Uses of Class
ffx.utilities.FFXBinding

Packages that use FFXBinding

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.commands
ffx.algorithms.commands.test
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.potential.cli	The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.commands
ffx.potential.commands.test
ffx.potential.utils	The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
ffx.realspace.commands
ffx.realspace.commands.test
ffx.utilities	The Utilities package implements a variety of useful Directory, File, Port, String, etc functionality.
ffx.xray.commands
ffx.xray.commands.test

Uses of FFXBinding in ffx.algorithms.cli

Constructors in ffx.algorithms.cli with parameters of type FFXBinding

Modifier	Constructor	Description
	AlgorithmsCommand(FFXBinding binding)

Uses of FFXBinding in ffx.algorithms.commands

Constructors in ffx.algorithms.commands with parameters of type FFXBinding

Modifier	Constructor	Description
	AnalyzeNEQ(FFXBinding binding)	AnalyzeNEQ Constructor.
	Anneal(FFXBinding binding)	Anneal Constructor.
	BAR(FFXBinding binding)	BAR Constructor.
	Cluster(FFXBinding binding)	Cluster constructor.
	Dynamics(FFXBinding binding)	Dynamics Constructor.
	ForEachFile(FFXBinding binding)	ForEachFile Constructor.
	GenZ(FFXBinding binding)	ManyBody Constructor.
	Histogram(FFXBinding binding)	Histogram Constructor.
	ManyBody(FFXBinding binding)	ManyBody Constructor.
	MBAR(FFXBinding binding)	MBAR Constructor.
	Minimize(FFXBinding binding)	Minimize Constructor.
	MinimizeCrystals(FFXBinding binding)	CrystalMin Constructor.
	MinimizeOpenMM(FFXBinding binding)	MinimizeOpenMM Constructor.
	MutatePDB(FFXBinding binding)	MutatePDB Constructor.
	SaveRotamers(FFXBinding binding)
	Scheduler(FFXBinding binding)	Scheduler Constructor.
	SortArc(FFXBinding binding)	SortArc Constructor.
	Superpose(FFXBinding binding)	Superpose Constructor.
	SuperposeCrystals(FFXBinding binding)
	Thermodynamics(FFXBinding binding)	Thermodynamics Constructor.
	TorsionScan(FFXBinding binding)

Uses of FFXBinding in ffx.algorithms.commands.test

Constructors in ffx.algorithms.commands.test with parameters of type FFXBinding

Modifier	Constructor	Description
	ApplyTorsions(FFXBinding binding)	ApplyTorsions Constructor.
	CoformerBindingSearch(FFXBinding binding)	Constructor.
	CreateRotamers(FFXBinding binding)	CreateRotamers Constructor.
	CrystalSearch(FFXBinding binding)	CrystalSearch Constructor.
	FindRestraints(FFXBinding binding)	FindRestraints Constructor.
	Freefix(FFXBinding binding)	Freefix Constructor.
	IdentifyRotamers(FFXBinding binding)	IdentifyRotamers Constructor.
	ManyBodyPhScan(FFXBinding binding)	ManyBodyPhScan Constructor.
	MinimizePh(FFXBinding binding)	MinimizePh Constructor.
	MostBar(FFXBinding binding)	MostBar Constructor.
	OSTGradient(FFXBinding binding)	OSTGradient Constructor.
	PhDynamics(FFXBinding binding)	PhDynamics Constructor.
	RaoBlackwellEstimator(FFXBinding binding)	RaoBlackwellEstimator Constructor.
	RepexThermo(FFXBinding binding)	RepexThermo Constructor.
	SortXPH(FFXBinding binding)	SortXPH Constructor.
	WeightedEnsemble(FFXBinding binding)	Constructor.

Uses of FFXBinding in ffx.algorithms.misc

Fields in ffx.algorithms.misc declared as FFXBinding

Modifier and Type	Field	Description
FFXBinding	AlgorithmsTest.binding

Uses of FFXBinding in ffx.potential.cli

Constructors in ffx.potential.cli with parameters of type FFXBinding

Modifier	Constructor	Description
	PotentialCommand(FFXBinding binding)	Create a Script using the supplied Binding.

