Superimpose chemical structures

import os
import re
from collections import OrderedDict
from ase import Atoms
import ase.io


def read_structures(path, fpatt, verbose=False):
    '''
    Read all the structures from `path` that match the `fpatt` pattern
    '''

    fpatt = re.compile(fpatt)

    out = {'II': OrderedDict(), 'III': OrderedDict(), 'IV': OrderedDict()}

    for fname in os.listdir(path):
        m = fpatt.match(fname)
        if m:
            symbol, oxs = m.group(1), m.group(2)
            out[oxs][symbol] = ase.io.read(os.path.join(path, fname))
        else:
            if verbose:
                print('ERROR ', fname)

    print('Read: ', ', '.join(['{}: {}'.format(k, len(v)) for k, v in out.items()]))

    return out

if __name__ == '__main__':

    path = 'AlPO-5-H'
    patt = r'([A-Za-z]+)\(([IV]+)\)-AlPO-5-O2-H\.traj'

    halpo = read_structures(path, patt)

    atoms = Atoms()

    for me, a in halpo['IV'].items():
        atoms = atoms + a

    transmittances = [0.8] * len(atoms)

    ase.io.write('Me-AlPO-5-H.pov', atoms,
        rotation='-15y',
        show_unit_cell=0,
        run_povray=True,
        display=False,
        pause=True,
        canvas_width=1024,
        camera_type='perspective',
        transmittances=transmittances)

    ase.io.write('Me-AlPO-5-H_0y.pov', atoms,
        rotation='',
        show_unit_cell=0,
        run_povray=True,
        display=False,
        pause=True,
        canvas_width=1024,
        camera_type='perspective',
        transmittances=transmittances)