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