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.
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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)