Package ffx.algorithms.commands.test
Class RepexThermo
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.Thermodynamics
ffx.algorithms.commands.test.RepexThermo
The RepexThermo command uses the Orthogonal Space Tempering with histogram replica exchange to estimate a free energy difference.
Usage:
ffxc test.RepexThermo [options] <filename> [file2...];
Usage:
ffxc test.RepexThermo [options] <filename> [file2...];
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Field Summary
Fields inherited from class ffx.algorithms.commands.Thermodynamics
additionalProperties, alchemicalOptions, barostatOptions, dynamicsOptions, filenames, lambdaParticleOptions, multiDynamicsOptions, orthogonalSpaceTempering, ostOptions, potential, randomSymopOptions, thermodynamicsOptions, topologies, topologyOptions, verbose, writeoutOptions
Fields inherited from class ffx.algorithms.cli.AlgorithmsCommand
activeAssembly, algorithmFunctions, algorithmListener, baseDir
Fields inherited from class ffx.utilities.FFXCommand
args, binding, color, help, logger, parseResult, version
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Constructor Summary
ConstructorsConstructorDescriptionRepexThermo Constructor.RepexThermo
(FFXBinding binding) RepexThermo Constructor.RepexThermo
(String[] args) RepexThermo constructor that sets the command line arguments. -
Method Summary
Methods inherited from class ffx.algorithms.commands.Thermodynamics
destroyPotentials, setProperties
Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand
getActiveAssemblies, getActiveAssembly, init, saveDirFile, setActiveAssembly, setBaseDir, updateTitle
Methods inherited from class ffx.utilities.FFXCommand
getCommand, helpString, listCommands, setBinding
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Constructor Details
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RepexThermo
public RepexThermo()RepexThermo Constructor. -
RepexThermo
RepexThermo Constructor.- Parameters:
binding
- The Binding to use.
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RepexThermo
RepexThermo constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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run
Execute this Command.- Overrides:
run
in classThermodynamics
- Returns:
- The current FFXCommand.
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getOST
- Overrides:
getOST
in classThermodynamics
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getPotential
- Overrides:
getPotential
in classThermodynamics
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getPotentials
Description copied from class:AlgorithmsCommand
Returns a List of all Potential objects associated with this script.- Overrides:
getPotentials
in classThermodynamics
- Returns:
- All Potentials. Sometimes empty, never null.
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