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core::pack::interaction_graph::LinearMemEdge Class Reference

#include <LinearMemoryInteractionGraph.hh>

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

 LinearMemEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 
virtual ~LinearMemEdge ()
 
virtual void set_sparse_aa_info (ObjexxFCL::FArray2_bool const &)
 
virtual void force_aa_neighbors (int node1aa, int node2aa)
 
virtual void force_all_aa_neighbors ()
 
virtual bool get_sparse_aa_info (int node1aa, int node2aa) const
 
virtual core::PackerEnergy get_two_body_energy (int const node1state, int const node2state) const
 
virtual void prepare_for_simulated_annealing ()
 
core::PackerEnergy get_current_two_body_energy () const
 
void acknowledge_state_change (int node_ind, int new_state, SparseMatrixIndex const &new_state_sparse_info, int bumped_recent_history_index, int new_state_recent_history_index, core::PackerEnergy &new_energy)
 
void acknowledge_state_zeroed (int node_ind)
 
void acknowledge_partial_state_change (int node_ind, int new_state, SparseMatrixIndex const &new_state_sparse_info, int bumped_recent_history_index, int new_state_recent_history_index)
 
core::PackerEnergy get_energy_following_partial_state_assignment ()
 
void reset_state_energies (int node_index, int state, int recent_history_id)
 
core::PackerEnergy get_energy_for_alt_state (bool store_rpes, int changing_node_index, int alternate_state, int alternate_state_recent_history_index, int other_node_curr_state, int other_node_state_recent_history_index)
 
void acknowledge_substitution (int substituted_node_index, core::PackerEnergy const curr_state_energy, int nodes_new_state, SparseMatrixIndex const &nodes_new_state_sparse_info, int bumped_recent_history_index, int new_state_recent_history_index, int neighbors_curr_state)
 
int get_two_body_table_size () const
 
virtual void declare_energies_final ()
 
void print_current_energy () const
 
ObjexxFCL::FArray2D< unsigned
char > const & 
get_sparse_aa_neighbor_info ()
 
virtual unsigned int count_static_memory () const
 
virtual unsigned int count_dynamic_memory () const
 
virtual void set_edge_weight (Real weight)
 
- Public Member Functions inherited from core::pack::interaction_graph::OnTheFlyEdge
virtual ~OnTheFlyEdge ()
 
 OnTheFlyEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 
void set_ProCorrection_values (int node_not_necessarily_proline, int state, core::PackerEnergy bb_nonprobb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_nonprobb_E, core::PackerEnergy sc_probb_E)
 
core::PackerEnergy get_proline_correction_for_node (int node_ind, int state) const
 
bool long_range_interactions_exist () const
 
bool short_range_interactions_exist () const
 
void note_long_range_interactions_exist ()
 
void note_short_range_interactions_exist ()
 
ResiduePairEvalType eval_type (int node_index) const
 
- Public Member Functions inherited from core::pack::interaction_graph::FixedBBEdge
virtual ~FixedBBEdge ()
 
 FixedBBEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 
- Public Member Functions inherited from core::pack::interaction_graph::EdgeBase
virtual ~EdgeBase ()
 copy constructor, do not use More...
 
 EdgeBase (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 main constructor for edge, no default nor copy constructors More...
 
int get_other_ind (int callers_index) const
 returns the index of the other node that the edge is incident upon More...
 
NodeBaseget_other_node (int callers_index) const
 returns a pointer to the other node that the edge is incident upon More...
 
int get_first_node_ind () const
 returns the index of the smaller-indexed node More...
 
int get_second_node_ind () const
 returns the index of the larger-indexed node More...
 
void set_pos_in_owners_list (std::list< EdgeBase * >::iterator edge_iterator)
 edge keeps iterator to its position in it's owner's edge list More...
 
void set_pos_in_node_edgevector (int callers_index, int position)
 edge keeps index it has in node_ind's edge vector More...
 
bool same_edge (int node1, int node2) const
 returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important More...
 
