schrodinger.trajectory.prody.crosscorrelation module

This module defines functions for calculating atomic properties from normal modes.

schrodinger.trajectory.prody.crosscorrelation.calcCrossCorr(modes, n_cpu=1)

Return cross-correlations matrix. For a 3-d model, cross-correlations matrix is an NxN matrix, where N is the number of atoms. Each element of this matrix is the trace of the submatrix corresponding to a pair of atoms. Covariance matrix may be calculated using all modes or a subset of modes of an NMA instance. For large systems, calculation of cross-correlations matrix may be time consuming. Optionally, multiple processors may be employed to perform calculations by passing n_cpu=2 or more.


Return covariance matrix calculated for given modes.