demokit.RMSF
- class demokit.RMSF(atomgroup, **kwargs)[source]
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 to be whole because periodic boundaries are not taken into account.
Run the analysis with
RMSF.run(), which stores the results in the arrayRMSF.results.rmsf.- __init__(atomgroup, **kwargs)[source]
- Parameters:
atomgroup (AtomGroup) – Atoms for which RMSF is calculated
verbose (bool (optional)) – Show detailed progress of the calculation if set to
True; the default isFalse.
- Raises:
ValueError – raised if negative values are calculated, which indicates that a numerical overflow or underflow occurred
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 [Wel62].
References
[Wel62]B. P. Welford. Note on a method for calculating corrected sums of squares and products. Technometrics, 4(3):419–420, 1962. doi:10.1080/00401706.1962.10490022.