test_suite.system_tests.peak

36 """TestCase class for the functional tests for the support of different peak intensity files.""" 37

38 - def __init__(self, methodName='runTest'):

39 """Skip the tests if the C modules are non-functional. 40 41 @keyword methodName: The name of the test. 42 @type methodName: str 43 """ 44 45 # Execute the base class method. 46 super(Peak_lists, self).__init__(methodName) 47 48 # Missing module. 49 if not dep_check.C_module_exp_fn and methodName in ['test_bug_17276_peak_lists', 'test_bug_20873_peak_lists', 'test_ccpn_analysis']: 50 # Store in the status object. 51 status.skipped_tests.append([methodName, 'Relax curve-fitting C module', self._skip_type])

52 53

54 - def setUp(self):

55 """Set up for all the functional tests.""" 56 57 # Create a data pipe. 58 self.interpreter.pipe.create('mf', 'mf')

59 60

61 - def test_bug_17276_peak_lists(self):

62 """Test catching U{bug #17276<https://web.archive.org/web/https://gna.org/bugs/?17276>}, the duplicated peak list reading failure submitted by Leanne Minall.""" 63 64 # Execute the script. 65 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bug_17276_peak_lists.py')

66 67

68 - def test_bug_20873_peak_lists(self):

69 """Test catching U{bug #20873<https://web.archive.org/web/https://gna.org/bugs/?20873>}, the custom peak intensity reading with a list of spectrum_ids submitted by Troels E. Linnet.""" 70 71 # The path to the files. 72 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists' 73 74 # First create a data pipe. 75 self.interpreter.pipe.create(pipe_name='origin rx', pipe_type='relax_fit', bundle='rx') 76 77 # Load the spin systems. 78 self.interpreter.sequence.read(file='test.seq', dir=path, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None) 79 80 # Load the intensities. 81 self.interpreter.spectrum.read_intensities(file='test.seq', dir=path, spectrum_id=['2', '0'], dim=1, int_method='height', int_col=[6, 7], spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None) 82 83 # The peak intensities. 84 data_2 = [337765.90000000002, 1697771.0, 867389.80000000005, 2339480.0, 2574062.0, 1609356.0, 2179341.0, 1563795.0, 1535896.0, 3578841.0] 85 data_0 = [636244.59999999998, 3015788.0, 1726064.0, 4039142.0, 4313824.0, 2927111.0, 4067343.0, 2921316.0, 3005234.0, 6352595.0] 86 87 # Data checks. 88 for i in range(len(cdp.mol[0].res)): 89 # Alias the spin. 90 spin = cdp.mol[0].res[i].spin[0] 91 92 # The intensities. 93 self.assertEqual(spin.peak_intensity['0'], data_0[i]) 94 self.assertEqual(spin.peak_intensity['2'], data_2[i])

95 96

97 - def test_ccpn_analysis(self):

98 """Test U{bug #17341<https://web.archive.org/web/https://gna.org/bugs/index.php?17341>}, the CCPN Analysis 2.1 peak list reading submitted by Madeleine Strickland.""" 99 100 # Execute the script. 101 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'peak_lists'+sep+'ccpn_analysis.py') 102 103 # Spectrum names. 104 names = ['T1A_0010', 'T1A_0020', 'T1A_0030', 'T1A_0050', 'T1A_0070', 'T1A_0100', 'T1A_0150', 'T1A_0200', 'T1A_0300', 'T1A_0400', 'T1A_0600', 'T1A_0800', 'T1A_1000', 'T1A_1200'] 105 106 # Relaxation times (in seconds). 107 times = [0.01, 0.02, 0.03, 0.05, 0.07, 0.1, 0.15, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 1.2] 108 109 # Check the spectrum IDs and relaxation times. 110 for i in range(len(times)): 111 self.assertEqual(cdp.spectrum_ids[i], names[i]) 112 self.assertEqual(cdp.relax_times[names[i]], times[i]) 113 114 # The peak heights. 115 heights = [ 116 [1.41e06, 1.33e06, 1.31e06, 1.31e06, 1.28e06, 1.20e06, 1.18e06, 1.07e06, 9.70e05, 8.47e05, 7.00e05, 5.25e05, 4.23e05, 3.10e05], 117 [1.79e06, 1.76e06, 1.71e06, 1.70e06, 1.66e06, 1.56e06, 1.51e06, 1.41e06, 1.24e06, 1.11e06, 8.43e05, 6.79e05, 5.04e05, 4.18e05] 118 ] 119 120 # Check the heights. 121 for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 122 # The data. 123 if res_num == 1501: 124 index = 0 125 elif res_num == 1504: 126 index = 1 127 128 # No data. 129 else: 130 # There should be no intensity data. 131 self.assert_(not hasattr(spin, 'peak_intensity')) 132 133 # Do not perform the height checks. 134 continue 135 136 # Check the data. 137 self.assert_(hasattr(spin, 'peak_intensity')) 138 139 # Check the values. 140 for i in range(len(times)): 141 self.assertEqual(spin.peak_intensity[names[i]], heights[index][i])

142 143

144 - def test_read_spins_peak_list_generic(self):

