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core::pack::interaction_graph::LazyNode Class Reference

#include <LazyInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::LazyNode:
Inheritance graph
[legend]

Public Member Functions

 LazyNode (InteractionGraphBase *owner, int node_id, int num_states)
 main constructor, no default or copy constructors More...
 
 ~LazyNode () override
 
void prepare_for_simulated_annealing () override
 
void print () const override
 
bool state_unassigned () const override
 
virtual core::PackerEnergy get_totalE () const
 
void assign_zero_state () override
 
void assign_state (int new_state)
 
void partial_assign_state (int new_state)
 
void complete_state_assignment ()
 
int get_current_state () const
 
core::PackerEnergy get_one_body_energy_current_state () const
 
core::PackerEnergy project_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_node_energy)
 
void commit_considered_substitution ()
 
core::PackerEnergy compute_pair_energy_for_current_state (int edge_making_energy_request)
 
void acknowledge_neighbors_state_substitution (int edge_to_altered_neighbor, core::PackerEnergy new_edge_energy, int other_node_new_state, SparseMatrixIndex const &other_node_new_state_sparse_info)
 
void acknowledge_neighbors_partial_state_substitution (int edge_to_altered_neighbor, int other_node_new_, SparseMatrixIndex const &other_node_new_state_sparse_info)
 
SparseMatrixIndex const & get_sparse_mat_info_for_curr_state () const
 
void print_internal_energies () const
 
void update_internal_energy_sums ()
 
unsigned int count_static_memory () const override
 
unsigned int count_dynamic_memory () const override
 memory accounting scheme More...
 
virtual int aatype_for_state (int state) const
 
- Public Member Functions inherited from core::pack::interaction_graph::OnTheFlyNode
 OnTheFlyNode (InteractionGraphBase *owner, int node_id, int num_states)
 main constructor, no default or copy constructors More...
 
 ~OnTheFlyNode () override
 
void set_rotamers (rotamer_set::RotamerSetCOP rotamers)
 
void zero_one_body_energies () override
 
void add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b) override
 
void update_one_body_energy (int state, core::PackerEnergy energy) override
 
virtual void set_one_body_energy (int state, core::PackerEnergy energy)
 
void add_to_one_body_energy (int state, core::PackerEnergy energy) override
 
virtual void zero_one_body_energy (int state)
 
int get_num_aa_types () const
 
utility::vector1< int > & get_num_states_for_aa_types ()
 
utility::vector1< int > const & get_num_states_for_aa_types () const
 
int get_num_states_for_aa_type (int aa_type)
 
SparseMatrixIndex const & get_sparse_mat_info_for_state (int state) const
 
int get_state_offset_for_aatype (int aatype) const
 
core::PackerEnergy get_one_body_energy (int state) const
 
bool distinguish_backbone_and_sidechain () const
 
void distinguish_backbone_and_sidechain (bool setting)
 
unsigned int count_dynamic_memory () const override
 
core::PackerEnergy compute_rotamer_pair_energy (int edge_making_energy_request, int state_this, int state_other) const
 
- Public Member Functions inherited from core::pack::interaction_graph::FixedBBNode
 ~FixedBBNode () override
 
 FixedBBNode (InteractionGraphBase *owner, int node_id, int num_states)
 
- Public Member Functions inherited from core::pack::interaction_graph::NodeBase
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...
 
EdgeBasefind_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...
 
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...
 
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...
 
EdgeBaseget_incident_edge (int index)
 
int get_index_of_adjacent_node (int index) const
 
NodeBase const * get_adjacent_node (int index) const
 
NodeBaseget_adjacent_node (int index)
 

Protected Member Functions

core::PackerEnergy get_curr_pd_energy_total () const
 
core::PackerEnergy get_alt_pd_energy_total () const
 
void set_alternate_state (int alt)
 
int get_alternate_state () const
 
void calc_deltaEpd (int alternate_state)
 
bool considering_alternate_state () const
 
- Protected Member Functions inherited from core::pack::interaction_graph::OnTheFlyNode
OnTheFlyEdgeget_incident_otf_edge (int edge)
 
OnTheFlyEdge const * get_incident_otf_edge (int edge) const
 
OnTheFlyNodeget_adjacent_otf_node (int index)
 
OnTheFlyNode const * get_adjacent_otf_node (int index) const
 
OnTheFlyInteractionGraphget_on_the_fly_owner ()
 
OnTheFlyInteractionGraph const * get_on_the_fly_owner () const
 
conformation::Residue const & get_rotamer (int state) const
 
BoundingSphere const & sc_bounding_sphere (int state) const
 
BoundingSphere const & bb_bounding_sphere () const
 
- Protected Member Functions inherited from core::pack::interaction_graph::NodeBase
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
 
InteractionGraphBaseget_owner ()
 

Private Member Functions

void update_internal_vectors ()
 
LazyEdge const * get_incident_lazy_edge (int index) const
 Pointer Downcasts. More...
 