Real edge_weight () const
 
InteractionGraphBase const * get_owner () const
 
InteractionGraphBaseget_owner ()
 

Static Public Attributes

static core::PackerEnergy const NOT_YET_COMPUTED_ENERGY = -1234
 

Protected Member Functions

void declare_energies_final_no_deletion ()
 
void prepare_for_simulated_annealing_no_deletion ()
 
bool pd_edge_table_all_zeros () const
 
- Protected Member Functions inherited from core::pack::interaction_graph::OnTheFlyEdge
core::PackerEnergy get_proline_correction (int which_node, int state) const
 
OnTheFlyNode const * get_otf_node (int which_node) const
 
OnTheFlyNodeget_otf_node (int which_node)
 

Private Member Functions

LinearMemNode const * get_linmem_node (int index) const
 
LinearMemNodeget_linmem_node (int index)
 
LinearMemoryInteractionGraph
const * 
get_linmem_ig_owner () const
 
LinearMemoryInteractionGraphget_linmem_ig_owner ()
 
void handle_bumped_recent_history_state_for_node (int node_substituted, int node_not_substituted, int bumped_recent_history_index)
 
void store_curr_state_energy ()
 
void wipe (int node)
 
 LinearMemEdge ()
 
 LinearMemEdge (LinearMemEdge const &)
 
LinearMemEdgeoperator= (LinearMemEdge const &)
 

Private Attributes

bool store_rpes_ [2]
 
ObjexxFCL::FArray2D
< core::PackerEnergy
stored_rpes_ [2]
 
ObjexxFCL::FArray2D< unsigned
char > 
sparse_aa_neighbors_
 
core::PackerEnergy curr_state_energy_
 
core::PackerEnergy alt_state_energy_
 
bool partial_state_assignment_
 
bool preped_for_sim_annealing_
 

Constructor & Destructor Documentation

core::pack::interaction_graph::LinearMemEdge::LinearMemEdge ( InteractionGraphBase owner,
int  first_node_ind,
int  second_node_ind 
)

References store_rpes_.

core::pack::interaction_graph::LinearMemEdge::~LinearMemEdge ( )
virtual
core::pack::interaction_graph::LinearMemEdge::LinearMemEdge ( )
private

Referenced by count_static_memory().

