soprano.collection.generate.molneigh

Generator producing molecular neighbourhoods

Functions

molecularNeighbourhoodGen(struct, mols[, ...])

Generator function to create a spherical molecular neighbourhood.

soprano.collection.generate.molneigh.molecularNeighbourhoodGen(struct, mols, central_mol=0, max_R=10, method='com', use_supercell=False)

Generator function to create a spherical molecular neighbourhood. Given a structure and its molecules as returned by the Molecules property, produce supercell structures that contain one molecule each, progressively further away from the one indicated as central.

Args:

struct (ase.Atoms): original structure

mols ([ase.AtomsSelection]): list of molecules, as returned by the

soprano.properties.linkage.Molecules

class.

central_mol (int): index of the molecule whose centre of mass is

considered central. Default is 0.

max_R (float): maximum radius of the neighbourhood sphere. Default is

10 Ang.

method (str): method to compute distance between molecules. ‘com’

means using the center of mass. ‘nearest’ means using

the closest atom. Default is ‘com’.

use_supercell (bool): if True, all returned structures will have a

cell large enough to contain the entire

neighbourhood. Default is False.

Returns:

molecularNeighbourhoodGen (generator): an iterator object that yields

structures within the given

spherical neighbourhood.