Rosetta 3.4
Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions
core::pack::interaction_graph::LazyEdge Class Reference

#include <LazyInteractionGraph.hh>

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List of all members.

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
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
virtual bool get_sparse_aa_info (int node1aa, int node2aa) const
 returns whether two amino acid types are represented as neighbors
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

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

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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apl
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core::pack::interaction_graph::LazyEdge::~LazyEdge ( ) [virtual]

LazyEdge::~LazyEdge()

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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.

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 ( ) [inline, protected]
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(), and NOT_YET_COMPUTED_ENERGY.

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(), and NOT_YET_COMPUTED_ENERGY.

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 
) [inline, static]

LazyEdge::get_alternate_state_energy_first_node

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apl
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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 
) [inline, static]

LazyEdge::get_alternate_state_energy_second_node

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

LazyEdge::get_current_two_body_energy

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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().

core::PackerEnergy core::pack::interaction_graph::LazyEdge::get_energy_following_partial_state_assignment ( )
FArray2D_int const & core::pack::interaction_graph::LazyEdge::get_offsets_for_aatypes ( )

LazyEdge::get_offsets_for_aatypes

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

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 core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_types().

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().

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().

bool core::pack::interaction_graph::LazyEdge::pd_edge_table_all_zeros ( ) const [inline, protected]
void core::pack::interaction_graph::LazyEdge::prepare_for_simulated_annealing ( ) [virtual]
void core::pack::interaction_graph::LazyEdge::prepare_for_simulated_annealing_no_deletion ( ) [inline, protected]
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 
) [inline, static]

LazyEdge::store_interaction_energy_first_node

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apl
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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 
) [inline, static]

LazyEdge::store_interaction_energy_second_node

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


Member Data Documentation


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