from ase.io import read, write
import numpy as np
from ase import Atoms

# Check that saving/loading pdb files correctly reproduces the atoms object.
#
# Loading will restore the cell from lengths/angles, so the best we can do
# is to recreate the scaled positions, not the absolute positions.

images = [
    Atoms(symbols='C8O8Ru64',
          pbc=np.array([ True,  True,  True], dtype=bool),
          cell=np.array(
      [[  9.46101634e+00,   5.46231901e+00,  -7.62683750e-07],
       [  0.00000000e+00,   1.09246400e+01,  -7.62683750e-07],
       [  0.00000000e+00,   0.00000000e+00,   2.14654300e+01]]),
          positions=np.array(
      [[  7.80131882e-01,   6.83747136e+00,   8.38204657e+00],
       [  5.51092271e+00,   9.56854231e+00,   8.38223568e+00],
       [  3.07270715e+00,   2.87955302e+00,   8.37140640e+00],
       [  7.80350536e+00,   5.61092571e+00,   8.37131213e+00],
       [  4.27438360e+00,   6.25264571e+00,   7.97264597e+00],
       [  9.00498640e+00,   8.98355980e+00,   7.97286435e+00],
       [  6.37288973e+00,   1.35474697e+01,   7.83982205e+00],
       [  1.64255024e+00,   1.08160090e+01,   7.83994023e+00],
       [  7.71235875e-01,   6.84831577e+00,   9.54503003e+00],
       [  5.50223518e+00,   9.57934418e+00,   9.54476437e+00],
       [  3.03497100e+00,   2.94960249e+00,   9.52997683e+00],
       [  7.76620880e+00,   5.68120179e+00,   9.52999700e+00],
       [  4.23008702e+00,   6.32508468e+00,   9.15933250e+00],
       [  8.96060688e+00,   9.05590199e+00,   9.15923442e+00],
       [  6.34874076e+00,   1.35969943e+01,   9.03839912e+00],
       [  1.61820848e+00,   1.08649253e+01,   9.01849841e+00],
       [  1.57683637e+00,   2.73116147e+00,  -2.54228044e-07],
       [  1.56720630e+00,   2.72722886e+00,   4.28570884e+00],
       [  7.88417713e-01,   1.36558046e+00,   2.15514407e+00],
       [  8.02210750e-01,   1.34385101e+00,   6.43536380e+00],
       [  3.94209046e+00,   4.09674123e+00,  -4.44898981e-07],
       [  3.95116212e+00,   4.10376637e+00,   4.28640956e+00],
       [  3.15367180e+00,   2.73116022e+00,   2.15514388e+00],
       [  3.15302826e+00,   2.73391087e+00,   6.47587998e+00],
       [  6.30734454e+00,   5.46232098e+00,  -6.35569919e-07],
       [  6.29772257e+00,   5.45840160e+00,   4.28564811e+00],
       [  5.51892683e+00,   4.09674051e+00,   2.15514369e+00],
       [  5.53267073e+00,   4.07509705e+00,   6.43527963e+00],
       [  8.67259863e+00,   6.82790073e+00,  -8.26240856e-07],
       [  8.68166544e+00,   6.83494012e+00,   4.28642358e+00],
       [  7.88417997e+00,   5.46231972e+00,   2.15514350e+00],
       [  7.88362942e+00,   5.46507502e+00,   6.47590212e+00],
       [  1.57683637e+00,   5.46232147e+00,  -4.44898981e-07],
       [  1.58727500e+00,   5.44486645e+00,   4.24854361e+00],
       [  7.88417713e-01,   4.09674046e+00,   2.15514388e+00],
       [  8.01608482e-01,   4.07705367e+00,   6.44578990e+00],
       [  3.94209046e+00,   6.82790123e+00,  -6.35569919e-07],
