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