def test_triclinic_cell(self):
cell = UnitCell(35.996, 41.601, 45.756, 67.40, 66.90, 74.85)
pos = Position(-15, -17, 190)
frac = cell.fractionalize(pos)
pos2 = cell.orthogonalize(frac)
self.assertAlmostEqual(pos.x, pos2.x, delta=1e-12)
self.assertAlmostEqual(pos.y, pos2.y, delta=1e-12)
self.assertAlmostEqual(pos.z, pos2.z, delta=1e-12)
def test_triclinic_cell(self):
cell = UnitCell(35.996, 41.601, 45.756, 67.40, 66.90, 74.85)
pos = Position(-15, -17, 190)
frac = cell.fractionalize(pos)
pos2 = cell.orthogonalize(frac)
self.assertAlmostEqual(pos.x, pos2.x, delta=1e-12)
self.assertAlmostEqual(pos.y, pos2.y, delta=1e-12)
self.assertAlmostEqual(pos.z, pos2.z, delta=1e-12)
# tested against values from uctbx:
# from cctbx import uctbx
# uc = uctbx.unit_cell((35.996, 41.601, 45.756, 67.40, 66.90, 74.85))
# uc.d_star_sq((-3, -2, 1))
# uc.d((3, 4, 5))
self.assertAlmostEqual(cell.calculate_1_d2([-3, -2, 1]),
0.0128229081865688, delta=1e-17)
self.assertAlmostEqual(cell.calculate_d([3, 4, 5]),
7.7319559244298, delta=1e-13)
# uc.metrical_matrix()
cctbx_mm = [1295.712016, 1730.643201, 2093.611536,
391.3591013825865, 646.1921687548228, 731.5043620154578]
mt = cell.metric_tensor()
for a, b in zip(mt.elements(), cctbx_mm):
self.assertAlmostEqual(a, b, delta=1e-12)
# uc.reciprocal_metrical_matrix()
cctbx_rmm = [0.00092792089082916, 0.000689632633981, 0.0006277651322979,
-0.000104162588996, -0.000250008091601, -0.000208806754807]
rmt = cell.reciprocal_metric_tensor()
for a, b in zip(rmt.elements(), cctbx_rmm):
self.assertAlmostEqual(a, b, delta=1e-15)
def test_ortho_cell(self):
cell = UnitCell(25.14, 39.50, 45.07, 90, 90, 90)
pos = Position(5, -6, 7)
frac = cell.fractionalize(pos)
self.assertAlmostEqual(frac.x, 0.198886, delta=1e-6)
self.assertAlmostEqual(frac.y, -0.151899, delta=1e-6)
self.assertAlmostEqual(frac.z, 0.155314, delta=1e-6)
pos2 = cell.orthogonalize(frac)
self.assertAlmostEqual(pos.x, pos2.x, delta=1e-12)
self.assertAlmostEqual(pos.y, pos2.y, delta=1e-12)
self.assertAlmostEqual(pos.z, pos2.z, delta=1e-12)
corner = cell.orthogonalize(Fractional(1, 1, 1))
self.assertAlmostEqual(corner.x, cell.a, delta=1e-12)
self.assertAlmostEqual(corner.y, cell.b, delta=1e-12)
self.assertAlmostEqual(corner.z, cell.c, delta=1e-12)
def test_pickling(self):
try:
import cPickle as pickle # Use cPickle on Python 2.7
except ImportError:
import pickle
cell = UnitCell(35.996, 41.601, 45.756, 67.40, 66.90, 74.85)
pkl_string = pickle.dumps(cell, protocol=pickle.HIGHEST_PROTOCOL)
result = pickle.loads(pkl_string)
self.assertTrue(isinstance(result, UnitCell))
self.assertEqual(cell.parameters, result.parameters)
def test_atom_to_site(self):
cell = UnitCell(35.996, 41.601, 45.756, 67.40, 66.90, 74.85)
atom = gemmi.Atom()
atom.aniso = gemmi.SMat33f(13.1, 20.1, 11.1, -3.5, 5.5, -0.4)
site = gemmi.SmallStructure.Site(atom, cell)
# tested against values from cctbx:
# from cctbx import uctbx, adptbx
# uc = uctbx.unit_cell((35.996, 41.601, 45.756, 67.40, 66.90, 74.85))
# aniso = (13.1, 20.1, 11.1, -3.5, 5.5, -0.4)
# ucif = adptbx.u_cart_as_u_cif(uc, aniso)
ucif = [11.537759976524049, 19.43436271641311, 11.1,
-8.078683096677723, 1.4787260755519491, -3.9018967241279157]
for a, b in zip(site.aniso.elements(), ucif):
self.assertAlmostEqual(a, b, delta=1e-6)
def test_pickling(self):
import os
try:
import cPickle as pickle # Use cPickle on Python 2.7
except ImportError:
import pickle
cell = UnitCell(35.996, 41.601, 45.756, 67.40, 66.90, 74.85)
with open("temp.pkl", "wb") as temp:
pickle.dump(cell, temp)
with open("temp.pkl", "rb") as temp:
result = pickle.load(temp)
self.assertTrue(isinstance(result, UnitCell))
self.assertEqual(cell.parameters, result.parameters)
os.remove("temp.pkl")
def test_triclinic_cell(self):
cell = UnitCell(35.996, 41.601, 45.756, 67.40, 66.90, 74.85)
# this would give syntax error with Python < 3.5
#o_f = cell.orthogonalization_matrix @ cell.fractionalization_matrix
o_f = cell.orthogonalization_matrix.multiply(
cell.fractionalization_matrix)
self.assertTrue(o_f.approx(gemmi.Mat33(), 1e-15))