145 """Test the reading of spins from a generic peak intensity list.""" 146 147 # Read the peak spins. 148 self.interpreter.spectrum.read_spins(file="generic_intensity.txt", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', res_num_col=1, res_name_col=2) 149 150 # Test some of the sequence. 151 self.assertEqual(len(cdp.mol), 1) 152 self.assertEqual(cdp.mol[0].name, None) 153 self.assertEqual(len(cdp.mol[0].res), 5) 154 155 # 1st residue. 156 self.assertEqual(cdp.mol[0].res[0].num, 20) 157 self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 158 self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 159 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 160 self.assertEqual(cdp.mol[0].res[0].spin[0].name, None) 161 162 # 2nd residue. 163 self.assertEqual(cdp.mol[0].res[1].num, 23) 164 self.assertEqual(cdp.mol[0].res[1].name, 'ALA') 165 self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 166 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 167 self.assertEqual(cdp.mol[0].res[1].spin[0].name, None) 168 169 # 3rd residue. 170 self.assertEqual(cdp.mol[0].res[2].num, 34) 171 self.assertEqual(cdp.mol[0].res[2].name, 'CYS') 172 self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 173 self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 174 self.assertEqual(cdp.mol[0].res[2].spin[0].name, None) 175 176 # 4th residue. 177 self.assertEqual(cdp.mol[0].res[3].num, 35) 178 self.assertEqual(cdp.mol[0].res[3].name, 'MET') 179 self.assertEqual(len(cdp.mol[0].res[3].spin), 1) 180 self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) 181 self.assertEqual(cdp.mol[0].res[3].spin[0].name, None) 182 183 # 5th residue. 184 self.assertEqual(cdp.mol[0].res[4].num, 36) 185 self.assertEqual(cdp.mol[0].res[4].name, 'LYS') 186 self.assertEqual(len(cdp.mol[0].res[4].spin), 1) 187 self.assertEqual(cdp.mol[0].res[4].spin[0].num, None) 188 self.assertEqual(cdp.mol[0].res[4].spin[0].name, None)

189 190

191 - def test_read_spins_peak_list_generic_with_spin_name(self):

192 """Test the reading of spins with spin name in columns from a generic peak intensity list.""" 193 194 # Read the peak spins. 195 self.interpreter.spectrum.read_spins(file='test.seq', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5) 196 197 # Test some of the sequence. 198 self.assertEqual(len(cdp.mol), 1) 199 self.assertEqual(cdp.mol[0].name, 'protein') 200 self.assertEqual(len(cdp.mol[0].res), 10) 201 202 # 1st residue. 203 self.assertEqual(cdp.mol[0].res[0].num, 10) 204 self.assertEqual(cdp.mol[0].res[0].name, 'L') 205 self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 206 self.assertEqual(cdp.mol[0].res[0].spin[0].num, 10) 207 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 208 209 # 2nd residue. 210 self.assertEqual(cdp.mol[0].res[1].num, 6) 211 self.assertEqual(cdp.mol[0].res[1].name, 'V') 212 self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 213 self.assertEqual(cdp.mol[0].res[1].spin[0].num, 6) 214 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N')

215 216

217 - def test_read_spins_peak_list_nmrview(self):

218 """Test the reading of an NMRView peak list.""" 219 220 # Read the peak list. 221 self.interpreter.spectrum.read_spins(file="cNTnC.xpk", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) 222 self.interpreter.spectrum.read_spins(file="cNTnC.xpk", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) 223 224 # Test some of the sequence. 225 self.assertEqual(len(cdp.mol), 1) 226 self.assertEqual(cdp.mol[0].name, None) 227 self.assertEqual(len(cdp.mol[0].res), 2) 228 229 # 1st residue. 230 self.assertEqual(cdp.mol[0].res[0].num, 70) 231 self.assertEqual(cdp.mol[0].res[0].name, None) 232 self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 233 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 234 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 235 self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) 236 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HN') 237 238 # 2nd residue. 239 self.assertEqual(cdp.mol[0].res[1].num, 72) 240 self.assertEqual(cdp.mol[0].res[1].name, None) 241 self.assertEqual(len(cdp.mol[0].res[1].spin), 2) 242 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 243 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 244 self.assertEqual(cdp.mol[0].res[1].spin[1].num, None) 245 self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'HN')

246 247

248 - def test_read_spins_peak_list_NMRPipe_seriesTab(self):

