Package ffx.algorithms.commands.test
Class FindRestraints
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.test.FindRestraints
The FindRestraints script identifies guest molecule atoms that should be restrained based on
their proximity to specific atoms in a host molecule.
Usage:
ffxc test.FindRestraints [options] <filename>
Usage:
ffxc test.FindRestraints [options] <filename>
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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
ConstructorsConstructorDescriptionFindRestraints Constructor.FindRestraints
(FFXBinding binding) FindRestraints Constructor.FindRestraints
(String[] args) FindRestraints constructor that sets the command line arguments. -
Method Summary
Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand
destroyPotentials, getActiveAssemblies, getActiveAssembly, getPotentials, 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
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Constructor Details
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FindRestraints
public FindRestraints()FindRestraints Constructor. -
FindRestraints
FindRestraints Constructor.- Parameters:
binding
- The Binding to use.
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FindRestraints
FindRestraints constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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getPotentialObject
Get the potential object.- Returns:
- The potential object.
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run
Execute this Command.- Overrides:
run
in classFFXCommand
- Returns:
- The current FFXCommand.
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