Uses of Package
ffx.algorithms.optimize

Packages that use ffx.algorithms.optimize

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.manybody

Classes in ffx.algorithms.optimize used by ffx.algorithms.cli

Class	Description
RotamerOptimization	Optimize protein side-chain conformations and nucleic acid backbone conformations using rotamers.
RotamerOptimization.Algorithm	Rotamer Optimization Methods.

Classes in ffx.algorithms.optimize used by ffx.algorithms.optimize

Class	Description
ConformationScan	This class is for a configuration optimization of two small systems.
Minimize	Minimize the potential energy of a system to an RMS gradient per atom convergence criteria.
Minimize.MinimizationEngine	Enumerates available molecular minimization engines; presently limited to the FFX reference engine and the OpenMM engine.
RotamerOptimization.Algorithm	Rotamer Optimization Methods.
RotamerOptimization.Direction
RotamerOptimization.DistanceMethod	Allows get2BodyDistance to find the shortest distance between any two rotamers or two residues.

Classes in ffx.algorithms.optimize used by ffx.algorithms.optimize.manybody

Class	Description
RotamerOptimization	Optimize protein side-chain conformations and nucleic acid backbone conformations using rotamers.
RotamerOptimization.DistanceMethod	Allows get2BodyDistance to find the shortest distance between any two rotamers or two residues.