249 """Test the reading of an NMRPipe seriesTab peak list.""" 250 251 # Read the peak list. 252 self.interpreter.spectrum.read_spins(file="seriesTab.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) 253 self.interpreter.spectrum.read_spins(file="seriesTab.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) 254 255 # Test some of the sequence. 256 self.assertEqual(len(cdp.mol), 1) 257 self.assertEqual(cdp.mol[0].name, None) 258 self.assertEqual(len(cdp.mol[0].res), 3) 259 260 # 1st residue. 261 self.assertEqual(cdp.mol[0].res[0].num, 62) 262 self.assertEqual(cdp.mol[0].res[0].name, 'W') 263 self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 264 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 265 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'NE1') 266 self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) 267 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HE1') 268 269 # 2nd residue. 270 self.assertEqual(cdp.mol[0].res[1].num, 10) 271 self.assertEqual(cdp.mol[0].res[1].name, 'L') 272 self.assertEqual(len(cdp.mol[0].res[1].spin), 2) 273 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 274 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 275 self.assertEqual(cdp.mol[0].res[1].spin[1].num, None) 276 self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'HN') 277 278 # 3rd residue. 279 self.assertEqual(cdp.mol[0].res[2].num, 6) 280 self.assertEqual(cdp.mol[0].res[2].name, 'V') 281 self.assertEqual(len(cdp.mol[0].res[2].spin), 2) 282 self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 283 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 284 self.assertEqual(cdp.mol[0].res[2].spin[1].num, None) 285 self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'HN')

286 287

288 - def test_read_spins_peak_list_NMRPipe_seriesTab_multi(self):

289 """Test the reading of an NMRPipe seriesTab peak list.""" 290 291 # Read the peak list. 292 self.interpreter.spectrum.read_spins(file="seriesTab_multi.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) 293 self.interpreter.spectrum.read_spins(file="seriesTab_multi.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) 294 295 # Test some of the sequence. 296 self.assertEqual(len(cdp.mol), 1) 297 self.assertEqual(cdp.mol[0].name, None) 298 self.assertEqual(len(cdp.mol[0].res), 5) 299 300 # 1st residue. 301 self.assertEqual(cdp.mol[0].res[0].num, 2) 302 self.assertEqual(cdp.mol[0].res[0].name, 'T') 303 self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 304 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 305 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 306 self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) 307 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HN') 308 309 # 2nd residue. 310 self.assertEqual(cdp.mol[0].res[1].num, 3) 311 self.assertEqual(cdp.mol[0].res[1].name, 'K') 312 self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 313 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 314 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 315 316 # 3rd residue. 317 self.assertEqual(cdp.mol[0].res[2].num, 4) 318 self.assertEqual(cdp.mol[0].res[2].name, 'A') 319 self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 320 self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 321 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 322 323 # 4th residue. 324 self.assertEqual(cdp.mol[0].res[3].num, 5) 325 self.assertEqual(cdp.mol[0].res[3].name, 'V') 326 self.assertEqual(len(cdp.mol[0].res[3].spin), 1) 327 self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) 328 self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N')

329 330

331 - def test_read_spins_peak_list_NMRPipe_seriesTab_multi_no_2dim(self):

332 """Test the reading of an NMRPipe seriesTab peak list, with no assignment for second dimension.""" 333 334 # Read the peak list. 335 self.interpreter.spectrum.read_spins(file="folded_sparky_corr_final_max_standard_trunc.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+'acbp_cpmg_disp_101MGuHCl_40C_041223', dim=1) 336 self.interpreter.spectrum.read_spins(file="folded_sparky_corr_final_max_standard_trunc.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+'acbp_cpmg_disp_101MGuHCl_40C_041223', dim=2) 337 338 # Test some of the sequence. 339 self.assertEqual(len(cdp.mol), 1) 340 self.assertEqual(cdp.mol[0].name, None) 341 self.assertEqual(len(cdp.mol[0].res), 1) 342 343 # 1st residue. 344 self.assertEqual(cdp.mol[0].res[0].num, 61) 345 self.assertEqual(cdp.mol[0].res[0].name, 'L') 346 self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 347 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 348 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 349 self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) 350 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HN')

351 352

353 - def test_read_spins_peak_list_sparky(self):

354 """Test the reading of spins from a Sparky peak list.""" 355 356 # Read the spins from peak list. 357 self.interpreter.spectrum.read_spins(file="ref_ave.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) 358 self.interpreter.spectrum.read_spins(file="ref_ave.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) 359 360 # Test some of the sequence. 361 self.assertEqual(len(cdp.mol), 1) 362 self.assertEqual(cdp.mol[0].name, None) 363 self.assertEqual(len(cdp.mol[0].res), 6) 364 365 # 1st residue. 366 self.assertEqual(cdp.mol[0].res[0].num, 3) 367 self.assertEqual(cdp.mol[0].res[0].name, 'LEU') 368 self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 369 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 370 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 371 self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) 372 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HN') 373 374 # 2nd residue. 375 self.assertEqual(cdp.mol[0].res[1].num, 4) 376 self.assertEqual(cdp.mol[0].res[1].name, 'GLY') 377 self.assertEqual(len(cdp.mol[0].res[1].spin), 2) 378 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 379 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 380 381 # 3rd residue. 382 self.assertEqual(cdp.mol[0].res[2].num, 5) 383 self.assertEqual(cdp.mol[0].res[2].name, 'SER') 384 self.assertEqual(len(cdp.mol[0].res[2].spin), 2) 385 self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 386 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 387 388 # 4th residue. 389 self.assertEqual(cdp.mol[0].res[3].num, 6) 390 self.assertEqual(cdp.mol[0].res[3].name, 'MET') 391 self.assertEqual(len(cdp.mol[0].res[3].spin), 2) 392 self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) 393 self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') 394 395 # 5th residue. 396 self.assertEqual(cdp.mol[0].res[4].num, 40) 397 self.assertEqual(cdp.mol[0].res[4].name, 'TRP') 398 self.assertEqual(len(cdp.mol[0].res[4].spin), 4) 399 self.assertEqual(cdp.mol[0].res[4].spin[0].num, None) 400 self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N') 401 self.assertEqual(cdp.mol[0].res[4].spin[1].num, None) 402 self.assertEqual(cdp.mol[0].res[4].spin[1].name, 'NE1') 403 404 # 6th residue. 405 self.assertEqual(cdp.mol[0].res[5].num, 55) 406 self.assertEqual(cdp.mol[0].res[5].name, 'ASN') 407 self.assertEqual(len(cdp.mol[0].res[5].spin), 2) 408 self.assertEqual(cdp.mol[0].res[5].spin[0].num, None) 409 self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N')

