test_suite.system_tests.model

64 """TestCase class for the functional tests of model-free analysis.""" 65

66 - def setUp(self):

67 """Set up for all the functional tests.""" 68 69 # Create the data pipe. 70 self.interpreter.pipe.create('mf', 'mf')

71 72

73 - def mesg_opt_debug(self, spin):

74 """Method for returning a string to help debug the minimisation. 75 76 @param spin: The SpinContainer of the optimised spin. 77 @type spin: SpinContainer instance 78 @return: The debugging string. 79 @rtype: str 80 """ 81 82 # Initialise the string. 83 string = 'Optimisation failure.\n\n' 84 85 # Create the string. 86 string = string + "%-18s%-25s\n" % ("System: ", SYSTEM) 87 string = string + "%-18s%-25s\n" % ("Release: ", RELEASE) 88 string = string + "%-18s%-25s\n" % ("Version: ", VERSION) 89 string = string + "%-18s%-25s\n" % ("Win32 version: ", (WIN32_VER[0] + " " + WIN32_VER[1] + " " + WIN32_VER[2] + " " + WIN32_VER[3])) 90 string = string + "%-18s%-25s\n" % ("Distribution: ", (DIST[0] + " " + DIST[1] + " " + DIST[2])) 91 string = string + "%-18s%-25s\n" % ("Architecture: ", (ARCH[0] + " " + ARCH[1])) 92 string = string + "%-18s%-25s\n" % ("Machine: ", MACH) 93 string = string + "%-18s%-25s\n" % ("Processor: ", PROC) 94 string = string + "%-18s%-25s\n" % ("Python version: ", PY_VER) 95 string = string + "%-18s%-25s\n" % ("Numpy version: ", NUMPY_VER) 96 string = string + "%-18s%-25s\n" % ("Libc version: ", (LIBC_VER[0] + " " + LIBC_VER[1])) 97 98 99 # Minimisation info. 100 string = string + '\n' 101 if spin.local_tm != None: 102 string = string + "%-15s %30.16g\n" % ('local_tm (ns):', spin.local_tm * 1e9) 103 if spin.s2 != None: 104 string = string + "%-15s %30.16g\n" % ('s2:', spin.s2) 105 if spin.s2f != None: 106 string = string + "%-15s %30.16g\n" % ('s2f:', spin.s2f) 107 if spin.s2s != None: 108 string = string + "%-15s %30.16g\n" % ('s2s:', spin.s2s) 109 if spin.te != None: 110 string = string + "%-15s %30.13g\n" % ('te (ps):', spin.te * 1e12) 111 if spin.tf != None: 112 string = string + "%-15s %30.13g\n" % ('tf (ps):', spin.tf * 1e12) 113 if spin.ts != None: 114 string = string + "%-15s %30.13g\n" % ('ts (ps):', spin.ts * 1e12) 115 if spin.rex != None: 116 string = string + "%-15s %30.17g\n" % ('rex:', spin.rex * (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2) 117 string = string + "%-15s %30.17g\n" % ('chi2:', spin.chi2) 118 string = string + "%-15s %30i\n" % ('iter:', spin.iter) 119 string = string + "%-15s %30i\n" % ('f_count:', spin.f_count) 120 string = string + "%-15s %30i\n" % ('g_count:', spin.g_count) 121 string = string + "%-15s %30i\n" % ('h_count:', spin.h_count) 122 string = string + "%-15s %30s\n" % ('warning:', spin.warning) 123 124 # Return the string. 125 return string

126 127

128 - def monte_carlo(self):

129 """Run Monte Carlo simulations for the optimised model-free model.""" 130 131 # Monte Carlo simulations. 132 self.interpreter.monte_carlo.setup(number=3) 133 self.interpreter.monte_carlo.create_data() 134 self.interpreter.monte_carlo.initial_values() 135 self.interpreter.minimise('newton') 136 #self.interpreter.eliminate() 137 self.interpreter.monte_carlo.error_analysis()

138 139

140 - def object_comparison(self, obj1=None, obj2=None, skip=None):

141 """Check if the contents of 2 objects are the same.""" 142 143 # The names are the same. 144 self.assertEqual(dir(obj1), dir(obj2)) 145 146 # Loop over the objects in the base objects. 147 for name in dir(obj1): 148 # Skip special objects. 149 if skip and name in skip: 150 continue 151 152 # Skip objects starting with '_'. 153 if search('^_', name): 154 continue 155 156 # Skip original class methods. 157 if name in list(obj1.__class__.__dict__.keys()): 158 continue 159 160 # Print out. 161 print(("\t" + name)) 162 163 # Get the sub-objects. 164 sub_obj1 = getattr(obj1, name) 165 sub_obj2 = getattr(obj2, name) 166 167 # Check that they are of the same type. 168 self.assertEqual(type(sub_obj1), type(sub_obj2)) 169 170 # Check that they are equal (converting to strings to avoid comparison nastiness). 171 self.assertEqual(str(sub_obj1), str(sub_obj2))

172 173

174 - def test_bug_14872_unicode_selection(self):

175 """Test catching bug #14872, the unicode string selection failure as submitted by Olivier Serve.""" 176 177 # Execute the script. 178 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_14872_unicode_selection.py')

179 180

181 - def test_bug_14941_local_tm_global_selection(self):

182 """Test catching bug #14941, the local tm global model selection problem as submitted by Mikaela Stewart (mikaela dot stewart att gmail dot com).""" 183 184 # Execute the script. 185 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_14941_local_tm_global_selection.py')

186 187

188 - def test_bug_15050(self):

189 """Test catching bug #15050, 'PipeContainer' object has no attribute 'diff_tensor' error as submitted by Tiago Pais (https://web.archive.org/web/https://gna.org/users/tpais).""" 190 191 # Execute the script. 192 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_15050.py')

193 194

195 - def test_bugs_12582_12591_12607(self):

196 """Test catching bugs #12582, #12591 and #12607 as submitted by Chris Brosey.""" 197 198 # Execute the script. 199 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bugs_12582_12591_12607.py') 200 201 # Test for bug #12607 (S2 changes because it is in the grid search when it should not be). 202 self.assertNotEqual(cdp.mol[0].res[1].spin[0].s2, 1.0)

203 204

205 - def test_bug_18790(self):

206 """Test catching bug #18790, the negative relaxation data RelaxError reported by Vitaly Vostrikov.""" 207 208 # Execute the script. 209 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_18790_negative_error.py')

210 211

212 - def test_create_m4(self):

213 """Creating model m4 with parameters {S2, te, Rex} using model_free.create_model().""" 214 215 # Execute the script. 216 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'create_m4.py') 217 218 # Test the model. 219 self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4') 220 self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['s2', 'te', 'rex'])

221 222

223 - def test_dauvergne_protocol(self):

224 """Check the execution of auto_analyses.dauvergne_protocol.""" 225 226 # Create a temporary directory for dumping files. 227 ds.tmpdir = mkdtemp() 228 229 # Execute the script. 230 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'dauvergne_protocol.py') 231 232 # Check the diffusion tensor. 233 self.assertEqual(cdp.diff_tensor.type, 'sphere') 234 self.assertAlmostEqual(cdp.diff_tensor.tm, 1e-8) 235 self.assertEqual(cdp.diff_tensor.fixed, True) 236 237 # The global minimisation info. 238 self.assertAlmostEqual(cdp.chi2, 4e-19) 239 240 # The spin ID info. 241 mol_names = ["sphere_mol1"] * 9 242 res_names = ["GLY"] * 9 243 res_nums = range(1, 10) 244 spin_names = ["N"] * 9 245 spin_nums = numpy.array(range(9)) * 2 + 1 246 247 # Check the spin data. 248 i = 0 249 for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 250 # The ID info. 251 self.assertEqual(mol_name, mol_names[i]) 252 self.assertEqual(res_name, res_names[i]) 253 self.assertEqual(res_num, res_nums[i]) 254 self.assertEqual(spin.name, spin_names[i]) 255 self.assertEqual(spin.num, spin_nums[i]) 256 257 # The data. 258 self.assertEqual(spin.select, True) 259 self.assertEqual(spin.fixed, False) 260 self.assertEqual(spin.proton_type, '1H') 261 self.assertEqual(spin.heteronuc_type, '15N') 262 self.assertEqual(spin.attached_proton, None) 263 self.assertEqual(spin.nucleus, None) 264 self.assertAlmostEqual(spin.r, 1.02 * 1e-10) 265 self.assertAlmostEqual(spin.csa, -172e-6) 266 267 # The model-free data. 268 self.assertEqual(spin.model, 'm2') 269 self.assertEqual(spin.equation, 'mf_orig') 270 self.assertEqual(len(spin.params), 2) 271 self.assertEqual(spin.params[0], 's2') 272 self.assertEqual(spin.params[1], 'te') 273 self.assertAlmostEqual(spin.s2, 0.8) 274 self.assertEqual(spin.s2f, None) 275 self.assertEqual(spin.s2s, None) 276 self.assertEqual(spin.local_tm, None) 277 self.assertAlmostEqual(spin.te, 20e-12) 278 self.assertEqual(spin.tf, None) 279 self.assertEqual(spin.ts, None) 280 self.assertEqual(spin.rex, None) 281 282 # The spin minimisation info. 283 self.assertEqual(spin.chi2, None) 284 self.assertEqual(spin.iter, None) 285 self.assertEqual(spin.f_count, None) 286 self.assertEqual(spin.g_count, None) 287 self.assertEqual(spin.h_count, None) 288 self.assertEqual(spin.warning, None) 289 290 # Increment the index. 291 i += 1

292 293

294 - def test_generate_ri(self):

295 """Back-calculate relaxation data.""" 296 297 # Execute the script. 298 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'generate_ri.py')

299 300

301 - def test_latex_table(self):

302 """Test the creation of a LaTeX table of model-free results, mimicking the latex_mf_table.py sample script.""" 303 304 # Execute the script. 305 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'latex_mf_table.py')

306 307

308 - def test_local_tm_10_S2_0_8_te_40(self):

309 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 310 311 # Setup the data pipe for optimisation. 312 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_local_tm_10_S2_0_8_te_40.py') 313 314 # The proton frequencies in MHz. 315 frq = ['400', '500', '600', '700', '800', '900', '1000'] 316 317 # Load the relaxation data. 318 for i in range(len(frq)): 319 self.interpreter.relax_data.read('NOE_%s'%frq[i], 'NOE', float(frq[i])*1e6, 'noe.%s.out' % frq[i], dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 320 self.interpreter.relax_data.read('R1_%s'%frq[i], 'R1', float(frq[i])*1e6, 'r1.%s.out' % frq[i], dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 321 self.interpreter.relax_data.read('R2_%s'%frq[i], 'R2', float(frq[i])*1e6, 'r2.%s.out' % frq[i], dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 322 323 # Set up the initial model-free parameter values (bypass the grid search for speed). 324 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 325 326 # Minimise. 327 self.interpreter.minimise('newton', 'gmw', 'back') 328 329 # Alias the relevent spin container. 330 spin = cdp.mol[0].res[0].spin[0] 331 332 # Check the values. 333 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

