Package ffx.algorithms.optimize.manybody

package ffx.algorithms.optimize.manybody

Related Packages

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

Classes

Class	Description
DistanceMatrix	Calculates a residue-residue distance matrix.
DistanceRegion	Compute the minimum distance between each pair of residues for all rotamer permutations.
EliminatedRotamers
EnergyExpansion
EnergyRegion
FourBodyEnergyRegion	Compute 4-Body energies.
GoldsteinPairRegion
ManyBodyCell	A cell used for optimization of a subdomain, its residues, its extent in fractional coordinates, its overall (linear) index, and its indices along the a, b, and c axes.
RotamerMatrixMC	Monte Carlo driver for DEE-MC.
RotamerMatrixMove	This implements single-rotamer changes in the framework of the rotamer energy matrices.
SelfEnergyRegion	Compute residue self-energy values in parallel across nodes.
ThreeBodyEnergyRegion	Compute 3-Body energy values in parallel across nodes.
TwoBodyEnergyRegion	Compute 2-Body energy values in parallel across nodes.