Uses of Class
ffx.algorithms.optimize.RotamerOptimization

Packages that use RotamerOptimization

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
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 RotamerOptimization in ffx.algorithms.cli

Methods in ffx.algorithms.cli with parameters of type RotamerOptimization

Modifier and Type	Method	Description
void	ManyBodyOptions.initRotamerOptimization(RotamerOptimization rotamerOptimization, MolecularAssembly activeAssembly)	initRotamerOptimization.

Uses of RotamerOptimization in ffx.algorithms.optimize.manybody

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

Modifier and Type	Method	Description
void	GoldsteinPairRegion.init(Residue[] residues, int i, int riA, int riB, int j, int rjC, int rjD, int[][] bidiResNeighbors, RotamerOptimization rotamerOptimization)	Initializes a ParallelRegion to attempt the elimination of riA,rjC by riB,rjD.

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

Modifier	Constructor	Description
	EliminatedRotamers(RotamerOptimization rO, DistanceMatrix dM, List<Residue> allResiduesList, int maxRotCheckDepth, double clashThreshold, double pairClashThreshold, double multiResClashThreshold, double nucleicPruningFactor, double nucleicPairsPruningFactor, double multiResPairClashAddn, boolean pruneClashes, boolean prunePairClashes, boolean print, Residue[] residues)
	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)
	RotamerMatrixMC(int[] rotamers, Residue[] residues, boolean useFullAMOEBAEnergy, RotamerOptimization rotamerOptimization)	The Rotamers array must be the same array as passed to any MCMove objects used (and not a copy).
	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)