410 411

412 - def test_read_spins_peak_list_sparky_export_ccpnmr_analysis(self):

413 """Test the reading of spins from a Sparky peak list exported from CcpNmr Analysis.""" 414 415 # Read the spins from peak list. 416 self.interpreter.spectrum.read_spins(file="peak_list_ccpnmr_analysis.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') 417 418 # Test some of the sequence. 419 self.assertEqual(len(cdp.mol), 1) 420 self.assertEqual(cdp.mol[0].name, None) 421 self.assertEqual(len(cdp.mol[0].res), 3) 422 423 # 1st residue. 424 self.assertEqual(cdp.mol[0].res[0].num, 76) 425 self.assertEqual(cdp.mol[0].res[0].name, 'L') 426 self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 427 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 428 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 429 430 # 2nd residue. 431 self.assertEqual(cdp.mol[0].res[1].num, 74) 432 self.assertEqual(cdp.mol[0].res[1].name, 'T') 433 self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 434 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 435 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 436 437 # 3rd residue. 438 self.assertEqual(cdp.mol[0].res[2].num, 31) 439 self.assertEqual(cdp.mol[0].res[2].name, 'T') 440 self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 441 self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 442 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 443 444 # Read the peak list intensity. 445 self.interpreter.spectrum.read_intensities(file="peak_list_ccpnmr_analysis.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 446 447 # Test the data. 448 self.assertEqual(list(cdp.mol[0].res[0].spin[0].peak_intensity.values())[0], 2.32E+05) 449 self.assertEqual(list(cdp.mol[0].res[1].spin[0].peak_intensity.values())[0], 2.01E+05) 450 self.assertEqual(list(cdp.mol[0].res[2].spin[0].peak_intensity.values())[0], 2.08E+05)

451 452

453 - def test_read_spins_peak_list_sparky_with_2dim_ass(self):

454 """Test the reading of spins from a Sparky peak list with two dimensional assignment""" 455 456 # Read the spins from peak list. 457 self.interpreter.spectrum.read_spins(file="sparky2dim.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) 458 self.interpreter.spectrum.read_spins(file="sparky2dim.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) 459 460 # Test some of the sequence. 461 self.assertEqual(len(cdp.mol), 1) 462 self.assertEqual(cdp.mol[0].name, None) 463 self.assertEqual(len(cdp.mol[0].res), 7) 464 465 # 1st residue. 466 self.assertEqual(cdp.mol[0].res[0].num, 62) 467 self.assertEqual(cdp.mol[0].res[0].name, 'W') 468 self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 469 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 470 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'NE1') 471 self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) 472 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HE1') 473 474 # 2nd residue. 475 self.assertEqual(cdp.mol[0].res[1].num, 10) 476 self.assertEqual(cdp.mol[0].res[1].name, 'L') 477 self.assertEqual(len(cdp.mol[0].res[1].spin), 2) 478 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 479 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 480 self.assertEqual(cdp.mol[0].res[1].spin[1].num, None) 481 self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'HN') 482 483 # 3rd residue. 484 self.assertEqual(cdp.mol[0].res[2].num, 6) 485 self.assertEqual(cdp.mol[0].res[2].name, 'V') 486 self.assertEqual(len(cdp.mol[0].res[2].spin), 2) 487 self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 488 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 489 self.assertEqual(cdp.mol[0].res[2].spin[1].num, None) 490 self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'HN') 491 492 # 4th residue. 493 self.assertEqual(cdp.mol[0].res[3].num, 2) 494 self.assertEqual(cdp.mol[0].res[3].name, 'T') 495 self.assertEqual(len(cdp.mol[0].res[3].spin), 2) 496 self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) 497 self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') 498 self.assertEqual(cdp.mol[0].res[3].spin[1].num, None) 499 self.assertEqual(cdp.mol[0].res[3].spin[1].name, 'HN') 500 501 # 5th residue. 502 self.assertEqual(cdp.mol[0].res[4].num, 3) 503 self.assertEqual(cdp.mol[0].res[4].name, 'K') 504 self.assertEqual(len(cdp.mol[0].res[4].spin), 1) 505 self.assertEqual(cdp.mol[0].res[4].spin[0].num, None) 506 self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N') 507 508 # 6th residue. 509 self.assertEqual(cdp.mol[0].res[5].num, 4) 510 self.assertEqual(cdp.mol[0].res[5].name, 'A') 511 self.assertEqual(len(cdp.mol[0].res[5].spin), 1) 512 self.assertEqual(cdp.mol[0].res[5].spin[0].num, None) 513 self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') 514 515 # 7th residue. 516 self.assertEqual(cdp.mol[0].res[6].num, 5) 517 self.assertEqual(cdp.mol[0].res[6].name, 'V') 518 self.assertEqual(len(cdp.mol[0].res[6].spin), 1) 519 self.assertEqual(cdp.mol[0].res[6].spin[0].num, None) 520 self.assertEqual(cdp.mol[0].res[6].spin[0].name, 'N')

