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HPatchInteractionGraph.hh File Reference

Interaction graph which implements a non-PD score that optimizes against surface hydrophobic patches. Computational Protein Design with Explicit Consideration of Surface Hydrophobic Patches. R. Jacak, A. Leaver-Fay, and B. Kuhlman. Proteins. 2012 Mar;80(3):825-38. More...

#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Residue.hh>
#include <utility/graph/DisjointSets.hh>
#include <core/pack/interaction_graph/HPatchInteractionGraph.fwd.hh>
#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/RotamerDots.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/sasa/util.hh>
#include <core/pack/interaction_graph/SurfacePotential.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray1.io.hh>
#include <ObjexxFCL/format.hh>
#include <vector>

Classes

struct  core::pack::interaction_graph::exposed_hydrophobic_data
 
class  core::pack::interaction_graph::HPatchNode< V, E, G >
 Defines a FirstClass node which will keep track of changes in the SASA and hpatch score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
 
class  core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
 Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable. More...
 
class  core::pack::interaction_graph::HPatchEdge< V, E, G >
 Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...
 
class  core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
 Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode) More...
 
class  core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
 Defines the interaction graph that will keep track of changes to the hpatch score. More...
 
class  core::pack::interaction_graph::HPatchNode< V, E, G >
 Defines a FirstClass node which will keep track of changes in the SASA and hpatch score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
 
class  core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
 Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable. More...
 
class  core::pack::interaction_graph::HPatchEdge< V, E, G >
 Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...
 
class  core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
 Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode) More...
 
class  core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
 Defines the interaction graph that will keep track of changes to the hpatch score. More...
 

Namespaces

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

Functions

static basic::Tracer core::pack::interaction_graph::TR_NODE ("core.pack.hpatchig.node")
 Tracer instance for this file. More...
 
static basic::Tracer core::pack::interaction_graph::TR_EDGE ("core.pack.hpatchig.edge")
 
static basic::Tracer core::pack::interaction_graph::TR_BGNODE ("core.pack.hpatchig.bgnode")
 
static basic::Tracer core::pack::interaction_graph::TR_BGEDGE ("core.pack.hpatchig.bgedge")
 
static basic::Tracer core::pack::interaction_graph::TR_HIG ("core.pack.hpatchig.ig")
 
static basic::Tracer core::pack::interaction_graph::TR_STATS ("core.pack.hpatchig.stats")
 

Detailed Description

Interaction graph which implements a non-PD score that optimizes against surface hydrophobic patches. Computational Protein Design with Explicit Consideration of Surface Hydrophobic Patches. R. Jacak, A. Leaver-Fay, and B. Kuhlman. Proteins. 2012 Mar;80(3):825-38.

Author
Ron Jacak (ron.j.nosp@m.acak.nosp@m.@gmai.nosp@m.l.co.nosp@m.m)
Andrew Leaver-Fay