Uses of Class
ffx.algorithms.cli.AlgorithmsScript

Packages that use AlgorithmsScript

Package	Description
ffx.algorithms.commands
ffx.algorithms.commands.test
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.realspace.commands
ffx.realspace.commands.test
ffx.xray.commands
ffx.xray.commands.test

Uses of AlgorithmsScript in ffx.algorithms.commands

Subclasses of AlgorithmsScript 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	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 AlgorithmsScript in ffx.algorithms.commands.test

Subclasses of AlgorithmsScript 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	MinimizePh	The MinimizePh command uses a limited-memory BFGS algorithm to minimize the energy of a CpHMD molecular system.
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	PhDynamics	The PhDynamics command implements constant pH molecular dynamics.
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 AlgorithmsScript in ffx.algorithms.misc

Fields in ffx.algorithms.misc declared as AlgorithmsScript

Modifier and Type	Field	Description
AlgorithmsScript	AlgorithmsTest.algorithmsScript

Uses of AlgorithmsScript in ffx.realspace.commands

Subclasses of AlgorithmsScript 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 AlgorithmsScript in ffx.realspace.commands.test

Subclasses of AlgorithmsScript 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 AlgorithmsScript in ffx.xray.commands

Subclasses of AlgorithmsScript 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	The X-ray ComputeFc script.
class	Deuterate	Deuterate changes exchangeable hydrogen atoms to deuterium atoms for a PDB file.
class	Dynamics	The X-ray Dynamics script.
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	SaveConformerPDB	The SaveConformerPDB script saves alternate conformers with proper alt loc labels.
class	Timer	The X-ray Timer script.

Uses of AlgorithmsScript in ffx.xray.commands.test

Subclasses of AlgorithmsScript in ffx.xray.commands.test

Modifier and Type	Class	Description
class	Alchemical	The Alchemical Changes script.
class	LambdaGradient	The X-ray test Lambda Gradient script.