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

Member Function Documentation

void core::pack::interaction_graph::LinearMemEdge::acknowledge_partial_state_change ( int  node_ind,
int  new_state,
SparseMatrixIndex const &  new_state_sparse_info,
int  bumped_recent_history_index,
int  new_state_recent_history_index 
)
void core::pack::interaction_graph::LinearMemEdge::acknowledge_state_change ( int  node_ind,
int  new_state,
SparseMatrixIndex const &  new_state_sparse_info,
int  bumped_recent_history_index,
int  new_state_recent_history_index,
core::PackerEnergy new_energy 
)
void core::pack::interaction_graph::LinearMemEdge::acknowledge_state_zeroed ( int  node_ind)
void core::pack::interaction_graph::LinearMemEdge::acknowledge_substitution ( int  substituted_node_index,
core::PackerEnergy const  curr_state_energy,
int  nodes_new_state,
SparseMatrixIndex const &  nodes_new_state_sparse_info,
int  bumped_recent_history_index,
int  new_state_recent_history_index,
int  neighbors_curr_state 
)
inline
unsigned int core::pack::interaction_graph::LinearMemEdge::count_dynamic_memory ( ) const
virtual
unsigned int core::pack::interaction_graph::LinearMemEdge::count_static_memory ( ) const
virtual
void core::pack::interaction_graph::LinearMemEdge::declare_energies_final ( )
virtual
void core::pack::interaction_graph::LinearMemEdge::declare_energies_final_no_deletion ( )
inlineprotected
void core::pack::interaction_graph::LinearMemEdge::force_aa_neighbors ( int  node1aa,
int  node2aa 
)
virtual
void core::pack::interaction_graph::LinearMemEdge::force_all_aa_neighbors ( )
virtual
core::PackerEnergy core::pack::interaction_graph::LinearMemEdge::get_current_two_body_energy ( ) const
core::PackerEnergy core::pack::interaction_graph::LinearMemEdge::get_energy_following_partial_state_assignment ( )
core::PackerEnergy core::pack::interaction_graph::LinearMemEdge::get_energy_for_alt_state ( bool  store_rpes,
int  changing_node_index,
int  alternate_state,
int  alternate_state_recent_history_index,
int  other_node_curr_state,
int  other_node_state_recent_history_index 
)
LinearMemoryInteractionGraph const * core::pack::interaction_graph::LinearMemEdge::get_linmem_ig_owner ( ) const
inlineprivate
LinearMemoryInteractionGraph * core::pack::interaction_graph::LinearMemEdge::get_linmem_ig_owner ( )
inlineprivate
LinearMemNode const * core::pack::interaction_graph::LinearMemEdge::get_linmem_node ( int  index) const
inlineprivate
LinearMemNode * core::pack::interaction_graph::LinearMemEdge::get_linmem_node ( int  index)
inlineprivate
bool core::pack::interaction_graph::LinearMemEdge::get_sparse_aa_info ( int  node1aa,
int  node2aa 
) const
virtual
ObjexxFCL::FArray2D< unsigned char > const & core::pack::interaction_graph::LinearMemEdge::get_sparse_aa_neighbor_info ( )
core::PackerEnergy core::pack::interaction_graph::LinearMemEdge::get_two_body_energy ( int const  node1state,
int const  node2state 
) const
virtual
int core::pack::interaction_graph::LinearMemEdge::get_two_body_table_size ( ) const
void core::pack::interaction_graph::LinearMemEdge::handle_bumped_recent_history_state_for_node ( int  node_substituted,
int  node_not_substituted,
int  bumped_recent_history_index 
)
private
LinearMemEdge& core::pack::interaction_graph::LinearMemEdge::operator= ( LinearMemEdge const &  )
private
bool core::pack::interaction_graph::LinearMemEdge::pd_edge_table_all_zeros ( ) const
inlineprotected
void core::pack::interaction_graph::LinearMemEdge::prepare_for_simulated_annealing ( )
virtual
void core::pack::interaction_graph::LinearMemEdge::prepare_for_simulated_annealing_no_deletion ( )
inlineprotected
void core::pack::interaction_graph::LinearMemEdge::print_current_energy ( ) const
void core::pack::interaction_graph::LinearMemEdge::reset_state_energies ( int  node_index,
int  state,
int  recent_history_id 
)
void core::pack::interaction_graph::LinearMemEdge::set_edge_weight ( Real  weight)
virtual

DANGER: this will not update the cached energies on the nodes this edge is incident upon.

Implements core::pack::interaction_graph::EdgeBase.

References core::pack::interaction_graph::EdgeBase::edge_weight(), NOT_YET_COMPUTED_ENERGY, and stored_rpes_.

void core::pack::interaction_graph::LinearMemEdge::set_sparse_aa_info ( ObjexxFCL::FArray2_bool const &  aa_neighbors)
virtual
void core::pack::interaction_graph::LinearMemEdge::store_curr_state_energy ( )
private
void core::pack::interaction_graph::LinearMemEdge::wipe ( int  node)
private

Member Data Documentation

core::PackerEnergy core::pack::interaction_graph::LinearMemEdge::alt_state_energy_
private
core::PackerEnergy core::pack::interaction_graph::LinearMemEdge::curr_state_energy_
private
core::PackerEnergy const core::pack::interaction_graph::LinearMemEdge::NOT_YET_COMPUTED_ENERGY = -1234
static
bool core::pack::interaction_graph::LinearMemEdge::partial_state_assignment_
private
bool core::pack::interaction_graph::LinearMemEdge::preped_for_sim_annealing_
private
ObjexxFCL::FArray2D< unsigned char > core::pack::interaction_graph::LinearMemEdge::sparse_aa_neighbors_
private
bool core::pack::interaction_graph::LinearMemEdge::store_rpes_[2]
private
ObjexxFCL::FArray2D< core::PackerEnergy > core::pack::interaction_graph::LinearMemEdge::stored_rpes_[2]
private

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