Package ffx.algorithms.commands.test


package ffx.algorithms.commands.test
  • Classes
    Class
    Description
    The ApplyTorsions script is used to apply a custom set of torsions to a side chain.
    CoformerBindingSearch is a Groovy script that generates a set of molecular orientations in vacuum and calculates the energy of each conformation.
    The CreateRotamers script creates a set of conformation dependent rotamers.
    The CrystalSearch script searches for minimum energy polymorphs for a given space group.
    The FindRestraints script identifies guest molecule atoms that should be restrained based on their proximity to specific atoms in a host molecule.
    The Freefix script calculates analytical free energy, entropy, and enthalpy corrections for flat-bottom harmonic restraints with inner and outer radii.
    The IdentifyRotamers script attempts to identify which rotamer each Residue in the system is in.
    The ManyBodyPhScan script runs a pH scan with ManyBody optimization by executing another FFXScript multiple times across a pH range.
    The MinimizePh command uses a limited-memory BFGS algorithm to minimize the energy of a CpHMD molecular system.
    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>
    OSTGradient tests the Orthogonal Space Tempering Potential.
    The PhDynamics command implements constant pH molecular dynamics.
    Use the Rao-Blackwell Estimator to estimate a free energy difference of protonation for a CpHMD system.
    The RepexThermo command uses the Orthogonal Space Tempering with histogram replica exchange to estimate a free energy difference.
    The SortXPH command unwinds .ARC files from CpHMD runs.
    WeightedEnsemble
    Usage: Accelerated Sampling with Weighted Ensemble
    ffxc test.WeightedEnsemble [options] <filename> [file2