521 522

523 - def test_read_spins_peak_list_sparky_with_no_int_col(self):

524 """Test the reading of spins from a Sparky peak list with no intensity column.""" 525 526 # Read the spins from peak list. 527 self.interpreter.spectrum.read_spins(file="sparky_wo_int.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) 528 self.interpreter.spectrum.read_spins(file="sparky_wo_int.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) 529 530 # Test some of the sequence. 531 self.assertEqual(len(cdp.mol), 1) 532 self.assertEqual(cdp.mol[0].name, None) 533 self.assertEqual(len(cdp.mol[0].res), 7) 534 535 # 1st residue. 536 self.assertEqual(cdp.mol[0].res[0].num, 62) 537 self.assertEqual(cdp.mol[0].res[0].name, 'W') 538 self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 539 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 540 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'NE1') 541 self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) 542 self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HE1') 543 544 # 2nd residue. 545 self.assertEqual(cdp.mol[0].res[1].num, 10) 546 self.assertEqual(cdp.mol[0].res[1].name, 'L') 547 self.assertEqual(len(cdp.mol[0].res[1].spin), 2) 548 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 549 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 550 self.assertEqual(cdp.mol[0].res[1].spin[1].num, None) 551 self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'HN') 552 553 # 3rd residue. 554 self.assertEqual(cdp.mol[0].res[2].num, 6) 555 self.assertEqual(cdp.mol[0].res[2].name, 'V') 556 self.assertEqual(len(cdp.mol[0].res[2].spin), 2) 557 self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 558 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 559 self.assertEqual(cdp.mol[0].res[2].spin[1].num, None) 560 self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'HN') 561 562 # 4th residue. 563 self.assertEqual(cdp.mol[0].res[3].num, 2) 564 self.assertEqual(cdp.mol[0].res[3].name, 'T') 565 self.assertEqual(len(cdp.mol[0].res[3].spin), 2) 566 self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) 567 self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') 568 self.assertEqual(cdp.mol[0].res[3].spin[1].num, None) 569 self.assertEqual(cdp.mol[0].res[3].spin[1].name, 'HN') 570 571 # 5th residue. 572 self.assertEqual(cdp.mol[0].res[4].num, 3) 573 self.assertEqual(cdp.mol[0].res[4].name, 'K') 574 self.assertEqual(len(cdp.mol[0].res[4].spin), 1) 575 self.assertEqual(cdp.mol[0].res[4].spin[0].num, None) 576 self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N') 577 578 # 6th residue. 579 self.assertEqual(cdp.mol[0].res[5].num, 4) 580 self.assertEqual(cdp.mol[0].res[5].name, 'A') 581 self.assertEqual(len(cdp.mol[0].res[5].spin), 1) 582 self.assertEqual(cdp.mol[0].res[5].spin[0].num, None) 583 self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') 584 585 # 7th residue. 586 self.assertEqual(cdp.mol[0].res[6].num, 5) 587 self.assertEqual(cdp.mol[0].res[6].name, 'V') 588 self.assertEqual(len(cdp.mol[0].res[6].spin), 1) 589 self.assertEqual(cdp.mol[0].res[6].spin[0].num, None) 590 self.assertEqual(cdp.mol[0].res[6].spin[0].name, 'N')

591 592

593 - def test_read_spins_peak_list_xeasy(self):

594 """Test the reading of spins from an XEasy peak list.""" 595 596 # Read the peak list. 597 self.interpreter.spectrum.read_spins(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') 598 599 # Test some of the sequence. 600 self.assertEqual(len(cdp.mol), 1) 601 self.assertEqual(cdp.mol[0].name, None) 602 self.assertEqual(len(cdp.mol[0].res), 21) 603 604 # 1st residue. 605 self.assertEqual(cdp.mol[0].res[0].num, 21) 606 self.assertEqual(cdp.mol[0].res[0].name, 'LEU') 607 self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 608 self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 609 self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 610 611 # 2nd residue. 612 self.assertEqual(cdp.mol[0].res[1].num, 79) 613 self.assertEqual(cdp.mol[0].res[1].name, 'TRP') 614 self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 615 self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) 616 self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'NE1') 617 618 # 3rd residue. 619 self.assertEqual(cdp.mol[0].res[2].num, 110) 620 self.assertEqual(cdp.mol[0].res[2].name, 'PHE') 621 self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 622 self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 623 self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 624 625 # 10th residue. 626 self.assertEqual(cdp.mol[0].res[9].num, 107) 627 self.assertEqual(cdp.mol[0].res[9].name, 'TRP') 628 self.assertEqual(len(cdp.mol[0].res[9].spin), 2) 629 self.assertEqual(cdp.mol[0].res[9].spin[0].num, None) 630 self.assertEqual(cdp.mol[0].res[9].spin[0].name, 'N') 631 self.assertEqual(cdp.mol[0].res[9].spin[1].num, None) 632 self.assertEqual(cdp.mol[0].res[9].spin[1].name, 'C')

