interaction_graph Directory Reference

Directory dependency graph for interaction_graph:

Files
file	AdditionalBackgroundNodesInteractionGraph.hh [code]
	Interaction graph which can handle some residues not changing during packing.
file	AminoAcidNeighborSparseMatrix.fwd.hh [code]
	Sparse Matrix class for rotamer pair energy storage forward declaration.
file	AminoAcidNeighborSparseMatrix.hh [code]
	Amino acid neighbor sparse matrix template class.
file	AnnealableGraphBase.cc [code]
	Base interface for annealable graphs.
file	AnnealableGraphBase.fwd.hh [code]
	Base interface for annealable graphs.
file	AnnealableGraphBase.hh [code]
file	DensePDInteractionGraph.cc [code]
	Dense Edge-Matrix, Pairwise Decomposable interaction graph class implementation.
file	DensePDInteractionGraph.fwd.hh [code]
file	DensePDInteractionGraph.hh [code]
	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 [code]
file	DoubleDensePDInteractionGraph.fwd.hh [code]
file	DoubleDensePDInteractionGraph.hh [code]
	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 [code]
	Interaction graph that computes each rotamer pair energy at most once.
file	DoubleLazyInteractionGraph.fwd.hh [code]
	Interaction graph that computes each rotamer pair energy at most once.
file	DoubleLazyInteractionGraph.hh [code]
	Interaction graph that computes each rotamer pair energy at most once.
file	FASTERInteractionGraph.cc [code]
file	FASTERInteractionGraph.fwd.hh [code]
file	FASTERInteractionGraph.hh [code]
file	FixedBBInteractionGraph.cc [code]
	Precomputed interaction graph class.
file	FixedBBInteractionGraph.fwd.hh [code]
	Interaction graph base class for fixed-backbone packing.
file	FixedBBInteractionGraph.hh [code]
	Interaction graph base class for fixed-backbone packing.
file	HPatchEnergy.cc [code]
file	HPatchEnergy.fwd.hh [code]
file	HPatchEnergy.hh [code]
file	HPatchEnergyCreator.hh [code]
file	HPatchInteractionGraph.fwd.hh [code]
	Forward header for an IG that designs against hydrophobic area on the surface of proteins.
file	HPatchInteractionGraph.hh [code]
	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 [code]
	Interaction graph base class.
file	InteractionGraphBase.fwd.hh [code]
	InteractionGraph base class forward declaration.
file	InteractionGraphBase.hh [code]
	Base interface for annealable graphs.
file	InteractionGraphFactory.cc [code]
	Interation graph factory class definition.
file	InteractionGraphFactory.fwd.hh [code]
	Interation graph factory class forward declaration.
file	InteractionGraphFactory.hh [code]
	Interation graph factory class declaration.
file	LazyInteractionGraph.cc [code]
	Interaction graph that computes each rotamer pair energy at most once.
file	LazyInteractionGraph.fwd.hh [code]
	Interaction graph that computes each rotamer pair energy at most once.
file	LazyInteractionGraph.hh [code]
	Interaction graph that computes each rotamer pair energy at most once.
file	LinearMemoryInteractionGraph.cc [code]
file	LinearMemoryInteractionGraph.fwd.hh [code]
file	LinearMemoryInteractionGraph.hh [code]
file	MultiplexedAnnealableGraph.cc [code]
	Multiplexing packing graph container.
file	MultiplexedAnnealableGraph.fwd.hh [code]
file	MultiplexedAnnealableGraph.hh [code]
	Multiplexing packing graph container.
file	OnTheFlyInteractionGraph.cc [code]
file	OnTheFlyInteractionGraph.fwd.hh [code]
file	OnTheFlyInteractionGraph.hh [code]
file	PDInteractionGraph.cc [code]
	Pairwise Decomposable interaction graph class.
file	PDInteractionGraph.fwd.hh [code]
	Sparse pairwise decomposable interaction graph forward declaration.
file	PDInteractionGraph.hh [code]
	Pairwise Decomposable interaction graph class header.
file	PrecomputedPairEnergiesInteractionGraph.cc [code]
	Precomputed interaction graph class.
file	PrecomputedPairEnergiesInteractionGraph.fwd.hh [code]
	Precomputed Pair Energies Interaction Graph forward declaration.
file	PrecomputedPairEnergiesInteractionGraph.hh [code]
	Precomputed interaction graph class header.
file	ResidueArrayAnnealingEvaluator.cc [code]
file	ResidueArrayAnnealingEvaluator.fwd.hh [code]
file	ResidueArrayAnnealingEvaluator.hh [code]
	Annealable interface for score terms evaluated over an array of residues.
file	RotamerDots.cc [code]
	RotamerDots classes files - ported from rosetta++.
file	RotamerDots.fwd.hh [code]
	RotamerDots classes, forward declaration - ported from rosetta++.
file	RotamerDots.hh [code]
	RotamerDots classes header files - ported from rosetta++.
file	SimpleInteractionGraph.cc [code]
file	SimpleInteractionGraph.fwd.hh [code]
file	SimpleInteractionGraph.hh [code]
file	SparseMatrixIndex.fwd.hh [code]
	Helper class for AminoAcidNeighborSparseMatrix forward declaration.
file	SparseMatrixIndex.hh [code]
file	SurfaceEnergy.cc [code]
file	SurfaceEnergy.fwd.hh [code]
file	SurfaceEnergy.hh [code]
file	SurfaceEnergyCreator.hh [code]
file	SurfaceInteractionGraph.fwd.hh [code]
	Forward header for an IG that designs against hydrophobic area on the surface of proteins.
file	SurfaceInteractionGraph.hh [code]
	Interaction graph which implements a non-PD, environment-dependent score for surface residues.
file	SurfacePotential.cc [code]
file	SurfacePotential.hh [code]
file	SymmLinMemInteractionGraph.cc [code]
file	SymmLinMemInteractionGraph.fwd.hh [code]
file	SymmLinMemInteractionGraph.hh [code]
file	SymmMinimalistInteractionGraph.cc [code]
file	SymmMinimalistInteractionGraph.fwd.hh [code]
file	SymmMinimalistInteractionGraph.hh [code]
file	SymmOnTheFlyInteractionGraph.cc [code]
file	SymmOnTheFlyInteractionGraph.fwd.hh [code]
file	SymmOnTheFlyInteractionGraph.hh [code]