LazyEdgeget_incident_lazy_edge (int index)
 
LazyNode const * get_adjacent_lazy_node (int index) const
 
LazyNodeget_adjacent_lazy_node (int index)
 
LazyInteractionGraph const * get_lazy_ig_owner () const
 
LazyInteractionGraphget_lazy_ig_owner ()
 
 LazyNode ()
 
 LazyNode (LazyNode const &)
 
LazyNodeoperator= (LazyNode const &)
 

Private Attributes

ObjexxFCL::FArray3D_int aa_offsets_for_edges_
 
ObjexxFCL::FArray2D_int num_states_for_aa_type_for_higher_indexed_neighbor_
 
std::vector
< ObjexxFCL::FArray1A
< core::PackerEnergy > > 
edge_matrix_ptrs_
 
std::vector< int > neighbors_curr_state_
 
std::vector< SparseMatrixIndexneighbors_curr_state_sparse_info_
 
int current_state_
 
SparseMatrixIndex curr_state_sparse_mat_info_
 
core::PackerEnergy curr_state_one_body_energy_
 
core::PackerEnergy curr_state_total_energy_
 
std::vector< core::PackerEnergycurr_state_two_body_energies_
 
int alternate_state_
 
SparseMatrixIndex alt_state_sparse_mat_info_
 
core::PackerEnergy alternate_state_one_body_energy_
 
core::PackerEnergy alternate_state_total_energy_
 
std::vector< core::PackerEnergyalternate_state_two_body_energies_
 
bool alternate_state_is_being_considered_
 
bool procrastinated_
 

Additional Inherited Members

- Public Types inherited from core::pack::interaction_graph::OnTheFlyNode
typedef std::pair< Vector, RealBoundingSphere
 

Constructor & Destructor Documentation

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

main constructor, no default or copy constructors

Parameters
par Global Read:
Global Write:
Remarks
References:
Author
apl
core::pack::interaction_graph::LazyNode::~LazyNode ( )
overridedefault
Parameters
par Global Read:
Global Write:
Remarks
References:
Author
apl
core::pack::interaction_graph::LazyNode::LazyNode ( )
private

Referenced by count_static_memory().

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

Member Function Documentation

int core::pack::interaction_graph::LazyNode::aatype_for_state ( int  state) const
virtual
void core::pack::interaction_graph::LazyNode::acknowledge_neighbors_partial_state_substitution ( int  edge_to_altered_neighbor,
int  other_node_new_state,
SparseMatrixIndex const &  other_node_new_state_sparse_info 
)
void core::pack::interaction_graph::LazyNode::acknowledge_neighbors_state_substitution ( int  edge_to_altered_neighbor,
core::PackerEnergy  new_edge_energy,
int  other_node_new_state,
SparseMatrixIndex const &  other_node_new_state_sparse_info 
)
inline
void core::pack::interaction_graph::LazyNode::assign_state ( int  new_state)
void core::pack::interaction_graph::LazyNode::assign_zero_state ( )
overridevirtual
void core::pack::interaction_graph::LazyNode::calc_deltaEpd ( int  alternate_state)
protected
void core::pack::interaction_graph::LazyNode::commit_considered_substitution ( )
void core::pack::interaction_graph::LazyNode::complete_state_assignment ( )
core::PackerEnergy core::pack::interaction_graph::LazyNode::compute_pair_energy_for_current_state ( int  edge_making_energy_request)
Parameters
par Global Read:
Global Write:
Remarks
References:
Author
apl

References core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), current_state_, and neighbors_curr_state_.

bool core::pack::interaction_graph::LazyNode::considering_alternate_state ( ) const
inlineprotected
unsigned int core::pack::interaction_graph::LazyNode::count_dynamic_memory ( ) const
overridevirtual
unsigned int core::pack::interaction_graph::LazyNode::count_static_memory ( ) const
overridevirtual
Parameters
par Global Read:
Global Write:
Remarks
References:
Author
apl

Implements core::pack::interaction_graph::OnTheFlyNode.

References LazyNode().

