Package ffx.algorithms.optimize.manybody

@ParametersAreNonnullByDefault package 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.

Since:

1.0

Author:

Michael J. Schnieders

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	The anneal package implements simulated annealing-based optimization, including an interface for annealing schedules and several concrete schedule implementations (linear, exponential, and flat-end) used to control temperature during optimization runs.

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.