633 634

635 - def test_read_peak_list_generic(self):

636 """Test the reading of a generic peak intensity list.""" 637 638 # Create the sequence data, and name the spins. 639 self.interpreter.residue.create(20, 'GLY') 640 self.interpreter.residue.create(23, 'ALA') 641 self.interpreter.residue.create(34, 'CYS') 642 self.interpreter.residue.create(35, 'MET') 643 self.interpreter.residue.create(36, 'LYS') 644 self.interpreter.spin.name(name='N') 645 646 # Relaxation delays. 647 delays = [0.0109016, 648 0.0218032, 649 0.0436064, 650 0.0436064, 651 0.0872128, 652 0.1744260, 653 0.3488510, 654 0.6977020, 655 1.3954000, 656 1.9949900] 657 658 # Load the data. 659 for i in range(10): 660 # Read the peak intensities. 661 self.interpreter.spectrum.read_intensities(file="generic_intensity.txt", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id=repr(i), int_method='height', int_col=i+3, res_num_col=1, res_name_col=2) 662 663 # Set the relaxation times. 664 self.interpreter.relax_fit.relax_time(time=delays[i], spectrum_id=repr(i)) 665 666 # The actual intensities. 667 heights = [[1.0000, 0.9714, 0.9602, 0.9626, 0.8839, 0.8327, 0.7088, 0.5098, 0.2410, 0.1116], 668 [1.0000, 0.9789, 0.9751, 0.9762, 0.9074, 0.8532, 0.7089, 0.5170, 0.2444, 0.1537], 669 [1.0000, 0.9659, 0.9580, 0.9559, 0.9325, 0.8460, 0.7187, 0.5303, 0.2954, 0.1683], 670 [1.0000, 0.9657, 0.9389, 0.9366, 0.9331, 0.8683, 0.7169, 0.5357, 0.2769, 0.1625], 671 [1.0000, 1.0060, 0.9556, 0.9456, 0.9077, 0.8411, 0.6788, 0.4558, 0.2448, 0.1569] 672 ] 673 674 # Test the data. 675 for i in range(10): 676 for j in range(5): 677 self.assertEqual(cdp.mol[0].res[j].spin[0].peak_intensity[repr(i)], heights[j][i])

678 679

680 - def test_read_peak_list_nmrview(self):

681 """Test the reading of an NMRView peak list.""" 682 683 # Create the sequence data, and name the spins. 684 self.interpreter.residue.create(70) 685 self.interpreter.residue.create(72) 686 self.interpreter.spin.name(name='N') 687 688 # Read the peak list. 689 self.interpreter.spectrum.read_intensities(file="cNTnC.xpk", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 690 691 # Test the data. 692 self.assertEqual(list(cdp.mol[0].res[0].spin[0].peak_intensity.values())[0], -0.1694) 693 self.assertEqual(list(cdp.mol[0].res[1].spin[0].peak_intensity.values())[0], -0.1142)

694 695

696 - def test_read_peak_list_NMRPipe_seriesTab(self):

697 """Test the reading of an NMRPipe seriesTab peak list.""" 698 699 # Create the sequence data, and name the spins. 700 self.interpreter.residue.create(res_num = 62) 701 self.interpreter.spin.name(name='NE1', spin_id=':62') 702 self.interpreter.residue.create(res_num = 10) 703 self.interpreter.spin.name(name='N', spin_id=':10') 704 self.interpreter.residue.create(res_num = 6) 705 self.interpreter.spin.name(name='N', spin_id=':6') 706 707 # Read the peak list. 708 self.interpreter.spectrum.read_intensities(file="seriesTab.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='point sum') 709 710 # Test the data. 711 self.assertEqual(cdp.mol[0].res[0].spin[0].peak_intensity['test'], +1.851056e+06) 712 self.assertEqual(cdp.mol[0].res[1].spin[0].peak_intensity['test'], +3.224387e+05) 713 self.assertEqual(cdp.mol[0].res[2].spin[0].peak_intensity['test'], +1.479366e+06)

714 715

716 - def test_read_peak_list_NMRPipe_seriesTab_multi(self):