334 335

336 - def test_local_tm_10_S2_0_8_te_40_test2(self):

337 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 338 339 # Setup the data pipe for optimisation. 340 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_local_tm_10_S2_0_8_te_40.py') 341 342 # The proton frequencies in MHz. 343 frq = ['400', '500', '600', '700', '800', '900', '1000'] 344 345 # Load the relaxation data. 346 for i in range(len(frq)): 347 self.interpreter.relax_data.read('NOE_%s'%frq[i], 'NOE', float(frq[i])*1e6, 'noe.%s.out' % frq[i], dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 348 self.interpreter.relax_data.read('R1_%s'%frq[i], 'R1', float(frq[i])*1e6, 'r1.%s.out' % frq[i], dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 349 self.interpreter.relax_data.read('R2_%s'%frq[i], 'R2', float(frq[i])*1e6, 'r2.%s.out' % frq[i], dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 350 351 # Set up the initial model-free parameter values (bypass the grid search for speed). 352 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 353 354 # Minimise. 355 self.interpreter.minimise('newton', 'gmw', 'back') 356 357 # Alias the relevent spin container. 358 spin = cdp.mol[0].res[0].spin[0] 359 360 # Check the values. 361 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

362 363

364 - def test_local_tm_10_S2_0_8_te_40_test3(self):

365 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 366 367 # Setup the data pipe for optimisation. 368 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_local_tm_10_S2_0_8_te_40.py') 369 370 # Load the relaxation data. 371 self.interpreter.relax_data.read('R2_700', 'R2', 700*1e6, 'r2.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 372 self.interpreter.relax_data.read('NOE_500', 'NOE', 500*1e6, 'noe.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 373 self.interpreter.relax_data.read('R1_500', 'R1', 500*1e6, 'r1.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 374 self.interpreter.relax_data.read('R1_900', 'R1', 900*1e6, 'r1.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 375 self.interpreter.relax_data.read('NOE_900', 'NOE', 900*1e6, 'noe.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 376 self.interpreter.relax_data.read('R2_900', 'R2', 900*1e6, 'r2.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 377 self.interpreter.relax_data.read('R1_700', 'R1', 700*1e6, 'r1.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 378 self.interpreter.relax_data.read('NOE_700', 'NOE', 700*1e6, 'noe.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 379 self.interpreter.relax_data.read('R2_500', 'R2', 500*1e6, 'r2.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 380 381 # Set up the initial model-free parameter values (bypass the grid search for speed). 382 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 383 384 # Minimise. 385 self.interpreter.minimise('newton', 'gmw', 'back') 386 387 # Alias the relevent spin container. 388 spin = cdp.mol[0].res[0].spin[0] 389 390 # Check the values. 391 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

392 393

394 - def test_m0_grid(self):

395 """Test the optimisation of the m0 model-free model against the tm0 parameter grid.""" 396 397 # Initialise. 398 cdp._model = 'm0' 399 cdp._value_test = self.value_test 400 401 # Setup the data pipe for optimisation. 402 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

403 404

405 - def test_m0_grid_vs_m1(self):

406 """Test the optimisation of the m1 model-free model against the tm0 parameter grid.""" 407 408 # Initialise. 409 cdp._model = 'm1' 410 cdp._value_test = self.value_test 411 412 # Setup the data pipe for optimisation. 413 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

414 415

416 - def test_m0_grid_vs_m2(self):

417 """Test the optimisation of the m2 model-free model against the tm0 parameter grid.""" 418 419 # Initialise. 420 cdp._model = 'm2' 421 cdp._value_test = self.value_test 422 423 # Setup the data pipe for optimisation. 424 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

425 426

427 - def test_m0_grid_vs_m3(self):

428 """Test the optimisation of the m3 model-free model against the tm0 parameter grid.""" 429 430 # Initialise. 431 cdp._model = 'm3' 432 cdp._value_test = self.value_test 433 434 # Setup the data pipe for optimisation. 435 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

436 437

438 - def test_m0_grid_vs_m4(self):

439 """Test the optimisation of the m4 model-free model against the tm0 parameter grid.""" 440 441 # Initialise. 442 cdp._model = 'm4' 443 cdp._value_test = self.value_test 444 445 # Setup the data pipe for optimisation. 446 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

447 448

449 - def test_m1_grid(self):

450 """Test the optimisation of the m1 model-free model against the tm1 parameter grid.""" 451 452 # Initialise. 453 cdp._model = 'm1' 454 cdp._value_test = self.value_test 455 456 # Setup the data pipe for optimisation. 457 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm1_grid.py')

458 459

460 - def test_m2_grid(self):

461 """Test the optimisation of the m2 model-free model against the tm2 parameter grid.""" 462 463 # Initialise. 464 cdp._model = 'm2' 465 cdp._value_test = self.value_test 466 467 # Setup the data pipe for optimisation. 468 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

469 470

471 - def test_m2_grid_vs_m4(self):

472 """Test the optimisation of the m4 model-free model against the tm2 parameter grid.""" 473 474 # Initialise. 475 cdp._model = 'm4' 476 cdp._value_test = self.value_test 477 478 # Setup the data pipe for optimisation. 479 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

480 481

482 - def test_m3_grid(self):

483 """Test the optimisation of the m3 model-free model against the tm3 parameter grid.""" 484 485 # Initialise. 486 cdp._model = 'm3' 487 cdp._value_test = self.value_test 488 489 # Setup the data pipe for optimisation. 490 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm3_grid.py')

491 492

493 - def test_m4_grid(self):

494 """Test the optimisation of the m4 model-free model against the tm4 parameter grid.""" 495 496 # Initialise. 497 cdp._model = 'm4' 498 cdp._value_test = self.value_test 499 500 # Setup the data pipe for optimisation. 501 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm4_grid.py')

502 503

504 - def test_m5_grid(self):

505 """Test the optimisation of the m5 model-free model against the tm5 parameter grid.""" 506 507 # Initialise. 508 cdp._model = 'm5' 509 cdp._value_test = self.value_test 510 511 # Setup the data pipe for optimisation. 512 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm5_grid.py')

513 514

515 - def test_m6_grid(self):

516 """Test the optimisation of the m6 model-free model against the tm6 parameter grid.""" 517 518 # Initialise. 519 cdp._model = 'm6' 520 cdp._value_test = self.value_test 521 522 # Setup the data pipe for optimisation. 523 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm6_grid.py')

524 525

526 - def test_m7_grid(self):

527 """Test the optimisation of the m7 model-free model against the tm7 parameter grid.""" 528 529 # Initialise. 530 cdp._model = 'm7' 531 cdp._value_test = self.value_test 532 533 # Setup the data pipe for optimisation. 534 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm7_grid.py')

535 536

537 - def test_m8_grid(self):

538 """Test the optimisation of the m8 model-free model against the tm8 parameter grid.""" 539 540 # Initialise. 541 cdp._model = 'm8' 542 cdp._value_test = self.value_test 543 544 # Setup the data pipe for optimisation. 545 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm8_grid.py')

546 547

548 - def test_m9_grid(self):

549 """Test the optimisation of the m9 model-free model against the tm9 parameter grid.""" 550 551 # Initialise. 552 cdp._model = 'm9' 553 cdp._value_test = self.value_test 554 555 # Setup the data pipe for optimisation. 556 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm9_grid.py')

557 558

559 - def test_omp_analysis(self):

560 """Try a very minimal model-free analysis on the OMP relaxation data.""" 561 562 # Execute the script. 563 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'omp_model_free.py') 564 565 # Alias the final data pipe. 566 dp = pipes.get_pipe('final') 567 568 # Some checks. 569 self.assertEqual(dp.mol[0].res[0].spin[0].select_sim, [True, False, True]) 570 self.assertEqual(dp.mol[0].res[1].spin[0].select_sim, [True, True, False]) 571 self.assertEqual(dp.mol[0].res[2].spin[0].select_sim, [True, True, True]) 572 self.assert_(not hasattr(dp.mol[0].res[3].spin[0], 'select_sim'))

573 574

575 - def test_opendx_s2_te_rex(self):

576 """Mapping the {S2, te, Rex} chi2 space through the OpenDX user function dx.map().""" 577 578 # Execute the script. 579 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opendx_s2_te_rex.py')

580 581

582 - def test_opendx_theta_phi_da(self):

583 """Mapping the {theta, phi, Da} chi2 space through the OpenDX user function dx.map().""" 584 585 # Path of the files. 586 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 587 588 # Read the PDF file and set the vectors. 589 self.interpreter.structure.read_pdb(file='pdb', dir=path, read_model=1) 590 self.interpreter.structure.load_spins('@N') 591 self.interpreter.structure.vectors(attached='H') 592 593 # Read the relaxation data. 594 self.interpreter.relax_data.read('R1_600', 'R1', 600.0*1e6, 'r1.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 595 self.interpreter.relax_data.read('R2_600', 'R2', 600.0*1e6, 'r2.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 596 self.interpreter.relax_data.read('NOE_600', 'NOE', 600.0*1e6, 'noe.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 597 self.interpreter.relax_data.read('R1_500', 'R1', 500.0*1e6, 'r1.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 598 self.interpreter.relax_data.read('R2_500', 'R2', 500.0*1e6, 'r2.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 599 self.interpreter.relax_data.read('NOE_500', 'NOE', 500.0*1e6, 'noe.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 600 601 # Setup other values. 602 self.interpreter.diffusion_tensor.init((1.601 * 1e7, 1.34, 72.4, 90-77.9), param_types=4) 603 self.interpreter.value.set([N15_CSA, NH_BOND_LENGTH], ['csa', 'r']) 604 self.interpreter.value.set([0.8, 50 * 1e-12, 0.0], ['s2', 'te', 'rex']) 605 self.interpreter.value.set('15N', 'heteronuc_type') 606 self.interpreter.value.set('1H', 'proton_type') 607 608 # Select the model. 609 self.interpreter.model_free.select_model(model='m4') 610 611 # Map the space. 612 self.interpreter.dx.map(params=['theta', 'phi', 'Da'], spin_id=':2', inc=2, lower=[0, 0, -0.5*1e7], upper=[pi, 2.0*pi, 1.0*1e7], file_prefix='devnull')

613 614

615 - def test_opendx_tm_s2_te(self):

