rmsfkit.RMSF

class rmsfkit.RMSF(atomgroup, **kwargs)

Calculate RMSF of given atoms across a trajectory.

Note

No RMSD-superposition is performed; it is assumed that the user is providing a trajectory where the protein of interest has been structurally aligned to a reference structure. The protein also has be whole because periodic boundaries are not taken into account.

Run the analysis with RMSF.run(), which stores the results in the array RMSF.results.rmsf.

__init__(atomgroup, **kwargs)

Parameters

• atomgroup (AtomGroup) – Atoms for which RMSF is calculated

• verbose (bool (optional)) – Show detailed progress of the calculation if set to True; the default is False.

Raises

ValueError – raised if negative values are calculated, which indicates that a numerical overflow or underflow occured

Notes

The root mean square fluctuation of an atom \(i\) is computed as the time average

\[\rho_i = \sqrt{\left\langle (\mathbf{x}_i - \langle\mathbf{x}_i\rangle)^2 \right\rangle}\]

No mass weighting is performed.

This method implements an algorithm for computing sums of squares while avoiding overflows and underflows :cite:p:`Welford1962`.

References

Methods

__init__(atomgroup, **kwargs)	Parameters atomgroup (AtomGroup) -- Atoms for which RMSF is calculated
run([start, stop, step, frames, verbose])	Perform the calculation