orgdisord.utils

Functions

get_molecules(atoms[, use_cell_indices])	Get the molecules from an atoms object.
get_new_labels(atoms)	Get the labels for a given atoms object in the style of JMOL/ MagresView
get_unique_atoms(atoms, sg[, symprec])	Return the unique atoms in an atoms object and the count of duplicates
molecule_collide(atom, atoms[, vdw_scale, ...])	Checks if an atom is colliding with a group of atoms defined by the initial_fractional_positions.
random_product(*args[, repeat])	Random selection from itertools.product(*args, **kwds) From https://docs.python.org/3/library/itertools.html#itertools-recipes
reload_as_molecular_crystal(images[, ...])	takes in a list of atoms, identifies molecules, unwraps molecules so that they're 'connected' across periodic boundaries TODO: Test wrap in parallel mode and in cheap mode.
standardise_cell(atoms[, symprec])	Convert an ASE Atoms object to the standardised unit cell according to spglib
unwrap_molecules(atoms[, wrap_each_molecule])
wrap_molecule(atoms[, max_dist])	Translates molecule such that no bit of the molecule sticks out passed max_dist in any direction.