616 """Mapping the {local_tm, S2, te} chi2 space through the OpenDX user function dx.map().""" 617 618 # Path of the files. 619 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 620 621 # Read the sequence. 622 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 623 624 # Read the relaxation data. 625 self.interpreter.relax_data.read('R1_600', 'R1', 600.0*1e6, 'r1.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 626 self.interpreter.relax_data.read('R2_600', 'R2', 600.0*1e6, 'r2.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 627 self.interpreter.relax_data.read('NOE_600', 'NOE', 600.0*1e6, 'noe.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 628 self.interpreter.relax_data.read('R1_500', 'R1', 500.0*1e6, 'r1.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 629 self.interpreter.relax_data.read('R2_500', 'R2', 500.0*1e6, 'r2.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 630 self.interpreter.relax_data.read('NOE_500', 'NOE', 500.0*1e6, 'noe.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 631 632 # Setup other values. 633 self.interpreter.value.set([N15_CSA, NH_BOND_LENGTH], ['csa', 'r']) 634 self.interpreter.value.set('15N', 'heteronuc_type') 635 self.interpreter.value.set('1H', 'proton_type') 636 637 # Select the model. 638 self.interpreter.model_free.select_model(model='tm2') 639 640 # Map the space. 641 self.interpreter.dx.map(params=['local_tm', 's2', 'te'], spin_id=':2', inc=2, lower=[5e-9, 0.0, 0.0], file_prefix='devnull')

642 643

644 - def test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149(self):

645 """Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 646 647 The optimisation options are: 648 - BFGS optimisation. 649 - Backtracking line search. 650 - Constrained. 651 652 The true data set is: 653 - S2 = 0.970 654 - te = 2048 ps 655 - Rex = 0.149 s^-1 656 """ 657 658 # Setup the data pipe for optimisation. 659 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 660 661 # Set up the initial model-free parameter values (bypass the grid search for speed). 662 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 663 664 # Minimise. 665 self.interpreter.minimise('bfgs', 'back') 666 667 # Alias the relevent spin container. 668 spin = cdp.mol[0].res[1].spin[0] 669 670 # Optimisation differences. 671 ########################### 672 673 # 32-bit Linux. 674 # iter: 203 675 # f_count: 955 676 # g_count: 209 677 678 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-devel/2009-05/msg00003.html). 679 # System: Linux 680 # Release: 2.6.28-gentoo-r5 681 # Version: #1 SMP Sat Apr 25 13:31:51 EDT 2009 682 # Win32 version: 683 # Distribution: 684 # Architecture: 32bit ELF 685 # Machine: i686 686 # Processor: Intel(R) Pentium(R) M processor 1.80GHz 687 # Python version: 2.5.4 688 # numpy version: 1.2.1 689 # 690 # s2: 0.9700000000012307 691 # te: 2048.0000002299716 692 # rex: 0.14899999997647859 693 # chi2: 1.9223825944220359e-20 694 # iter: 157 695 # f_count: 722 696 # g_count: 164 697 # h_count: 0 698 # warning: None 699 700 # 32-bit i686 Linux. 701 # System: Linux 702 # Release: 2.6.33.7-desktop-2mnb 703 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 704 # Win32 version: 705 # Distribution: mandrake 2010.2 Official 706 # Architecture: 32bit ELF 707 # Machine: i686 708 # Processor: i686 709 # Python version: 2.6.5 710 # Numpy version: 1.4.1 711 # Libc version: glibc 2.0 712 # 713 # s2: 0.9700000000016741 714 # te (ps): 2048.000000312 715 # rex: 0.14899999996808433 716 # chi2: 3.5466670276032307e-20 717 # iter: 158 718 # f_count: 744 719 # g_count: 165 720 # h_count: 0 721 # warning: None 722 723 # 32-bit i686 Linux. 724 # System: Linux 725 # Release: 2.6.33.7-desktop-2mnb 726 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 727 # Win32 version: 728 # Distribution: mandrake 2010.2 Official 729 # Architecture: 32bit ELF 730 # Machine: i686 731 # Processor: i686 732 # Python version: 2.6.5 733 # Numpy version: 1.4.1 734 # Libc version: glibc 2.0 735 # 736 # s2: 0.9700000000016741 737 # te: 2048.000000312 738 # rex: 0.14899999996808433 739 # chi2: 3.5466670276032307e-20 740 # iter: 158 741 # f_count: 744 742 # g_count: 165 743 # h_count: 0 744 # warning: None 745 746 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-users/2011-01/msg00029.html). 747 # System: Linux 748 # Release: 2.6.28-17-generic 749 # Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 750 # Win32 version: 751 # Distribution: Ubuntu 9.04 jaunty 752 # Architecture: 32bit ELF 753 # Machine: i686 754 # Processor: 755 # Python version: 2.6.2 756 # Numpy version: 1.2.1 757 # Libc version: glibc 2.4 758 # 759 # s2: 0.970000000000951 760 # te (ps): 2048.000000178 761 # rex: 0.14899999998189395 762 # chi2: 1.1498599057727952e-20 763 # iter: 154 764 # f_count: 598 765 # g_count: 161 766 # h_count: 0 767 # warning: None 768 769 # 64-bit x86_64 Linux. 770 # System: Linux 771 # Release: 2.6.24.7-server-2mnb 772 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 773 # Win32 version: 774 # Distribution: mandriva 2008.1 Official 775 # Architecture: 64bit ELF 776 # Machine: x86_64 777 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 778 # Python version: 2.5.2 779 # Numpy version: 1.2.0 780 # Libc version: glibc 2.2.5 781 # 782 # s2: 0.9699999999999785 783 # te: 2047.9999999962433 784 # rex: 0.14900000000039709 785 # chi2: 5.2479491342506911e-24 786 # iter: 162 787 # f_count: 758 788 # g_count: 169 789 # h_count: 0 790 # warning: None 791 792 # 32-bit Windows. 793 # iter: 156 794 # f_count: 701 795 # g_count: 163 796 797 # 32-bit powerpc Darwin (https://web.archive.org/web/https://gna.org/bugs/?12573, http://www.nmr-relax.com/mail.gna.org/public/relax-users/2008-10/msg00089.html). 798 # System: Darwin 799 # Release: 9.5.0 800 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; root:xnu-1228.7.58~1/RELEASE_PPC 801 # Win32 version: 802 # Distribution: 803 # Architecture: 32bit 804 # Machine: Power Macintosh 805 # Processor: powerpc 806 # Python version: 2.5.2 807 # numpy version: 1.1.1 808 # 809 # s2: 0.9699999999999861 810 # te: 2047.9999999978033 811 # rex: 0.14900000000028032 812 # chi2: 1.8533903598853284e-24 813 # iter: 156 814 # f_count: 695 815 # g_count: 162 816 # h_count: 0 817 # warning: None 818 819 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14173). 820 # System: Darwin 821 # Release: 9.8.0 822 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 823 # Win32 version: 824 # Distribution: 825 # Architecture: 32bit 826 # Machine: i386 827 # Processor: i386 828 # Python version: 2.6.2 829 # numpy version: 1.3.0 830 # 831 # s2: 0.9700000000009170 832 # te: 2048.0000001751678 833 # rex: 0.14899999998256069 834 # chi2: 1.1151721805269898e-20 835 # iter: 175 836 # f_count: 735 837 # g_count: 182 838 # h_count: 0 839 # warning: None 840 841 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14173). 842 # System: Darwin 843 # Release: 9.8.0 844 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 845 # Win32 version: 846 # Distribution: 847 # Architecture: 64bit 848 # Machine: i386 849 # Processor: i386 850 # Python version: 2.6.2 851 # numpy version: 1.3.0 852 # 853 # s2: 0.9699999999999785 854 # te: 2047.9999999962433 855 # rex: 0.14900000000039709 856 # chi2: 5.2479491342506911e-24 857 # iter: 162 858 # f_count: 758 859 # g_count: 169 860 # h_count: 0 861 # warning: None 862 863 # Optimisation values. 864 select = True 865 s2 = 0.9699999999999995 866 te = 2048.000000000022283 867 rex = 0.14900000000000566 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 868 chi2 = 3.1024517431117421e-27 869 iter = [154, 156, 157, 158, 162, 175, 203] 870 f_count = [598, 695, 701, 722, 735, 744, 758, 955] 871 g_count = [161, 162, 163, 164, 165, 169, 182, 209] 872 h_count = 0 873 warning = None 874 875 # Test the values. 876 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 877 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

878 879

880 - def test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149(self):

881 """Constrained BFGS opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 882 883 The optimisation options are: 884 - BFGS optimisation. 885 - More and Thuente line search. 886 - Constrained. 887 888 The true data set is: 889 - S2 = 0.970 890 - te = 2048 ps 891 - Rex = 0.149 s^-1 892 """ 893 894 # Setup the data pipe for optimisation. 895 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 896 897 # Set up the initial model-free parameter values (bypass the grid search for speed). 898 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 899 900 # Minimise. 901 self.interpreter.minimise('bfgs', 'mt') 902 903 # Alias the relevent spin container. 904 spin = cdp.mol[0].res[1].spin[0] 905 906 # Optimisation differences. 907 ########################### 908 909 # 32-bit Linux. 910 # f_count: 388 911 # g_count: 388 912 913 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-devel/2009-05/msg00003.html). 914 # System: Linux 915 # Release: 2.6.28-gentoo-r5 916 # Version: #1 SMP Sat Apr 25 13:31:51 EDT 2009 917 # Win32 version: 918 # Distribution: 919 # Architecture: 32bit ELF 920 # Machine: i686 921 # Processor: Intel(R) Pentium(R) M processor 1.80GHz 922 # Python version: 2.5.4 923 # numpy version: 1.2.1 924 # 925 # s2: 0.9700000000000604 926 # te: 2048.0000000114946 927 # rex: 0.14899999999885985 928 # chi2: 4.762657780645096e-23 929 # iter: 120 930 # f_count: 386 931 # g_count: 386 932 # h_count: 0 933 # warning: None 934 935 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-users/2011-01/msg00029.html). 936 # System: Linux 937 # Release: 2.6.28-17-generic 938 # Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 939 # Win32 version: 940 # Distribution: Ubuntu 9.04 jaunty 941 # Architecture: 32bit ELF 942 # Machine: i686 943 # Processor: 944 # Python version: 2.6.2 945 # Numpy version: 1.2.1 946 # Libc version: glibc 2.4 947 # 948 # s2: 0.9700000000000614 949 # te (ps): 2048.000000012 950 # rex: 0.14899999999883881 951 # chi2: 4.9272178768519757e-23 952 # iter: 120 953 # f_count: 381 954 # g_count: 381 955 # h_count: 0 956 # warning: None 957 958 # 64-bit x86_64 Linux. 959 # System: Linux 960 # Release: 2.6.24.7-server-2mnb 961 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 962 # Win32 version: 963 # Distribution: mandriva 2008.1 Official 964 # Architecture: 64bit ELF 965 # Machine: x86_64 966 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 967 # Python version: 2.5.2 968 # Numpy version: 1.2.0 969 # Libc version: glibc 2.2.5 970 # 971 # s2: 0.9700000000000603 972 # te: 2048.0000000114601 973 # rex: 0.14899999999886163 974 # chi2: 4.7289676642197204e-23 975 # iter: 120 976 # f_count: 384 977 # g_count: 384 978 # h_count: 0 979 # warning: None 980 981 # 32-bit powerpc Darwin (https://web.archive.org/web/https://gna.org/bugs/?12573, http://www.nmr-relax.com/mail.gna.org/public/relax-users/2008-10/msg00089.html). 982 # System: Darwin 983 # Release: 9.5.0 984 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 985 # root:xnu-1228.7.58~1/RELEASE_PPC 986 # Win32 version: 987 # Distribution: 988 # Architecture: 32bit 989 # Machine: Power Macintosh 990 # Processor: powerpc 991 # Python version: 2.5.2 992 # numpy version: 1.1.1 993 # 994 # s2: 0.9700000000000607 995 # te: 2048.0000000115510 996 # rex: 0.14899999999885080 997 # chi2: 4.8056261450870388e-23 998 # iter: 120 999 # f_count: 377 1000 # g_count: 377 1001 # h_count: 0 1002 # warning: None 1003 1004 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14174). 1005 # System: Darwin 1006 # Release: 9.8.0 1007 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1008 # Win32 version: 1009 # Distribution: 1010 # Architecture: 32bit 1011 # Machine: i386 1012 # Processor: i386 1013 # Python version: 2.6.2 1014 # numpy version: 1.3.0 1015 # 1016 # s2: 0.9700000000000604 1017 # te: 2048.0000000114997 1018 # rex: 0.14899999999886168 1019 # chi2: 4.7647467884964078e-23 1020 # iter: 120 1021 # f_count: 386 1022 # g_count: 386 1023 # h_count: 0 1024 # warning: None 1025 1026 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14174). 1027 # System: Darwin 1028 # Release: 9.8.0 1029 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1030 # Win32 version: 1031 # Distribution: 1032 # Architecture: 64bit 1033 # Machine: i386 1034 # Processor: i386 1035 # Python version: 2.6.2 1036 # numpy version: 1.3.0 1037 # 1038 # s2: 0.9700000000000603 1039 # te: 2048.0000000114601 1040 # rex: 0.14899999999886163 1041 # chi2: 4.7289676642197204e-23 1042 # iter: 120 1043 # f_count: 384 1044 # g_count: 384 1045 # h_count: 0 1046 # warning: None 1047 1048 # Optimisation values. 1049 select = True 1050 s2 = 0.9700000000000580 1051 te = 2048.000000011044449 1052 rex = 0.148999999998904 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1053 chi2 = 4.3978813282102374e-23 1054 iter = 120 1055 f_count = [377, 381, 384, 386, 388] 1056 g_count = [377, 381, 384, 386, 388] 1057 h_count = 0 1058 warning = None 1059 1060 # Test the values. 1061 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1062 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1063 1064

