Uses of Package
ffx.algorithms.cli

Packages that use ffx.algorithms.cli

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).

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

Class	Description
BarostatOptions	Represents command line options for scripts that use a barostat/NPT.
DynamicsOptions	Represents command line options for scripts that run molecular dynamics.
LambdaParticleOptions	Represents command line options for scripts that utilize a mobile lambda particle, such as Thermodynamics.
ThermodynamicsOptions	Represents command line options for scripts that calculate thermodynamics.
ThermodynamicsOptions.ThermodynamicsAlgorithm	Represents categories of thermodynamics algorithms that must be handled differently.

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

Class	Description
DynamicsOptions	Represents command line options for scripts that run molecular dynamics.

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

Class	Description
AlgorithmsScript	Base class for scripts in the Algorithms package, providing some key functions.

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

Class	Description
ManyBodyOptions	Represents command line options for scripts that use a many-body expansion for global optimization.

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

Class	Description
DynamicsOptions	Represents command line options for scripts that run molecular dynamics.
LambdaParticleOptions	Represents command line options for scripts that utilize a mobile lambda particle, such as Thermodynamics.
OSTOptions	Represents command line options for scripts that utilize variants of the Orthogonal Space Tempering (OST) algorithm.