Uses of Class
ffx.utilities.FFXCommand

Packages that use FFXCommand

Package	Description
ffx	Force Field X implements fixed charge and polarizable atomic multipole molecular mechanics potentials, local and global optimization, molecular dynamics, free energy differences, etc, with special support for crystal space groups.
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.commands
ffx.algorithms.commands.test
ffx.potential.cli	The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.commands
ffx.potential.commands.test
ffx.realspace.commands
ffx.realspace.commands.test
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.
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 FFXCommand in ffx

Methods in ffx that return FFXCommand

Modifier and Type	Method	Description
static FFXCommand	Main.ffxScript(String[] args)	A main entry point that runs a script and return a refernce to the result.
static FFXCommand	Main.runScript(ModelingShell shell, File commandLineFile, List<String> argList)

Uses of FFXCommand in ffx.algorithms.cli

Subclasses of FFXCommand in ffx.algorithms.cli

Modifier and Type	Class	Description
class	AlgorithmsCommand	Base class for scripts in the Algorithms package, providing some key functions.

Uses of FFXCommand in ffx.algorithms.commands

Subclasses of FFXCommand in ffx.algorithms.commands

Modifier and Type	Class	Description
class	AnalyzeNEQ	Performs analysis of Non-equilibrium work simulations.
class	Anneal	The Anneal script.
class	BAR	The BAR script finds the free energy difference across a lambda window.
class	Cluster	The Cluster script clusters structures utilizing RMSD.
class	Dynamics	The Dynamics script implements molecular and stochastic dynamics algorithms.
class	ForEachFile	Run an FFX command on a series of files.
class	GenZ	The ReductionPartition script performs a discrete optimization using a many-body expansion and elimination expressions.
class	Histogram	The Histogram script prints out a Orthogonal Space histogram from a *.his file.
class	ManyBody	The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.
class	MBAR	Perform MBAR calculation or necessary energy evaluations.
class	Minimize	The Minimize script uses a limited-memory BFGS algorithm to minimize the energy of a molecular system.
class	MinimizeCrystals	The MinimizeCrystals script uses a limited-memory BFGS algorithm to minimize the energy of a crystal, including both coordinates and unit cell parameters.
class	MinimizeOpenMM	The Minimize script uses OpenMM accelerated L-BFGS algorithm to minimize the energy of a molecular system.
class	MutatePDB	The MutatePDB script mutates residue(s) of a PDB file.
class	PhDynamics	The PhDynamics command implements constant pH molecular dynamics.
class	PhMinimize	The MinimizePh command uses a limited-memory BFGS algorithm to minimize the energy of a CpHMD molecular system.
class	SaveRotamers	The SaveRotamers script saves out rotamers.
class	Scheduler	Run a Parallel Java Job Scheduler on a cluster with multiple nodes.
class	SortArc	The SortArc script sort Monte Carlo archive files by lambda value.
class	Superpose	The Superpose script superposes molecules in an arc/multiple model pdb file (all versus all or one versus all) or in two pdb/xyz files.
class	SuperposeCrystals
class	Thermodynamics	The Thermodynamics script uses the Transition-Tempered Orthogonal Space Random Walk algorithm to estimate a free energy.
class	TorsionScan	The TorsionSearch command enumerates conformations of a molecule using torsional scans around rotatable bonds.

Uses of FFXCommand in ffx.algorithms.commands.test

Subclasses of FFXCommand in ffx.algorithms.commands.test

Modifier and Type	Class	Description
class	ApplyTorsions	The ApplyTorsions script is used to apply a custom set of torsions to a side chain.
class	CoformerBindingSearch	CoformerBindingSearch is a Groovy script that generates a set of molecular orientations in vacuum and calculates the energy of each conformation.
class	CreateRotamers	The CreateRotamers script creates a set of conformation dependent rotamers.
class	CrystalSearch	The CrystalSearch script searches for minimum energy polymorphs for a given space group.
class	FindRestraints	The FindRestraints script identifies guest molecule atoms that should be restrained based on their proximity to specific atoms in a host molecule.
class	Freefix	The Freefix script calculates analytical free energy, entropy, and enthalpy corrections for flat-bottom harmonic restraints with inner and outer radii.
class	IdentifyRotamers	The IdentifyRotamers script attempts to identify which rotamer each Residue in the system is in.
class	ManyBodyPhScan	The ManyBodyPhScan script runs a pH scan with ManyBody optimization by executing another FFXScript multiple times across a pH range.
class	MostBar	The MostBar script uses a single set of archive file(s) from a Metropolized Orthogonal Space Tempering run to evaluate free energy via the Bennett Acceptance Ratio Usage: ffxc test.MostBar [options] <structures1>
class	OSTGradient	OSTGradient tests the Orthogonal Space Tempering Potential.
class	RaoBlackwellEstimator	Use the Rao-Blackwell Estimator to estimate a free energy difference of protonation for a CpHMD system.
class	RepexThermo	The RepexThermo command uses the Orthogonal Space Tempering with histogram replica exchange to estimate a free energy difference.
class	SortXPH	The SortXPH command unwinds .ARC files from CpHMD runs.
class	WeightedEnsemble	WeightedEnsemble Usage: Accelerated Sampling with Weighted Ensemble ffxc test.WeightedEnsemble [options] <filename> [file2

Uses of FFXCommand in ffx.potential.cli

Subclasses of FFXCommand in ffx.potential.cli

Modifier and Type	Class	Description
class	PotentialCommand	Base class for scripts in the Potentials package, providing some key functions.