1065 - def test_opt_constr_cd_back_S2_0_970_te_2048_Rex_0_149(self):

1066 """Constrained coordinate descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1067 1068 The optimisation options are: 1069 - Coordinate descent optimisation. 1070 - Backtracking line search. 1071 - Constrained. 1072 1073 The true data set is: 1074 - S2 = 0.970 1075 - te = 2048 ps 1076 - Rex = 0.149 s^-1 1077 """ 1078 1079 # Setup the data pipe for optimisation. 1080 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 1081 1082 # Set up the initial model-free parameter values (bypass the grid search for speed). 1083 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1084 1085 # Minimise. 1086 self.interpreter.minimise('cd', 'back', max_iter=50) 1087 1088 # Alias the relevent spin container. 1089 spin = cdp.mol[0].res[1].spin[0] 1090 1091 # Optimisation differences. 1092 ########################### 1093 1094 # 64-bit x86_64 Linux. 1095 # System: Linux 1096 # Release: 2.6.24.7-server-2mnb 1097 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1098 # Win32 version: 1099 # Distribution: mandriva 2008.1 Official 1100 # Architecture: 64bit ELF 1101 # Machine: x86_64 1102 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1103 # Python version: 2.5.2 1104 # Numpy version: 1.2.0 1105 # Libc version: glibc 2.2.5 1106 # 1107 # s2: 0.9097900390625000 1108 # te: 25.0000000000000 1109 # rex: 1.24017333984375000 1110 # chi2: 53.476155463267176 1111 # iter: 50 1112 # f_count: 131 1113 # g_count: 51 1114 # h_count: 0 1115 # warning: Maximum number of iterations reached 1116 1117 # Optimisation values. 1118 select = True 1119 s2 = 0.9097900390625 1120 te = 25.00000000000000 1121 rex = 1.24017333984375 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1122 chi2 = 53.476155463267176 1123 iter = 50 1124 f_count = 131 1125 g_count = 51 1126 h_count = 0 1127 warning = 'Maximum number of iterations reached' 1128 1129 # Test the values. 1130 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1131 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1132 1133

1134 - def test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149(self):

1135 """Constrained coordinate descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1136 1137 The optimisation options are: 1138 - Coordinate descent optimisation. 1139 - More and Thuente line search. 1140 - Constrained. 1141 1142 The true data set is: 1143 - S2 = 0.970 1144 - te = 2048 ps 1145 - Rex = 0.149 s^-1 1146 """ 1147 1148 # Setup the data pipe for optimisation. 1149 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 1150 1151 # Set up the initial model-free parameter values (bypass the grid search for speed). 1152 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1153 1154 # Minimise. 1155 self.interpreter.minimise('cd', 'mt') 1156 1157 # Alias the relevent spin container. 1158 spin = cdp.mol[0].res[1].spin[0] 1159 1160 # Optimisation differences. 1161 ########################### 1162 1163 # 32-bit Linux. 1164 # f_count: 738 1165 # g_count: 738 1166 1167 # 32-bit i686 Linux. 1168 # System: Linux 1169 # Release: 2.6.33.7-desktop-2mnb 1170 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1171 # Win32 version: 1172 # Distribution: mandrake 2010.2 Official 1173 # Architecture: 32bit ELF 1174 # Machine: i686 1175 # Processor: i686 1176 # Python version: 2.6.5 1177 # Numpy version: 1.4.1 1178 # Libc version: glibc 2.0 1179 # 1180 # s2: 0.9700000000219662 1181 # te: 2048.000001534 1182 # rex: 0.14899999946980566 1183 # chi2: 2.3474910055938013e-18 1184 # iter: 200 1185 # f_count: 874 1186 # g_count: 874 1187 # h_count: 0 1188 # warning: None 1189 1190 # 64-bit x86_64 Linux. 1191 # System: Linux 1192 # Release: 2.6.24.7-server-2mnb 1193 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1194 # Win32 version: 1195 # Distribution: mandriva 2008.1 Official 1196 # Architecture: 64bit ELF 1197 # Machine: x86_64 1198 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1199 # Python version: 2.5.2 1200 # Numpy version: 1.2.0 1201 # Libc version: glibc 2.2.5 1202 # 1203 # s2: 0.9700000000219674 1204 # te: 2048.0000015341870 1205 # rex: 0.14899999946977982 1206 # chi2: 2.3477234248531005e-18 1207 # iter: 198 1208 # f_count: 757 1209 # g_count: 757 1210 # h_count: 0 1211 # warning: None 1212 1213 # 32-bit powerpc Darwin (https://web.archive.org/web/https://gna.org/bugs/?12573, http://www.nmr-relax.com/mail.gna.org/public/relax-users/2008-10/msg00089.html). 1214 # System: Darwin 1215 # Release: 9.5.0 1216 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1217 # root:xnu-1228.7.58~1/RELEASE_PPC 1218 # Win32 version: 1219 # Distribution: 1220 # Architecture: 32bit 1221 # Machine: Power Macintosh 1222 # Processor: powerpc 1223 # Python version: 2.5.2 1224 # numpy version: 1.1.1 1225 # 1226 # s2: 0.9700000000219674 1227 # te: 2048.0000015341870 1228 # rex: 0.14899999946977982 1229 # chi2: 2.3477234248531005e-18 1230 # iter: 198 1231 # f_count: 757 1232 # g_count: 757 1233 # h_count: 0 1234 # warning: None 1235 1236 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14175). 1237 # System: Darwin 1238 # Release: 9.8.0 1239 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1240 # Win32 version: 1241 # Distribution: 1242 # Architecture: 64bit 1243 # Machine: i386 1244 # Processor: i386 1245 # Python version: 2.6.2 1246 # numpy version: 1.3.0 1247 # 1248 # s2: 0.9700000000219674 1249 # te: 2048.0000015341870 1250 # rex: 0.14899999946977982 1251 # chi2: 2.3477234248531005e-18 1252 # iter: 198 1253 # f_count: 757 1254 # g_count: 757 1255 # h_count: 0 1256 # warning: None 1257 1258 # Optimisation values. 1259 select = True 1260 s2 = 0.9700000000219674 1261 te = 2048.000001534187049 1262 rex = 0.14899999946977982 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1263 chi2 = 2.3477234248531005e-18 1264 iter = [198, 200] 1265 f_count = [738, 757, 874] 1266 g_count = [738, 757, 874] 1267 h_count = 0 1268 warning = None 1269 1270 # Test the values. 1271 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1272 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1273 1274

1275 - def test_opt_constr_newton_gmw_back_S2_0_970_te_2048_Rex_0_149(self):

