Uses of Package
ffx.algorithms
Packages that use ffx.algorithms
Package
Description
The Algorithms package has support for local and global optimization, molecular dynamics
simulations, and calculation of free energy differences.
The Algorithms CLI package defines options for PicoCLI command line scripts.
The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and
via OpenMM.
The MC package implements a variety of Monte Carlo moves for optimization and simulation
algorithms.
The Misc package contains a few miscellaneous algorithms.
The Optimize package contains local and global optimization algorithms using pure Java and OpenMM
code paths.
The Thermodynamics package computes free energy differences using Orthogonal Space Tempering
(OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
The UI package provides views and controllers for manipulating molecular systems.
The X-ray package implements support for X-ray and Neutron refinement.
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Classes in ffx.algorithms used by ffx.algorithmsClassDescriptionAlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional functionality such as molecular dynamics and L-BFGS local optimization.The AlgorithmListener will be notified at regular intervals during an algorithm.
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Classes in ffx.algorithms used by ffx.algorithms.cliClassDescriptionAlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional functionality such as molecular dynamics and L-BFGS local optimization.The AlgorithmListener will be notified at regular intervals during an algorithm.
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Classes in ffx.algorithms used by ffx.algorithms.dynamicsClassDescriptionThe AlgorithmListener will be notified at regular intervals during an algorithm.Algorithms that can be gracefully terminated early should implement this interface.
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Classes in ffx.algorithms used by ffx.algorithms.mcClassDescriptionThe AlgorithmListener will be notified at regular intervals during an algorithm.
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Classes in ffx.algorithms used by ffx.algorithms.miscClassDescriptionThe AlgorithmListener will be notified at regular intervals during an algorithm.
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Classes in ffx.algorithms used by ffx.algorithms.optimizeClassDescriptionThe AlgorithmListener will be notified at regular intervals during an algorithm.Algorithms that can be gracefully terminated early should implement this interface.
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Classes in ffx.algorithms used by ffx.algorithms.optimize.annealClassDescriptionThe AlgorithmListener will be notified at regular intervals during an algorithm.Algorithms that can be gracefully terminated early should implement this interface.
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Classes in ffx.algorithms used by ffx.algorithms.optimize.manybodyClassDescriptionThe AlgorithmListener will be notified at regular intervals during an algorithm.
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Classes in ffx.algorithms used by ffx.algorithms.thermodynamicsClassDescriptionThe AlgorithmListener will be notified at regular intervals during an algorithm.
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Classes in ffx.algorithms used by ffx.uiClassDescriptionAlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional functionality such as molecular dynamics and L-BFGS local optimization.The AlgorithmListener will be notified at regular intervals during an algorithm.AlgorithmUtils, on top of the core functionality of PotentialsUtils, implements additional functionality such as molecular dynamics and L-BFGS local optimization.
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Classes in ffx.algorithms used by ffx.xrayClassDescriptionThe AlgorithmListener will be notified at regular intervals during an algorithm.Algorithms that can be gracefully terminated early should implement this interface.