Uses of Class
ffx.algorithms.cli.AlgorithmsCommand
Packages that use AlgorithmsCommand
Package
Description
The Misc package contains a few miscellaneous algorithms.
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Uses of AlgorithmsCommand in ffx.algorithms.commands
Subclasses of AlgorithmsCommand in ffx.algorithms.commandsModifier and TypeClassDescriptionclass
Performs analysis of Non-equilibrium work simulations.class
The Anneal script.class
The BAR script finds the free energy difference across a lambda window.class
The Cluster script clusters structures utilizing RMSD.class
The Dynamics script implements molecular and stochastic dynamics algorithms.class
Run an FFX command on a series of files.class
The ReductionPartition script performs a discrete optimization using a many-body expansion and elimination expressions.class
The Histogram script prints out a Orthogonal Space histogram from a *.his file.class
The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.class
Perform MBAR calculation or necessary energy evaluations.class
The Minimize script uses a limited-memory BFGS algorithm to minimize the energy of a molecular system.class
The MinimizeCrystals script uses a limited-memory BFGS algorithm to minimize the energy of a crystal, including both coordinates and unit cell parameters.class
The Minimize script uses OpenMM accelerated L-BFGS algorithm to minimize the energy of a molecular system.class
The MutatePDB script mutates residue(s) of a PDB file.class
The SaveRotamers script saves out rotamers.class
Run a Parallel Java Job Scheduler on a cluster with multiple nodes.class
The SortArc script sort Monte Carlo archive files by lambda value.class
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
class
The Thermodynamics script uses the Transition-Tempered Orthogonal Space Random Walk algorithm to estimate a free energy.class
The TorsionSearch command enumerates conformations of a molecule using torsional scans around rotatable bonds. -
Uses of AlgorithmsCommand in ffx.algorithms.commands.test
Subclasses of AlgorithmsCommand in ffx.algorithms.commands.testModifier and TypeClassDescriptionclass
The ApplyTorsions script is used to apply a custom set of torsions to a side chain.class
CoformerBindingSearch is a Groovy script that generates a set of molecular orientations in vacuum and calculates the energy of each conformation.class
The CreateRotamers script creates a set of conformation dependent rotamers.class
The CrystalSearch script searches for minimum energy polymorphs for a given space group.class
The FindRestraints script identifies guest molecule atoms that should be restrained based on their proximity to specific atoms in a host molecule.class
The Freefix script calculates analytical free energy, entropy, and enthalpy corrections for flat-bottom harmonic restraints with inner and outer radii.class
The IdentifyRotamers script attempts to identify which rotamer each Residue in the system is in.class
The ManyBodyPhScan script runs a pH scan with ManyBody optimization by executing another FFXScript multiple times across a pH range.class
The MinimizePh command uses a limited-memory BFGS algorithm to minimize the energy of a CpHMD molecular system.class
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 tests the Orthogonal Space Tempering Potential.class
The PhDynamics command implements constant pH molecular dynamics.class
Use the Rao-Blackwell Estimator to estimate a free energy difference of protonation for a CpHMD system.class
The RepexThermo command uses the Orthogonal Space Tempering with histogram replica exchange to estimate a free energy difference.class
The SortXPH command unwinds .ARC files from CpHMD runs.class
WeightedEnsemble
Usage: Accelerated Sampling with Weighted Ensemble
ffxc test.WeightedEnsemble [options] <filename> [file2 -
Uses of AlgorithmsCommand in ffx.algorithms.misc
Fields in ffx.algorithms.misc declared as AlgorithmsCommand -
Uses of AlgorithmsCommand in ffx.realspace.commands
Subclasses of AlgorithmsCommand in ffx.realspace.commandsModifier and TypeClassDescriptionclass
The Real Space Annealing script.class
The Real Space Dynamics script.class
Run GenZ for ensemble generation.class
The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.class
The Real Space Minimize script. -
Uses of AlgorithmsCommand in ffx.realspace.commands.test
Subclasses of AlgorithmsCommand in ffx.realspace.commands.testModifier and TypeClassDescriptionclass
The Alchemical Changes script.class
The Real Space Annealing script. -
Uses of AlgorithmsCommand in ffx.xray.commands
Subclasses of AlgorithmsCommand in ffx.xray.commandsModifier and TypeClassDescriptionclass
The X-ray Annealing script.class
Use AverageMTZ to provide two MTZ files and an iteration for a cumulative moving average.class
The CIF2MTZ script saves a CIF file to MTZ format.class
The X-ray ComputeFc script.class
Deuterate changes exchangeable hydrogen atoms to deuterium atoms for a PDB file.class
The X-ray Dynamics script.class
The GenZ script for calculating free energy changes.class
The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.class
The X-ray Minimize script.class
The X-ray ModelvsData script.class
The MTZInfo script prints out MTZ reflection file header info.class
The SaveConformerPDB script saves alternate conformers with proper alt loc labels.class
The X-ray Timer script. -
Uses of AlgorithmsCommand in ffx.xray.commands.test
Subclasses of AlgorithmsCommand in ffx.xray.commands.testModifier and TypeClassDescriptionclass
The Alchemical Changes script.class
The X-ray test Lambda Gradient script.