1276 """Constrained Newton opt, GMW Hessian mod, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1277 1278 The optimisation options are: 1279 - Newton optimisation. 1280 - GMW Hessian modification. 1281 - Backtracking line search. 1282 - Constrained. 1283 1284 The true data set is: 1285 - S2 = 0.970 1286 - te = 2048 ps 1287 - Rex = 0.149 s^-1 1288 """ 1289 1290 # Setup the data pipe for optimisation. 1291 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 1292 1293 # Set up the initial model-free parameter values (bypass the grid search for speed). 1294 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1295 1296 # Minimise. 1297 self.interpreter.minimise('newton', 'gmw', 'back') 1298 1299 # Alias the relevent spin container. 1300 spin = cdp.mol[0].res[1].spin[0] 1301 1302 # Optimisation differences. 1303 ########################### 1304 1305 # 32-bit Linux. 1306 # f_count: 55 1307 # g_count: 23 1308 1309 # 32-bit i686 Linux. 1310 # System: Linux 1311 # Release: 2.6.33.7-desktop-2mnb 1312 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1313 # Win32 version: 1314 # Distribution: mandrake 2010.2 Official 1315 # Architecture: 32bit ELF 1316 # Machine: i686 1317 # Processor: i686 1318 # Python version: 2.6.5 1319 # Numpy version: 1.4.1 1320 # Libc version: glibc 2.0 1321 # 1322 # s2: 0.9699999999999992 1323 # te: 2048 1324 # rex: 0.14900000000002034 1325 # chi2: 1.1701970207791308e-27 1326 # iter: 18 1327 # f_count: 57 1328 # g_count: 23 1329 # h_count: 18 1330 # warning: None 1331 1332 # 64-bit x86_64 Linux. 1333 # System: Linux 1334 # Release: 2.6.24.7-server-2mnb 1335 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1336 # Win32 version: 1337 # Distribution: mandriva 2008.1 Official 1338 # Architecture: 64bit ELF 1339 # Machine: x86_64 1340 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1341 # Python version: 2.5.2 1342 # Numpy version: 1.2.0 1343 # Libc version: glibc 2.2.5 1344 # 1345 # s2: 0.9699999999999995 1346 # te: 2048.0000000000473 1347 # rex: 0.14900000000001926 1348 # chi2: 7.9357208397255696e-28 1349 # iter: 18 1350 # f_count: 55 1351 # g_count: 23 1352 # h_count: 18 1353 # warning: None 1354 1355 # 32-bit powerpc Darwin (https://web.archive.org/web/https://gna.org/bugs/?12573, http://www.nmr-relax.com/mail.gna.org/public/relax-users/2008-10/msg00089.html). 1356 # System: Darwin 1357 # Release: 9.5.0 1358 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1359 # root:xnu-1228.7.58~1/RELEASE_PPC 1360 # Win32 version: 1361 # Distribution: 1362 # Architecture: 32bit 1363 # Machine: Power Macintosh 1364 # Processor: powerpc 1365 # Python version: 2.5.2 1366 # numpy version: 1.1.1 1367 # 1368 # s2: 0.9699999999999993 1369 # te: 2048.0000000000427 1370 # rex: 0.14900000000002098 1371 # chi2: 5.7085251917483392e-28 1372 # iter: 18 1373 # f_count: 94 1374 # g_count: 23 1375 # h_count: 18 1376 # warning: None 1377 1378 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14177). 1379 # System: Darwin 1380 # Release: 9.8.0 1381 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1382 # Win32 version: 1383 # Distribution: 1384 # Architecture: 32bit 1385 # Machine: i386 1386 # Processor: i386 1387 # Python version: 2.6.2 1388 # numpy version: 1.3.0 1389 # 1390 # s2: 0.9699999999999994 1391 # te: 2048.0000000000455 1392 # rex: 0.14900000000001823 1393 # chi2: 7.3040158179665562e-28 1394 # iter: 18 1395 # f_count: 55 1396 # g_count: 23 1397 # h_count: 18 1398 # warning: None 1399 1400 # Optimisation values. 1401 select = True 1402 s2 = 0.9699999999999994 1403 te = 2048.000000000045020 1404 rex = 0.14900000000001817 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1405 chi2 = 7.3040158179665562e-28 1406 iter = 18 1407 f_count = [55, 57, 94] 1408 g_count = [23] 1409 h_count = 18 1410 warning = None 1411 1412 # Test the values. 1413 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1414 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1415 1416

1417 - def test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149(self):

1418 """Constrained Newton opt, GMW Hessian mod, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1419 1420 The optimisation options are: 1421 - Newton optimisation. 1422 - GMW Hessian modification. 1423 - More and Thuente line search. 1424 - Constrained. 1425 1426 The true data set is: 1427 - S2 = 0.970 1428 - te = 2048 ps 1429 - Rex = 0.149 s^-1 1430 """ 1431 1432 # Setup the data pipe for optimisation. 1433 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 1434 1435 # Set up the initial model-free parameter values (bypass the grid search for speed). 1436 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1437 1438 # Minimise. 1439 self.interpreter.minimise('newton', 'gmw', 'mt') 1440 1441 # Monte Carlo simulations. 1442 self.monte_carlo() 1443 1444 # Alias the relevent spin container. 1445 spin = cdp.mol[0].res[1].spin[0] 1446 1447 # Optimisation differences. 1448 ########################### 1449 1450 # 32-bit Linux. 1451 # f_count: 159, 95 1452 # g_count: 159 1453 1454 # 32-bit i686 Linux. 1455 # System: Linux 1456 # Release: 2.6.33.7-desktop-2mnb 1457 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1458 # Win32 version: 1459 # Distribution: mandrake 2010.2 Official 1460 # Architecture: 32bit ELF 1461 # Machine: i686 1462 # Processor: i686 1463 # Python version: 2.6.5 1464 # Numpy version: 1.4.1 1465 # Libc version: glibc 2.0 1466 # 1467 # s2: 0.9699999999999994 1468 # te: 2048 1469 # rex: 0.14900000000002014 1470 # chi2: 7.9326439528899843e-28 1471 # iter: 22 1472 # f_count: 95 1473 # g_count: 95 1474 # h_count: 22 1475 # warning: None 1476 1477 # 64-bit x86_64 Linux. 1478 # System: Linux 1479 # Release: 2.6.24.7-server-2mnb 1480 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1481 # Win32 version: 1482 # Distribution: mandriva 2008.1 Official 1483 # Architecture: 64bit ELF 1484 # Machine: x86_64 1485 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1486 # Python version: 2.5.2 1487 # Numpy version: 1.2.0 1488 # Libc version: glibc 2.2.5 1489 # 1490 # s2: 0.9699999999999994 1491 # te: 2048.0000000000446 1492 # rex: 0.14900000000001615 1493 # chi2: 8.3312601381368332e-28 1494 # iter: 22 1495 # f_count: 91 1496 # g_count: 91 1497 # h_count: 22 1498 # warning: None 1499 1500 # 64-bit x86_64 Linux (Not sure why there is a difference here, maybe this is gcc or blas/lapack - Python and numpy versions are identical). 1501 # f_count: 153 1502 # g_count: 153 1503 1504 # 32-bit powerpc Darwin (https://web.archive.org/web/https://gna.org/bugs/?12573, http://www.nmr-relax.com/mail.gna.org/public/relax-users/2008-10/msg00089.html). 1505 # System: Darwin 1506 # Release: 9.5.0 1507 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1508 # root:xnu-1228.7.58~1/RELEASE_PPC 1509 # Win32 version: 1510 # Distribution: 1511 # Architecture: 32bit 1512 # Machine: Power Macintosh 1513 # Processor: powerpc 1514 # Python version: 2.5.2 1515 # numpy version: 1.1.1 1516 # 1517 # s2: 0.9699999999999993 1518 # te: 2048.0000000000409 1519 # rex: 0.14900000000002178 1520 # chi2: 6.8756889983348349e-28 1521 # iter: 22 1522 # f_count: 160 1523 # g_count: 160 1524 # h_count: 22 1525 # warning: None 1526 1527 # 32-bit Windows. 1528 # f_count: 165 1529 # g_count: 165 1530 1531 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14176). 1532 # System: Darwin 1533 # Release: 9.8.0 1534 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1535 # Win32 version: 1536 # Distribution: 1537 # Architecture: 32bit 1538 # Machine: i386 1539 # Processor: i386 1540 # Python version: 2.6.2 1541 # numpy version: 1.3.0 1542 # 1543 # s2: 0.9699999999999994 1544 # te: 2048.0000000000446 1545 # rex: 0.14900000000001609 1546 # chi2: 8.3312601381368332e-28 1547 # iter: 22 1548 # f_count: 91 1549 # g_count: 91 1550 # h_count: 22 1551 # warning: None 1552 1553 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14176). 1554 # System: Darwin 1555 # Release: 9.8.0 1556 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1557 # Win32 version: 1558 # Distribution: 1559 # Architecture: 64bit 1560 # Machine: i386 1561 # Processor: i386 1562 # Python version: 2.6.2 1563 # numpy version: 1.3.0 1564 # 1565 # s2: 0.9699999999999994 1566 # te: 2048.0000000000446 1567 # rex: 0.14900000000001609 1568 # chi2: 8.3312601381368332e-28 1569 # iter: 22 1570 # f_count: 91 1571 # g_count: 91 1572 # h_count: 22 1573 # warning: None 1574 1575 # Optimisation values. 1576 select = True 1577 s2 = 0.9699999999999993 1578 te = 2048.000000000041837 1579 rex = 0.14900000000002225 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1580 chi2 = 6.8756889983348349e-28 1581 iter = 22 1582 f_count = [91, 95, 153, 159, 160, 165] 1583 g_count = [91, 95, 153, 159, 160, 165] 1584 h_count = 22 1585 warning = None 1586 1587 # Test the values. 1588 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1589 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1590 1591

1592 - def test_opt_constr_sd_back_S2_0_970_te_2048_Rex_0_149(self):

1593 """Constrained steepest descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1594 1595 The optimisation options are: 1596 - Steepest descent optimisation. 1597 - Backtracking line search. 1598 - Constrained. 1599 1600 The true data set is: 1601 - S2 = 0.970 1602 - te = 2048 ps 1603 - Rex = 0.149 s^-1 1604 """ 1605 1606 # Setup the data pipe for optimisation. 1607 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 1608 1609 # Set up the initial model-free parameter values (bypass the grid search for speed). 1610 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1611 1612 # Minimise. 1613 self.interpreter.minimise('sd', 'back', max_iter=50) 1614 1615 # Alias the relevent spin container. 1616 spin = cdp.mol[0].res[1].spin[0] 1617 1618 # Optimisation differences. 1619 ########################### 1620 1621 # 64-bit x86_64 Linux. 1622 # System: Linux 1623 # Release: 2.6.24.7-server-2mnb 1624 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1625 # Win32 version: 1626 # Distribution: mandriva 2008.1 Official 1627 # Architecture: 64bit ELF 1628 # Machine: x86_64 1629 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1630 # Python version: 2.5.2 1631 # Numpy version: 1.2.0 1632 # Libc version: glibc 2.2.5 1633 # 1634 # s2: 0.9157922083468916 1635 # te: 0.3056865872253 1636 # rex: 0.34008409798064831 1637 # chi2: 68.321956795340569 1638 # iter: 50 1639 # f_count: 134 1640 # g_count: 51 1641 # h_count: 0 1642 # warning: Maximum number of iterations reached 1643 1644 # Optimisation values. 1645 select = True 1646 s2 = 0.91579220834688024 1647 te = 0.30568658722531733 1648 rex = 0.34008409798366124 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1649 chi2 = 68.321956795264342 1650 iter = 50 1651 f_count = 134 1652 g_count = 51 1653 h_count = 0 1654 warning = 'Maximum number of iterations reached' 1655 1656 # Test the values. 1657 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1658 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1659 1660

1661 - def test_opt_constr_sd_mt_S2_0_970_te_2048_Rex_0_149(self):

