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core::pack::interaction_graph::SymmOnTheFlyEdge Class Referenceabstract

#include <SymmOnTheFlyInteractionGraph.hh>

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

virtual ~SymmOnTheFlyEdge ()
 
 SymmOnTheFlyEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 
void add_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
 
virtual unsigned int count_static_memory () const =0
 
virtual unsigned int count_dynamic_memory () 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
 
void set_residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit)
 
unsigned char residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit, int whichnode_restypegroup, int othernode_restypegroup) const
 
virtual void set_sparse_aa_info (ObjexxFCL::FArray2_bool const &)
 fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...
 
virtual bool get_sparse_aa_info (int, int) const
 fullfilling base class virtual member request – however, this function does not quite make sense for a symmetric otf ig, so this is just stubbed out to return true. More...
 
virtual void force_aa_neighbors (int, int)
 fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...
 
virtual void force_all_aa_neighbors ()
 fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...
 
virtual core::PackerEnergy get_two_body_energy (int const, int const ) const =0
 
- 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...
 
virtual void declare_energies_final ()=0
 
virtual void prepare_for_simulated_annealing ()=0
 
Real edge_weight () const
 
virtual void set_edge_weight (Real weight)=0
 
InteractionGraphBase const * get_owner () const
 
InteractionGraphBaseget_owner ()
 

Protected Member Functions

core::PackerEnergy get_proline_correction (int which_node, int state) const
 
SymmOnTheFlyNode const * get_otf_node (int which_node) const
 
SymmOnTheFlyNodeget_otf_node (int which_node)
 
SymmOnTheFlyInteractionGraph
const * 
get_otf_owner () const
 
SymmOnTheFlyInteractionGraphget_otf_owner ()
 

Private Attributes

ObjexxFCL::FArray4D< unsigned
char > 
restypegroup_adjacency_
 
utility::vector1
< core::PackerEnergy
proline_corrections_ [2]
 
ResiduePairEvalType eval_types_ [2]
 
bool long_range_interactions_exist_
 
bool short_range_interactions_exist_
 

Constructor & Destructor Documentation

core::pack::interaction_graph::SymmOnTheFlyEdge::~SymmOnTheFlyEdge ( )
virtual
core::pack::interaction_graph::SymmOnTheFlyEdge::SymmOnTheFlyEdge ( InteractionGraphBase owner,
int  first_node_ind,
int  second_node_ind 
)

Member Function Documentation

void core::pack::interaction_graph::SymmOnTheFlyEdge::add_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 
)
unsigned int core::pack::interaction_graph::SymmOnTheFlyEdge::count_dynamic_memory ( ) const
virtual
virtual unsigned int core::pack::interaction_graph::SymmOnTheFlyEdge::count_static_memory ( ) const
pure virtual
ResiduePairEvalType core::pack::interaction_graph::SymmOnTheFlyEdge::eval_type ( int  node_index) const
inline
virtual void core::pack::interaction_graph::SymmOnTheFlyEdge::force_aa_neighbors ( int  ,
int   
)
inlinevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

virtual void core::pack::interaction_graph::SymmOnTheFlyEdge::force_all_aa_neighbors ( )
inlinevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

SymmOnTheFlyNode const* core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_node ( int  which_node) const
inlineprotected
SymmOnTheFlyNode* core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_node ( int  which_node)
inlineprotected
SymmOnTheFlyInteractionGraph const * core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_owner ( ) const
inlineprotected
SymmOnTheFlyInteractionGraph * core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_owner ( )
inlineprotected
core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_proline_correction ( int  which_node,
int  state 
) const
inlineprotected
core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_proline_correction_for_node ( int  node_ind,
int  state 
) const
inline
virtual bool core::pack::interaction_graph::SymmOnTheFlyEdge::get_sparse_aa_info ( int  ,
int   
) const
inlinevirtual

fullfilling base class virtual member request – however, this function does not quite make sense for a symmetric otf ig, so this is just stubbed out to return true.

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

virtual core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_two_body_energy ( int  const,
int  const 
) const
pure virtual
bool core::pack::interaction_graph::SymmOnTheFlyEdge::long_range_interactions_exist ( ) const
inline
void core::pack::interaction_graph::SymmOnTheFlyEdge::note_long_range_interactions_exist ( )
inline
void core::pack::interaction_graph::SymmOnTheFlyEdge::note_short_range_interactions_exist ( )
inline
unsigned char core::pack::interaction_graph::SymmOnTheFlyEdge::residues_adjacent_for_subunit_pair ( int  which_node,
int  other_node_subunit,
int  whichnode_restypegroup,
int  othernode_restypegroup 
) const
void core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair ( int  which_node,
int  other_node_subunit 
)
virtual void core::pack::interaction_graph::SymmOnTheFlyEdge::set_sparse_aa_info ( ObjexxFCL::FArray2_bool const &  )
inlinevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

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

bool core::pack::interaction_graph::SymmOnTheFlyEdge::short_range_interactions_exist ( ) const
inline

Member Data Documentation

ResiduePairEvalType core::pack::interaction_graph::SymmOnTheFlyEdge::eval_types_[2]
private

Referenced by SymmOnTheFlyEdge().

bool core::pack::interaction_graph::SymmOnTheFlyEdge::long_range_interactions_exist_
private
utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmOnTheFlyEdge::proline_corrections_[2]
private
ObjexxFCL::FArray4D< unsigned char > core::pack::interaction_graph::SymmOnTheFlyEdge::restypegroup_adjacency_
private

Dimensions: naatypes x naatypes x n_subunits x 2 aa_adjacency( l, k, j, i ); i = 1 or 2, repesnting either the lower or upper node respectively, the residue of which lives in the asymmetric unit j = 1..n_subunits, representing the subunit of origin for the other node's residue k = amino acid type for node i l = amino acid type for the other node

Referenced by residues_adjacent_for_subunit_pair(), and set_residues_adjacent_for_subunit_pair().

bool core::pack::interaction_graph::SymmOnTheFlyEdge::short_range_interactions_exist_
private

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