Package ffx.xray.commands
Class Deuterate
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.xray.commands.Deuterate
Deuterate changes exchangeable hydrogen atoms to deuterium atoms for a PDB file.
Usage:
ffxc xray.Deuterate <pdbfile1>
Usage:
ffxc xray.Deuterate <pdbfile1>
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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
ConstructorsConstructorDescriptionDeuterate constructor.Deuterate
(FFXBinding binding) Deuterate constructor.Deuterate constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionReturns a List of all Potential objects associated with this script.run()
Execute the script.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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Deuterate
public Deuterate()Deuterate constructor. -
Deuterate
Deuterate constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Deuterate
Deuterate constructor.- Parameters:
binding
- The Binding to use.
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Method Details
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run
Execute the script.- Overrides:
run
in classFFXCommand
- Returns:
- The current FFXCommand.
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getPotentials
Description copied from class:AlgorithmsCommand
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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