Package ffx.potential.commands

Class Solvator

java.lang.Object

ffx.utilities.FFXCommand

ffx.potential.cli.PotentialCommand

ffx.potential.commands.Solvator

public class Solvator
extends PotentialCommand

The Solvator script puts a box of solvent around a solute.
Usage:
ffxc Solvator [options] <filename>

Field Summary

Fields inherited from class ffx.potential.cli.PotentialCommand

activeAssembly, baseDir, potentialFunctions

Fields inherited from class ffx.utilities.FFXCommand

args, binding, color, help, logger, parseResult, version

Constructor Summary

Constructors

Constructor	Description
Solvator()
Solvator(FFXBinding binding)
Solvator(String[] args)

Method Summary

Modifier and Type	Method	Description
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this command.
File	getWrittenFile()
Solvator	run()	Execute this Command.
void	setProperties(org.apache.commons.configuration2.Configuration additionalProps)

Methods inherited from class ffx.potential.cli.PotentialCommand

createOutputFile, destroyPotentials, getActiveAssemblies, getActiveAssembly, getActiveAssembly, getBaseDirString, getPotentialsFromAssemblies, init, parseFilePath, saveByExtension, saveByExtension, saveByOriginalExtension, saveByOriginalExtension, setActiveAssembly

Methods inherited from class ffx.utilities.FFXCommand

getCommand, helpString, listCommands, setBinding

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

Solvator

public Solvator()

Solvator

public Solvator(FFXBinding binding)

Solvator

public Solvator(String[] args)

Method Details

setProperties

public void setProperties(org.apache.commons.configuration2.Configuration additionalProps)

run

public Solvator run()

Description copied from class: FFXCommand

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getWrittenFile

public File getWrittenFile()

getPotentials

public List<Potential> getPotentials()

Description copied from class: PotentialCommand

Returns a List of all Potential objects associated with this command. Should be written to tolerate nulls, as many tests run help() and exit without instantiating their Potentials.

Overrides:

getPotentials in class PotentialCommand

Returns:

All Potentials. Sometimes empty, never null.