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core::pack::interaction_graph::LazyEdge Class Reference

#include <LazyInteractionGraph.hh>

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Public Member Functions

 LazyEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 
virtual ~LazyEdge ()
 
virtual void set_sparse_aa_info (FArray2_bool const &)
 
virtual void force_aa_neighbors (int node1aa, int node2aa)
 re-allocates two-body energy table after forcing a pair of amino acids to become neighbors that were not initially declared to be neighbors More...
 
virtual void force_all_aa_neighbors ()
 re-allocates two-body energy table after forcing a pair of amino acids to become neighbors that were not initially declared to be neighbors More...
 
virtual bool get_sparse_aa_info (int node1aa, int node2aa) const
 returns whether two amino acid types are represented as neighbors More...
 
virtual core::PackerEnergy get_two_body_energy (int const node1state, int const node2state) const
 
virtual void declare_energies_final ()
 
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, 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)
 
core::PackerEnergy get_energy_following_partial_state_assignment ()
 
void acknowledge_substitution (int substituted_node_index, core::PackerEnergy const curr_state_energy, int nodes_new_state, SparseMatrixIndex const &nodes_new_state_sparse_info)
 
void set_edge_weight (Real weight)
 
core::PackerEnergyget_edge_table_ptr ()
 
int get_two_body_table_size () const
 
void print_current_energy () const
 
bool build_sc_only_rotamer ()
 
FArray2D_int const & get_offsets_for_aatypes ()
 
utility::vector1< int > const & get_second_node_num_states_per_aa ()
 
ObjexxFCL::FArray2D
< core::PackerEnergy
get_aa_submatrix_energies (int node1aa, int node2aa) const
 
virtual unsigned int count_static_memory () const
 
virtual unsigned int count_dynamic_memory () const
 
- 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)
 
virtual void set_sparse_aa_info (ObjexxFCL::FArray2_bool const &sparse_conn_info)=0
 
- 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 Member Functions

static core::PackerEnergy get_alternate_state_energy_first_node (int first_node_alt_state, int second_node_orig_state, SparseMatrixIndex const &second_node_orig_state_sparse_info, int first_node_state_offset_minus_1, int second_node_curr_num_states_per_aatype, int aa_neighbor_offset, FArray1< core::PackerEnergy > &edge_energy_table)
 
static core::PackerEnergy get_alternate_state_energy_second_node (int first_node_orig_state, int second_node_alt_state, SparseMatrixIndex const &first_node_orig_state_sparse_info, SparseMatrixIndex const &second_node_alternate_state_sparse_info, int second_node_alt_state_num_states_per_aatype, int aa_neighbor_offset, FArray1< core::PackerEnergy > &edge_energy_table)
 
static void store_interaction_energy_first_node (SparseMatrixIndex const &second_node_orig_state_sparse_info, int first_node_state_offset_minus_1, int second_node_curr_num_states_per_aatype, int aa_neighbor_offset, FArray1< core::PackerEnergy > &edge_energy_table, core::PackerEnergy interaction_energy)
 
static void store_interaction_energy_second_node (SparseMatrixIndex const &first_node_orig_state_sparse_info, SparseMatrixIndex const &second_node_alternate_state_sparse_info, int second_node_alt_state_num_states_per_aatype, int aa_neighbor_offset, FArray1< core::PackerEnergy > &edge_energy_table, core::PackerEnergy interaction_energy)
 

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

void get_energy_for_state_pair (int nodes_states[2], SparseMatrixIndex sparse_matrix_indices[2])
 
LazyNode const * get_lazy_node (int index) const
 
LazyNodeget_lazy_node (int index)
 
LazyInteractionGraph const * get_lazy_ig_owner () const
 
LazyInteractionGraphget_lazy_ig_owner ()
 
void wipe_two_body_energies_for_node_state (int node, int state)
 
 LazyEdge ()
 
 LazyEdge (LazyEdge const &)
 
LazyEdgeoperator= (LazyEdge const &)
 

Private Attributes

AminoAcidNeighborSparseMatrix
< core::PackerEnergy
two_body_energies_
 
core::PackerEnergy curr_state_energy_
 
bool partial_state_assignment_
 
bool ran_annealing_since_pair_energy_table_cleared_
 

Constructor & Destructor Documentation

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

LazyEdge::LazyEdge

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

LazyEdge::~LazyEdge()

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core::pack::interaction_graph::LazyEdge::LazyEdge ( )
private

Referenced by count_static_memory().

