Uses of Class
ffx.algorithms.optimize.manybody.EnergyExpansion
Packages that use EnergyExpansion
Package
Description
The Optimize package contains local and global optimization algorithms using pure Java and OpenMM
code paths.
The manybody package implements many-body rotamer optimization infrastructure,
including distance matrices, an energy expansion (self, two-body, three-body,
and four-body), Dead-end elimination criteria, Goldstein elimination criteria,
and supporting data structures for efficient optimization.
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Uses of EnergyExpansion in ffx.algorithms.optimize
Methods in ffx.algorithms.optimize that return EnergyExpansion -
Uses of EnergyExpansion in ffx.algorithms.optimize.manybody
Methods in ffx.algorithms.optimize.manybody with parameters of type EnergyExpansionModifier and TypeMethodDescriptionvoid
EnergyRegion.init
(EnergyExpansion eE, Residue[] residues, int[] rotamers, boolean threeBodyTerm) void
EliminatedRotamers.setEnergyExpansion
(EnergyExpansion eE) Constructors in ffx.algorithms.optimize.manybody with parameters of type EnergyExpansionModifierConstructorDescriptionFourBodyEnergyRegion
(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, double superpositionThreshold) SelfEnergyRegion
(RotamerOptimization rO, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, BufferedWriter energyWriter, Comm world, int numProc, boolean pruneClashes, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles) ThreeBodyEnergyRegion
(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, BufferedWriter energyWriter, Comm world, int numProc, double superpositionThreshold, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles) TwoBodyEnergyRegion
(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, BufferedWriter energyWriter, Comm world, int numProc, boolean prunePairClashes, double superpositionThreshold, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles)