test_suite.system_tests.structure

39 """Class for testing the structural objects.""" 40

41 - def setUp(self):

42 """Set up for all the functional tests.""" 43 44 # Create the data pipe. 45 self.interpreter.pipe.create('mf', 'mf')

46 47

48 - def test_alt_loc_missing(self):

49 """Test that a RelaxError occurs when the alternate location indicator is present but not specified.""" 50 51 # Path of the structure file. 52 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 53 54 # Load the file, load the spins, and attach the protons. 55 self.assertRaises(RelaxError, self.interpreter.structure.read_pdb, '1OGT_trunc.pdb', dir=path)

56 57

58 - def test_bug_sr_2998_broken_conect_records(self):

59 """Test the bug reported as the U{support request #2998<https://web.archive.org/web/https://gna.org/support/?2998>}, the broken CONECT records.""" 60 61 # Path of the structure file. 62 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 63 64 # Load the file. 65 self.interpreter.structure.read_pdb('1RTE_trunc.pdb', dir=path)

66 67

68 - def test_bug_20470_alternate_location_indicator(self):

69 """Catch U{bug #20470<https://web.archive.org/web/https://gna.org/bugs/?20470>}, the alternate location indicator problem.""" 70 71 # Path of the structure file. 72 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 73 74 # Load the file, load the spins, and attach the protons. 75 self.interpreter.structure.read_pdb('1OGT_trunc.pdb', dir=path, alt_loc='A') 76 self.interpreter.structure.load_spins(spin_id='@N', ave_pos=True) 77 self.interpreter.sequence.attach_protons()

78 79

80 - def test_bug_21187_corrupted_pdb(self):

81 """Catch U{bug #21187<https://web.archive.org/web/https://gna.org/bugs/?21187>}, the corrupted PDB with all proton atoms numbers set to zero.""" 82 83 # Path of the structure file. 84 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 85 86 # Load the file. 87 self.interpreter.structure.read_pdb('bug_21187_molecule.pdb', dir=path) 88 89 # Load the @N, @H, and @NE1 spins (needed to create the :60@0 spin to trigger the bug later). 90 self.interpreter.structure.load_spins(spin_id='@N', ave_pos=True) 91 self.interpreter.structure.load_spins(spin_id='@NE1', ave_pos=True) 92 self.interpreter.structure.load_spins(spin_id='@H', ave_pos=True) 93 94 # Load the :60@HE1 spin - this clashes with the :60@H spin as both have the spin ID of ':60@0'. 95 self.interpreter.structure.load_spins(spin_id='@HE1', ave_pos=True)

96 97

98 - def test_bug_21522_master_record_atom_count(self):

99 """Catch U{bug #21522<https://web.archive.org/web/https://gna.org/bugs/?21522>}, the structure.write_pdb user function creating an incorrect MASTER record. 100 101 This also triggers U{bug #21520<https://web.archive.org/web/https://gna.org/bugs/?21520>}, the failure of the structure.write_pdb user function when creating the MASTER record due to too many ATOM and HETATM records being present. 102 """ 103 104 # Create 2 models. 105 self.interpreter.structure.add_model(model_num=1) 106 self.interpreter.structure.add_model(model_num=2) 107 108 # Add a single atom. 109 self.interpreter.structure.add_atom(atom_name='N', res_name='Pro', res_num=2, pos=[1., 2., 3.], element='N') 110 111 # Create a PDB file. 112 file = DummyFileObject() 113 self.interpreter.structure.write_pdb(file=file, force=True) 114 115 # The file contents, as they should be. 116 contents = [ 117 "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011. \n", 118 "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM). \n", 119 "MODEL 1 \n", 120 "ATOM 1 N Pro A 2 1.000 2.000 3.000 1.00 0.00 N \n", 121 "TER 2 Pro A 2 \n", 122 "ENDMDL \n", 123 "MODEL 2 \n", 124 "ATOM 1 N Pro A 2 1.000 2.000 3.000 1.00 0.00 N \n", 125 "TER 2 Pro A 2 \n", 126 "ENDMDL \n", 127 "MASTER 0 0 0 0 0 0 0 0 1 1 0 0 \n", 128 "END \n" 129 ] 130 131 # Check the created PDB file. 132 lines = file.readlines() 133 for i in range(len(lines)): 134 self.assertEqual(contents[i], lines[i])

135 136

137 - def test_delete_empty(self):

138 """Test the deletion of non-existent structural data.""" 139 140 # Delete all structural data. 141 self.interpreter.structure.delete()

142 143

144 - def test_delete_multi_pipe(self):

145 """Test the deletion of structural data in only one pipe.""" 146 147 # Create a structure with a single atom. 148 self.interpreter.structure.add_atom(atom_name='PIV', res_name='M1', res_num=1, pos=[0., 1., 2.], element='S') 149 150 # Create a new data pipe. 151 self.interpreter.pipe.create('new', 'N-state') 152 153 # Create a structure with a single atom. 154 self.interpreter.structure.add_atom(atom_name='PIV', res_name='M1', res_num=2, pos=[4., 5., 6.], element='S') 155 156 # Delete all structural data. 157 self.interpreter.structure.delete() 158 159 # Checks. 160 self.assert_(hasattr(cdp, 'structure')) 161 self.assertEqual(len(cdp.structure.structural_data), 0) 162 self.interpreter.pipe.switch('mf') 163 self.assert_(hasattr(cdp, 'structure')) 164 self.assertEqual(len(cdp.structure.structural_data), 1)

165 166

167 - def test_displacement(self):

168 """Test of the structure.displacement user function.""" 169 170 # Path of the structure file. 171 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 172 173 # Load the file as two models. 174 self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path, set_model_num=1) 175 self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path, set_model_num=2) 176 177 # A rotation. 178 R = zeros((3, 3), float64) 179 euler_to_R_zyz(1.3, 0.4, 4.5, R) 180 181 # Rotate the second model. 182 self.interpreter.structure.rotate(R, model=2) 183 184 # Calculate the displacement. 185 self.interpreter.structure.displacement() 186 187 # Shift a third structure back using the calculated displacement. 188 self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path, set_model_num=3) 189 self.interpreter.structure.rotate(R, model=3) 190 191 # The data to check. 192 models = [1, 2] 193 trans_vect = [ 194 [[0.0, 0.0, 0.0], 195 [ 2.270857972754659, -1.811667138656451, 1.878400649688508]], 196 [[ -2.270857972754659, 1.811667138656451, -1.878400649688508], 197 [0.0, 0.0, 0.0]] 198 ] 199 dist = [ 200 [0.0000000000000000, 3.4593818457148173], 201 [3.4593818457148173, 0.0000000000000000] 202 ] 203 rot_axis = [ 204 [None, 205 [ 0.646165066909452, 0.018875759848125, -0.762964227206007]], 206 [[ -0.646165066909452, -0.018875759848125, 0.762964227206007], 207 None] 208 ] 209 angle = [ 210 [0.0000000000000000, 0.6247677290742989], 211 [0.6247677290742989, 0.0000000000000000] 212 ] 213 214 # Test the results. 215 self.assert_(hasattr(cdp.structure, 'displacements')) 216 for i in range(len(models)): 217 for j in range(len(models)): 218 # Check the translation. 219 self.assertAlmostEqual(cdp.structure.displacements._translation_distance[models[i]][models[j]], dist[i][j]) 220 for k in range(3): 221 self.assertAlmostEqual(cdp.structure.displacements._translation_vector[models[i]][models[j]][k], trans_vect[i][j][k]) 222 223 # Check the rotation. 224 self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[models[i]][models[j]], angle[i][j]) 225 if rot_axis[i][j] != None: 226 for k in range(3): 227 self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[models[i]][models[j]][k], rot_axis[i][j][k]) 228 229 # Save the results. 230 self.tmpfile = mktemp() 231 self.interpreter.state.save(self.tmpfile, dir=None, force=True) 232 233 # Reset relax. 234 self.interpreter.reset() 235 236 # Load the results. 237 self.interpreter.state.load(self.tmpfile) 238 239 # Test the re-loaded data. 240 self.assert_(hasattr(cdp.structure, 'displacements')) 241 for i in range(len(models)): 242 for j in range(len(models)): 243 # Check the translation. 244 self.assertAlmostEqual(cdp.structure.displacements._translation_distance[models[i]][models[j]], dist[i][j]) 245 for k in range(3): 246 self.assertAlmostEqual(cdp.structure.displacements._translation_vector[models[i]][models[j]][k], trans_vect[i][j][k]) 247 248 # Check the rotation. 249 self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[models[i]][models[j]], angle[i][j]) 250 if rot_axis[i][j] != None: 251 for k in range(3): 252 self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[models[i]][models[j]][k], rot_axis[i][j][k])

253 254

255 - def test_load_spins_mol_cat(self):

256 """Test the loading of spins from different molecules into one molecule container.""" 257 258 # Path of the files. 259 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose' 260 261 # Read the PDBs. 262 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_1.pdb', dir=path, set_mol_name='L1') 263 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_2.pdb', dir=path, set_mol_name='L2') 264 265 # Load a few protons. 266 self.interpreter.structure.load_spins('#L1:900@C1', mol_name_target='Lactose') 267 self.interpreter.structure.load_spins('#L2:900@C2', mol_name_target='Lactose') 268 269 # Check the spin data. 270 self.assertEqual(len(cdp.mol), 1) 271 self.assertEqual(cdp.mol[0].name, 'Lactose') 272 self.assertEqual(len(cdp.mol[0].res), 1) 273 self.assertEqual(cdp.mol[0].res[0].name, 'UNK') 274 self.assertEqual(cdp.mol[0].res[0].num, 900) 275 self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 276 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'C1') 277 self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 278 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'C2') 279 self.assertEqual(cdp.mol[0].res[0].spin[1].num, 2)

280 281

282 - def test_load_internal_results(self):

283 """Load the PDB file using the information in a results file (using the internal structural object).""" 284 285 # Path of the files. 286 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 287 288 # Read the results file. 289 self.interpreter.results.read(file='str_internal', dir=path) 290 291 # Test the structure metadata. 292 self.assert_(hasattr(cdp, 'structure')) 293 self.assert_(hasattr(cdp.structure, 'structural_data')) 294 self.assert_(len(cdp.structure.structural_data)) 295 self.assert_(len(cdp.structure.structural_data[0].mol)) 296 297 mol = cdp.structure.structural_data[0].mol[0] 298 self.assertEqual(mol.file_name, 'Ap4Aase_res1-12.pdb') 299 self.assertEqual(mol.file_path, '') 300 self.assertEqual(mol.file_model, 1) 301 self.assertEqual(mol.file_mol_num, 1) 302 303 # The real atomic data. 304 atom_name = ['N', 'CA', '1HA', '2HA', 'C', 'O', '1HT', '2HT', '3HT', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', 'HG', 'CD1', '1HD1', '2HD1', '3HD1', 'CD2', '1HD2', '2HD2', '3HD2', 'C', 'O', 'N', 'H', 'CA', '1HA', '2HA', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'OG', 'HG', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', 'SD', 'CE', '1HE', '2HE', '3HE', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', 'OD1', 'OD2', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'OG', 'HG', 'C', 'O', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', 'CD', 'OE1', 'OE2', 'C', 'O', 'N', 'H', 'CA', '1HA', '2HA', 'C', 'O'] 305 bonded = [[]]*174 306 chain_id = [None]*174 307 element = ['N', 'C', 'H', 'H', 'C', 'O', 'H', 'H', 'H', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'O', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'S', 'C', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'O', 'O', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'O', 'H', 'C', 'O', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'O', 'O', 'C', 'O', 'N', 'H', 'C', 'H', 'H', 'C', 'O'] 308 pdb_record = ['ATOM']*174 309 res_name = ['GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY'] 310 res_num = [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12] 311 seg_id = [None]*174 312 x = [8.442, 7.469, 8.013, 6.825, 6.610, 6.827, 9.398, 8.180, 8.448, 5.613, 5.281, 4.714, 5.222, 3.646, 3.332, 2.800, 4.319, 4.853, 3.587, 6.162, 4.805, 4.075, 3.593, 4.074, 4.475, 3.498, 3.572, 2.025, 1.965, 1.609, 1.176, 1.823, 0.176, 0.096, 0.509, -0.789, 0.474, 0.809, -0.595, 0.707, 4.264, 4.364, 4.809, 4.697, 5.561, 6.220, 6.156, 4.659, 4.746, 3.786, 3.770, 2.851, 2.368, 1.785, 1.177, 1.165, 2.360, 1.690, 3.546, 3.804, 3.814, 3.563, 4.442, 4.984, 5.411, 6.192, 4.872, 6.068, 6.868, 5.332, 6.747, 6.155, 5.409, 6.977, 5.721, 3.369, 2.255, 3.703, 4.604, 2.753, 1.851, 3.329, 4.182, 3.644, 2.319, 1.992, 1.854, 2.419, 1.251, 3.451, 4.359, 3.267, 2.246, 4.223, 4.054, 4.040, 5.573, 6.142, 3.488, 4.276, 2.795, 1.828, 2.929, 2.810, 1.772, 0.912, 2.067, 1.505, 0.464, 2.138, 0.938, 2.273, 4.268, 4.585, 5.076, 4.776, 6.392, 6.925, 7.120, 7.968, 7.464, 6.130, 6.384, 6.135, 4.210, 4.246, 6.325, 5.263, 7.477, 8.281, 7.587, 7.039, 9.047, 9.133, 9.654, 9.590, 10.670, 9.215, 9.190, 10.055, 8.012, 7.007, 7.361, 6.144, 5.925, 5.555, 6.329, 4.814, 4.894, 4.761] 313 y = [10.188, 9.889, 9.712, 10.745, 8.674, 7.991, 10.291, 11.073, 9.416, 8.385, 9.152, 7.243, 6.302, 7.443, 6.483, 7.963, 8.253, 7.605, 8.842, 9.327, 10.088, 7.251, 8.285, 6.099, 5.309, 5.986, 4.953, 6.396, 7.471, 6.106, 5.775, 5.225, 4.796, 4.954, 3.787, 4.949, 6.853, 7.828, 6.775, 6.720, 6.853, 8.068, 6.222, 5.251, 6.956, 6.273, 7.706, 7.634, 8.841, 6.847, 5.889, 7.360, 6.511, 8.230, 7.620, 8.669, 9.269, 9.652, 8.174, 9.362, 7.546, 6.604, 8.253, 9.095, 7.354, 7.976, 6.886, 6.258, 5.824, 5.499, 6.846, 5.570, 5.985, 5.190, 4.766, 8.771, 8.245, 9.789, 10.161, 10.351, 10.605, 11.610, 11.341, 12.287, 12.322, 11.787, 13.410, 9.322, 9.015, 8.776, 9.052, 7.758, 7.826, 7.990, 8.977, 7.248, 7.894, 8.285, 6.370, 6.214, 5.342, 5.431, 3.973, 3.943, 3.230, 3.234, 2.212, 3.991, 3.892, 3.624, 5.960, 5.908, 3.339, 3.179, 2.980, 3.150, 2.375, 2.876, 2.616, 3.262, 1.675, 3.264, 4.305, 2.758, 4.055, 2.299, 0.876, 0.258, 0.312, 0.871, -1.106, -1.253, -1.489, -2.564, -1.049, -1.041, -1.011, -0.052, -1.970, -2.740, -1.931, -2.037, -1.962, -2.949, -2.983, -3.917, -4.588, -4.488, -3.289, -3.932] 314 z = [6.302, 7.391, 8.306, 7.526, 7.089, 6.087, 6.697, 5.822, 5.604, 7.943, 9.155, 7.752, 7.908, 8.829, 9.212, 8.407, 9.880, 10.560, 10.415, 9.754, 8.900, 6.374, 5.909, 5.719, 6.139, 4.391, 4.081, 4.415, 4.326, 5.367, 3.307, 2.640, 3.889, 4.956, 3.700, 3.430, 2.493, 2.814, 2.633, 1.449, 3.403, 3.572, 2.369, 2.281, 1.371, 0.855, 1.868, 0.359, 0.149, -0.269, -0.055, -1.268, -1.726, -0.608, 0.037, -1.377, 0.162, 0.731, -2.354, -2.175, -3.496, -3.603, -4.606, -4.199, -5.387, -5.803, -6.196, -4.563, -5.146, -4.350, -3.001, -1.895, -1.241, -1.307, -2.472, -5.551, -5.582, -6.328, -6.269, -7.274, -6.735, -7.913, -8.518, -7.133, -8.791, -9.871, -8.395, -8.346, -8.584, -8.977, -8.732, -10.002, -10.355, -11.174, -11.584, -11.936, -10.759, -11.425, -9.403, -8.469, -9.921, -11.030, -9.410, -8.336, -10.080, -9.428, -10.291, -11.333, -11.606, -12.128, -10.723, -11.893, -9.781, -10.959, -8.768, -7.344, -8.971, -9.765, -7.642, -7.816, -7.251, -6.715, -6.584, -5.765, -7.175, -6.955, -9.288, -9.222, -9.654, -9.696, -10.009, -10.928, -10.249, -10.194, -9.475, -11.596, -11.540, -11.813, -12.724, -13.193, -13.137, -8.947, -7.774, -9.383, -10.338, -8.477, -8.138, -9.017, -7.265, -6.226] 315 316 # Test the atomic data. 317 mol = cdp.structure.structural_data[0].mol[0] 318 for i in range(len(mol.atom_name)): 319 self.assertEqual(mol.atom_name[i], atom_name[i]) 320 self.assertEqual(mol.bonded[i], bonded[i]) 321 self.assertEqual(mol.chain_id[i], chain_id[i]) 322 self.assertEqual(mol.element[i], element[i]) 323 self.assertEqual(mol.pdb_record[i], pdb_record[i]) 324 self.assertEqual(mol.res_name[i], res_name[i]) 325 self.assertEqual(mol.res_num[i], res_num[i]) 326 self.assertEqual(mol.seg_id[i], seg_id[i]) 327 self.assertEqual(mol.x[i], x[i]) 328 self.assertEqual(mol.y[i], y[i]) 329 self.assertEqual(mol.z[i], z[i])

330 331

332 - def test_load_internal_results2(self):

333 """Load the PDB file using the information in a results file (using the internal structural object).""" 334 335 # Path of the files. 336 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 337 338 # Read the results file. 339 self.interpreter.results.read(file=path+sep+'str_internal')

340 341

342 - def test_metadata_xml(self):

343 """Test the storage and loading of metadata into an XML state file.""" 344 345 # Load the file. 346 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 347 self.interpreter.structure.read_pdb('1UBQ.pdb', dir=path) 348 349 # Delete a big chunk of the molecule. 350 self.interpreter.structure.delete(":35-76") 351 352 # Delete all waters. 353 self.interpreter.structure.delete(":HOH") 354 355 # Write out the results file. 356 self.tmpfile = mktemp() + '.bz2' 357 self.interpreter.results.write(self.tmpfile, dir=None) 358 359 # Create a new data pipe and load the results. 360 self.interpreter.pipe.create('xml text', 'mf') 361 self.interpreter.results.read(self.tmpfile) 362 363 # What the data should look like. 364 helices = [ 365 ['H1', 'A', 'ILE', 23, 'A', 'GLU', 34, 1, 12] 366 ] 367 sheets = [ 368 [1, 'BET', 5, 'GLY', 'A', 10, None, 'VAL', 'A', 17, None, 0, None, None, None, None, None, None, None, None, None, None], 369 [2, 'BET', 5, 'MET', 'A', 1, None, 'THR', 'A', 7, None, -1, None, None, None, None, None, None, None, None, None, None] 370 ] 371 372 # Check the helix data. 373 self.assert_(hasattr(cdp.structure, 'helices')) 374 self.assertEqual(len(cdp.structure.helices), 1) 375 self.assertEqual(cdp.structure.helices[0], helices[0]) 376 377 # Check the sheet data. 378 self.assert_(hasattr(cdp.structure, 'sheets')) 379 self.assertEqual(len(cdp.structure.sheets), 2) 380 self.assertEqual(cdp.structure.sheets[0], sheets[0]) 381 self.assertEqual(cdp.structure.sheets[1], sheets[1])

382 383

384 - def test_read_gaussian_strychnine(self):

385 """Load the structure from the 'strychnine_opt_cdcl3_b3lyp_gaussian.log.bz2' compressed Gaussian log file.""" 386 387 # Path of the files. 388 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 389 390 # Read the XYZ file. 391 self.interpreter.structure.read_gaussian(file='strychnine_opt_cdcl3_b3lyp_gaussian.log.bz2', dir=path, set_mol_name='strychnine') 392 393 # Test the molecule data. 394 self.assertEqual(len(cdp.structure.structural_data), 1) 395 self.assertEqual(len(cdp.structure.structural_data[0].mol), 1) 396 397 # Load the carbon atoms and test it. 398 self.interpreter.structure.load_spins('@C') 399 self.assertEqual(count_spins(), 21) 400 401 # Load the protons. 402 self.interpreter.structure.load_spins('@H') 403 self.assertEqual(count_spins(), 43) 404 405 # And now all the rest of the atoms. 406 self.interpreter.structure.load_spins() 407 408 # The actual data. 409 data = [ 410 [ 5, 'C', -0.258837, -2.073956, -0.558021], 411 [ 6, 'C', -0.824223, -1.406962, -1.808433], 412 [ 7, 'C', -1.741283, -0.250780, -1.378644], 413 [ 8, 'C', -0.819735, 0.828965, -0.783392], 414 [ 9, 'C', 0.003153, 0.334416, 0.415455], 415 [10, 'C', 2.358372, 0.448322, 0.162421], 416 [11, 'C', 3.667689, 0.888405, -0.010558], 417 [12, 'C', 4.632616, -0.056196, -0.360560], 418 [13, 'C', 4.303015, -1.398582, -0.525823], 419 [14, 'C', 2.988069, -1.825141, -0.331972], 420 [15, 'C', 2.015427, -0.899636, 0.012625], 421 [16, 'C', 0.561728, -1.122705, 0.360284], 422 [17, 'C', 0.390886, -1.834862, 1.723978], 423 [18, 'C', -1.067936, -2.282629, 1.709808], 424 [19, 'C', -2.708975, -2.252045, -0.131301], 425 [20, 'C', -2.815469, -0.775379, -0.431910], 426 [21, 'C', -3.718174, 0.023460, 0.134879], 427 [22, 'C', -3.726395, 1.516213, -0.058936], 428 [23, 'C', -1.423939, 2.193179, -0.407936], 429 [24, 'C', -0.372897, 3.059448, 0.332496], 430 [25, 'C', 1.064718, 2.558120, 0.325331], 431 [26, 'H', 0.399932, -2.896344, -0.855386], 432 [27, 'H', -1.364146, -2.140645, -2.409934], 433 [28, 'H', -0.007016, -1.035292, -2.430851], 434 [29, 'H', -2.229948, 0.177326, -2.261725], 435 [30, 'H', -0.101863, 1.055799, -1.581061], 436 [31, 'H', -0.582210, 0.470722, 1.326014], 437 [32, 'H', 3.918694, 1.929549, 0.116264], 438 [33, 'H', 5.656588, 0.267474, -0.505165], 439 [34, 'H', 5.068478, -2.115052, -0.797816], 440 [35, 'H', 2.736463, -2.873299, -0.445917], 441 [36, 'H', 1.059165, -2.698455, 1.760657], 442 [37, 'H', 0.631843, -1.189746, 2.570301], 443 [38, 'H', -1.243126, -3.142405, 2.361743], 444 [39, 'H', -1.719677, -1.470258, 2.058429], 445 [40, 'H', -3.410692, -2.541912, 0.651788], 446 [41, 'H', -2.971493, -2.840572, -1.016009], 447 [42, 'H', -4.455619, -0.395106, 0.813636], 448 [43, 'H', -3.834304, 1.785629, -1.118252], 449 [44, 'H', -4.559845, 1.966160, 0.480526], 450 [45, 'H', -1.736135, 2.699031, -1.329897], 451 [46, 'H', -0.354638, 4.078330, -0.048526], 452 [47, 'H', -0.690723, 3.116119, 1.378208], 453 [ 1, 'O', -2.547545, 2.139059, 0.472310], 454 [ 2, 'O', 2.015408, 3.324289, 0.213156], 455 [ 3, 'N', 1.207610, 1.203922, 0.478894], 456 [ 4, 'N', -1.350394, -2.624460, 0.301178] 457 ] 458 459 # Check the data. 460 i = 0 461 for spin in spin_loop(): 462 self.assertEqual(spin.num, data[i][0]) 463 self.assertEqual(spin.name, data[i][1]) 464 self.assertEqual(spin.element, data[i][1]) 465 self.assertEqual(spin.pos[0], data[i][2]) 466 self.assertEqual(spin.pos[1], data[i][3]) 467 self.assertEqual(spin.pos[2], data[i][4]) 468 469 # Increment the spin index. 470 i += 1

471 472

473 - def test_read_merge(self):

474 """Test the merging of two molecules into one.""" 475 476 # Path of the files. 477 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 478 479 # Read the PDB files. 480 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-6.pdb', dir=path, set_mol_name='Ap4Aase', set_model_num=1) 481 self.interpreter.structure.read_pdb(file='Ap4Aase_res7-12.pdb', dir=path, set_mol_name='Ap4Aase', set_model_num=1, merge=True) 482 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=path, set_mol_name='Ap4Aase', set_model_num=2) 483 484 # Check that everything is ok. 485 cdp.structure.validate_models()

486 487

488 - def test_read_not_pdb(self):

489 """Test the reading of a file by structure.read_pdb that is not a PDB.""" 490 491 # Path of the files. 492 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'saved_states' 493 494 # Read the non-PDB file. 495 self.interpreter.structure.read_pdb(file='basic_single_pipe.bz2', dir=path)

496 497

498 - def test_read_pdb_internal1(self):

499 """Load the '1F35_N_H_molmol.pdb' PDB file (using the internal structural object PDB reader).""" 500 501 # Path of the files. 502 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 503 504 # Read the PDB. 505 self.interpreter.structure.read_pdb(file='1F35_N_H_molmol.pdb', dir=path) 506 507 # Test the molecule name. 508 self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name, '1F35_N_H_molmol_mol1') 509 510 # Load a single atom and test it. 511 self.interpreter.structure.load_spins('#1F35_N_H_molmol_mol1:3@N') 512 self.assertEqual(count_spins(), 1) 513 514 # Try loading a few protons. 515 self.interpreter.structure.load_spins('@*H*') 516 517 # And now all the rest of the atoms. 518 self.interpreter.structure.load_spins() 519 520 # Extract a N-Ca vector. 521 self.interpreter.interatom.define(spin_id1='@CA', spin_id2='#1F35_N_H_molmol_mol1:3@N') 522 self.interpreter.interatom.unit_vectors() 523 print(cdp.interatomic[0]) 524 self.assert_(hasattr(cdp.interatomic[0], 'vector'))

525 526

527 - def test_read_pdb_internal2(self):

528 """Load the 'Ap4Aase_res1-12.pdb' PDB file (using the internal structural object PDB reader).""" 529 530 # Path of the files. 531 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 532 533 # Read the PDB. 534 self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=path) 535 536 # Try loading a few protons. 537 self.interpreter.structure.load_spins('@*H*') 538 539 # And now all the rest of the atoms. 540 self.interpreter.structure.load_spins()

541 542

543 - def test_read_pdb_internal3(self):

544 """Load the 'gromacs.pdb' PDB file (using the internal structural object PDB reader).""" 545 546 # Path of the files. 547 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'phthalic_acid' 548 549 # Read the PDB. 550 self.interpreter.structure.read_pdb(file='gromacs.pdb', dir=path) 551 552 # Try loading a few protons, without positions averaging across models. 553 self.interpreter.structure.load_spins('@*H*', ave_pos=False) 554 555 # A test. 556 self.assertEqual(len(cdp.mol[0].res[0].spin[0].pos), 2) 557 558 # And now all the rest of the atoms. 559 self.interpreter.structure.load_spins()

560 561

562 - def test_read_pdb_internal4(self):

563 """Load the 'tylers_peptide_trunc.pdb' PDB file (using the internal structural object PDB reader).""" 564 565 # Path of the files. 566 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 567 568 # Read the PDB. 569 self.interpreter.structure.read_pdb(file='tylers_peptide_trunc.pdb', dir=path) 570 571 # Try loading a few protons. 572 self.interpreter.structure.load_spins('@*H*') 573 574 # And now all the rest of the atoms. 575 self.interpreter.structure.load_spins()

576 577

578 - def test_read_pdb_internal5(self):

579 """Load the 'lactose_MCMM4_S1_1.pdb' PDB file (using the internal structural object PDB reader).""" 580 581 # Path of the files. 582 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose' 583 584 # Read the PDB. 585 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_1.pdb', dir=path) 586 587 # Try loading a few protons. 588 self.interpreter.structure.load_spins('@*H*') 589 590 # And now all the rest of the atoms. 591 self.interpreter.structure.load_spins()

592 593

594 - def test_read_pdb_internal6(self):

595 """Load the 'lactose_MCMM4_S1_1.pdb' and 'lactose_MCMM4_S1_2.pdb' PDB files as 2 separate structures (using the internal structural object PDB reader).""" 596 597 # Path of the files. 598 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose' 599 600 # Read the PDB twice. 601 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_1.pdb', dir=path) 602 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_2.pdb', dir=path) 603 604 # Try loading a few protons. 605 self.interpreter.structure.load_spins('@*H*') 606 607 # And now all the rest of the atoms. 608 self.interpreter.structure.load_spins()

609 610

611 - def test_read_pdb_internal7(self):

612 """Load the 'lactose_MCMM4_S1_1.pdb' PDB file twice as 2 separate structures (using the internal structural object PDB reader).""" 613 614 # Path of the files. 615 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose' 616 617 # Read the PDB twice. 618 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_1.pdb', dir=path) 619 self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_1.pdb', dir=path) 620 621 # Try loading a few protons. 622 self.interpreter.structure.load_spins('@*H*') 623 624 # And now all the rest of the atoms. 625 self.interpreter.structure.load_spins()

626 627

628 - def test_read_pdb_mol_2_model_internal(self):

629 """Load a few 'lactose_MCMM4_S1_*.pdb' PDB files as models (using the internal structural object PDB reader).""" 630 631 # Path of the files. 632 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose' 633 634 # Files. 635 files = ['lactose_MCMM4_S1_1.pdb', 636 'lactose_MCMM4_S1_2.pdb', 637 'lactose_MCMM4_S1_3.pdb'] 638 639 # Read the PDBs. 640 self.interpreter.structure.read_pdb(file=files[0], dir=path, set_model_num=1) 641 self.interpreter.structure.read_pdb(file=files[1], dir=path, set_model_num=1) 642 self.interpreter.structure.read_pdb(file=files[2], dir=path, set_model_num=1) 643 644 # Try loading a few protons. 645 self.interpreter.structure.load_spins('@*H*') 646 647 # And now all the rest of the atoms. 648 self.interpreter.structure.load_spins() 649 650 # Test the structural data. 651 self.assert_(hasattr(cdp, 'structure')) 652 self.assert_(hasattr(cdp.structure, 'structural_data')) 653 self.assertEqual(len(cdp.structure.structural_data), 1) 654 self.assertEqual(len(cdp.structure.structural_data[0].mol), 3) 655 656 i = 0 657 for mol in cdp.structure.structural_data[0].mol: 658 self.assertEqual(mol.file_name, files[i]) 659 self.assertEqual(mol.file_path, path) 660 self.assertEqual(mol.file_model, 1) 661 self.assertEqual(mol.file_mol_num, 1) 662 i = i + 1

663 664

665 - def test_read_pdb_model_2_mol_internal(self):

666 """Load the 2 models of the 'gromacs.pdb' PDB file as separate molecules of the same model (using the internal structural object PDB reader).""" 667 668 # Path of the files. 669 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'phthalic_acid' 670 671 # Read the PDB models. 672 self.interpreter.structure.read_pdb(file='gromacs.pdb', dir=path, read_model=1, set_model_num=1) 673 self.interpreter.structure.read_pdb(file='gromacs.pdb', dir=path, read_model=2, set_model_num=1) 674 675 # Try loading a few protons. 676 self.interpreter.structure.load_spins('@*H*') 677 678 # And now all the rest of the atoms. 679 self.interpreter.structure.load_spins() 680 681 # Test the structural data. 682 self.assert_(hasattr(cdp, 'structure')) 683 self.assert_(hasattr(cdp.structure, 'structural_data')) 684 self.assertEqual(len(cdp.structure.structural_data), 1) 685 self.assertEqual(len(cdp.structure.structural_data[0].mol), 2) 686 687 i = 0 688 for mol in cdp.structure.structural_data[0].mol: 689 self.assertEqual(mol.file_name, 'gromacs.pdb') 690 self.assertEqual(mol.file_path, path) 691 self.assertEqual(mol.file_model, i+1) 692 self.assertEqual(mol.file_mol_num, 1) 693 i = i + 1

694 695

696 - def test_read_pdb_complex_internal(self):

697 """Test the packing of models and molecules using 'gromacs.pdb' and 'lactose_MCMM4_S1_*.pdb' (using the internal structural object PDB reader).""" 698 699 # Path of the files. 700 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 701 702 # Read the PDB models. 703 self.interpreter.structure.read_pdb(file='gromacs.pdb', dir=path+sep+'phthalic_acid') 704 self.interpreter.structure.read_pdb(file='lactose'+sep+'lactose_MCMM4_S1_1.pdb', dir=path, set_model_num=1, set_mol_name='lactose_MCMM4_S1') 705 self.interpreter.structure.read_pdb(file='lactose'+sep+'lactose_MCMM4_S1_2.pdb', dir=path, set_model_num=2, set_mol_name='lactose_MCMM4_S1') 706 self.interpreter.structure.read_pdb(file='lactose'+sep+'lactose_MCMM4_S1_3.pdb', dir=path, set_model_num=1, set_mol_name='lactose_MCMM4_S1b') 707 self.interpreter.structure.read_pdb(file='lactose'+sep+'lactose_MCMM4_S1_4.pdb', dir=path, set_model_num=2, set_mol_name='lactose_MCMM4_S1b') 708 709 # Try loading a few protons. 710 self.interpreter.structure.load_spins('@*H*') 711 712 # And now all the rest of the atoms. 713 self.interpreter.structure.load_spins() 714 715 # Test the structural data. 716 self.assert_(hasattr(cdp, 'structure')) 717 self.assert_(hasattr(cdp.structure, 'structural_data')) 718 self.assertEqual(len(cdp.structure.structural_data), 2) 719 self.assertEqual(len(cdp.structure.structural_data[0].mol), 3) 720 self.assertEqual(len(cdp.structure.structural_data[1].mol), 3) 721 722 files = [['gromacs.pdb', 'lactose_MCMM4_S1_1.pdb', 'lactose_MCMM4_S1_3.pdb'], 723 ['gromacs.pdb', 'lactose_MCMM4_S1_2.pdb', 'lactose_MCMM4_S1_4.pdb']] 724 paths = [[path+sep+'phthalic_acid', path+sep+'lactose', path+sep+'lactose'], 725 [path+sep+'phthalic_acid', path+sep+'lactose', path+sep+'lactose']] 726 models = [[1, 1, 1], [2, 1, 1]] 727 728 for i in range(len(cdp.structure.structural_data)): 729 for j in range(len(cdp.structure.structural_data[i].mol)): 730 mol = cdp.structure.structural_data[i].mol[j] 731 self.assertEqual(mol.file_name, files[i][j]) 732 self.assertEqual(mol.file_path, paths[i][j]) 733 self.assertEqual(mol.file_model, models[i][j]) 734 self.assertEqual(mol.file_mol_num, 1)

735 736

737 - def test_read_pdb_1UBQ(self):

738 """Test the reading of the complete 1UBQ PDB file.""" 739 740 # Load the file. 741 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 742 self.interpreter.structure.read_pdb('1UBQ.pdb', dir=path) 743 744 # Check the data. 745 self.assert_(hasattr(cdp, 'structure')) 746 self.assert_(hasattr(cdp.structure, 'structural_data')) 747 self.assertEqual(len(cdp.structure.structural_data), 1) 748 self.assertEqual(len(cdp.structure.structural_data[0].mol), 1) 749 750 # Check the first atom. 751 self.assertEqual(cdp.structure.structural_data[0].mol[0].atom_num[0], 1) 752 self.assertEqual(cdp.structure.structural_data[0].mol[0].atom_name[0], 'N') 753 self.assertEqual(cdp.structure.structural_data[0].mol[0].chain_id[0], 'A') 754 self.assertEqual(cdp.structure.structural_data[0].mol[0].res_name[0], 'MET') 755 self.assertEqual(cdp.structure.structural_data[0].mol[0].res_num[0], 1) 756 self.assertEqual(cdp.structure.structural_data[0].mol[0].x[0], 27.340) 757 self.assertEqual(cdp.structure.structural_data[0].mol[0].y[0], 24.430) 758 self.assertEqual(cdp.structure.structural_data[0].mol[0].z[0], 2.614) 759 self.assertEqual(cdp.structure.structural_data[0].mol[0].element[0], 'N') 760 761 # Check the last atom (from the last water HETATM record). 762 self.assertEqual(cdp.structure.structural_data[0].mol[0].atom_num[-1], 661) 763 self.assertEqual(cdp.structure.structural_data[0].mol[0].atom_name[-1], 'O') 764 self.assertEqual(cdp.structure.structural_data[0].mol[0].chain_id[-1], None) 765 self.assertEqual(cdp.structure.structural_data[0].mol[0].res_name[-1], 'HOH') 766 self.assertEqual(cdp.structure.structural_data[0].mol[0].res_num[-1], 58) 767 self.assertEqual(cdp.structure.structural_data[0].mol[0].x[-1], 37.667) 768 self.assertEqual(cdp.structure.structural_data[0].mol[0].y[-1], 43.421) 769 self.assertEqual(cdp.structure.structural_data[0].mol[0].z[-1], 17.000) 770 self.assertEqual(cdp.structure.structural_data[0].mol[0].element[-1], 'O')

771 772

773 - def test_read_write_pdb_1UBQ(self):

