|
| file | AdditionalBackgroundNodesInteractionGraph.hh |
| | Interaction graph which can handle some residues not changing during packing.
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| |
| file | AminoAcidNeighborSparseMatrix.fwd.hh |
| | Sparse Matrix class for rotamer pair energy storage forward declaration.
|
| |
| file | AminoAcidNeighborSparseMatrix.hh |
| | Amino acid neighbor sparse matrix template class.
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| |
| file | DensePDInteractionGraph.cc |
| | Dense Edge-Matrix, Pairwise Decomposable interaction graph class implementation.
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| |
| file | DensePDInteractionGraph.fwd.hh |
| | Helper class for AminoAcidNeighborSparseMatrix forward declaration.
|
| |
| 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.
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| |
| 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.
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| |
| 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.
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| |
| file | HPatchEnergy.cc |
| |
| file | HPatchEnergy.fwd.hh |
| | HPatch energy method, a score based on exact SASA calculations and a new patch identification algorithm, forward header file.
|
| |
| file | HPatchEnergy.hh |
| | HPatch energy method, a score based on exact SASA calculations and a new patch identification algorithm, header file.
|
| |
| file | HPatchEnergyCreator.hh |
| | Declaration for the class that connects HPatchEnergy with the ScoringManager.
|
| |
| 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.
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| |
| file | InteractionGraphBase.cc |
| | Interaction graph base class.
|
| |
| file | InteractionGraphBase.fwd.hh |
| | InteractionGraph base class forward declaration.
|
| |
| file | InteractionGraphBase.hh |
| | Interaction graph base class header.
|
| |
| 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 | 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 | 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 |
| | Sparse matrix index class to work with AminoAcidNeighborSparseMatrix class.
|
| |
| file | SurfaceEnergy.cc |
| |
| file | SurfaceEnergy.fwd.hh |
| | Forward header file for SurfaceEnergy; Not really a CD1B energy; this class is needed for optE.
|
| |
| file | SurfaceEnergy.hh |
| | Header file for SurfaceEnergy; Not really a CD1B energy; this class is needed for optE.
|
| |
| file | SurfaceEnergyCreator.hh |
| | Declaration for the class that connects SurfaceEnergy with the ScoringManager.
|
| |
| 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 |
| | Class which keeps reads the residue hydrophobic ASA database file and calculates surface residue energies.
|
| |
| file | SurfacePotential.hh |
| | Class which keeps reads the residue hydrophobic ASA database file and calculates surface residue energies.
|
| |
| 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 |
| |
1.8.7