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. @reference 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. @reference 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. | |