774 """Test the reading and writing of the 1UBQ PDB file.""" 775 776 # Load the file. 777 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 778 self.interpreter.structure.read_pdb('1UBQ.pdb', dir=path) 779 780 # Delete a big chunk of the molecule. 781 self.interpreter.structure.delete(":35-76") 782 783 # Delete all waters. 784 self.interpreter.structure.delete(":HOH") 785 786 # Write out the file. 787 self.tmpfile = mktemp() + '.pdb' 788 self.interpreter.structure.write_pdb(self.tmpfile) 789 790 # Read the contents of the file. 791 file = open(self.tmpfile) 792 lines = file.readlines() 793 file.close() 794 795 # What the contents should be. 796 real_data = [ 797 "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011. \n", 798 "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM). \n", 799 "HELIX 1 H1 ILE A 23 GLU A 34 1 12 \n", 800 "SHEET 1 BET 5 GLY A 10 VAL A 17 0 \n", 801 "SHEET 2 BET 5 MET A 1 THR A 7 -1 \n", 802 "ATOM 1 N MET A 1 27.340 24.430 2.614 1.00 0.00 N \n", 803 "ATOM 2 CA MET A 1 26.266 25.413 2.842 1.00 0.00 C \n", 804 "ATOM 3 C MET A 1 26.913 26.639 3.531 1.00 0.00 C \n", 805 "ATOM 4 O MET A 1 27.886 26.463 4.263 1.00 0.00 O \n", 806 "ATOM 5 CB MET A 1 25.112 24.880 3.649 1.00 0.00 C \n", 807 "ATOM 6 CG MET A 1 25.353 24.860 5.134 1.00 0.00 C \n", 808 "ATOM 7 SD MET A 1 23.930 23.959 5.904 1.00 0.00 S \n", 809 "ATOM 8 CE MET A 1 24.447 23.984 7.620 1.00 0.00 C \n", 810 "ATOM 9 N GLN A 2 26.335 27.770 3.258 1.00 0.00 N \n", 811 "ATOM 10 CA GLN A 2 26.850 29.021 3.898 1.00 0.00 C \n", 812 "ATOM 11 C GLN A 2 26.100 29.253 5.202 1.00 0.00 C \n", 813 "ATOM 12 O GLN A 2 24.865 29.024 5.330 1.00 0.00 O \n", 814 "ATOM 13 CB GLN A 2 26.733 30.148 2.905 1.00 0.00 C \n", 815 "ATOM 14 CG GLN A 2 26.882 31.546 3.409 1.00 0.00 C \n", 816 "ATOM 15 CD GLN A 2 26.786 32.562 2.270 1.00 0.00 C \n", 817 "ATOM 16 OE1 GLN A 2 27.783 33.160 1.870 1.00 0.00 O \n", 818 "ATOM 17 NE2 GLN A 2 25.562 32.733 1.806 1.00 0.00 N \n", 819 "ATOM 18 N ILE A 3 26.849 29.656 6.217 1.00 0.00 N \n", 820 "ATOM 19 CA ILE A 3 26.235 30.058 7.497 1.00 0.00 C \n", 821 "ATOM 20 C ILE A 3 26.882 31.428 7.862 1.00 0.00 C \n", 822 "ATOM 21 O ILE A 3 27.906 31.711 7.264 1.00 0.00 O \n", 823 "ATOM 22 CB ILE A 3 26.344 29.050 8.645 1.00 0.00 C \n", 824 "ATOM 23 CG1 ILE A 3 27.810 28.748 8.999 1.00 0.00 C \n", 825 "ATOM 24 CG2 ILE A 3 25.491 27.771 8.287 1.00 0.00 C \n", 826 "ATOM 25 CD1 ILE A 3 27.967 28.087 10.417 1.00 0.00 C \n", 827 "ATOM 26 N PHE A 4 26.214 32.097 8.771 1.00 0.00 N \n", 828 "ATOM 27 CA PHE A 4 26.772 33.436 9.197 1.00 0.00 C \n", 829 "ATOM 28 C PHE A 4 27.151 33.362 10.650 1.00 0.00 C \n", 830 "ATOM 29 O PHE A 4 26.350 32.778 11.395 1.00 0.00 O \n", 831 "ATOM 30 CB PHE A 4 25.695 34.498 8.946 1.00 0.00 C \n", 832 "ATOM 31 CG PHE A 4 25.288 34.609 7.499 1.00 0.00 C \n", 833 "ATOM 32 CD1 PHE A 4 24.147 33.966 7.038 1.00 0.00 C \n", 834 "ATOM 33 CD2 PHE A 4 26.136 35.346 6.640 1.00 0.00 C \n", 835 "ATOM 34 CE1 PHE A 4 23.812 34.031 5.677 1.00 0.00 C \n", 836 "ATOM 35 CE2 PHE A 4 25.810 35.392 5.267 1.00 0.00 C \n", 837 "ATOM 36 CZ PHE A 4 24.620 34.778 4.853 1.00 0.00 C \n", 838 "ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 0.00 N \n", 839 "ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 0.00 C \n", 840 "ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 0.00 C \n", 841 "ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 0.00 O \n", 842 "ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 0.00 C \n", 843 "ATOM 42 CG1 VAL A 5 30.211 33.394 14.304 1.00 0.00 C \n", 844 "ATOM 43 CG2 VAL A 5 29.957 31.838 12.352 1.00 0.00 C \n", 845 "ATOM 44 N LYS A 6 27.751 35.867 13.740 1.00 0.00 N \n", 846 "ATOM 45 CA LYS A 6 27.691 37.315 14.143 1.00 0.00 C \n", 847 "ATOM 46 C LYS A 6 28.469 37.475 15.420 1.00 0.00 C \n", 848 "ATOM 47 O LYS A 6 28.213 36.753 16.411 1.00 0.00 O \n", 849 "ATOM 48 CB LYS A 6 26.219 37.684 14.307 1.00 0.00 C \n", 850 "ATOM 49 CG LYS A 6 25.884 39.139 14.615 1.00 0.00 C \n", 851 "ATOM 50 CD LYS A 6 24.348 39.296 14.642 1.00 0.00 C \n", 852 "ATOM 51 CE LYS A 6 23.865 40.723 14.749 1.00 0.00 C \n", 853 "ATOM 52 NZ LYS A 6 22.375 40.720 14.907 1.00 0.00 N \n", 854 "ATOM 53 N THR A 7 29.426 38.430 15.446 1.00 0.00 N \n", 855 "ATOM 54 CA THR A 7 30.225 38.643 16.662 1.00 0.00 C \n", 856 "ATOM 55 C THR A 7 29.664 39.839 17.434 1.00 0.00 C \n", 857 "ATOM 56 O THR A 7 28.850 40.565 16.859 1.00 0.00 O \n", 858 "ATOM 57 CB THR A 7 31.744 38.879 16.299 1.00 0.00 C \n", 859 "ATOM 58 OG1 THR A 7 31.737 40.257 15.824 1.00 0.00 O \n", 860 "ATOM 59 CG2 THR A 7 32.260 37.969 15.171 1.00 0.00 C \n", 861 "ATOM 60 N LEU A 8 30.132 40.069 18.642 1.00 0.00 N \n", 862 "ATOM 61 CA LEU A 8 29.607 41.180 19.467 1.00 0.00 C \n", 863 "ATOM 62 C LEU A 8 30.075 42.538 18.984 1.00 0.00 C \n", 864 "ATOM 63 O LEU A 8 29.586 43.570 19.483 1.00 0.00 O \n", 865 "ATOM 64 CB LEU A 8 29.919 40.890 20.938 1.00 0.00 C \n", 866 "ATOM 65 CG LEU A 8 29.183 39.722 21.581 1.00 0.00 C \n", 867 "ATOM 66 CD1 LEU A 8 29.308 39.750 23.095 1.00 0.00 C \n", 868 "ATOM 67 CD2 LEU A 8 27.700 39.721 21.228 1.00 0.00 C \n", 869 "ATOM 68 N THR A 9 30.991 42.571 17.998 1.00 0.00 N \n", 870 "ATOM 69 CA THR A 9 31.422 43.940 17.553 1.00 0.00 C \n", 871 "ATOM 70 C THR A 9 30.755 44.351 16.277 1.00 0.00 C \n", 872 "ATOM 71 O THR A 9 31.207 45.268 15.566 1.00 0.00 O \n", 873 "ATOM 72 CB THR A 9 32.979 43.918 17.445 1.00 0.00 C \n", 874 "ATOM 73 OG1 THR A 9 33.174 43.067 16.265 1.00 0.00 O \n", 875 "ATOM 74 CG2 THR A 9 33.657 43.319 18.672 1.00 0.00 C \n", 876 "ATOM 75 N GLY A 10 29.721 43.673 15.885 1.00 0.00 N \n", 877 "ATOM 76 CA GLY A 10 28.978 43.960 14.678 1.00 0.00 C \n", 878 "ATOM 77 C GLY A 10 29.604 43.507 13.393 1.00 0.00 C \n", 879 "ATOM 78 O GLY A 10 29.219 43.981 12.301 1.00 0.00 O \n", 880 "ATOM 79 N LYS A 11 30.563 42.623 13.495 1.00 0.00 N \n", 881 "ATOM 80 CA LYS A 11 31.191 42.012 12.331 1.00 0.00 C \n", 882 "ATOM 81 C LYS A 11 30.459 40.666 12.130 1.00 0.00 C \n", 883 "ATOM 82 O LYS A 11 30.253 39.991 13.133 1.00 0.00 O \n", 884 "ATOM 83 CB LYS A 11 32.672 41.717 12.505 1.00 0.00 C \n", 885 "ATOM 84 CG LYS A 11 33.280 41.086 11.227 1.00 0.00 C \n", 886 "ATOM 85 CD LYS A 11 34.762 40.799 11.470 1.00 0.00 C \n", 887 "ATOM 86 CE LYS A 11 35.614 40.847 10.240 1.00 0.00 C \n", 888 "ATOM 87 NZ LYS A 11 35.100 40.073 9.101 1.00 0.00 N \n", 889 "ATOM 88 N THR A 12 30.163 40.338 10.886 1.00 0.00 N \n", 890 "ATOM 89 CA THR A 12 29.542 39.020 10.653 1.00 0.00 C \n", 891 "ATOM 90 C THR A 12 30.494 38.261 9.729 1.00 0.00 C \n", 892 "ATOM 91 O THR A 12 30.849 38.850 8.706 1.00 0.00 O \n", 893 "ATOM 92 CB THR A 12 28.113 39.049 10.015 1.00 0.00 C \n", 894 "ATOM 93 OG1 THR A 12 27.280 39.722 10.996 1.00 0.00 O \n", 895 "ATOM 94 CG2 THR A 12 27.588 37.635 9.715 1.00 0.00 C \n", 896 "ATOM 95 N ILE A 13 30.795 37.015 10.095 1.00 0.00 N \n", 897 "ATOM 96 CA ILE A 13 31.720 36.289 9.176 1.00 0.00 C \n", 898 "ATOM 97 C ILE A 13 30.955 35.211 8.459 1.00 0.00 C \n", 899 "ATOM 98 O ILE A 13 30.025 34.618 9.040 1.00 0.00 O \n", 900 "ATOM 99 CB ILE A 13 32.995 35.883 9.934 1.00 0.00 C \n", 901 "ATOM 100 CG1 ILE A 13 33.306 34.381 9.840 1.00 0.00 C \n", 902 "ATOM 101 CG2 ILE A 13 33.109 36.381 11.435 1.00 0.00 C \n", 903 "ATOM 102 CD1 ILE A 13 34.535 34.028 10.720 1.00 0.00 C \n", 904 "ATOM 103 N THR A 14 31.244 34.986 7.197 1.00 0.00 N \n", 905 "ATOM 104 CA THR A 14 30.505 33.884 6.512 1.00 0.00 C \n", 906 "ATOM 105 C THR A 14 31.409 32.680 6.446 1.00 0.00 C \n", 907 "ATOM 106 O THR A 14 32.619 32.812 6.125 1.00 0.00 O \n", 908 "ATOM 107 CB THR A 14 30.091 34.393 5.078 1.00 0.00 C \n", 909 "ATOM 108 OG1 THR A 14 31.440 34.513 4.487 1.00 0.00 O \n", 910 "ATOM 109 CG2 THR A 14 29.420 35.756 5.119 1.00 0.00 C \n", 911 "ATOM 110 N LEU A 15 30.884 31.485 6.666 1.00 0.00 N \n", 912 "ATOM 111 CA LEU A 15 31.677 30.275 6.639 1.00 0.00 C \n", 913 "ATOM 112 C LEU A 15 31.022 29.288 5.665 1.00 0.00 C \n", 914 "ATOM 113 O LEU A 15 29.809 29.395 5.545 1.00 0.00 O \n", 915 "ATOM 114 CB LEU A 15 31.562 29.686 8.045 1.00 0.00 C \n", 916 "ATOM 115 CG LEU A 15 32.631 29.444 9.060 1.00 0.00 C \n", 917 "ATOM 116 CD1 LEU A 15 33.814 30.390 9.030 1.00 0.00 C \n", 918 "ATOM 117 CD2 LEU A 15 31.945 29.449 10.436 1.00 0.00 C \n", 919 "ATOM 118 N GLU A 16 31.834 28.412 5.125 1.00 0.00 N \n", 920 "ATOM 119 CA GLU A 16 31.220 27.341 4.275 1.00 0.00 C \n", 921 "ATOM 120 C GLU A 16 31.440 26.079 5.080 1.00 0.00 C \n", 922 "ATOM 121 O GLU A 16 32.576 25.802 5.461 1.00 0.00 O \n", 923 "ATOM 122 CB GLU A 16 31.827 27.262 2.894 1.00 0.00 C \n", 924 "ATOM 123 CG GLU A 16 31.363 28.410 1.962 1.00 0.00 C \n", 925 "ATOM 124 CD GLU A 16 31.671 28.291 0.498 1.00 0.00 C \n", 926 "ATOM 125 OE1 GLU A 16 30.869 28.621 -0.366 1.00 0.00 O \n", 927 "ATOM 126 OE2 GLU A 16 32.835 27.861 0.278 1.00 0.00 O \n", 928 "ATOM 127 N VAL A 17 30.310 25.458 5.384 1.00 0.00 N \n", 929 "ATOM 128 CA VAL A 17 30.288 24.245 6.193 1.00 0.00 C \n", 930 "ATOM 129 C VAL A 17 29.279 23.227 5.641 1.00 0.00 C \n", 931 "ATOM 130 O VAL A 17 28.478 23.522 4.725 1.00 0.00 O \n", 