Uses of FFXBinding in ffx.potential.commands

Constructors in ffx.potential.commands with parameters of type FFXBinding

Modifier	Constructor	Description
	Biotype(FFXBinding binding)
	Cart2Frac(FFXBinding binding)
	ChainBreaks(FFXBinding binding)
	Density(FFXBinding binding)
	Energy(FFXBinding binding)
	ExportQE(FFXBinding binding)
	Fasta(FFXBinding binding)
	FeatureMap(FFXBinding binding)
	FFtoXML(FFXBinding binding)
	Frac2Cart(FFXBinding binding)
	ImportCIF(FFXBinding binding)
	MoveIntoUnitCell(FFXBinding binding)
	NucleicAcidAnalysis(FFXBinding binding)
	PhEnergy(FFXBinding binding)	Energy constructor.
	PrepareSpaceGroups(FFXBinding binding)
	SaveAsP1(FFXBinding binding)
	SaveAsPDB(FFXBinding binding)
	SaveAsXYZ(FFXBinding binding)
	Solvator(FFXBinding binding)
	Timer(FFXBinding binding)
	Volume(FFXBinding binding)
	VolumeArc(FFXBinding binding)
	WriteRestraints(FFXBinding binding)

Uses of FFXBinding in ffx.potential.commands.test

Constructors in ffx.potential.commands.test with parameters of type FFXBinding

Modifier	Constructor	Description
	Gradient(FFXBinding binding)	Gradient constructor.
	LambdaGradient(FFXBinding binding)	LambdaGradient Constructor
	PhGradient(FFXBinding binding)	Constructor with Binding.
	PrmToProperty(FFXBinding binding)	PrmToProperty Constructor.
	ReorderAtoms(FFXBinding binding)	Constructor using Binding.
	SaveAsConstantPhPDB(FFXBinding binding)	SaveAsConstantPhPDB constructor.

Uses of FFXBinding in ffx.potential.utils

Fields in ffx.potential.utils declared as FFXBinding

Modifier and Type	Field	Description
FFXBinding	PotentialTest.binding

Uses of FFXBinding in ffx.realspace.commands

Constructors in ffx.realspace.commands with parameters of type FFXBinding

Modifier	Constructor	Description
	Anneal(FFXBinding binding)	Anneal constructor.
	Dynamics(FFXBinding binding)	Dynamics constructor.
	GenZ(FFXBinding binding)	GenZ Constructor.
	ManyBody(FFXBinding binding)	ManyBody constructor.
	Minimize(FFXBinding binding)	Minimize constructor.

Uses of FFXBinding in ffx.realspace.commands.test

Constructors in ffx.realspace.commands.test with parameters of type FFXBinding

Modifier	Constructor	Description
	Alchemical(FFXBinding binding)	Alchemical constructor.
	LambdaGradient(FFXBinding binding)	LambdaGradient constructor.

Uses of FFXBinding in ffx.utilities

Fields in ffx.utilities declared as FFXBinding

Modifier and Type	Field	Description
FFXBinding	FFXCommand.binding	The Binding that provides variables to this Command.

Methods in ffx.utilities with parameters of type FFXBinding

Modifier and Type	Method	Description
void	FFXCommand.setBinding(FFXBinding binding)	Set the Binding that provides variables to this Command.

Constructors in ffx.utilities with parameters of type FFXBinding

Modifier	Constructor	Description
	FFXCommand(FFXBinding binding)	Default constructor for an FFX Command.

Uses of FFXBinding in ffx.xray.commands

Constructors in ffx.xray.commands with parameters of type FFXBinding

Modifier	Constructor	Description
	Anneal(FFXBinding binding)	Anneal constructor.
	AverageMTZ(FFXBinding binding)	AverageMTZ constructor.
	CIFtoMTZ(FFXBinding binding)	CIF2MTZ constructor.
	ComputeFc(FFXBinding binding)	ComputeFc constructor.
	Deuterate(FFXBinding binding)	Deuterate constructor.
	Dynamics(FFXBinding binding)	Dynamics constructor.
	GenZ(FFXBinding binding)	GenZ Constructor.
	ManyBody(FFXBinding binding)	ManyBody constructor.
	Minimize(FFXBinding binding)	Minimize constructor.
	ModelvsData(FFXBinding binding)	ModelvsData constructor.
	MTZInfo(FFXBinding binding)	MTZInfo constructor.
	SaveConformerPDB(FFXBinding binding)	SaveConformerPDB constructor.
	Timer(FFXBinding binding)	Timer constructor.

Uses of FFXBinding in ffx.xray.commands.test

Constructors in ffx.xray.commands.test with parameters of type FFXBinding

Modifier	Constructor	Description
	Alchemical(FFXBinding binding)	Alchemical constructor.
	LambdaGradient(FFXBinding binding)	LambdaGradient constructor.