Package ffx.algorithms.commands
Class Dynamics
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.Dynamics
The Dynamics script implements molecular and stochastic dynamics algorithms.
Usage:
ffxc Dynamics [options] <filename> [file2...]
Usage:
ffxc Dynamics [options] <filename> [file2...]
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Field Summary
FieldsModifier and TypeFieldDescriptionCreation of a public field to try and make the JUnit test work, original code does not declare this as a public field.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
ConstructorsConstructorDescriptionDynamics()
Dynamics Constructor.Dynamics
(FFXBinding binding) Dynamics Constructor.Dynamics constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionReturns a List of all Potential objects associated with this script.run()
Execute this Command.Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand
destroyPotentials, getActiveAssemblies, getActiveAssembly, init, saveDirFile, setActiveAssembly, setBaseDir, updateTitle
Methods inherited from class ffx.utilities.FFXCommand
getCommand, helpString, listCommands, setBinding
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Field Details
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potential
Creation of a public field to try and make the JUnit test work, original code does not declare this as a public field. Originally it is declared in the run method. -
molDyn
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Constructor Details
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Dynamics
public Dynamics()Dynamics Constructor. -
Dynamics
Dynamics Constructor.- Parameters:
binding
- The Binding to use.
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Dynamics
Dynamics constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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getMolecularDynamics
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getPotentialObject
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run
Execute this Command.- Overrides:
run
in classFFXCommand
- Returns:
- The current FFXCommand.
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getPotentials
Returns a List of all Potential objects associated with this script.- Overrides:
getPotentials
in classAlgorithmsCommand
- Returns:
- All Potentials. Sometimes empty, never null.
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