932 "ATOM 131 CB VAL A 17 29.903 24.590 7.665 1.00 0.00 C \n", 933 "ATOM 132 CG1 VAL A 17 30.862 25.496 8.389 1.00 0.00 C \n", 934 "ATOM 133 CG2 VAL A 17 28.476 25.135 7.705 1.00 0.00 C \n", 935 "ATOM 134 N GLU A 18 29.380 22.057 6.232 1.00 0.00 N \n", 936 "ATOM 135 CA GLU A 18 28.468 20.940 5.980 1.00 0.00 C \n", 937 "ATOM 136 C GLU A 18 27.819 20.609 7.316 1.00 0.00 C \n", 938 "ATOM 137 O GLU A 18 28.449 20.674 8.360 1.00 0.00 O \n", 939 "ATOM 138 CB GLU A 18 29.213 19.697 5.506 1.00 0.00 C \n", 940 "ATOM 139 CG GLU A 18 29.728 19.755 4.060 1.00 0.00 C \n", 941 "ATOM 140 CD GLU A 18 28.754 20.061 2.978 1.00 0.00 C \n", 942 "ATOM 141 OE1 GLU A 18 27.546 19.992 2.985 1.00 0.00 O \n", 943 "ATOM 142 OE2 GLU A 18 29.336 20.423 1.904 1.00 0.00 O \n", 944 "ATOM 143 N PRO A 19 26.559 20.220 7.288 1.00 0.00 N \n", 945 "ATOM 144 CA PRO A 19 25.829 19.825 8.494 1.00 0.00 C \n", 946 "ATOM 145 C PRO A 19 26.541 18.732 9.251 1.00 0.00 C \n", 947 "ATOM 146 O PRO A 19 26.333 18.536 10.457 1.00 0.00 O \n", 948 "ATOM 147 CB PRO A 19 24.469 19.332 7.952 1.00 0.00 C \n", 949 "ATOM 148 CG PRO A 19 24.299 20.134 6.704 1.00 0.00 C \n", 950 "ATOM 149 CD PRO A 19 25.714 20.108 6.073 1.00 0.00 C \n", 951 "ATOM 150 N SER A 20 27.361 17.959 8.559 1.00 0.00 N \n", 952 "ATOM 151 CA SER A 20 28.054 16.835 9.210 1.00 0.00 C \n", 953 "ATOM 152 C SER A 20 29.258 17.318 9.984 1.00 0.00 C \n", 954 "ATOM 153 O SER A 20 29.930 16.477 10.606 1.00 0.00 O \n", 955 "ATOM 154 CB SER A 20 28.523 15.820 8.182 1.00 0.00 C \n", 956 "ATOM 155 OG SER A 20 28.946 16.445 6.967 1.00 0.00 O \n", 957 "ATOM 156 N ASP A 21 29.599 18.599 9.828 1.00 0.00 N \n", 958 "ATOM 157 CA ASP A 21 30.796 19.083 10.566 1.00 0.00 C \n", 959 "ATOM 158 C ASP A 21 30.491 19.162 12.040 1.00 0.00 C \n", 960 "ATOM 159 O ASP A 21 29.367 19.523 12.441 1.00 0.00 O \n", 961 "ATOM 160 CB ASP A 21 31.155 20.515 10.048 1.00 0.00 C \n", 962 "ATOM 161 CG ASP A 21 31.923 20.436 8.755 1.00 0.00 C \n", 963 "ATOM 162 OD1 ASP A 21 32.493 19.374 8.456 1.00 0.00 O \n", 964 "ATOM 163 OD2 ASP A 21 31.838 21.402 7.968 1.00 0.00 O \n", 965 "ATOM 164 N THR A 22 31.510 18.936 12.852 1.00 0.00 N \n", 966 "ATOM 165 CA THR A 22 31.398 19.064 14.286 1.00 0.00 C \n", 967 "ATOM 166 C THR A 22 31.593 20.553 14.655 1.00 0.00 C \n", 968 "ATOM 167 O THR A 22 32.159 21.311 13.861 1.00 0.00 O \n", 969 "ATOM 168 CB THR A 22 32.492 18.193 14.995 1.00 0.00 C \n", 970 "ATOM 169 OG1 THR A 22 33.778 18.739 14.516 1.00 0.00 O \n", 971 "ATOM 170 CG2 THR A 22 32.352 16.700 14.630 1.00 0.00 C \n", 972 "ATOM 171 N ILE A 23 31.113 20.863 15.860 1.00 0.00 N \n", 973 "ATOM 172 CA ILE A 23 31.288 22.201 16.417 1.00 0.00 C \n", 974 "ATOM 173 C ILE A 23 32.776 22.519 16.577 1.00 0.00 C \n", 975 "ATOM 174 O ILE A 23 33.233 23.659 16.384 1.00 0.00 O \n", 976 "ATOM 175 CB ILE A 23 30.520 22.300 17.764 1.00 0.00 C \n", 977 "ATOM 176 CG1 ILE A 23 29.006 22.043 17.442 1.00 0.00 C \n", 978 "ATOM 177 CG2 ILE A 23 30.832 23.699 18.358 1.00 0.00 C \n", 979 "ATOM 178 CD1 ILE A 23 28.407 22.948 16.366 1.00 0.00 C \n", 980 "ATOM 179 N GLU A 24 33.548 21.526 16.950 1.00 0.00 N \n", 981 "ATOM 180 CA GLU A 24 35.031 21.722 17.069 1.00 0.00 C \n", 982 "ATOM 181 C GLU A 24 35.615 22.190 15.759 1.00 0.00 C \n", 983 "ATOM 182 O GLU A 24 36.532 23.046 15.724 1.00 0.00 O \n", 984 "ATOM 183 CB GLU A 24 35.667 20.383 17.447 1.00 0.00 C \n", 985 "ATOM 184 CG GLU A 24 37.128 20.293 17.872 1.00 0.00 C \n", 986 "ATOM 185 CD GLU A 24 37.561 18.851 18.082 1.00 0.00 C \n", 987 "ATOM 186 OE1 GLU A 24 37.758 18.024 17.195 1.00 0.00 O \n", 988 "ATOM 187 OE2 GLU A 24 37.628 18.599 19.313 1.00 0.00 O \n", 989 "ATOM 188 N ASN A 25 35.139 21.624 14.662 1.00 0.00 N \n", 990 "ATOM 189 CA ASN A 25 35.590 21.945 13.302 1.00 0.00 C \n", 991 "ATOM 190 C ASN A 25 35.238 23.382 12.920 1.00 0.00 C \n", 992 "ATOM 191 O ASN A 25 36.066 24.109 12.333 1.00 0.00 O \n", 993 "ATOM 192 CB ASN A 25 35.064 20.957 12.255 1.00 0.00 C \n", 994 "ATOM 193 CG ASN A 25 35.541 21.418 10.871 1.00 0.00 C \n", 995 "ATOM 194 OD1 ASN A 25 36.772 21.623 10.676 1.00 0.00 O \n", 996 "ATOM 195 ND2 ASN A 25 34.628 21.595 9.920 1.00 0.00 N \n", 997 "ATOM 196 N VAL A 26 34.007 23.745 13.250 1.00 0.00 N \n", 998 "ATOM 197 CA VAL A 26 33.533 25.097 12.978 1.00 0.00 C \n", 999 "ATOM 198 C VAL A 26 34.441 26.099 13.684 1.00 0.00 C \n", 1000 "ATOM 199 O VAL A 26 34.883 27.090 13.093 1.00 0.00 O \n", 1001 "ATOM 200 CB VAL A 26 32.060 25.257 13.364 1.00 0.00 C \n", 1002 "ATOM 201 CG1 VAL A 26 31.684 26.749 13.342 1.00 0.00 C \n", 1003 "ATOM 202 CG2 VAL A 26 31.152 24.421 12.477 1.00 0.00 C \n", 1004 "ATOM 203 N LYS A 27 34.734 25.822 14.949 1.00 0.00 N \n", 1005 "ATOM 204 CA LYS A 27 35.596 26.715 15.736 1.00 0.00 C \n", 1006 "ATOM 205 C LYS A 27 36.975 26.826 15.107 1.00 0.00 C \n", 1007 "ATOM 206 O LYS A 27 37.579 27.926 15.159 1.00 0.00 O \n", 1008 "ATOM 207 CB LYS A 27 35.715 26.203 17.172 1.00 0.00 C \n", 1009 "ATOM 208 CG LYS A 27 34.343 26.445 17.898 1.00 0.00 C \n", 1010 "ATOM 209 CD LYS A 27 34.509 26.077 19.360 1.00 0.00 C \n", 1011 "ATOM 210 CE LYS A 27 33.206 26.311 20.122 1.00 0.00 C \n", 1012 "ATOM 211 NZ LYS A 27 33.455 25.910 21.546 1.00 0.00 N \n", 1013 "ATOM 212 N ALA A 28 37.499 25.743 14.571 1.00 0.00 N \n", 1014 "ATOM 213 CA ALA A 28 38.794 25.761 13.880 1.00 0.00 C \n", 1015 "ATOM 214 C ALA A 28 38.728 26.591 12.611 1.00 0.00 C \n", 1016 "ATOM 215 O ALA A 28 39.704 27.346 12.277 1.00 0.00 O \n", 1017 "ATOM 216 CB ALA A 28 39.285 24.336 13.566 1.00 0.00 C \n", 1018 "ATOM 217 N LYS A 29 37.633 26.543 11.867 1.00 0.00 N \n", 1019 "ATOM 218 CA LYS A 29 37.471 27.391 10.668 1.00 0.00 C \n", 1020 "ATOM 219 C LYS A 29 37.441 28.882 11.052 1.00 0.00 C \n", 1021 "ATOM 220 O LYS A 29 38.020 29.772 10.382 1.00 0.00 O \n", 1022 "ATOM 221 CB LYS A 29 36.193 27.058 9.911 1.00 0.00 C \n", 1023 "ATOM 222 CG LYS A 29 36.153 25.620 9.409 1.00 0.00 C \n", 1024 "ATOM 223 CD LYS A 29 34.758 25.280 8.900 1.00 0.00 C \n", 1025 "ATOM 224 CE LYS A 29 34.793 24.264 7.767 1.00 0.00 C \n", 1026 "ATOM 225 NZ LYS A 29 34.914 24.944 6.441 1.00 0.00 N \n", 1027 "ATOM 226 N ILE A 30 36.811 29.170 12.192 1.00 0.00 N \n", 1028 "ATOM 227 CA ILE A 30 36.731 30.570 12.645 1.00 0.00 C \n", 1029 "ATOM 228 C ILE A 30 38.148 30.981 13.069 1.00 0.00 C \n", 1030 "ATOM 229 O ILE A 30 38.544 32.150 12.856 1.00 0.00 O \n", 1031 "ATOM 230 CB ILE A 30 35.708 30.776 13.806 1.00 0.00 C \n", 1032 "ATOM 231 CG1 ILE A 30 34.228 30.630 13.319 1.00 0.00 C \n", 1033 "ATOM 232 CG2 ILE A 30 35.874 32.138 14.512 1.00 0.00 C \n", 1034 "ATOM 233 CD1 ILE A 30 33.284 30.504 14.552 1.00 0.00 C \n", 1035 "ATOM 234 N GLN A 31 38.883 30.110 13.713 1.00 0.00 N \n", 1036 "ATOM 235 CA GLN A 31 40.269 30.508 14.115 1.00 0.00 C \n", 1037 "ATOM 236 C GLN A 31 41.092 30.808 12.851 1.00 0.00 C \n", 1038 "ATOM 237 O GLN A 31 41.828 31.808 12.681 1.00 0.00 O \n", 1039 "ATOM 238 CB GLN A 31 40.996 29.399 14.865 1.00 0.00 C \n", 1040 "ATOM 239 CG GLN A 31 42.445 29.848 15.182 1.00 0.00 C \n", 1041 "ATOM 240 CD GLN A 31 43.090 28.828 16.095 1.00 0.00 C \n", 1042 "ATOM 241 OE1 GLN A 31 42.770 27.655 15.906 1.00 0.00 O \n", 1043 "ATOM 242 NE2 GLN A 31 43.898 29.252 17.050 1.00 0.00 N \n", 1044 "ATOM 243 N ASP A 32 41.001 29.878 11.931 1.00 0.00 N \n", 1045 "ATOM 244 CA ASP A 32 41.718 30.022 10.643 1.00 0.00 C \n", 1046 "ATOM 245 C ASP A 32 41.399 31.338 9.967 1.00 0.00 C \n", 1047 "ATOM 246 O ASP A 32 42.260 32.036 9.381 1.00 0.00 O \n", 1048 "ATOM 247 CB ASP A 32 41.398 28.780 9.810 1.00 0.00 C \n", 1049 "ATOM 248 CG ASP A 32 42.626 28.557 8.928 1.00 0.00 C \n", 1050 "ATOM 249 OD1 ASP A 32 43.666 28.262 9.539 1.00 0.00 O \n", 1051 "ATOM 250 OD2 ASP A 32 42.430 28.812 7.728 1.00 0.00 O \n", 1052 "ATOM 251 N LYS A 33 40.117 31.750 9.988 1.00 0.00 N \n", 1053 "ATOM 252 CA LYS A 33 39.808 32.994 9.233 1.00 0.00 C \n", 1054 "ATOM 253 C LYS A 33 39.837 34.271 9.995 1.00 0.00 C \n", 1055 "ATOM 254 O LYS A 33 40.164 35.323 9.345 1.00 0.00 O \n", 1056 "ATOM 255 CB LYS A 33 38.615 32.801 8.320 1.00 0.00 C \n", 1057 "ATOM 256 CG LYS A 33 37.220 32.822 8.827 1.00 0.00 C \n", 1058 "ATOM 257 CD LYS A 33 36.351 33.613 7.838 1.00 0.00 C \n", 1059 "ATOM 258 CE LYS A 33 36.322 32.944 6.477 1.00 0.00 C \n", 1060 "ATOM 259 NZ LYS A 33 35.768 33.945 5.489 1.00 0.00 N \n", 1061 "ATOM 260 N GLU A 34 39.655 34.335 11.285 1.00 0.00 N \n", 1062 "ATOM 261 CA GLU A 34 39.676 35.547 12.072 1.00 0.00 C \n", 1063 "ATOM 262 C GLU A 34 40.675 35.527 13.200 1.00 0.00 C \n", 1064 "ATOM 263 O GLU A 34 40.814 36.528 13.911 1.00 0.00 O \n", 1065 "ATOM 264 CB GLU A 34 38.290 35.814 12.698 1.00 0.00 C \n", 1066 "ATOM 265 CG GLU A 34 37.156 35.985 11.688 1.00 0.00 C \n", 1067 "ATOM 266 CD GLU A 34 37.192 37.361 11.033 1.00 0.00 C \n", 1068 "ATOM 267 OE1 GLU A 34 37.519 38.360 11.645 1.00 0.00 O \n", 1069 "ATOM 268 OE2 GLU A 34 36.861 37.320 9.822 1.00 0.00 O \n", 1070 "TER 269 GLU A 34 \n", 1071 "MASTER 0 0 0 0 0 0 0 0 268 1 0 0 \n", 1072 "END \n" 1073 ] 1074 1075 # Check the data. 1076 for i in range(len(real_data)): 1077 self.assertEqual(real_data[i], lines[i])

