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SurfaceInteractionGraph.hh File Reference

Interaction graph which implements a non-PD, environment-dependent score for surface residues. More...

#include <core/pack/interaction_graph/AdditionalBackgroundNodesInteractionGraph.hh>
#include <core/pack/interaction_graph/InteractionGraphBase.hh>
#include <core/pack/interaction_graph/LinearMemoryInteractionGraph.hh>
#include <core/pack/interaction_graph/SurfaceInteractionGraph.fwd.hh>
#include <core/pack/interaction_graph/SurfacePotential.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <vector>
#include <utility/vector1.hh>

Classes

class  core::pack::interaction_graph::SurfaceNode< V, E, G >
 Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
 
class  core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
 Defines a BackgroundResidue node which will contribute to changes in surface energy due to state changes on neighboring nodes, and not because of state changes to it. More...
 
class  core::pack::interaction_graph::SurfaceEdge< V, E, G >
 Defines a Surface edge which will be used in determining surface energy. More...
 
class  core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
 Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode) More...
 
class  core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
 Defines the interaction graph that will keep track of changes to the surface score. More...
 
class  core::pack::interaction_graph::SurfaceNode< V, E, G >
 Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
 
class  core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
 Defines a BackgroundResidue node which will contribute to changes in surface energy due to state changes on neighboring nodes, and not because of state changes to it. More...
 
class  core::pack::interaction_graph::SurfaceEdge< V, E, G >
 Defines a Surface edge which will be used in determining surface energy. More...
 
class  core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
 Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode) More...
 
class  core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
 Defines the interaction graph that will keep track of changes to the surface score. More...
 

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::pack
 
 core::pack::interaction_graph
 

Functions

static basic::Tracer TR_NODE ("core.pack.surfaceig.node")
 Tracer instance for this file. More...
 
static basic::Tracer TR_EDGE ("core.pack.surfaceig.edge")
 
static basic::Tracer TR_BGNODE ("core.pack.surfaceig.bgnode")
 
static basic::Tracer TR_BGEDGE ("core.pack.surfaceig.bgedge")
 
static basic::Tracer TR_SIG ("core.pack.surfaceig.sig")
 
static basic::Tracer TR_STATS ("core.pack.surfaceig.stats")
 

Detailed Description

Interaction graph which implements a non-PD, environment-dependent score for surface residues.

Author
Ron Jacak (ron.j.nosp@m.acak.nosp@m.@gmai.nosp@m.l.co.nosp@m.m)

Function Documentation

static basic::Tracer TR_BGEDGE ( "core.pack.surfaceig.bgedge"  )
static
static basic::Tracer TR_BGNODE ( "core.pack.surfaceig.bgnode"  )
static
static basic::Tracer TR_EDGE ( "core.pack.surfaceig.edge"  )
static
static basic::Tracer TR_NODE ( "core.pack.surfaceig.node"  )
static

Tracer instance for this file.

static basic::Tracer TR_SIG ( "core.pack.surfaceig.sig"  )
static

Referenced by core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::blanket_assign_state_0(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::blanket_reset_alt_state_total_hASAs(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::commit_considered_substitution(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::consider_substitution(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::create_background_node(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::create_new_edge(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::create_new_node(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::detect_background_residue_and_first_class_residue_neighbors(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::initialize(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::prepare_graph_for_simulated_annealing(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::print_internal_energies_for_current_state_assignment(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_errorfull_deltaE_threshold(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_network_state(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_num_background_residues(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_pose(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_residue_as_background_residue(), and core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::update_internal_energy_totals_surface().

static basic::Tracer TR_STATS ( "core.pack.surfaceig.stats"  )
static