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interaction_graph Directory Reference
Directory dependency graph for interaction_graph:
src/core/pack/interaction_graph

Files

file  AdditionalBackgroundNodesInteractionGraph.hh
 Interaction graph which can handle some residues not changing during packing.
 
file  AminoAcidNeighborSparseMatrix.fwd.hh
 Sparse Matrix class for rotamer pair energy storage forward declaration.
 
file  AminoAcidNeighborSparseMatrix.hh
 Amino acid neighbor sparse matrix template class.
 
file  AnnealableGraphBase.cc
 Base interface for annealable graphs.
 
file  AnnealableGraphBase.fwd.hh
 Base interface for annealable graphs.
 
file  AnnealableGraphBase.hh
 
file  DensePDInteractionGraph.cc
 Dense Edge-Matrix, Pairwise Decomposable interaction graph class implementation.
 
file  DensePDInteractionGraph.fwd.hh
 
file  DensePDInteractionGraph.hh
 Dense Edge-Matrix, Pairwise Decomposable interaction graph class header This graph does not take advantage of the memory-saving AANeighborSparseMatrix for the storage of RPEs (rotamer pair energies); for this reason it's a little bit faster and weights a little less than the PDInteractionGraph for fixed-sequence repackings – memory becomes a significant issue for design simulations, and this graph should not be used for that purpose.
 
file  DoubleDensePDInteractionGraph.cc
 
file  DoubleDensePDInteractionGraph.fwd.hh
 
file  DoubleDensePDInteractionGraph.hh
 Double-The-Memory interaction graph which stores interaction energies for a rotamer and all of its neighbors in a single row in memory.
 
file  DoubleLazyInteractionGraph.cc
 Interaction graph that computes each rotamer pair energy at most once.
 
file  DoubleLazyInteractionGraph.fwd.hh
 Interaction graph that computes each rotamer pair energy at most once.
 
file  DoubleLazyInteractionGraph.hh
 Interaction graph that computes each rotamer pair energy at most once.
 
file  FASTERInteractionGraph.cc
 
file  FASTERInteractionGraph.fwd.hh
 
file  FASTERInteractionGraph.hh
 
file  FASTERInteractionGraphTests.fwd.hh
 
file  FixedBBInteractionGraph.cc
 Precomputed interaction graph class.
 
file  FixedBBInteractionGraph.fwd.hh
 Interaction graph base class for fixed-backbone packing.
 
file  FixedBBInteractionGraph.hh
 Interaction graph base class for fixed-backbone packing.
 
file  HPatchEnergy.cc
 
file  HPatchEnergy.fwd.hh
 
file  HPatchEnergy.hh
 
file  HPatchEnergyCreator.hh
 
file  HPatchInteractionGraph.fwd.hh
 Forward header for an IG that designs against hydrophobic area on the surface of proteins.
 
file  HPatchInteractionGraph.hh
 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.
 
file  InteractionGraphBase.cc
 Interaction graph base class.
 
file  InteractionGraphBase.fwd.hh
 InteractionGraph base class forward declaration.
 
file  InteractionGraphBase.hh
 Base interface for annealable graphs.
 
file  InteractionGraphFactory.cc
 Interation graph factory class definition.
 
file  InteractionGraphFactory.fwd.hh
 Interation graph factory class forward declaration.
 
file  InteractionGraphFactory.hh
 Interation graph factory class declaration.
 
file  LazyInteractionGraph.cc
 Interaction graph that computes each rotamer pair energy at most once.
 
file  LazyInteractionGraph.fwd.hh
 Interaction graph that computes each rotamer pair energy at most once.
 
file  LazyInteractionGraph.hh
 Interaction graph that computes each rotamer pair energy at most once.
 
file  LinearMemoryInteractionGraph.cc
 
file  LinearMemoryInteractionGraph.fwd.hh
 
file  LinearMemoryInteractionGraph.hh
 
file  MultiplexedAnnealableGraph.cc
 Multiplexing packing graph container.
 
file  MultiplexedAnnealableGraph.fwd.hh
 
file  MultiplexedAnnealableGraph.hh
 Multiplexing packing graph container.
 
file  NPDHBondInteractionGraph.cc
 Non-templated helper functions for the NPDHBondInteractionGraph.
 
file  NPDHBondInteractionGraph.fwd.hh
 Forward header for an IG that assigns hydrogen bonds a (non-pairwise-decomposable) weight.
 
file  NPDHBondInteractionGraph.hh
 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.
 
file  NPDHBSimpleInteractionGraph.cc
 
file  NPDHBSimpleInteractionGraph.fwd.hh
 Data structure for representing changing energies for a Pose undergoing rotamer substitutions with the non-pairwise decomposable hydrogen bond potential.
 
file  NPDHBSimpleInteractionGraph.hh
 
file  OnTheFlyInteractionGraph.cc
 
file  OnTheFlyInteractionGraph.fwd.hh
 
file  OnTheFlyInteractionGraph.hh
 
file  PDInteractionGraph.cc
 Pairwise Decomposable interaction graph class.
 
file  PDInteractionGraph.fwd.hh
 Sparse pairwise decomposable interaction graph forward declaration.
 
file  PDInteractionGraph.hh
 Pairwise Decomposable interaction graph class header.
 
file  PrecomputedPairEnergiesInteractionGraph.cc
 Precomputed interaction graph class.
 
file  PrecomputedPairEnergiesInteractionGraph.fwd.hh
 Precomputed Pair Energies Interaction Graph forward declaration.
 
file  PrecomputedPairEnergiesInteractionGraph.hh
 Precomputed interaction graph class header.
 
file  ResidueArrayAnnealingEvaluator.cc
 
file  ResidueArrayAnnealingEvaluator.fwd.hh
 
file  ResidueArrayAnnealingEvaluator.hh
 Annealable interface for score terms evaluated over an array of residues.
 
file  RotamerDots.cc
 RotamerDots classes files - ported from rosetta++.
 
file  RotamerDots.fwd.hh
 RotamerDots classes, forward declaration - ported from rosetta++.
 
file  RotamerDots.hh
 RotamerDots classes header files - ported from rosetta++.
 
file  SimpleInteractionGraph.cc
 
file  SimpleInteractionGraph.fwd.hh
 
file  SimpleInteractionGraph.hh
 
file  SparseMatrixIndex.fwd.hh
 Helper class for AminoAcidNeighborSparseMatrix forward declaration.
 
file  SparseMatrixIndex.hh
 
file  SurfaceEnergy.cc
 
file  SurfaceEnergy.fwd.hh
 
file  SurfaceEnergy.hh
 
file  SurfaceEnergyCreator.hh
 
file  SurfaceInteractionGraph.fwd.hh
 Forward header for an IG that designs against hydrophobic area on the surface of proteins.
 
file  SurfaceInteractionGraph.hh
 Interaction graph which implements a non-PD, environment-dependent score for surface residues.
 
file  SurfacePotential.cc
 
file  SurfacePotential.hh
 
file  SymmLinMemInteractionGraph.cc
 
file  SymmLinMemInteractionGraph.fwd.hh
 
file  SymmLinMemInteractionGraph.hh
 
file  SymmMinimalistInteractionGraph.cc
 
file  SymmMinimalistInteractionGraph.fwd.hh
 
file  SymmMinimalistInteractionGraph.hh
 
file  SymmOnTheFlyInteractionGraph.cc
 
file  SymmOnTheFlyInteractionGraph.fwd.hh
 
file  SymmOnTheFlyInteractionGraph.hh
 
file  util.cc
 Simple utilities for interaction graphs.
 
file  util.hh
 Simple utilities for interaction graphs.