LazyNode const * core::pack::interaction_graph::LazyNode::get_adjacent_lazy_node ( int  index) const
inlineprivate
LazyNode * core::pack::interaction_graph::LazyNode::get_adjacent_lazy_node ( int  index)
inlineprivate
core::PackerEnergy core::pack::interaction_graph::LazyNode::get_alt_pd_energy_total ( ) const
inlineprotected
int core::pack::interaction_graph::LazyNode::get_alternate_state ( ) const
inlineprotected

References alternate_state_.

core::PackerEnergy core::pack::interaction_graph::LazyNode::get_curr_pd_energy_total ( ) const
inlineprotected
int core::pack::interaction_graph::LazyNode::get_current_state ( ) const
inline
LazyEdge const * core::pack::interaction_graph::LazyNode::get_incident_lazy_edge ( int  index) const
inlineprivate
LazyEdge * core::pack::interaction_graph::LazyNode::get_incident_lazy_edge ( int  index)
inlineprivate
LazyInteractionGraph const * core::pack::interaction_graph::LazyNode::get_lazy_ig_owner ( ) const
inlineprivate
LazyInteractionGraph * core::pack::interaction_graph::LazyNode::get_lazy_ig_owner ( )
inlineprivate
core::PackerEnergy core::pack::interaction_graph::LazyNode::get_one_body_energy_current_state ( ) const
inline
SparseMatrixIndex const & core::pack::interaction_graph::LazyNode::get_sparse_mat_info_for_curr_state ( ) const
inline
virtual core::PackerEnergy core::pack::interaction_graph::LazyNode::get_totalE ( ) const
inlinevirtual
LazyNode& core::pack::interaction_graph::LazyNode::operator= ( LazyNode const &  )
private
void core::pack::interaction_graph::LazyNode::partial_assign_state ( int  new_state)
void core::pack::interaction_graph::LazyNode::prepare_for_simulated_annealing ( )
overridevirtual
Parameters
par Global Read:
Global Write:
Remarks
References:
Author
apl

Implements core::pack::interaction_graph::NodeBase.

References core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date(), and update_internal_vectors().

void core::pack::interaction_graph::LazyNode::print ( ) const
overridevirtual
void core::pack::interaction_graph::LazyNode::print_internal_energies ( ) const
core::PackerEnergy core::pack::interaction_graph::LazyNode::project_deltaE_for_substitution ( int  alternate_state,
core::PackerEnergy prev_node_energy 
)
inline
void core::pack::interaction_graph::LazyNode::set_alternate_state ( int  alt)
inlineprotected

References alternate_state_.

bool core::pack::interaction_graph::LazyNode::state_unassigned ( ) const
inlineoverridevirtual
void core::pack::interaction_graph::LazyNode::update_internal_energy_sums ( )
void core::pack::interaction_graph::LazyNode::update_internal_vectors ( )
private

Member Data Documentation

ObjexxFCL::FArray3D_int core::pack::interaction_graph::LazyNode::aa_offsets_for_edges_
private
SparseMatrixIndex core::pack::interaction_graph::LazyNode::alt_state_sparse_mat_info_
private
int core::pack::interaction_graph::LazyNode::alternate_state_
private
bool core::pack::interaction_graph::LazyNode::alternate_state_is_being_considered_
private
core::PackerEnergy core::pack::interaction_graph::LazyNode::alternate_state_one_body_energy_
private
core::PackerEnergy core::pack::interaction_graph::LazyNode::alternate_state_total_energy_
private
std::vector< core::PackerEnergy > core::pack::interaction_graph::LazyNode::alternate_state_two_body_energies_
private
core::PackerEnergy core::pack::interaction_graph::LazyNode::curr_state_one_body_energy_
private
SparseMatrixIndex core::pack::interaction_graph::LazyNode::curr_state_sparse_mat_info_
private
core::PackerEnergy core::pack::interaction_graph::LazyNode::curr_state_total_energy_
private
std::vector< core::PackerEnergy > core::pack::interaction_graph::LazyNode::curr_state_two_body_energies_
private
int core::pack::interaction_graph::LazyNode::current_state_
private
std::vector< ObjexxFCL::FArray1A< core::PackerEnergy > > core::pack::interaction_graph::LazyNode::edge_matrix_ptrs_
private
std::vector< int > core::pack::interaction_graph::LazyNode::neighbors_curr_state_
private
std::vector< SparseMatrixIndex > core::pack::interaction_graph::LazyNode::neighbors_curr_state_sparse_info_
private
ObjexxFCL::FArray2D_int core::pack::interaction_graph::LazyNode::num_states_for_aa_type_for_higher_indexed_neighbor_
private
bool core::pack::interaction_graph::LazyNode::procrastinated_
private

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