interaction_graph Directory Reference

Directory dependency graph for 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	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.