soprano.measure

measure.py

Contains utility functions for measuring distances and other quantities at the level of a single ase.Atoms object.

Functions

bondDistance(s, i, j[, bond_matrix])	Return the distance in number of bonds between two atoms.
euclideanDistance(s, i, j[, periodic])	Return the distance between two atoms, in Angstroms.

soprano.measure.bondDistance(s, i, j, bond_matrix=None)

Return the distance in number of bonds between two atoms. Returns -1 if the two atoms are not connected. Requires NetworkX to be installed to work.

Parameters:

s (ase.Atoms): the structure on which to compute the distance

i (int): index of the first atom

j (int): index of the second atom

bond_matrix (np.ndarray): pre-computed bond matrix to use. If not

provided, will be calculated with default

parameters

Returns:

r (int): computed bond distance

soprano.measure.euclideanDistance(s, i, j, periodic=True)

Return the distance between two atoms, in Angstroms.

Parameters:

s (ase.Atoms): the structure on which to compute the distance

i (int): index of the first atom

j (int): index of the second atom

periodic (bool): whether to account for periodic boundaries when

computing the distance; default is True

Returns:

r (float): computed distance