1662 """Constrained steepest descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1663 1664 The optimisation options are: 1665 - Steepest descent optimisation. 1666 - More and Thuente line search. 1667 - Constrained. 1668 1669 The true data set is: 1670 - S2 = 0.970 1671 - te = 2048 ps 1672 - Rex = 0.149 s^-1 1673 """ 1674 1675 # Setup the data pipe for optimisation. 1676 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 1677 1678 # Set up the initial model-free parameter values (bypass the grid search for speed). 1679 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1680 1681 # Minimise. 1682 self.interpreter.minimise('sd', 'mt', max_iter=50) 1683 1684 # Alias the relevent spin container. 1685 spin = cdp.mol[0].res[1].spin[0] 1686 1687 # Optimisation differences. 1688 ########################### 1689 1690 # 64-bit x86_64 Linux. 1691 # System: Linux 1692 # Release: 2.6.24.7-server-2mnb 1693 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1694 # Win32 version: 1695 # Distribution: mandriva 2008.1 Official 1696 # Architecture: 64bit ELF 1697 # Machine: x86_64 1698 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1699 # Python version: 2.5.2 1700 # Numpy version: 1.2.0 1701 # Libc version: glibc 2.2.5 1702 # 1703 # s2: 0.9161999495781851 1704 # te: 0.1231968757090 1705 # rex: 0.16249110939079675 1706 # chi2: 73.843613548025075 1707 # iter: 50 1708 # f_count: 108 1709 # g_count: 108 1710 # h_count: 0 1711 # warning: Maximum number of iterations reached 1712 1713 # Optimisation values. 1714 select = True 1715 s2 = 0.91619994957822126 1716 te = 0.12319687570987945 1717 rex = 0.16249110942961512 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1718 chi2 = 73.843613546506191 1719 iter = 50 1720 f_count = 108 1721 g_count = 108 1722 h_count = 0 1723 warning = 'Maximum number of iterations reached' 1724 1725 # Test the values. 1726 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1727 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1728 1729

1730 - def test_opt_grid_search_S2_0_970_te_2048_Rex_0_149(self):

1731 """Constrained grid search {S2=0.970, te=2048, Rex=0.149}. 1732 1733 The optimisation options are: 1734 - Constrained grid search. 1735 1736 The true data set is: 1737 - S2 = 0.970 1738 - te = 2048 ps 1739 - Rex = 0.149 s^-1 1740 """ 1741 1742 # Setup the data pipe for optimisation. 1743 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_S2_0_970_te_2048_Rex_0_149.py') 1744 1745 # Grid search. 1746 self.interpreter.grid_search(inc=11) 1747 1748 # Alias the relevent spin container. 1749 spin = cdp.mol[0].res[1].spin[0] 1750 1751 # Optimisation differences. 1752 ########################### 1753 1754 # 64-bit x86_64 Linux. 1755 # System: Linux 1756 # Release: 2.6.24.7-server-2mnb 1757 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1758 # Win32 version: 1759 # Distribution: mandriva 2008.1 Official 1760 # Architecture: 64bit ELF 1761 # Machine: x86_64 1762 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1763 # Python version: 2.5.2 1764 # Numpy version: 1.2.0 1765 # Libc version: glibc 2.2.5 1766 # 1767 # s2: 1 1768 # te: 0 1769 # rex: 0 1770 # chi2: 3.9844117908982288 1771 # iter: 1331 1772 # f_count: 1331 1773 # g_count: 0 1774 # h_count: 0 1775 # warning: None 1776 1777 # Optimisation values. 1778 select = True 1779 s2 = 1.0 1780 te = 0.0 1781 rex = 0.0 1782 chi2 = 3.9844117908982288 1783 iter = 1331 1784 f_count = 1331 1785 g_count = 0 1786 h_count = 0 1787 warning = None 1788 1789 # Test the values. 1790 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1791 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1792 1793

1794 - def test_read_relax_data(self):

1795 """Reading of relaxation data using the user function relax_data.read().""" 1796 1797 # Path of the files. 1798 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 1799 1800 # Read the sequence. 1801 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 1802 1803 # Read the relaxation data. 1804 self.interpreter.relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.0 * 1e6, file='r1.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 1805 1806 # Test the data and error. 1807 self.assertEqual(cdp.mol[0].res[1].spin[0].ri_data['R1_600'], 1.3874977659397683) 1808 self.assertEqual(cdp.mol[0].res[1].spin[0].ri_data_err['R1_600'], 0.027749955318795365)

1809 1810

1811 - def test_read_results_1_2(self):

