Uses of Class
ffx.algorithms.optimize.manybody.EnergyExpansion

Packages that use EnergyExpansion

Package	Description
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.manybody	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.

Uses of EnergyExpansion in ffx.algorithms.optimize

Methods in ffx.algorithms.optimize that return EnergyExpansion

Modifier and Type	Method	Description
EnergyExpansion	RotamerOptimization.getEnergyExpansion()

Uses of EnergyExpansion in ffx.algorithms.optimize.manybody

Methods in ffx.algorithms.optimize.manybody with parameters of type EnergyExpansion

Modifier and Type	Method	Description
void	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 EnergyExpansion

Modifier	Constructor	Description
	FourBodyEnergyRegion(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)