Uses of Interface
ffx.algorithms.AlgorithmFunctions

Packages that use AlgorithmFunctions

Package	Description
ffx.algorithms	The Algorithms package has support for local and global optimization, molecular dynamics simulations, and calculation of free energy differences.
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.

Uses of AlgorithmFunctions in ffx.algorithms

Classes in ffx.algorithms that implement AlgorithmFunctions

Modifier and Type	Class	Description
class	AlgorithmUtils	AlgorithmUtils, on top of the core functionality of PotentialsUtils, implements additional functionality such as molecular dynamics and L-BFGS local optimization.

Uses of AlgorithmFunctions in ffx.algorithms.cli

Fields in ffx.algorithms.cli declared as AlgorithmFunctions

Modifier and Type	Field	Description
AlgorithmFunctions	AlgorithmsScript.algorithmFunctions	An instance of AlgorithmFunctions passed into the current context.

Methods in ffx.algorithms.cli with parameters of type AlgorithmFunctions

Modifier and Type	Method	Description
void	MultiDynamicsOptions.distribute(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, AlgorithmFunctions algorithmFunctions, int rank, int worldSize)	If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
void	MultiDynamicsOptions.distribute(MolecularAssembly[] molecularAssemblies, Potential[] potentials, CrystalPotential crystalPotential, AlgorithmFunctions algorithmFunctions, int rank, int worldSize)	If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
MolecularAssembly	MultiDynamicsOptions.openFile(AlgorithmFunctions algorithmFunctions, TopologyOptions topologyOptions, int threadsPer, String toOpen, int topNum, AlchemicalOptions alchemicalOptions, File structureFile, int rank)	Opens a file and processes it.

Uses of AlgorithmFunctions in ffx.ui

Classes in ffx.ui that implement AlgorithmFunctions

Modifier and Type	Class	Description
class	UIUtils	UIUtils implements core and extended functionality for many Force Field X algorithms and scripts, such as opening and closing structure files, basic force field evaluations, molecular dynamics, etc.

Methods in ffx.ui that return AlgorithmFunctions

Modifier and Type	Method	Description
AlgorithmFunctions	ModelingShell.getUIAlgorithmUtils()