1812 """Read a relax 1.2 model-free results file using the user function results.read().""" 1813 1814 # Read the results. 1815 self.interpreter.results.read(file='results_1.2', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 1816 1817 # Debugging print out. 1818 print(cdp) 1819 1820 # The spin specific data. 1821 num = [3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35] 1822 select = [False, False, False, False, False, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, False, False, False] 1823 model = ['m6', 'm8', 'm6', 'm6', 'm5', 'm5', 'm6', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm8'] 1824 params = [['s2f', 'tf', 's2', 'ts'], ['s2f', 'tf', 's2', 'ts', 'rex'], ['s2f', 'tf', 's2', 'ts'], ['s2f', 'tf', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 'tf', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 's2', 'ts'], ['s2f', 'tf', 's2', 'ts', 'rex']] 1825 s2 = [0.36670427146403667, 0.29007016882193892, 0.32969827132809559, 0.32795333510352148, 0.48713005133752196, 0.40269538236298569, 0.40700811448591556, 0.4283551026406261, 0.51176783207279875, 0.40593664887508263, 0.39437732735324443, 0.51457448574034614, 0.3946900969237977, 0.44740698217286901, 0.48527716982891644, 0.40845486062540021, 0.45839900995265137, 0.52650140958170921, 0.4293599736020427, 0.4057313062564018, 0.49877862202992485, 0.2592017578673716] 1826 s2f = [0.74487419686217116, 0.75358958979175727, 0.77751085082436211, 0.79095600331751026, 0.81059857999556584, 0.83190224667917501, 0.80119109731193627, 0.83083248649122576, 0.86030420847112021, 0.84853537580616367, 0.82378413185968968, 0.82419108009774422, 0.85121172821954216, 0.8736616181472916, 0.84117641395909415, 0.82881488883235521, 0.82697284935760407, 0.85172375147802715, 0.81366357660551614, 0.80525752789388483, 0.87016608774434312, 0.72732036363757913] 1827 s2s = [0.49230363061145249, 0.38491796164819009, 0.4240433056059994, 0.41462904855388333, 0.60095102971952741, 0.48406574687168274, 0.50800379067049317, 0.51557336720143987, 0.59486845122178478, 0.47839684761453399, 0.47873867934666214, 0.62433881919629686, 0.46368028522041266, 0.51210557140148982, 0.57690296800513374, 0.49281795745831319, 0.55430962492751434, 0.61815983018913379, 0.5276873464009153, 0.50385285725620466, 0.57319933407525203, 0.35637907423767778] 1828 tf = [51.972302580836775, 40.664901270582988, 28.130299965023671, 33.804249387275249, None, None, 39.01236115991609, None, None, None, None, None, None, None, None, None, None, None, None, None, None, 44.039078787981225] 1829 ts = [4485.91415175767, 4102.7781982031429, 3569.2837792404325, 6879.5308400989479, 3372.9879908647699, 4029.0617588044606, 4335.5290462417324, 4609.1336532777468, 2628.5638771308277, 3618.1332115807745, 6208.3028336637644, 3763.0843884066526, 3847.9994107906346, 2215.2061317769703, 2936.1282626562524, 3647.0715185456729, 3803.6990762708042, 2277.5259401416288, 3448.4496004396187, 3884.6917561878495, 1959.3267951363712, 4100.8496898773756] 1830 rex = [None, 0.37670424516405815, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, 0.71472288436387088] 1831 1832 # Relaxation data. 1833 ri_ids = ['R1_500', 'R2_500', 'NOE_500', 'R1_600', 'R2_600', 'NOE_600', 'R1_750', 'R2_750', 'NOE_750'] 1834 types_list = ['R1', 'R2', 'NOE', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 1835 frqs_list = [500000000.0] * 3 + [600000000.0] * 3 + [750000000.0] * 3 1836 ri_type = {} 1837 frqs = {} 1838 for i in range(len(ri_ids)): 1839 ri_type[ri_ids[i]] = types_list[i] 1840 frqs[ri_ids[i]] = frqs_list[i] 1841 1842 ri_data = {} 1843 ri_data['R1_500'] = [2.2480000000000002, 2.2679999999999998, 2.2309999999999999, 2.383, 2.1960000000000002, 2.3570000000000002, 2.3340000000000001, 2.3999999999999999, 2.2839999999999998, 2.3889999999999998, 2.375, 2.274, 2.407, 2.3220000000000001, 2.2130000000000001, 2.351, 2.3260000000000001, 2.2949999999999999, 2.2829999999999999, 2.302, 2.2719999999999998, 2.2280000000000002] 1844 ri_data['R2_500'] = [5.3419999999999996, 5.3730000000000002, 5.1280000000000001, 5.6749999999999998, 5.9669999999999996, 5.8410000000000002, 5.774, 6.0419999999999998, 6.3129999999999997, 5.9210000000000003, 6.1269999999999998, 6.1120000000000001, 6.0570000000000004, 5.6399999999999997, 6.2809999999999997, 5.8890000000000002, 5.875, 6.1429999999999998, 5.7370000000000001, 5.5490000000000004, 5.7110000000000003, 5.4020000000000001] 1845 ri_data['NOE_500'] = [0.4617, 0.46560000000000001, 0.61670000000000003, 0.60860000000000003, 0.68869999999999998, 0.6663, 0.58620000000000005, 0.64939999999999998, 0.61070000000000002, 0.61180000000000001, 0.73129999999999995, 0.69650000000000001, 0.65139999999999998, 0.4929, 0.65920000000000001, 0.63029999999999997, 0.64380000000000004, 0.53500000000000003, 0.63839999999999997, 0.65000000000000002, 0.49909999999999999, 0.45979999999999999] 1846 ri_data['R1_600'] = [1.8879999999999999, 1.992, 2.0270000000000001, 1.9790000000000001, 1.9399999999999999, 2.0550000000000002, 2.0030000000000001, 2.0139999999999998, 1.982, 2.1000000000000001, 2.008, 1.927, 2.1019999999999999, 2.0830000000000002, 1.9910000000000001, 2.036, 1.9990000000000001, 1.9490000000000001, 1.976, 1.9870000000000001, 2.0, 1.9379999999999999] 1847 ri_data['R2_600'] = [5.6100000000000003, 5.7869999999999999, 5.4029999999999996, 6.1849999999999996, 6.3150000000000004, 5.9809999999999999, 6.1600000000000001, 6.2460000000000004, 6.4340000000000002, 6.0069999999999997, 6.399, 6.6799999999999997, 6.1369999999999996, 5.952, 6.3239999999999998, 5.9699999999999998, 6.3979999999999997, 6.4379999999999997, 6.1139999999999999, 6.0960000000000001, 6.3250000000000002, 6.1050000000000004] 1848 ri_data['NOE_600'] = [0.62929999999999997, 0.64429999999999998, 0.5393, 0.71509999999999996, 0.73870000000000002, 0.75580000000000003, 0.64239999999999997, 0.74429999999999996, 0.69440000000000002, 0.73140000000000005, 0.7681, 0.73399999999999999, 0.75680000000000003, 0.62470000000000003, 0.73529999999999995, 0.73740000000000006, 0.73080000000000001, 0.6603, 0.70899999999999996, 0.69040000000000001, 0.59199999999999997, 0.56830000000000003] 1849 ri_data['R1_750'] = [1.6220000000000001, 1.706, 1.73, 1.665, 1.627, 1.768, 1.706, 1.7030000000000001, 1.7649999999999999, 1.8129999999999999, 1.675, 1.6339999999999999, 1.845, 1.7829999999999999, 1.764, 1.7470000000000001, 1.681, 1.647, 1.6850000000000001, 1.667, 1.7010000000000001, 1.6850000000000001] 1850 ri_data['R2_750'] = [6.2619999999999996, 6.5359999999999996, 5.8959999999999999, 6.6840000000000002, 6.8819999999999997, 6.7569999999999997, 6.5620000000000003, 7.0030000000000001, 6.9740000000000002, 6.649, 6.9829999999999997, 7.2309999999999999, 6.4429999999999996, 6.6840000000000002, 6.8070000000000004, 6.4850000000000003, 6.9400000000000004, 6.944, 6.4640000000000004, 6.4889999999999999, 6.9009999999999998, 6.9539999999999997] 1851 ri_data['NOE_750'] = [0.61909999999999998, 0.65890000000000004, 0.72009999999999996, 0.71009999999999995, 0.75219999999999998, 0.80420000000000003, 0.70020000000000004, 0.81999999999999995, 0.81040000000000001, 0.83409999999999995, 0.81299999999999994, 0.81910000000000005, 0.7782, 0.74760000000000004, 0.8115, 0.7379, 0.81100000000000005, 0.78249999999999997, 0.75729999999999997, 0.78259999999999996, 0.75139999999999996, 0.65210000000000001] 1852 1853 ri_data_err = {} 1854 ri_data_err['R1_500'] = [0.044999999999999998, 0.044999999999999998, 0.044499999999999998, 0.048000000000000001, 0.043999999999999997, 0.047, 0.0465, 0.048000000000000001, 0.045499999999999999, 0.048000000000000001, 0.047500000000000001, 0.045499999999999999, 0.048000000000000001, 0.0465, 0.044499999999999998, 0.047, 0.0465, 0.045499999999999999, 0.045499999999999999, 0.045999999999999999, 0.045499999999999999, 0.044499999999999998] 1855 ri_data_err['R2_500'] = [0.107, 0.1075, 0.10249999999999999, 0.1135, 0.11899999999999999, 0.11650000000000001, 0.11600000000000001, 0.121, 0.1265, 0.11799999999999999, 0.123, 0.122, 0.1215, 0.1125, 0.17599999999999999, 0.11749999999999999, 0.11749999999999999, 0.123, 0.1145, 0.111, 0.1145, 0.108] 1856 ri_data_err['NOE_500'] = [0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003] 1857 ri_data_err['R1_600'] = [0.037999999999999999, 0.040000000000000001, 0.040500000000000001, 0.0395, 0.0385, 0.041000000000000002, 0.040000000000000001, 0.040500000000000001, 0.040000000000000001, 0.042000000000000003, 0.041500000000000002, 0.039, 0.042000000000000003, 0.042000000000000003, 0.0395, 0.040500000000000001, 0.040000000000000001, 0.039, 0.0395, 0.040000000000000001, 0.040500000000000001, 0.039] 1858 ri_data_err['R2_600'] = [0.1125, 0.11550000000000001, 0.108, 0.1235, 0.1265, 0.1275, 0.123, 0.125, 0.1285, 0.12, 0.128, 0.13350000000000001, 0.1225, 0.11899999999999999, 0.1265, 0.1195, 0.128, 0.129, 0.1225, 0.122, 0.1265, 0.1225] 1859 ri_data_err['NOE_600'] = [0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003] 1860 ri_data_err['R1_750'] = [0.032500000000000001, 0.034000000000000002, 0.035000000000000003, 0.033500000000000002, 0.032500000000000001, 0.035499999999999997, 0.034000000000000002, 0.034000000000000002, 0.035499999999999997, 0.036499999999999998, 0.033500000000000002, 0.032500000000000001, 0.036999999999999998, 0.035499999999999997, 0.035499999999999997, 0.035000000000000003, 0.033500000000000002, 0.033000000000000002, 0.034000000000000002, 0.033000000000000002, 0.034000000000000002, 0.033500000000000002] 1861 ri_data_err['R2_750'] = [0.1255, 0.1305, 0.11799999999999999, 0.13400000000000001, 0.13800000000000001, 0.13550000000000001, 0.13150000000000001, 0.14050000000000001, 0.13950000000000001, 0.13300000000000001, 0.14000000000000001, 0.14449999999999999, 0.129, 0.13400000000000001, 0.13600000000000001, 0.1295, 0.13850000000000001, 0.13900000000000001, 0.1295, 0.13, 0.13800000000000001, 0.13900000000000001] 1862 ri_data_err['NOE_750'] = [0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003, 0.050000000000000003] 1863 1864 # Misc tests. 1865 self.assertEqual(cdp.pipe_type, 'mf') 1866 self.assertEqual(cdp.hybrid_pipes, []) 1867 1868 # Diffusion tensor tests. 1869 self.assertEqual(cdp.diff_tensor.type, 'sphere') 1870 self.assertEqual(cdp.diff_tensor.tm, 6.2029050826362826e-09) 1871 1872 # Global minimisation statistic tests. 1873 self.assertEqual(cdp.chi2, 88.0888600975) 1874 self.assertEqual(cdp.iter, 1) 1875 self.assertEqual(cdp.f_count, 20) 1876 self.assertEqual(cdp.g_count, 2) 1877 self.assertEqual(cdp.h_count, 1) 1878 self.assertEqual(cdp.warning, None) 1879 1880 # Global relaxation data tests. 1881 self.assertEqual(cdp.ri_ids, ri_ids) 1882 for ri_id in ri_ids: 1883 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 1884 self.assertEqual(cdp.frq[ri_id], frqs[ri_id]) 1885 1886 # Loop over the residues of the original data. 1887 j = 0 1888 for i in xrange(len(cdp.mol[0].res)): 1889 # Aliases 1890 res = cdp.mol[0].res[i] 1891 spin = cdp.mol[0].res[i].spin[0] 1892 1893 # Debugging print out. 1894 print(res) 1895 print(spin) 1896 1897 # Spin info tests. 1898 self.assertEqual(res.num, num[i]) 1899 self.assertEqual(res.name, 'XXX') 1900 self.assertEqual(spin.num, None) 1901 self.assertEqual(spin.name, None) 1902 self.assertEqual(spin.select, select[i]) 1903 self.assertEqual(spin.fixed, False) 1904 1905 # Skip deselected spins. 1906 if not select[i]: 1907 continue 1908 1909 # Structural info. 1910 self.assertEqual(spin.heteronuc_type, '15N') 1911 self.assertEqual(spin.proton_type, '1H') 1912 self.assertEqual(spin.attached_proton, None) 1913 self.assertEqual(spin.nucleus, None) 1914 1915 # Model-free tests. 1916 self.assertEqual(spin.model, model[j]) 1917 self.assertEqual(spin.equation, 'mf_ext') 1918 self.assertEqual(spin.params, params[j]) 1919 self.assertEqual(spin.s2, s2[j]) 1920 self.assertEqual(spin.s2f, s2f[j]) 1921 self.assertEqual(spin.s2s, s2s[j]) 1922 self.assertEqual(spin.local_tm, None) 1923 self.assertEqual(spin.te, None) 1924 if tf[j] != None: 1925 tf[j] = tf[j]*1e-12 1926 self.assertEqual(spin.tf, tf[j]) 1927 self.assertEqual(spin.ts, ts[j]*1e-12) 1928 if rex[j] != None: 1929 rex[j] = rex[j]/(2.0*pi*500000000.0)**2 1930 self.assertEqual(spin.rex, rex[j]) 1931 self.assertEqual(spin.r, 1.0200000000000001e-10) 1932 self.assertEqual(spin.csa, -0.00016999999999999999) 1933 1934 # Minimisation statistic tests. 1935 self.assertEqual(spin.chi2, None) 1936 self.assertEqual(spin.iter, None) 1937 self.assertEqual(spin.f_count, None) 1938 self.assertEqual(spin.g_count, None) 1939 self.assertEqual(spin.h_count, None) 1940 self.assertEqual(spin.warning, None) 1941 1942 # Relaxation data tests. 1943 for ri_id in cdp.ri_ids: 1944 print(ri_id) 1945 self.assertEqual(spin.ri_data[ri_id], ri_data[ri_id][j]) 1946 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[ri_id][j]) 1947 1948 # Secondary index. 1949 j = j + 1

1950 1951

1952 - def test_read_results_1_2_pse4(self):