717 """Test the reading of an NMRPipe seriesTab peak list.""" 718 719 # Create the sequence data, and name the spins. 720 self.interpreter.residue.create(res_num = 2) 721 self.interpreter.spin.name(name='N', spin_id=':2') 722 self.interpreter.residue.create(res_num = 3) 723 self.interpreter.spin.name(name='N', spin_id=':3') 724 self.interpreter.residue.create(res_num = 4) 725 self.interpreter.spin.name(name='N', spin_id=':4') 726 self.interpreter.residue.create(res_num = 5) 727 self.interpreter.spin.name(name='N', spin_id=':5') 728 self.interpreter.residue.create(res_num = 6) 729 self.interpreter.spin.name(name='N', spin_id=':6') 730 731 # Read the peak list. 732 self.interpreter.spectrum.read_intensities(file="seriesTab_multi.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='auto', int_method='point sum') 733 734 # Test the data. 735 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A0'], 1179448.0) 736 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A0'], 4407306.0) 737 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A0'], 3480382.0) 738 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A0'], 4306408.0) 739 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A0'], 3454030.0) 740 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A1'], 1411799.256) 741 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A1'], 5263645.5558) 742 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A1'], 4159404.5282) 743 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A1'], 5147018.8416) 744 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A1'], 4132401.492) 745 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A2'], 1411209.532) 746 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A2'], 5262764.0946) 747 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A2'], 4159404.5282) 748 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A2'], 5147018.8416) 749 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A2'], 4133092.298) 750 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A3'], 1408496.8016) 751 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A3'], 5264527.017) 752 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A3'], 4162536.872) 753 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A3'], 5146588.2008) 754 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A3'], 4134128.507) 755 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A4'], 1411327.4768) 756 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A4'], 5258797.5192) 757 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A4'], 4163232.9484) 758 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A4'], 5162952.5512) 759 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A4'], 4119966.984) 760 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A5'], 1414040.2072) 761 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A5'], 5275104.5514) 762 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A5'], 4150703.5732) 763 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A5'], 5151755.8904) 764 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A5'], 4128947.462) 765 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A6'], 1406727.6296) 766 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A6'], 5265849.2088) 767 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A6'], 4158360.4136) 768 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A6'], 5149172.0456) 769 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A6'], 4130674.477) 770 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A7'], 1415691.4344) 771 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A7'], 5267171.4006) 772 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A7'], 4144438.8856) 773 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A7'], 5137114.1032) 774 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A7'], 4127911.253) 775 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A8'], 1401184.224) 776 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A8'], 5264527.017) 777 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A8'], 4149659.4586) 778 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A8'], 5144004.356) 779 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A8'], 4133783.104) 780 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].peak_intensity['Z_A9'], 1415573.4896) 781 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].peak_intensity['Z_A9'], 5261882.6334) 782 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].peak_intensity['Z_A9'], 4138870.2744) 783 self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].peak_intensity['Z_A9'], 5123764.2384) 784 self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].peak_intensity['Z_A9'], 4128602.059)

785 786

787 - def test_read_peak_list_sparky(self):

788 """Test the reading of an Sparky peak list.""" 789 790 # Create the sequence data, and name the spins. 791 self.interpreter.residue.create(3) 792 self.interpreter.residue.create(4) 793 self.interpreter.residue.create(5) 794 self.interpreter.residue.create(6) 795 self.interpreter.spin.name(name='N') 796 797 # Read the peak list. 798 self.interpreter.spectrum.read_intensities(file="ref_ave.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 799 800 # Test the data. 801 self.assertEqual(list(cdp.mol[0].res[0].spin[0].peak_intensity.values())[0], 6262) 802 self.assertEqual(list(cdp.mol[0].res[1].spin[0].peak_intensity.values())[0], 148614) 803 self.assertEqual(list(cdp.mol[0].res[2].spin[0].peak_intensity.values())[0], 166842) 804 self.assertEqual(list(cdp.mol[0].res[3].spin[0].peak_intensity.values())[0], 128690)

805 806

807 - def test_read_peak_list_sparky_double(self):

808 """Test the reading of two Sparky peak lists simultaneously.""" 809 810 # Create the sequence data, and name the spins. 811 self.interpreter.residue.create(3) 812 self.interpreter.residue.create(4) 813 self.interpreter.residue.create(5) 814 self.interpreter.residue.create(6) 815 self.interpreter.spin.name(name='N') 816 817 # Read the peak list. 818 self.interpreter.spectrum.read_intensities(file=["ref_ave.list", "sat_ave.list"], dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id=['ref', 'sat'], int_method='height') 819 820 # Test the data. 821 self.assertEqual(cdp.mol[0].res[0].spin[0].peak_intensity['ref'], 6262) 822 self.assertEqual(cdp.mol[0].res[0].spin[0].peak_intensity['sat'], 2535.0) 823 self.assertEqual(cdp.mol[0].res[1].spin[0].peak_intensity['ref'], 148614) 824 self.assertEqual(cdp.mol[0].res[1].spin[0].peak_intensity['sat'], 5050.0) 825 self.assertEqual(cdp.mol[0].res[2].spin[0].peak_intensity['ref'], 166842) 826 self.assertEqual(cdp.mol[0].res[2].spin[0].peak_intensity['sat'], 51643.0) 827 self.assertEqual(cdp.mol[0].res[3].spin[0].peak_intensity['ref'], 128690) 828 self.assertEqual(cdp.mol[0].res[3].spin[0].peak_intensity['sat'], 53663.0)

829 830

831 - def test_read_peak_list_xeasy(self):

