Package ffx.algorithms.commands

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