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

Member Function Documentation

void core::pack::interaction_graph::LazyEdge::acknowledge_partial_state_change ( int  node_ind,
int  new_state,
SparseMatrixIndex const &  new_state_sparse_info 
)
void core::pack::interaction_graph::LazyEdge::acknowledge_state_change ( int  node_ind,
int  new_state,
SparseMatrixIndex const &  new_state_sparse_info,
core::PackerEnergy new_energy 
)
void core::pack::interaction_graph::LazyEdge::acknowledge_state_zeroed ( int  node_ind)
void core::pack::interaction_graph::LazyEdge::acknowledge_substitution ( int  substituted_node_index,
core::PackerEnergy const  curr_state_energy,
int  nodes_new_state,
SparseMatrixIndex const &  nodes_new_state_sparse_info 
)
inline
bool core::pack::interaction_graph::LazyEdge::build_sc_only_rotamer ( )
inline
unsigned int core::pack::interaction_graph::LazyEdge::count_dynamic_memory ( ) const
virtual
unsigned int core::pack::interaction_graph::LazyEdge::count_static_memory ( ) const
virtual

LazyEdge::getMemoryUsageInBytes

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Implements core::pack::interaction_graph::OnTheFlyEdge.

References LazyEdge().

void core::pack::interaction_graph::LazyEdge::declare_energies_final ( )
virtual

LazyEdge::declare_energies_final

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

void core::pack::interaction_graph::LazyEdge::declare_energies_final_no_deletion ( )
inlineprotected
void core::pack::interaction_graph::LazyEdge::force_aa_neighbors ( int  node1aa,
int  node2aa 
)
virtual

re-allocates two-body energy table after forcing a pair of amino acids to become neighbors that were not initially declared to be neighbors

Parameters
node1aa- [in] - the amino acid type for the node with the smaller index
node2aa- [in] - the amino acid type for the node with the larger index

Implements core::pack::interaction_graph::FixedBBEdge.

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::blanket_set(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::force_aa_neighbors(), NOT_YET_COMPUTED_ENERGY, ran_annealing_since_pair_energy_table_cleared_, and two_body_energies_.

void core::pack::interaction_graph::LazyEdge::force_all_aa_neighbors ( )
virtual

re-allocates two-body energy table after forcing a pair of amino acids to become neighbors that were not initially declared to be neighbors

Parameters
node1aa- [in] - the amino acid type for the node with the smaller index
node2aa- [in] - the amino acid type for the node with the larger index

Implements core::pack::interaction_graph::FixedBBEdge.

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::blanket_set(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::force_all_aa_neighbors(), NOT_YET_COMPUTED_ENERGY, ran_annealing_since_pair_energy_table_cleared_, and two_body_energies_.

ObjexxFCL::FArray2D< core::PackerEnergy > core::pack::interaction_graph::LazyEdge::get_aa_submatrix_energies ( int  node1aa,
int  node2aa 
) const
core::PackerEnergy core::pack::interaction_graph::LazyEdge::get_alternate_state_energy_first_node ( int  first_node_alt_state,
int  second_node_orig_state,
SparseMatrixIndex const &  second_node_orig_state_sparse_info,
int  first_node_state_offset_minus_1,
int  second_node_curr_num_states_per_aatype,
int  aa_neighbor_offset,
FArray1< core::PackerEnergy > &  edge_energy_table 
)
inlinestatic

LazyEdge::get_alternate_state_energy_first_node

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References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get().

core::PackerEnergy core::pack::interaction_graph::LazyEdge::get_alternate_state_energy_second_node ( int  first_node_orig_state,
int  second_node_alt_state,
SparseMatrixIndex const &  first_node_orig_state_sparse_info,
SparseMatrixIndex const &  second_node_alternate_state_sparse_info,
int  second_node_alt_state_num_states_per_aatype,
int  aa_neighbor_offset,
FArray1< core::PackerEnergy > &  edge_energy_table 
)
inlinestatic

LazyEdge::get_alternate_state_energy_second_node

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References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get().

core::PackerEnergy core::pack::interaction_graph::LazyEdge::get_current_two_body_energy ( ) const

LazyEdge::get_current_two_body_energy

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References curr_state_energy_.

Referenced by core::pack::interaction_graph::LazyNode::update_internal_energy_sums().

core::PackerEnergy & core::pack::interaction_graph::LazyEdge::get_edge_table_ptr ( )

LazyEdge::get_edge_table_ptr

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References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::getMatrixPointer(), and two_body_energies_.

