Uses of Class
ffx.algorithms.cli.AlgorithmsCommand

Packages that use AlgorithmsCommand
  • Uses of AlgorithmsCommand in ffx.algorithms.commands

    Modifier and Type
    Class
    Description
    class 
    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

    Modifier and Type
    Class
    Description
    class 
    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

    Modifier and Type
    Field
    Description
    AlgorithmsTest.algorithmsScript
     
  • Uses of AlgorithmsCommand in ffx.realspace.commands

    Modifier and Type
    Class
    Description
    class 
    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

    Modifier and Type
    Class
    Description
    class 
    The Alchemical Changes script.
    class 
    The Real Space Annealing script.
  • Uses of AlgorithmsCommand in ffx.xray.commands

    Modifier and Type
    Class
    Description
    class 
    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

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