1078 1079

1080 - def test_read_xyz_internal1(self):

1081 """Load the 'Indol_test.xyz' XYZ file (using the internal structural object XYZ reader).""" 1082 1083 # Path of the files. 1084 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 1085 1086 # Read the XYZ file. 1087 self.interpreter.structure.read_xyz(file='Indol_test.xyz', dir=path) 1088 1089 # Test the molecule name. 1090 self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name, 'Indol_test_mol1') 1091 1092 # Load a single atom and test it. 1093 self.interpreter.structure.load_spins('#Indol_test_mol1@3') 1094 self.assertEqual(count_spins(), 1) 1095 1096 # Try loading a few protons. 1097 self.interpreter.structure.load_spins('@*H*') 1098 1099 # And now all the rest of the atoms. 1100 self.interpreter.structure.load_spins()

1101 1102

1103 - def test_read_xyz_internal2(self):

1104 """Load the 'SSS-cluster4-new-test.xyz' XYZ file (using the internal structural object XYZ reader).""" 1105 1106 # Path of the files. 1107 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 1108 1109 # Read the XYZ file. 1110 self.interpreter.structure.read_xyz(file='SSS-cluster4-new-test.xyz', dir=path, read_model=[1]) 1111 1112 # Test the molecule name. 1113 self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name, 'SSS-cluster4-new-test_mol1') 1114 1115 # Load a single atom and test it. 1116 self.interpreter.structure.load_spins('#SSS-cluster4-new-test_mol1@2') 1117 self.assertEqual(count_spins(), 1) 1118 1119 # Test the spin coordinates. 1120 a=return_spin('#SSS-cluster4-new-test_mol1@2') 1121 self.assertAlmostEqual(a.pos[0], -12.398) 1122 self.assertAlmostEqual(a.pos[1], -15.992) 1123 self.assertAlmostEqual(a.pos[2], 11.448) 1124 1125 # Try loading a few protons. 1126 #self.interpreter.structure.load_spins('@H') 1127 1128 # And now all the rest of the atoms. 1129 self.interpreter.structure.load_spins() 1130 1131 # Extract a vector between first two spins. 1132 self.interpreter.interatom.define(spin_id1='@2', spin_id2='@10') 1133 self.interpreter.interatom.unit_vectors() 1134 self.assertAlmostEqual(cdp.interatomic[0].vector[0], -0.4102707) 1135 self.assertAlmostEqual(cdp.interatomic[0].vector[1], 0.62128879) 1136 self.assertAlmostEqual(cdp.interatomic[0].vector[2], -0.6675913)

1137 1138

1139 - def test_read_xyz_strychnine(self):

1140 """Load the 'strychnine.xyz' XYZ file (using the internal structural object XYZ reader).""" 1141 1142 # Path of the files. 1143 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 1144 1145 # Read the XYZ file. 1146 self.interpreter.structure.read_xyz(file='strychnine.xyz', dir=path, set_mol_name='strychnine') 1147 1148 # Test the molecule data. 1149 self.assertEqual(len(cdp.structure.structural_data), 1) 1150 self.assertEqual(len(cdp.structure.structural_data[0].mol), 1) 1151 1152 # Load the carbon atoms and test it. 1153 self.interpreter.structure.load_spins('@C') 1154 self.assertEqual(count_spins(), 21) 1155 1156 # Load the protons. 1157 self.interpreter.structure.load_spins('@H') 1158 self.assertEqual(count_spins(), 43) 1159 1160 # And now all the rest of the atoms. 1161 self.interpreter.structure.load_spins()

1162 1163

1164 - def test_rmsd(self):

1165 """Test the structure.rmsd user function.""" 1166 1167 # Set up 3 models. 1168 self.interpreter.structure.add_model(model_num=1) 1169 self.interpreter.structure.add_model(model_num=2) 1170 self.interpreter.structure.add_model(model_num=4) 1171 1172 # Check that the models were correctly created. 1173 self.assert_(hasattr(cdp, 'structure')) 1174 self.assert_(hasattr(cdp.structure, 'structural_data')) 1175 self.assertEqual(len(cdp.structure.structural_data), 3) 1176 1177 # Create a structure with some atoms. 1178 self.interpreter.structure.add_atom(atom_name='A', res_name='UNK', res_num=1, pos=[[1., 0., -1.], [0., 0., 0.], [-1., 0., 1.]], element='S') 1179 self.interpreter.structure.add_atom(atom_name='A', res_name='UNK', res_num=2, pos=[[1., 2., -1.], [0., 2., 0.], [-1., 2., 1.]], element='S') 1180 self.interpreter.structure.add_atom(atom_name='A', res_name='UNK', res_num=3, pos=[[1., 20., -1.], [0., 20., 0.], [-1., 20., 1.]], element='S') 1181 1182 # Check the internal atomic info. 1183 self.assertEqual(cdp.structure.structural_data[0].mol[0].x, [1., 1., 1.]) 1184 self.assertEqual(cdp.structure.structural_data[0].mol[0].y, [0., 2., 20.]) 1185 self.assertEqual(cdp.structure.structural_data[0].mol[0].z, [-1., -1., -1.]) 1186 self.assertEqual(cdp.structure.structural_data[1].mol[0].x, [0., 0., 0.]) 1187 self.assertEqual(cdp.structure.structural_data[1].mol[0].y, [0., 2., 20.]) 1188 self.assertEqual(cdp.structure.structural_data[1].mol[0].z, [0., 0., 0.]) 1189 self.assertEqual(cdp.structure.structural_data[2].mol[0].x, [-1., -1., -1.]) 1190 self.assertEqual(cdp.structure.structural_data[2].mol[0].y, [0., 2., 20.]) 1191 self.assertEqual(cdp.structure.structural_data[2].mol[0].z, [1., 1., 1.]) 1192 1193 # Calculate the RMSD. 1194 self.interpreter.structure.rmsd() 1195 1196 # Checks. 1197 self.assert_(hasattr(cdp.structure, 'rmsd')) 1198 self.assertAlmostEqual(cdp.structure.rmsd, 2./3*sqrt(2))

1199 1200

1201 - def test_rmsd_ubi(self):

1202 """Test the structure.rmsd user function on the truncated ubiquitin ensemble.""" 1203 1204 # Load the structure. 1205 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 1206 self.interpreter.structure.read_pdb('trunc_ubi_pcs.pdb', dir=path) 1207 1208 # Calculate the RMSD. 1209 self.interpreter.structure.rmsd() 1210 1211 # Checks (the values match the VMD 1.9.1 RMSD numbers). 1212 self.assert_(hasattr(cdp.structure, 'rmsd')) 1213 self.assertAlmostEqual(cdp.structure.rmsd, 0.77282758781333061)

1214 1215

1216 - def test_superimpose_fit_to_first(self):

1217 """Test of the structure.superimpose user function, fitting to the first structure.""" 1218 1219 # Path of the structure file. 1220 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam' 1221 1222 # Load the two rotated structures. 1223 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=1, set_mol_name='CaM') 1224 self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path, set_model_num=2, set_mol_name='CaM') 1225 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=3, set_mol_name='CaM') 1226 1227 # Superimpose the backbone heavy atoms. 1228 self.interpreter.structure.superimpose(method='fit to first', atom_id='@N,C,CA,O') 1229 1230 # Check that the two structures now have the same atomic coordinates. 1231 model1 = cdp.structure.structural_data[0].mol[0] 1232 model2 = cdp.structure.structural_data[1].mol[0] 1233 model3 = cdp.structure.structural_data[2].mol[0] 1234 for i in range(len(model1.atom_name)): 1235 # Check model 2. 1236 self.assertAlmostEqual(model1.x[i], model2.x[i], 2) 1237 self.assertAlmostEqual(model1.y[i], model2.y[i], 2) 1238 self.assertAlmostEqual(model1.z[i], model2.z[i], 2) 1239 1240 # Check model 3. 1241 self.assertAlmostEqual(model1.x[i], model3.x[i], 2) 1242 self.assertAlmostEqual(model1.y[i], model3.y[i], 2) 1243 self.assertAlmostEqual(model1.z[i], model3.z[i], 2)

1244 1245

1246 - def test_superimpose_fit_to_mean(self):

1247 """Test of the structure.superimpose user function, fitting to the mean structure.""" 1248 1249 # Path of the structure file. 1250 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam' 1251 1252 # Load the two rotated structures. 1253 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=1, set_mol_name='CaM') 1254 self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path, set_model_num=2, set_mol_name='CaM') 1255 1256 # Superimpose the backbone heavy atoms. 1257 self.interpreter.structure.superimpose(method='fit to mean', atom_id='@N,C,CA,O') 1258 1259 # Check that the two structures now have the same atomic coordinates. 1260 model1 = cdp.structure.structural_data[0].mol[0] 1261 model2 = cdp.structure.structural_data[1].mol[0] 1262 for i in range(len(model1.atom_name)): 1263 self.assertAlmostEqual(model1.x[i], model2.x[i], 2) 1264 self.assertAlmostEqual(model1.y[i], model2.y[i], 2) 1265 self.assertAlmostEqual(model1.z[i], model2.z[i], 2)

1266 1267

1268 - def test_superimpose_fit_to_mean2(self):

1269 """Second test of the structure.superimpose user function, fitting to the mean structure.""" 1270 1271 # Path of the structure file. 1272 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam' 1273 1274 # Load the two rotated structures. 1275 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=1, set_mol_name='CaM') 1276 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=2, set_mol_name='CaM') 1277 self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path, set_model_num=3, set_mol_name='CaM') 1278 1279 # Transpose model 3. 1280 self.interpreter.structure.translate([20.0, 0.0, 0.0], model=3) 1281 1282 # Superimpose the backbone heavy atoms. 1283 self.interpreter.structure.superimpose(models=[2, 3], method='fit to mean', atom_id='@N,C,CA,O') 1284 1285 # Check that the two structures now have the same atomic coordinates as the original, but shifted 10 Angstrom in x. 1286 model1 = cdp.structure.structural_data[0].mol[0] 1287 model2 = cdp.structure.structural_data[1].mol[0] 1288 model3 = cdp.structure.structural_data[2].mol[0] 1289 for i in range(len(model1.atom_name)): 1290 # Check model 2. 1291 self.assertAlmostEqual(model1.x[i] + 10, model2.x[i], 2) 1292 self.assertAlmostEqual(model1.y[i], model2.y[i], 2) 1293 self.assertAlmostEqual(model1.z[i], model2.z[i], 2) 1294 1295 # Check model 3. 1296 self.assertAlmostEqual(model2.x[i], model3.x[i], 2) 1297 self.assertAlmostEqual(model2.y[i], model3.y[i], 2) 1298 self.assertAlmostEqual(model2.z[i], model3.z[i], 2)

