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

Packages that use DistanceMatrix

Package	Description
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 DistanceMatrix in ffx.algorithms.optimize.manybody

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

Modifier and Type	Method	Description
void	DistanceRegion.init(DistanceMatrix dM, MolecularAssembly molecularAssembly, Residue[] allResiduesArray, AlgorithmListener algorithmListener, DistanceMatrix.NeighborDistances[][] distanceMatrix)

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

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)
	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)