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

Packages that use EliminatedRotamers

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

Uses of EliminatedRotamers in ffx.algorithms.optimize

Methods in ffx.algorithms.optimize that return EliminatedRotamers

Modifier and Type	Method	Description
EliminatedRotamers	RotamerOptimization.getEliminatedRotamers()

Uses of EliminatedRotamers in ffx.algorithms.optimize.manybody

Constructors in ffx.algorithms.optimize.manybody with parameters of type EliminatedRotamers

Modifier	Constructor	Description
	EnergyExpansion(RotamerOptimization rO, DistanceMatrix dM, EliminatedRotamers eR, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, List<Residue> allResiduesList, int[][] resNeighbors, boolean threeBodyTerm, boolean decomposeOriginal, boolean usingBoxOptimization, boolean verbose, boolean pruneClashes, boolean prunePairClashes, boolean master)
	FourBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, double superpositionThreshold)
	RotamerMatrixMove(boolean useAllElims, int[] rotamers, Residue[] residues, RotamerOptimization rotamerOptimization, EliminatedRotamers eliminatedRotamers, boolean monteCarloTesting)	Constructs the RotamerMatrixMove set; at present, a new object must be made if rotamers or residues are changed outside the scope of this class.
	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)