Class PhGradient

java.lang.Object

ffx.utilities.FFXCommand

ffx.potential.cli.PotentialCommand

ffx.potential.commands.test.PhGradient

public class PhGradient
extends PotentialCommand

The Gradient script evaluates the consistency of the energy and gradient for CpHMD.
Usage:
ffxc test.PhGradient [options] <filename>

Field Summary

Fields

Modifier and Type	Field	Description
HashMap<String,double[]>	endstateEnergyMap
double	minEnergy
String	minLambdaList
int	nESVFailures
int	nFailures

Fields inherited from class PotentialCommand

activeAssembly, baseDir, potentialFunctions

Fields inherited from class FFXCommand

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

Constructor Summary

Constructors

Constructor	Description
PhGradient()	Default constructor.
PhGradient(FFXBinding binding)	Constructor with Binding.
PhGradient(String[] args)	Constructor that sets command-line args.

Method Summary

Modifier and Type	Method	Description
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this command.
PhGradient	run()	Execute the script.

Methods inherited from class PotentialCommand

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

Methods inherited from class FFXCommand

getCommand, helpString, listCommands, setBinding

Methods inherited from class Object

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

Field Details

endstateEnergyMap

public HashMap<String,double[]> endstateEnergyMap

nFailures

public int nFailures

nESVFailures

public int nESVFailures

minEnergy

public double minEnergy

minLambdaList

public String minLambdaList

Constructor Details

PhGradient

public PhGradient()

Default constructor.

PhGradient

public PhGradient(FFXBinding binding)

Constructor with Binding.

Parameters:

binding - Binding

PhGradient

public PhGradient(String[] args)

Constructor that sets command-line args.

Parameters:

args - Args

Method Details

run

public PhGradient run()

Execute the script.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

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.