Uses of FFXCommand in ffx.potential.commands

Subclasses of FFXCommand in ffx.potential.commands

Modifier and Type	Class	Description
class	Biotype	Print out Biotype records for the atoms in an XYZ file.
class	Cart2Frac	Convert from Cartesian to fractional coordinates.
class	ChainBreaks	Fix chain breaks in a PDB file.
class	Density	Calculate the mean system density for single topology systems.
class	Energy	Compute the force field potential energy.
class	ExportQE	Generate Quantum Espresso (QE) input from an XYZ file.
class	Fasta	Fasta outputs a sub-sequence from a FASTA file.
class	FeatureMap	Create a Feature Map for a given protein structure.
class	FFtoXML	The FFtoXML command saves a force field as an XML file usable by OpenMM.
class	Frac2Cart	Convert from fractional to Cartesian coordinates.
class	ImportCIF	Convert a CIF file to PDB/XYZ format.
class	MoveIntoUnitCell	Move the center of mass of each molecule into the unit cell.
class	NucleicAcidAnalysis	Calculates nucleic acid torsions as well as information regarding the sugar pucker.
class	PhEnergy	The Energy script evaluates the energy of a system.
class	PrepareSpaceGroups	Create sub-directories for selected space groups.
class	SaveAsP1	Expand the system to P1 and then save it.
class	SaveAsPDB	Save the system as a PDB file.
class	SaveAsXYZ	Save the system as an XYZ (or ARC) file.
class	Solvator	The Solvator script puts a box of solvent around a solute.
class	Timer	The Timer command evaluates the wall clock time for energy and forces.
class	Volume	Calculate the surface area and volume using the GaussVol (default) or Connolly algorithm.
class	VolumeArc	Calculate the surface area and volume using the GaussVol (default) or Connolly algorithm for each snapshot in an ARC file.
class	WriteRestraints	WriteRestraints logs "restrain-position" properties for a PDB/XYZ file.

Uses of FFXCommand in ffx.potential.commands.test

Subclasses of FFXCommand in ffx.potential.commands.test

Modifier and Type	Class	Description
class	Gradient	The Gradient script evaluates the consistency of the energy and gradient.
class	LambdaGradient	The LambdaGradient script tests numeric gradients w.r.t. lambda against numeric, finite-difference gradients Usage: ffxc test.LambdaGradient [options] <filename> [file2...]
class	PhGradient	The Gradient script evaluates the consistency of the energy and gradient for CpHMD.
class	PrmToProperty	The PrmToProperty script converts a TINKER *.prm file to Java properties.
class	ReorderAtoms	The ReorderAtoms script sorts the atoms within an XYZ file based on atomic weight.
class	SaveAsConstantPhPDB	Save a PDB file that includes all titrating tautomer hydrogen atoms.

Uses of FFXCommand in ffx.realspace.commands

Subclasses of FFXCommand in ffx.realspace.commands

Modifier and Type	Class	Description
class	Anneal	The Real Space Annealing script.
class	Dynamics	The Real Space Dynamics script.
class	GenZ	Run GenZ for ensemble generation.
class	ManyBody	The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.
class	Minimize	The Real Space Minimize script.

Uses of FFXCommand in ffx.realspace.commands.test

Subclasses of FFXCommand in ffx.realspace.commands.test

Modifier and Type	Class	Description
class	Alchemical	The Alchemical Changes script.
class	LambdaGradient	The Real Space Annealing script.

Uses of FFXCommand in ffx.ui

Methods in ffx.ui that return FFXCommand

Modifier and Type	Method	Description
FFXCommand	ModelingShell.runFFXScript(File file, List<String> argList)	runFFXScript - Execute a FFX script.
FFXCommand	ModelingShell.runFFXScript(Class<? extends FFXCommand> className, List<String> argList)	runFFXScript - Execute a compiled FFX command.

Method parameters in ffx.ui with type arguments of type FFXCommand

Modifier and Type	Method	Description
FFXCommand	ModelingShell.runFFXScript(Class<? extends FFXCommand> className, List<String> argList)	runFFXScript - Execute a compiled FFX command.

Uses of FFXCommand in ffx.utilities

Methods in ffx.utilities that return FFXCommand

Modifier and Type	Method	Description
FFXCommand	FFXCommand.run()	Execute this Command.

Methods in ffx.utilities that return types with arguments of type FFXCommand

Modifier and Type	Method	Description
static Class<? extends FFXCommand>	FFXCommand.getCommand(String name)	Use the System ClassLoader to find the requested Command.

Uses of FFXCommand in ffx.xray.commands

Subclasses of FFXCommand in ffx.xray.commands

Modifier and Type	Class	Description
class	Anneal	The X-ray Annealing script.
class	AverageMTZ	Use AverageMTZ to provide two MTZ files and an iteration for a cumulative moving average.
class	CIFtoMTZ	The CIF2MTZ script saves a CIF file to MTZ format.
class	ComputeFc	Compute structure factors and save them to an MTZ file.
class	Deuterate	Deuterate changes exchangeable hydrogen atoms to deuterium atoms for a PDB file.
class	Dynamics	The X-ray Dynamics script.
class	EditPDB	EditPDB edits a PDB model for use in experimental refinement.
class	GenZ	The GenZ script for calculating free energy changes.
class	ManyBody	The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.
class	Minimize	The X-ray Minimize script.
class	ModelvsData	The X-ray ModelvsData script.
class	MTZInfo	The MTZInfo script prints out MTZ reflection file header info.
class	Timer	The X-ray Timer script.

Uses of FFXCommand in ffx.xray.commands.test

Subclasses of FFXCommand in ffx.xray.commands.test

Modifier and Type	Class	Description
class	Alchemical	The Alchemical Changes script.
class	Gradient	The Gradient script evaluates the consistency of the energy and gradient.
class	LambdaGradient	The X-ray test Lambda Gradient script.