def test_readingCIFs(self):
from analyseClusters import Crystal
#arbitrarily divide in 2 parts
myCrystal = Crystal.fromZp1Cif('mfa_tfa_tfa_pcm_f16_translated.cif',
nAtomsPerMol=15)
self.assertEqual(
[len(m.aseAtoms) for m in myCrystal.asymmetricMolecules], [15, 15])
#P-1 structure with z'=1
myCrystal = Crystal.fromCif('mfa_tfa_tfa_pcm_f16_translated.cif')
self.assertTrue(len(myCrystal.asymmetricMolecules), 2)
self.assertEqual(
[len(x.aseAtoms) for x in myCrystal.asymmetricMolecules], [30, 30])
#Originally P1 with z'=4 (already expanded the symmetry and reduced to P1)
myCrystal = Crystal.fromCif('tfa_ffa_tfa_pcm_p21c.cif')
self.assertTrue(len(myCrystal.asymmetricMolecules), 4)
self.assertEqual(
[len(x.aseAtoms) for x in myCrystal.asymmetricMolecules], [30] * 4)
def test_changingCellParams(self):
from analyseClusters import latticeParameters, Crystal
myCrystal = Crystal.fromZp1Cif('expStructuresTFA.cif')
np.testing.assert_array_almost_equal(
np.array(latticeParameters(myCrystal.aseCell)),
np.array([6.9136, 7.2915, 14.1096, 78.1106, 80.0763, 64.8556]))
#swap (a,b,c) -> (c,a,b)
np.testing.assert_array_almost_equal(
latticeParameters(
np.dot(np.array([[0., 0., 1.], [1., 0., 0.], [0., 1., 0.]]),
myCrystal.aseCell)),
np.array([14.1096, 6.9136, 7.2915, 64.8556, 78.1106, 80.0763]))
newCrystal = myCrystal.clone(
np.array([[0., 0., 1.], [1., 0., 0.], [0., 1., 0.]]))
np.testing.assert_array_almost_equal(
latticeParameters(newCrystal.aseCell),
np.array([14.1096, 6.9136, 7.2915, 64.8556, 78.1106, 80.0763]))
def test_indicesAcidicHydrogens(self):
from analyseClusters import Crystal
myCrystal = Crystal.fromZp1Cif('mfa_tfa_tfa_pcm_f16_translated.cif')
self.assertTrue(myCrystal.asymmetricMolecules[0].
indicesAcidicHydrogens() == [18, 23])