1299 1300

1301 - def test_web_of_motion_12(self):

1302 """Check the operation of the structure.web_of_motion user function using structural models 1 and 2 (of 3).""" 1303 1304 # Load the file. 1305 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 1306 self.interpreter.structure.read_pdb('web_of_motion.pdb', dir=path) 1307 1308 # Run the structure.web_of_motion user function and collect the results in a dummy file object. 1309 file = DummyFileObject() 1310 self.interpreter.structure.web_of_motion(file=file, models=[1, 2]) 1311 1312 # The result. 1313 result = [ 1314 "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011. ", 1315 "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM). ", 1316 "ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00 0.00 N ", 1317 "ATOM 2 N LEU A 4 9.211 -9.425 26.970 1.00 0.00 N ", 1318 "ATOM 3 H LEU A 4 8.575 -8.953 27.963 1.00 0.00 H ", 1319 "ATOM 4 H LEU A 4 9.085 -9.743 27.919 1.00 0.00 H ", 1320 "ATOM 5 CA LEU A 4 10.302 -8.195 26.930 1.00 0.00 C ", 1321 "ATOM 6 CA LEU A 4 10.077 -8.221 26.720 1.00 0.00 C ", 1322 "ATOM 7 CB LEU A 4 9.494 -7.221 26.051 1.00 0.00 C ", 1323 "ATOM 8 CB LEU A 4 9.297 -7.096 26.024 1.00 0.00 C ", 1324 "ATOM 9 CG LEU A 4 10.107 -5.862 25.665 1.00 0.00 C ", 1325 "ATOM 10 CG LEU A 4 10.061 -5.803 25.679 1.00 0.00 C ", 1326 "ATOM 11 CD1 LEU A 4 11.182 -6.007 24.608 1.00 0.00 C ", 1327 "ATOM 12 CD1 LEU A 4 11.029 -6.002 24.507 1.00 0.00 C ", 1328 "ATOM 13 CD2 LEU A 4 9.036 -4.875 25.171 1.00 0.00 C ", 1329 "ATOM 14 CD2 LEU A 4 9.120 -4.618 25.384 1.00 0.00 C ", 1330 "ATOM 15 C LEU A 4 10.999 -7.436 28.046 1.00 0.00 C ", 1331 "ATOM 16 C LEU A 4 10.625 -7.721 28.047 1.00 0.00 C ", 1332 "TER 17 LEU A 4 ", 1333 "CONECT 1 2 ", 1334 "CONECT 2 1 ", 1335 "CONECT 3 4 ", 1336 "CONECT 4 3 ", 1337 "CONECT 5 6 ", 1338 "CONECT 6 5 ", 1339 "CONECT 7 8 ", 1340 "CONECT 8 7 ", 1341 "CONECT 9 10 ", 1342 "CONECT 10 9 ", 1343 "CONECT 11 12 ", 1344 "CONECT 12 11 ", 1345 "CONECT 13 14 ", 1346 "CONECT 14 13 ", 1347 "CONECT 15 16 ", 1348 "CONECT 16 15 ", 1349 "MASTER 0 0 0 0 0 0 0 0 16 1 16 0 ", 1350 "END " 1351 ] 1352 1353 # Check the created PDB file. 1354 lines = file.readlines() 1355 for i in range(len(lines)): 1356 self.assertEqual(result[i]+'\n', lines[i])

1357 1358

1359 - def test_web_of_motion_13(self):

1360 """Check the operation of the structure.web_of_motion user function using structural models 1 and 3 (of 3).""" 1361 1362 # Load the file. 1363 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 1364 self.interpreter.structure.read_pdb('web_of_motion.pdb', dir=path) 1365 1366 # Run the structure.web_of_motion user function and collect the results in a dummy file object. 1367 file = DummyFileObject() 1368 self.interpreter.structure.web_of_motion(file=file, models=[1, 3]) 1369 1370 # The result. 1371 result = [ 1372 "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011. ", 1373 "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM). ", 1374 "ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00 0.00 N ", 1375 "ATOM 2 N LEU A 4 7.761 -6.392 27.161 1.00 0.00 N ", 1376 "ATOM 3 H LEU A 4 8.575 -8.953 27.963 1.00 0.00 H ", 1377 "ATOM 4 H LEU A 4 7.278 -6.195 28.026 1.00 0.00 H ", 1378 "ATOM 5 CA LEU A 4 10.302 -8.195 26.930 1.00 0.00 C ", 1379 "ATOM 6 CA LEU A 4 9.256 -6.332 27.183 1.00 0.00 C ", 1380 "ATOM 7 CB LEU A 4 9.494 -7.221 26.051 1.00 0.00 C ", 1381 "ATOM 8 CB LEU A 4 9.799 -5.331 26.144 1.00 0.00 C ", 1382 "ATOM 9 CG LEU A 4 10.107 -5.862 25.665 1.00 0.00 C ", 1383 "ATOM 10 CG LEU A 4 10.293 -5.882 24.803 1.00 0.00 C ", 1384 "ATOM 11 CD1 LEU A 4 11.182 -6.007 24.608 1.00 0.00 C ", 1385 "ATOM 12 CD1 LEU A 4 9.404 -6.984 24.274 1.00 0.00 C ", 1386 "ATOM 13 CD2 LEU A 4 9.036 -4.875 25.171 1.00 0.00 C ", 1387 "ATOM 14 CD2 LEU A 4 10.355 -4.772 23.792 1.00 0.00 C ", 1388 "ATOM 15 C LEU A 4 10.999 -7.436 28.046 1.00 0.00 C ", 1389 "ATOM 16 C LEU A 4 9.816 -6.033 28.572 1.00 0.00 C ", 1390 "TER 17 LEU A 4 ", 1391 "CONECT 1 2 ", 1392 "CONECT 2 1 ", 1393 "CONECT 3 4 ", 1394 "CONECT 4 3 ", 1395 "CONECT 5 6 ", 1396 "CONECT 6 5 ", 1397 "CONECT 7 8 ", 1398 "CONECT 8 7 ", 1399 "CONECT 9 10 ", 1400 "CONECT 10 9 ", 1401 "CONECT 11 12 ", 1402 "CONECT 12 11 ", 1403 "CONECT 13 14 ", 1404 "CONECT 14 13 ", 1405 "CONECT 15 16 ", 1406 "CONECT 16 15 ", 1407 "MASTER 0 0 0 0 0 0 0 0 16 1 16 0 ", 1408 "END " 1409 ] 1410 1411 # Check the created PDB file. 1412 lines = file.readlines() 1413 for i in range(len(lines)): 1414 self.assertEqual(result[i]+'\n', lines[i])

1415 1416

1417 - def test_web_of_motion_all(self):

1418 """Check the operation of the structure.web_of_motion user function using all structural models.""" 1419 1420 # Load the file. 1421 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' 1422 self.interpreter.structure.read_pdb('web_of_motion.pdb', dir=path) 1423 1424 # Run the structure.web_of_motion user function and collect the results in a dummy file object. 1425 file = DummyFileObject() 1426 self.interpreter.structure.web_of_motion(file=file) 1427 1428 # The result. 1429 result = [ 1430 "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011. ", 1431 "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM). ", 1432 "ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00 0.00 N ", 1433 "ATOM 2 N LEU A 4 9.211 -9.425 26.970 1.00 0.00 N ", 1434 "ATOM 3 N LEU A 4 7.761 -6.392 27.161 1.00 0.00 N ", 1435 "ATOM 4 H LEU A 4 8.575 -8.953 27.963 1.00 0.00 H ", 1436 "ATOM 5 H LEU A 4 9.085 -9.743 27.919 1.00 0.00 H ", 1437 "ATOM 6 H LEU A 4 7.278 -6.195 28.026 1.00 0.00 H ", 1438 "ATOM 7 CA LEU A 4 10.302 -8.195 26.930 1.00 0.00 C ", 1439 "ATOM 8 CA LEU A 4 10.077 -8.221 26.720 1.00 0.00 C ", 1440 "ATOM 9 CA LEU A 4 9.256 -6.332 27.183 1.00 0.00 C ", 1441 "ATOM 10 CB LEU A 4 9.494 -7.221 26.051 1.00 0.00 C ", 1442 "ATOM 11 CB LEU A 4 9.297 -7.096 26.024 1.00 0.00 C ", 1443 "ATOM 12 CB LEU A 4 9.799 -5.331 26.144 1.00 0.00 C ", 1444 "ATOM 13 CG LEU A 4 10.107 -5.862 25.665 1.00 0.00 C ", 1445 "ATOM 14 CG LEU A 4 10.061 -5.803 25.679 1.00 0.00 C ", 1446 "ATOM 15 CG LEU A 4 10.293 -5.882 24.803 1.00 0.00 C ", 1447 "ATOM 16 CD1 LEU A 4 11.182 -6.007 24.608 1.00 0.00 C ", 1448 "ATOM 17 CD1 LEU A 4 11.029 -6.002 24.507 1.00 0.00 C ", 1449 "ATOM 18 CD1 LEU A 4 9.404 -6.984 24.274 1.00 0.00 C ", 1450 "ATOM 19 CD2 LEU A 4 9.036 -4.875 25.171 1.00 0.00 C ", 1451 "ATOM 20 CD2 LEU A 4 9.120 -4.618 25.384 1.00 0.00 C ", 1452 "ATOM 21 CD2 LEU A 4 10.355 -4.772 23.792 1.00 0.00 C ", 1453 "ATOM 22 C LEU A 4 10.999 -7.436 28.046 1.00 0.00 C ", 1454 "ATOM 23 C LEU A 4 10.625 -7.721 28.047 1.00 0.00 C ", 1455 "ATOM 24 C LEU A 4 9.816 -6.033 28.572 1.00 0.00 C ", 1456 "TER 25 LEU A 4 ", 1457 "CONECT 1 2 3 ", 1458 "CONECT 2 1 3 ", 1459 "CONECT 3 1 2 ", 1460 "CONECT 4 5 6 ", 1461 "CONECT 5 4 6 ", 1462 "CONECT 6 4 5 ", 1463 "CONECT 7 8 9 ", 1464 "CONECT 8 7 9 ", 1465 "CONECT 9 7 8 ", 1466 "CONECT 10 11 12 ", 1467 "CONECT 11 10 12 ", 1468 "CONECT 12 10 11 ", 1469 "CONECT 13 14 15 ", 1470 "CONECT 14 13 15 ", 1471 "CONECT 15 13 14 ", 1472 "CONECT 16 17 18 ", 1473 "CONECT 17 16 18 ", 1474 "CONECT 18 16 17 ", 1475 "CONECT 19 20 21 ", 1476 "CONECT 20 19 21 ", 1477 "CONECT 21 19 20 ", 1478 "CONECT 22 23 24 ", 1479 "CONECT 23 22 24 ", 1480 "CONECT 24 22 23 ", 1481 "MASTER 0 0 0 0 0 0 0 0 24 1 24 0 ", 1482 "END " 1483 ] 1484 1485 # Check the created PDB file. 1486 lines = file.readlines() 1487 for i in range(len(lines)): 1488 self.assertEqual(result[i]+'\n', lines[i])

Source Code for Module test_suite.system_tests.structure