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