Optimization and Sampling Commands for Testing Purposes

Command	Purpose
test.ApplyTorsions	The ApplyTorsions command is used to apply a custom set of torsions to a side-chain.
test.CoformerBindingSearch	Calculates interaction energies of different molecular orientations and saves low energy orientations.
test.CreateRotamers	The CreateRotamers command creates a set of conformation dependent rotamers.
test.CrystalSearch	The CrystalSearch command searches for minimum energy polymorphs for a given space group.
test.IdentifyRotamers	The IdentifyRotamers command attempts to identify which rotamer each Residue in the system is in.
test.ManyBodyPhScan	The ManyBodyPhScan command runs a pH Scan with ManyBody.
test.MinimizePh	The MinimizePh command uses a limited-memory BFGS algorithm to minimize the energy of a CpHMD molecular system.
test.OSTBias	The OSTBias command tests the Orthogonal Space Tempering Potential.
PhDynamics	The PhDynamics command implements constant pH molecular dynamics.
test.RaoBlackwellEstimator	Use the Rao-Blackwell Estimator to estimate a free energy difference of protonation for a CpHMD system.
test.SortXPh	The SortXPH command unwinds .ARC files from CpHMD runs.