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_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)