       [  3.95243122e+00,   6.81073405e+00,   4.32065689e+00],
       [  3.15367180e+00,   5.46232022e+00,   2.15514369e+00],
       [  3.16456215e+00,   5.44150374e+00,   6.44566316e+00],
       [  6.30734454e+00,   8.19348098e+00,  -8.26240856e-07],
       [  6.31780039e+00,   8.17600912e+00,   4.24852811e+00],
       [  5.51892588e+00,   6.82789997e+00,   2.15514350e+00],
       [  5.53216899e+00,   6.80824683e+00,   6.44574538e+00],
       [  8.67259863e+00,   9.55906073e+00,  -1.01691179e-06],
       [  8.68296348e+00,   9.54187626e+00,   4.32068356e+00],
       [  7.88417997e+00,   8.19347972e+00,   2.15514331e+00],
       [  7.89512792e+00,   8.17267187e+00,   6.44565547e+00],
       [  1.57683637e+00,   8.19348147e+00,  -6.35569919e-07],
       [  1.58115689e+00,   8.20071292e+00,   4.29055653e+00],
       [  7.88417713e-01,   6.82790046e+00,   2.15514369e+00],
       [  7.91948666e-01,   6.82222698e+00,   6.48549188e+00],
       [  3.94209046e+00,   9.55906123e+00,  -8.26240856e-07],
       [  3.93358820e+00,   9.55894698e+00,   4.29187459e+00],
       [  3.15367180e+00,   8.19348022e+00,   2.15514350e+00],
       [  3.15825664e+00,   8.18574447e+00,   6.38108109e+00],
       [  6.30734454e+00,   1.09246410e+01,  -1.01691179e-06],
       [  6.31166355e+00,   1.09318806e+01,   4.29057142e+00],
       [  5.51892588e+00,   9.55905997e+00,   2.15514331e+00],
       [  5.52249944e+00,   9.55339051e+00,   6.48545486e+00],
       [  8.67259863e+00,   1.22902207e+01,  -1.20758273e-06],
       [  8.66410508e+00,   1.22901152e+01,   4.29183559e+00],
       [  7.88418091e+00,   1.09246403e+01,   2.15514312e+00],
       [  7.88880125e+00,   1.09169018e+01,   6.38105940e+00],
       [  1.57683637e+00,   1.09246415e+01,  -8.26240856e-07],
       [  1.58687157e+00,   1.09077863e+01,   4.32193338e+00],
       [  7.88417713e-01,   9.55906046e+00,   2.15514350e+00],
       [  7.78394031e-01,   9.52397919e+00,   6.44162756e+00],
       [  3.94209046e+00,   1.22902212e+01,  -1.01691179e-06],
       [  3.95166143e+00,   1.22749617e+01,   4.26568019e+00],
       [  3.15367180e+00,   1.09246402e+01,   2.15514331e+00],
       [  3.19235336e+00,   1.09175437e+01,   6.44091634e+00],
       [  6.30734454e+00,   1.36558010e+01,  -1.20758273e-06],
       [  6.31737307e+00,   1.36389093e+01,   4.32189961e+00],
       [  5.51892588e+00,   1.22902200e+01,   2.15514312e+00],
       [  5.50895045e+00,   1.22551312e+01,   6.44172685e+00],
       [  8.67259863e+00,   1.50213807e+01,  -1.39825367e-06],
       [  8.68213569e+00,   1.50061426e+01,   4.26566744e+00],
       [  7.88418091e+00,   1.36558003e+01,   2.15514293e+00],
       [  7.92283529e+00,   1.36487476e+01,   6.44087611e+00]])),
]


atoms1 = images[0]
write('grumbles.pdb', atoms1)
atoms2 = read('grumbles.pdb')

spos1 = (atoms1.get_scaled_positions() + 0.5) % 1.0
spos2 = (atoms2.get_scaled_positions() + 0.5) % 1.0

for a, b in zip(spos1, spos2):
    print(a, b)

err = np.abs(spos1 - spos2).max()
print(err)
assert err < 2e-4