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

core::PackerEnergy core::pack::interaction_graph::LazyEdge::get_energy_following_partial_state_assignment ( )
void core::pack::interaction_graph::LazyEdge::get_energy_for_state_pair ( int  nodes_states[2],
SparseMatrixIndex  sparse_matrix_indices_[2] 
)
private
LazyInteractionGraph const * core::pack::interaction_graph::LazyEdge::get_lazy_ig_owner ( ) const
inlineprivate
LazyInteractionGraph * core::pack::interaction_graph::LazyEdge::get_lazy_ig_owner ( )
inlineprivate
LazyNode const * core::pack::interaction_graph::LazyEdge::get_lazy_node ( int  index) const
inlineprivate
LazyNode * core::pack::interaction_graph::LazyEdge::get_lazy_node ( int  index)
inlineprivate
FArray2D_int const & core::pack::interaction_graph::LazyEdge::get_offsets_for_aatypes ( )
utility::vector1< int > const & core::pack::interaction_graph::LazyEdge::get_second_node_num_states_per_aa ( )

LazyEdge::get_second_node_num_states_per_aa

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References get_lazy_node(), and core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_types().

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

bool core::pack::interaction_graph::LazyEdge::get_sparse_aa_info ( int  node1aa,
int  node2aa 
) const
virtual

returns whether two amino acid types are represented as neighbors

Implements core::pack::interaction_graph::FixedBBEdge.

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_sparse_aa_info(), and two_body_energies_.

core::PackerEnergy core::pack::interaction_graph::LazyEdge::get_two_body_energy ( int const  node1state,
int const  node2state 
) const
virtual
int core::pack::interaction_graph::LazyEdge::get_two_body_table_size ( ) const

LazyEdge::get_two_body_table_size

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References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_table_size(), and two_body_energies_.

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

LazyEdge& core::pack::interaction_graph::LazyEdge::operator= ( LazyEdge const &  )
private
bool core::pack::interaction_graph::LazyEdge::pd_edge_table_all_zeros ( ) const
inlineprotected
void core::pack::interaction_graph::LazyEdge::prepare_for_simulated_annealing ( )
virtual
void core::pack::interaction_graph::LazyEdge::prepare_for_simulated_annealing_no_deletion ( )
inlineprotected
void core::pack::interaction_graph::LazyEdge::print_current_energy ( ) const
void core::pack::interaction_graph::LazyEdge::set_edge_weight ( Real  weight)
virtual
void core::pack::interaction_graph::LazyEdge::set_sparse_aa_info ( FArray2_bool const &  aa_neighbors)
virtual
void core::pack::interaction_graph::LazyEdge::store_interaction_energy_first_node ( SparseMatrixIndex const &  second_node_orig_state_sparse_info,
int  first_node_state_offset_minus_1,
int  second_node_curr_num_states_per_aatype,
int  aa_neighbor_offset,
FArray1< core::PackerEnergy > &  edge_energy_table,
core::PackerEnergy  interaction_energy 
)
inlinestatic

LazyEdge::store_interaction_energy_first_node

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apl
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References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set().

Referenced by core::pack::interaction_graph::LazyNode::project_deltaE_for_substitution().

void core::pack::interaction_graph::LazyEdge::store_interaction_energy_second_node ( SparseMatrixIndex const &  first_node_orig_state_sparse_info,
SparseMatrixIndex const &  second_node_alternate_state_sparse_info,
int  second_node_alt_state_num_states_per_aatype,
int  aa_neighbor_offset,
FArray1< core::PackerEnergy > &  edge_energy_table,
core::PackerEnergy  interaction_energy 
)
inlinestatic

LazyEdge::store_interaction_energy_second_node

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@parGlobal Read:
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apl
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References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set().

Referenced by core::pack::interaction_graph::LazyNode::project_deltaE_for_substitution().

void core::pack::interaction_graph::LazyEdge::wipe_two_body_energies_for_node_state ( int  node,
int  state 
)
private

Member Data Documentation

core::PackerEnergy core::pack::interaction_graph::LazyEdge::curr_state_energy_
private
core::PackerEnergy const core::pack::interaction_graph::LazyEdge::NOT_YET_COMPUTED_ENERGY = -1234
static
bool core::pack::interaction_graph::LazyEdge::partial_state_assignment_
private
bool core::pack::interaction_graph::LazyEdge::ran_annealing_since_pair_energy_table_cleared_
private
AminoAcidNeighborSparseMatrix< core::PackerEnergy > core::pack::interaction_graph::LazyEdge::two_body_energies_
mutableprivate

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