pos = Position(-15, -17, 190)
frac = cell.fractionalize(pos)
pos2 = cell.orthogonalize(frac)
self.assertAlmostEqual(pos.x, pos2.x, delta=1e-12)
self.assertAlmostEqual(pos.y, pos2.y, delta=1e-12)
self.assertAlmostEqual(pos.z, pos2.z, delta=1e-12)
# tested against values from uctbx:
# from cctbx import uctbx
# uc = uctbx.unit_cell((35.996, 41.601, 45.756, 67.40, 66.90, 74.85))
# uc.d_star_sq((-3, -2, 1))
# uc.d((3, 4, 5))
self.assertAlmostEqual(cell.calculate_1_d2([-3, -2, 1]),
0.0128229081865688,
delta=1e-17)
self.assertAlmostEqual(cell.calculate_d([3, 4, 5]),
7.7319559244298,
delta=1e-13)
# uc.metrical_matrix()
cctbx_mm = [
1295.712016, 1730.643201, 2093.611536, 391.3591013825865,
646.1921687548228, 731.5043620154578
]
mt = cell.metric_tensor()
assert_almost_equal_seq(self, mt.elements_pdb(), cctbx_mm, delta=1e-12)
# uc.reciprocal_metrical_matrix()
cctbx_rmm = [
0.00092792089082916, 0.000689632633981, 0.0006277651322979,
-0.000104162588996, -0.000250008091601, -0.000208806754807
]
rmt = cell.reciprocal_metric_tensor()
assert_almost_equal_seq(self,
rmt.elements_pdb(),
cctbx_rmm,
delta=1e-15)
def test_ortho_cell(self):
cell = UnitCell(25.14, 39.50, 45.07, 90, 90, 90)
pos = Position(5, -6, 7)
frac = cell.fractionalize(pos)
self.assertAlmostEqual(frac.x, 0.198886, delta=1e-6)
self.assertAlmostEqual(frac.y, -0.151899, delta=1e-6)
self.assertAlmostEqual(frac.z, 0.155314, delta=1e-6)
pos2 = cell.orthogonalize(frac)
self.assertAlmostEqual(pos.x, pos2.x, delta=1e-12)
self.assertAlmostEqual(pos.y, pos2.y, delta=1e-12)
self.assertAlmostEqual(pos.z, pos2.z, delta=1e-12)
corner = cell.orthogonalize(gemmi.Fractional(1, 1, 1))
self.assertAlmostEqual(corner.x, cell.a, delta=1e-12)
self.assertAlmostEqual(corner.y, cell.b, delta=1e-12)
self.assertAlmostEqual(corner.z, cell.c, delta=1e-12)
rec = cell.reciprocal()
self.assertEqual([rec.alpha, rec.beta, rec.gamma], [90, 90, 90])
self.assertAlmostEqual(rec.a, 1 / cell.a, delta=1e-17)
def test_triclinic_cell(self):
cell = UnitCell(35.996, 41.601, 45.756, 67.40, 66.90, 74.85)
pos = Position(-15, -17, 190)
frac = cell.fractionalize(pos)
pos2 = cell.orthogonalize(frac)
self.assertAlmostEqual(pos.x, pos2.x, delta=1e-12)
self.assertAlmostEqual(pos.y, pos2.y, delta=1e-12)
self.assertAlmostEqual(pos.z, pos2.z, delta=1e-12)
# tested against values from uctbx:
# from cctbx import uctbx
# uc = uctbx.unit_cell((35.996, 41.601, 45.756, 67.40, 66.90, 74.85))
# uc.d_star_sq((-3, -2, 1))
# uc.d((3, 4, 5))
self.assertAlmostEqual(cell.calculate_1_d2(-3, -2, 1),
0.0128229081865688,
delta=1e-17)
self.assertAlmostEqual(cell.calculate_d(3, 4, 5),
7.7319559244298,
delta=1e-13)
def test_dummy_cell(self):
cell = UnitCell()
self.assertEqual([cell.a, cell.b, cell.c], [1, 1, 1])
self.assertEqual([cell.alpha, cell.beta, cell.gamma], [90, 90, 90])
self.assertEqual(cell.volume, 1.0)
detector_bulge_correction = rec.split()[1:3]
detector_bulge_correction_uncertainty = rec.split()[3:5] # More guessing...
# if rec.startswith('Image'): rec.split()[1] # I think this only means something to Precognition's indexer
if rec.startswith('Resolution'):
resolution_range = rec.split()[1:3]
if rec.startswith('Wavelength'):
wavelength_range = rec.split()[1:3]
# Convert angles to radians and prepare matrices for calculation
# o1 \in [0,pi)
# o2 \in [0,2pi)
M = np.array(missetting_matrix, dtype=float).reshape((3,3))
o1 = np.deg2rad(float(omega_polar_orientation[0]))
o2 = np.deg2rad(float(omega_polar_orientation[1]))
gonio_phi = np.deg2rad(float(goniometer[2]))
cell = UnitCell(*[float(i) for i in unit_cell]) # i is an iterating variable
# Get rotation matrix from B to U
R = get_rotation_matrix(np.array([0., 0., -1.]), o1)
temp = get_rotation_matrix(np.array([0., 1., 0.]), o2)
R = temp@R
temp = get_rotation_matrix(([email protected]([0., 1., 0.])[:,None])[:,0], gonio_phi)
R = temp@R
# Create transposed orthogonalization matrix
O = np.vstack((
cell.orthogonalize(Fractional(1., 0., 0.)).tolist(),
cell.orthogonalize(Fractional(0., 1., 0.)).tolist(),
cell.orthogonalize(Fractional(0., 0., 1.)).tolist(),
)).T
