pack::interaction_graph::PDNode::update_one_body_energies(), core::pack::interaction_graph::LazyEdge::wipe_two_body_energies_for_node_state(), core::pack::interaction_graph::FASTERNode::zero_one_body_energies(), core::pack::interaction_graph::DoubleDensePDNode::zero_one_body_energies(), core::pack::interaction_graph::DensePDNode::zero_one_body_energies(), and core::pack::interaction_graph::PDNode::zero_one_body_energies().

InteractionGraphBase const* core::pack::interaction_graph::NodeBase::get_owner ( ) const
inlineprotected

Definition at line 155 of file InteractionGraphBase.hh.

References owner_.

Referenced by core::pack::interaction_graph::DoubleLazyNode::get_dlazy_ig_owner(), core::pack::interaction_graph::DensePDNode::get_dpdig_owner(), core::pack::interaction_graph::DoubleDensePDNode::get_dpdig_owner(), core::pack::interaction_graph::FASTERNode::get_fasterig_owner(), protocols::flexpack::interaction_graph::FlexbbNode::get_flexbbig_owner(), core::pack::interaction_graph::LazyNode::get_lazy_ig_owner(), core::pack::interaction_graph::LinearMemNode::get_linmem_ig_owner(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_minimalistflexbbig_owner(), protocols::flexpack::interaction_graph::OTFFlexbbNode::get_otfflexbbig_owner(), core::pack::interaction_graph::PDNode::get_pdig_owner(), core::pack::interaction_graph::SymmMinimalistNode::get_symmin_ig_owner(), and core::pack::interaction_graph::SymmLinearMemNode::get_symmlinmem_ig_owner().

InteractionGraphBase* core::pack::interaction_graph::NodeBase::get_owner ( )
inlineprotected

Definition at line 161 of file InteractionGraphBase.hh.

References owner_.

NodeBase& core::pack::interaction_graph::NodeBase::operator= ( NodeBase &  )
private
virtual void core::pack::interaction_graph::NodeBase::prepare_for_simulated_annealing ( )
pure virtual

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

virtual bool core::pack::interaction_graph::NodeBase::state_unassigned ( ) const
pure virtual

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

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
@parGlobal Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

Definition at line 342 of file InteractionGraphBase.cc.

References adjacent_node_, adjacent_node_ind_, edge_vector_up_to_date_, incident_edge_list_, incident_edge_vector_, node_index_, num_edges_to_smaller_indexed_nodes_, and num_incident_edges_.

Referenced by core::pack::interaction_graph::FASTERNode::update_internal_vectors(), core::pack::interaction_graph::SymmMinimalistNode::update_internal_vectors(), core::pack::interaction_graph::DoubleDensePDNode::update_internal_vectors(), core::pack::interaction_graph::DensePDNode::update_internal_vectors(), core::pack::interaction_graph::SymmLinearMemNode::update_internal_vectors(), core::pack::interaction_graph::LazyNode::update_internal_vectors(), core::pack::interaction_graph::DoubleLazyNode::update_internal_vectors(), core::pack::interaction_graph::PDNode::update_internal_vectors(), core::pack::interaction_graph::LinearMemNode::update_internal_vectors(), and protocols::flexpack::interaction_graph::FlexbbNode::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::OnTheFlyNode, core::pack::interaction_graph::SymmOnTheFlyNode, protocols::flexpack::interaction_graph::FlexbbNode, core::pack::interaction_graph::PDNode, core::pack::interaction_graph::DensePDNode, core::pack::interaction_graph::DoubleDensePDNode, and core::pack::interaction_graph::FASTERNode.

virtual void core::pack::interaction_graph::NodeBase::zero_one_body_energies ( )
pure virtual

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

Member Data Documentation

std::vector< NodeBase* > core::pack::interaction_graph::NodeBase::adjacent_node_
private

Definition at line 177 of file InteractionGraphBase.hh.

Referenced by count_dynamic_memory(), get_adjacent_node(), and update_edge_vector().

std::vector< int > core::pack::interaction_graph::NodeBase::adjacent_node_ind_
private

Definition at line 176 of file InteractionGraphBase.hh.

Referenced by count_dynamic_memory(), get_index_of_adjacent_node(), and update_edge_vector().

bool core::pack::interaction_graph::NodeBase::edge_vector_up_to_date_
private

Definition at line 178 of file InteractionGraphBase.hh.

Referenced by add_edge(), drop_all_edges(), drop_edge(), get_adjacent_node(), get_edge_vector_up_to_date(), get_incident_edge(), get_index_of_adjacent_node(), and update_edge_vector().

std::list< EdgeBase* > core::pack::interaction_graph::NodeBase::incident_edge_list_
private

Definition at line 174 of file InteractionGraphBase.hh.

Referenced by add_edge(), count_dynamic_memory(), depth_first_connected_component_counting(), drop_all_edges(), drop_edge(), edge_list_begin(), edge_list_end(), find_edge(), and update_edge_vector().

std::vector< EdgeBase* > core::pack::interaction_graph::NodeBase::incident_edge_vector_
private

Definition at line 175 of file InteractionGraphBase.hh.

Referenced by count_dynamic_memory(), get_incident_edge(), and update_edge_vector().

int core::pack::interaction_graph::NodeBase::node_index_
private

Definition at line 169 of file InteractionGraphBase.hh.

Referenced by add_edge(), depth_first_connected_component_counting(), drop_edge(), find_edge(), get_node_index(), and update_edge_vector().

int core::pack::interaction_graph::NodeBase::num_edges_to_larger_indexed_nodes_
private

Definition at line 173 of file InteractionGraphBase.hh.

Referenced by add_edge(), drop_edge(), and get_num_edges_to_larger_indexed_nodes().

int core::pack::interaction_graph::NodeBase::num_edges_to_smaller_indexed_nodes_
private

Definition at line 172 of file InteractionGraphBase.hh.

Referenced by add_edge(), drop_edge(), get_num_edges_to_smaller_indexed_nodes(), and update_edge_vector().

int core::pack::interaction_graph::NodeBase::num_incident_edges_
private

Definition at line 171 of file InteractionGraphBase.hh.

Referenced by add_edge(), drop_edge(), get_num_incident_edges(), and update_edge_vector().

int core::pack::interaction_graph::NodeBase::num_states_
private

Definition at line 170 of file InteractionGraphBase.hh.

Referenced by get_num_states().

InteractionGraphBase* core::pack::interaction_graph::NodeBase::owner_
private

Definition at line 179 of file InteractionGraphBase.hh.

Referenced by depth_first_connected_component_counting(), and get_owner().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:27:03 for Rosetta 3.5 by   doxygen 1.8.4