832 """Test the reading of an XEasy peak list.""" 833 834 # Create the sequence data, and name the spins. 835 self.interpreter.residue.create(15) 836 self.interpreter.residue.create(21) 837 self.interpreter.residue.create(22) 838 self.interpreter.residue.create(29) 839 self.interpreter.residue.create(52) 840 self.interpreter.residue.create(69) 841 self.interpreter.residue.create(70) 842 self.interpreter.residue.create(73) 843 self.interpreter.residue.create(79) 844 self.interpreter.residue.create(84) 845 self.interpreter.residue.create(87) 846 self.interpreter.residue.create(95) 847 self.interpreter.residue.create(96) 848 self.interpreter.residue.create(100) 849 self.interpreter.residue.create(104) 850 self.interpreter.residue.create(107) 851 self.interpreter.residue.create(110) 852 self.interpreter.residue.create(112) 853 self.interpreter.residue.create(120) 854 self.interpreter.residue.create(141) 855 self.interpreter.residue.create(165) 856 self.interpreter.spin.name(name='N') 857 858 # Read the peak list. 859 self.interpreter.spectrum.read_intensities(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 860 861 # Test the data. 862 self.assertEqual(list(cdp.mol[0].res[ 0].spin[0].peak_intensity.values())[0], 9.714e+03) 863 self.assertEqual(list(cdp.mol[0].res[ 1].spin[0].peak_intensity.values())[0], 7.919e+03) 864 self.assertEqual(list(cdp.mol[0].res[ 2].spin[0].peak_intensity.values())[0], 1.356e+04) 865 self.assertEqual(list(cdp.mol[0].res[ 3].spin[0].peak_intensity.values())[0], 9.884e+03) 866 self.assertEqual(list(cdp.mol[0].res[ 4].spin[0].peak_intensity.values())[0], 2.041e+04) 867 self.assertEqual(list(cdp.mol[0].res[ 5].spin[0].peak_intensity.values())[0], 9.305e+03) 868 self.assertEqual(list(cdp.mol[0].res[ 6].spin[0].peak_intensity.values())[0], 3.154e+04) 869 self.assertEqual(list(cdp.mol[0].res[ 7].spin[0].peak_intensity.values())[0], 9.180e+03) 870 self.assertEqual(list(cdp.mol[0].res[ 9].spin[0].peak_intensity.values())[0], 1.104e+04) 871 self.assertEqual(list(cdp.mol[0].res[10].spin[0].peak_intensity.values())[0], 7.680e+03) 872 self.assertEqual(list(cdp.mol[0].res[11].spin[0].peak_intensity.values())[0], 5.206e+03) 873 self.assertEqual(list(cdp.mol[0].res[12].spin[0].peak_intensity.values())[0], 2.863e+04) 874 self.assertEqual(list(cdp.mol[0].res[14].spin[0].peak_intensity.values())[0], 9.271e+03) 875 self.assertEqual(list(cdp.mol[0].res[15].spin[0].peak_intensity.values())[0], 7.919e+03) 876 self.assertEqual(list(cdp.mol[0].res[16].spin[0].peak_intensity.values())[0], 9.962e+03) 877 self.assertEqual(list(cdp.mol[0].res[17].spin[0].peak_intensity.values())[0], 1.260e+04) 878 self.assertEqual(list(cdp.mol[0].res[18].spin[0].peak_intensity.values())[0], 1.545e+04) 879 self.assertEqual(list(cdp.mol[0].res[19].spin[0].peak_intensity.values())[0], 1.963e+04) 880 self.assertEqual(list(cdp.mol[0].res[20].spin[0].peak_intensity.values())[0], 1.918e+04)

881 882

883 - def test_read_peak_list_xeasy_2(self):

884 """Test the reading of an XEasy peak list (2).""" 885 886 # Create the sequence data, and name the spins. 887 self.interpreter.residue.create(79) 888 self.interpreter.spin.name(name='NE1') 889 890 # Read the peak list. 891 self.interpreter.spectrum.read_intensities(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 892 893 # Test the data. 894 self.assertEqual(list(cdp.mol[0].res[0].spin[0].peak_intensity.values())[0], 1.532e+04)

895 896

897 - def test_read_peak_list_xeasy_3(self):

898 """Test the reading of an XEasy peak list (3).""" 899 900 # Create the sequence data, and name the spins. 901 self.interpreter.residue.create(100) 902 self.interpreter.spin.name(name='C') 903 904 # Read the peak list. 905 self.interpreter.spectrum.read_intensities(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 906 907 # Test the data. 908 self.assertEqual(list(cdp.mol[0].res[0].spin[0].peak_intensity.values())[0], 6.877e+03)

909 910

911 - def test_read_peak_list_xeasy_4(self):

912 """Test the reading of an XEasy peak list (4).""" 913 914 # Create the sequence data, and name the spins. 915 self.interpreter.residue.create(107) 916 self.interpreter.spin.name(name='C') 917 918 # Read the peak list. 919 self.interpreter.spectrum.read_intensities(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 920 921 # Test the data. 922 self.assertEqual(list(cdp.mol[0].res[0].spin[0].peak_intensity.values())[0], 7.123e+03)

Source Code for Module test_suite.system_tests.peak_lists