molFit_quaternions¶

Functions¶

molFit_quaternions.alignAllMol(dcdData)¶

This function takes trajectories from Dataset dcdData attribute, and apply the following procedure for each frames in dcdData array:

First, computes appropriate dot products are computed with the first frames coordinates. Then, the matrix to be solved for eigenvalues and eigenvectors is constructed and solved

Parameters:	dcdData (`numpy.ndarray`) – array containing trajectory coordinates for wanted frames with shape (atoms, frames, coordinates)
Returns:	A list of 4 by 4 rotation matrices to be applied on dcdData array

This procedure is based on the [Horn_1987] and [Theobald_2005] papers.

References:

[Horn_1987]

https://doi.org/10.1364/JOSAA.4.000629

[Theobald_2005]

https://doi.org/10.1107/S0108767305015266

molFit_quaternions.applyRotation(dcdData, qM)¶

Apply a rotation using given rotation matrix qM on given dcd data.

Returns:	rotated dcd data