Module statistics

Module for handling all types of structural statistics.

Functions

float atomic_rmsd(coord, verbosity=0)
Determine the RMSD for the given atomic coordinates.

calc_mean_structure(coord=None, mean=None, weights=None)
Average the coordinates.

rank-1 numpy float64 array per_atom_rmsd(coord, verbosity=0)
Determine the per-atom RMSDs for the given atomic coordinates.

Variables

__package__ = 'lib.structure'

Imports: array, float64, mean, ones, sqrt, std, zeros, norm

Function Details

atomic_rmsd(coord, verbosity=0)

Determine the RMSD for the given atomic coordinates.

This is the per atom RMSD to the mean structure.

Parameters:

• coord (rank-3 numpy array) - The array of molecular coordinates. The first dimension corresponds to the model, the second the atom, the third the coordinate.

Returns: float

The RMSD value.

calc_mean_structure(coord=None, mean=None, weights=None)

Average the coordinates.

Parameters:

• coord (list of numpy rank-2, Nx3 arrays) - The list of coordinates of all models to superimpose. The first index is the models, the second is the atomic positions, and the third is the xyz coordinates.
• weights (list of float) - The weights for each structure.
• mean (numpy rank-2, Nx3 array) - The data storage for the mean structure.

per_atom_rmsd(coord, verbosity=0)

Determine the per-atom RMSDs for the given atomic coordinates.

This is the per atom RMSD to the mean structure.

Parameters:

• coord (rank-3 numpy array) - The array of molecular coordinates. The first dimension corresponds to the model, the second the atom, the third the coordinate.

Returns: rank-1 numpy float64 array

The list of RMSD values for each atom.