Package ffx.algorithms.commands
Class MinimizeOpenMM
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.MinimizeOpenMM
The Minimize script uses OpenMM accelerated L-BFGS algorithm to minimize the
energy of a molecular system.
Usage:
ffxc MinimizeOpenMM [options] <filename>
Usage:
ffxc MinimizeOpenMM [options] <filename>
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Field Summary
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
ConstructorsConstructorDescriptionMinimizeOpenMM Constructor.MinimizeOpenMM
(FFXBinding binding) MinimizeOpenMM Constructor.MinimizeOpenMM
(String[] args) MinimizeOpenMM 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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Constructor Details
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MinimizeOpenMM
public MinimizeOpenMM()MinimizeOpenMM Constructor. -
MinimizeOpenMM
MinimizeOpenMM Constructor.- Parameters:
binding
- The Binding to use.
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MinimizeOpenMM
MinimizeOpenMM 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 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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