1953 """Read the truncated relax 1.2 model-free results file for PSE-4.""" 1954 1955 # Read the results. 1956 self.interpreter.results.read(file='pse4_trunc', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 1957 1958 # Debugging print out. 1959 print(cdp) 1960 1961 # The spin specific data. 1962 num = [24, 27] 1963 name = ['ser', 'gln'] 1964 eqi = [None, 'mf_ext'] 1965 select = [False, True] 1966 model = [None, 'm5'] 1967 params = [[], ['s2f', 's2', 'ts']] 1968 s2 = [None, 0.86578779694713515] 1969 s2f = [None, 0.88618694421409949] 1970 s2s = [None, 0.97698098871784322] 1971 s2s_sim = [[None, None, None], 1972 [0.95852080081635382, 0.97574415413309512, 0.97293450506144197]] 1973 tf = [None, None] 1974 ts = [None, 598.8142249659868e-12] 1975 rex = [None, None] 1976 r = [None, 1.0200000000000001e-10] 1977 csa = [None, -0.00017199999999999998] 1978 ri_ids = ['R1_800', 'NOE_800', 'R1_600', 'R2_600', 'NOE_600', 'R1_500', 'R2_500', 'NOE_500'] 1979 ri_type_list = ['R1', 'NOE', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 1980 frq_list = [799744000.0]*2 + [599737000.0]*3 + [499719000.0]*3 1981 ri_data_list = [[], 1982 [0.6835, 0.81850000000000001, 0.98409999999999997, 16.5107, 0.79796699999999998, 1.3174999999999999, 15.381500000000001, 0.73046900000000003]] 1983 ri_data_err_list = [[], 1984 [0.026957200000000001, 0.025881000000000001, 0.0243073, 0.497137, 0.028663000000000001, 0.038550000000000001, 0.40883999999999998, 0.022016299999999999]] 1985 ri_type = {} 1986 frq = {} 1987 ri_data = [{}, {}] 1988 ri_data_err = [{}, {}] 1989 for i in range(len(ri_ids)): 1990 ri_type[ri_ids[i]] = ri_type_list[i] 1991 frq[ri_ids[i]] = frq_list[i] 1992 ri_data[1][ri_ids[i]] = ri_data_list[1][i] 1993 ri_data_err[1][ri_ids[i]] = ri_data_err_list[1][i] 1994 1995 # Misc tests. 1996 self.assertEqual(cdp.pipe_type, 'mf') 1997 self.assertEqual(cdp.hybrid_pipes, []) 1998 1999 # Diffusion tensor tests. 2000 self.assertEqual(cdp.diff_tensor.type, 'ellipsoid') 2001 self.assertEqual(cdp.diff_tensor.tm, 1.2682770910095516e-08) 2002 self.assertEqual(cdp.diff_tensor.tm_err, 2.4053909822304126e-11) 2003 self.assertEqual(cdp.diff_tensor.tm_sim[0], 1.2666656725867738e-08) 2004 self.assertEqual(cdp.diff_tensor.tm_sim[1], 1.2689812011679408e-08) 2005 self.assertEqual(cdp.diff_tensor.tm_sim[2], 1.2698266641804573e-08) 2006 2007 # Global minimisation statistic tests. 2008 self.assertEqual(cdp.chi2, 935.13348627485448) 2009 self.assertEqual(cdp.chi2_sim[0], 898.0981500197106) 2010 self.assertEqual(cdp.chi2_sim[1], 904.11113814725172) 2011 self.assertEqual(cdp.chi2_sim[2], 902.03890817023728) 2012 self.assertEqual(cdp.iter, 1) 2013 self.assertEqual(cdp.iter_sim[0], 23) 2014 self.assertEqual(cdp.iter_sim[1], 30) 2015 self.assertEqual(cdp.iter_sim[2], 16) 2016 self.assertEqual(cdp.f_count, 21) 2017 self.assertEqual(cdp.f_count_sim[0], 61) 2018 self.assertEqual(cdp.f_count_sim[1], 501) 2019 self.assertEqual(cdp.f_count_sim[2], 59) 2020 self.assertEqual(cdp.g_count, 2) 2021 self.assertEqual(cdp.g_count_sim[0], 27) 2022 self.assertEqual(cdp.g_count_sim[1], 34) 2023 self.assertEqual(cdp.g_count_sim[2], 20) 2024 self.assertEqual(cdp.h_count, 1) 2025 self.assertEqual(cdp.h_count_sim[0], 23) 2026 self.assertEqual(cdp.h_count_sim[1], 30) 2027 self.assertEqual(cdp.h_count_sim[2], 16) 2028 self.assertEqual(cdp.warning, None) 2029 self.assertEqual(cdp.warning_sim[0], None) 2030 self.assertEqual(cdp.warning_sim[1], None) 2031 self.assertEqual(cdp.warning_sim[2], None) 2032 2033 # Global relaxation data tests. 2034 self.assertEqual(cdp.ri_ids, ri_ids) 2035 for ri_id in ri_ids: 2036 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 2037 self.assertEqual(cdp.frq[ri_id], frq[ri_id]) 2038 2039 # Loop over the residues of the original data. 2040 for i in xrange(len(cdp.mol[0].res)): 2041 # Aliases 2042 res = cdp.mol[0].res[i] 2043 spin = cdp.mol[0].res[i].spin[0] 2044 2045 # Debugging print out. 2046 print(res) 2047 print(spin) 2048 2049 # Spin info tests. 2050 self.assertEqual(res.num, num[i]) 2051 self.assertEqual(res.name, name[i]) 2052 self.assertEqual(spin.num, None) 2053 self.assertEqual(spin.name, None) 2054 self.assertEqual(spin.select, select[i]) 2055 self.assertEqual(spin.fixed, False) 2056 2057 # Structural info. 2058 self.assertEqual(spin.heteronuc_type, '15N') 2059 self.assertEqual(spin.proton_type, '1H') 2060 self.assertEqual(spin.attached_proton, 'H') 2061 #FIXME 2062 #self.assertEqual(spin.nucleus, 'N') 2063 2064 # Model-free tests. 2065 self.assertEqual(spin.model, model[i]) 2066 self.assertEqual(spin.equation, eqi[i]) 2067 self.assertEqual(spin.params, params[i]) 2068 self.assertEqual(spin.s2, s2[i]) 2069 self.assertEqual(spin.s2f, s2f[i]) 2070 self.assertEqual(spin.s2s, s2s[i]) 2071 self.assertEqual(spin.local_tm, None) 2072 self.assertEqual(spin.te, None) 2073 self.assertEqual(spin.tf, tf[i]) 2074 self.assertEqual(spin.ts, ts[i]) 2075 self.assertEqual(spin.rex, rex[i]) 2076 self.assertEqual(spin.r, r[i]) 2077 self.assertEqual(spin.csa, csa[i]) 2078 for j in range(3): 2079 self.assertEqual(spin.s2s_sim[j], s2s_sim[i][j]) 2080 2081 # Minimisation statistic tests. 2082 self.assertEqual(spin.chi2, None) 2083 self.assertEqual(spin.iter, None) 2084 self.assertEqual(spin.f_count, None) 2085 self.assertEqual(spin.g_count, None) 2086 self.assertEqual(spin.h_count, None) 2087 self.assertEqual(spin.warning, None) 2088 2089 # Relaxation data tests. 2090 if i == 0: 2091 self.assertEqual(spin.ri_data, {}) 2092 self.assertEqual(spin.ri_data_err, {}) 2093 else: 2094 for ri_id in ri_ids: 2095 self.assertEqual(spin.ri_data[ri_id], ri_data[i][ri_id]) 2096 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[i][ri_id])

2097 2098

2099 - def test_read_results_1_2_tem1(self):

2100 """Read the truncated relax 1.2 model-free results file for TEM-1.""" 2101 2102 # Read the results. 2103 self.interpreter.results.read(file='tem1_trunc', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 2104 2105 # Debugging print out. 2106 print(cdp) 2107 2108 # The spin specific data. 2109 num = [26, 27, 29, 30, 31, 32, 33, 34] 2110 name = ['His', 'Pro', 'Thr', 'Leu', 'Val', 'Lys', 'Val', 'Lys'] 2111 eqi = [None, None, None, 'mf_ext', 'mf_orig', 'mf_orig', None, 'mf_orig'] 2112 select = [False, False, False, True, True, True, False, True] 2113 model = [None, None, None, 'm5', 'm2', 'm1', None, 'm1'] 2114 params = [None, None, None, ['s2f', 's2', 'ts'], ['s2', 'te'], ['s2'], None, ['s2']] 2115 s2 = [None, None, None, 0.85674161305142216, 0.89462664243726608, 0.90201790111143165, None, 0.92099297347361675] 2116 s2f = [None, None, None, 0.88220054271390302, None, None, None, None] 2117 s2s = [None, None, None, 0.97114156200339452, None, None, None, None] 2118 te = [None, None, None, None, 43.262426916926735*1e-12, None, None, None] 2119 tf = [None, None, None, None, None, None, None, None] 2120 ts = [None, None, None, 2385.912514843546*1e-12, None, None, None, None] 2121 rex = [None, None, None, None, None, None, None, None] 2122 r = [None, None, None, 1.0200000000000001e-10, 1.0200000000000001e-10, 1.0200000000000001e-10, None, 1.0200000000000001e-10] 2123 csa = [None, None, None, -0.00017199999999999998, -0.00017199999999999998, -0.00017199999999999998, None, -0.00017199999999999998] 2124 ri_ids = ['R1_800', 'R2_800', 'R1_600', 'R2_600', 'NOE_600', 'R1_500', 'R2_500', 'NOE_500'] 2125 ri_type_list = ['R1', 'R2', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 2126 frq_list = [799812000.0]*2 + [599739000.0]*3 + [499827000.0]*3 2127 ri_data_list = [[], 2128 [], 2129 [], 2130 [0.75680000000000003, 18.797999999999998, 1.0747, 16.477, 0.86873100000000003, 1.2625999999999999, 15.3367, 0.77803197999999996], 2131 [0.75019999999999998, 19.201599999999999, 1.0617000000000001, 17.652899999999999, 0.73757200000000001, 1.3165, 15.949, 0.72442474000000001], 2132 [0.75860000000000005, 19.303799999999999, 1.0605, 16.593699999999998, 0.79137500000000005, 1.3425, 15.327199999999999, 0.83449132000000004], 2133 [], 2134 [0.71919999999999995, 20.165400000000002, 1.0729, 17.291899999999998, 0.80444599999999999, 1.2971999999999999, 15.9963, 0.73164684999999996]] 2135 ri_data_err_list = [[], 2136 [], 2137 [], 2138 [0.028001600000000001, 0.21729999999999999, 0.031166300000000001, 0.44487900000000002, 0.043210699999999998, 0.054291800000000001, 0.69015199999999999, 0.038901600000000001], 2139 [0.028899999999999999, 0.25640000000000002, 0.030789299999999999, 0.476628, 0.036686799999999999, 0.0566095, 0.71770500000000004, 0.036221200000000002], 2140 [0.033399999999999999, 0.2233, 0.030754500000000001, 0.44802999999999998, 0.039363000000000002, 0.057727500000000001, 0.689724, 0.041724600000000001], 2141 [], 2142 [0.027699999999999999, 0.52810000000000001, 0.031399999999999997, 0.46688099999999999, 0.040013100000000003, 0.055779599999999999, 0.71983399999999997, 0.036582299999999998]] 2143 ri_type = {} 2144 frq = {} 2145 ri_data = [] 2146 ri_data_err = [] 2147 for i in range(len(ri_data_list)): 2148 ri_data.append({}) 2149 ri_data_err.append({}) 2150 2151 for i in range(len(ri_ids)): 2152 ri_type[ri_ids[i]] = ri_type_list[i] 2153 frq[ri_ids[i]] = frq_list[i] 2154 for j in range(len(ri_data_list)): 2155 if len(ri_data_list[j]): 2156 ri_data[j][ri_ids[i]] = ri_data_list[j][i] 2157 ri_data_err[j][ri_ids[i]] = ri_data_err_list[j][i] 2158 2159 chi2 = [None, None, None, 7.9383923597292441, 10.93852890925343, 3.1931459495488084, None, 8.3598891989018611] 2160 iter = [None, None, None, 55, 10, 3, None, 3] 2161 f_count = [None, None, None, 170, 148, 10, None, 10] 2162 g_count = [None, None, None, 60, 14, 6, None, 6] 2163 h_count = [None, None, None, 55, 10, 3, None, 3] 2164 2165 # Misc tests. 2166 self.assertEqual(cdp.pipe_type, 'mf') 2167 self.assertEqual(cdp.hybrid_pipes, []) 2168 2169 # Diffusion tensor tests. 2170 self.assertEqual(cdp.diff_tensor.type, 'ellipsoid') 2171 self.assertEqual(cdp.diff_tensor.tm, 1.2526607261882971e-08) 2172 self.assertEqual(cdp.diff_tensor.Da, 2784606.8835473624) 2173 self.assertEqual(cdp.diff_tensor.Dr, 0.097243698709517518) 2174 self.assertEqual(cdp.diff_tensor.alpha, 48.852555276419558 / 360.0 * 2.0 * pi) 2175 self.assertEqual(cdp.diff_tensor.beta, 9.7876096346750447 / 360.0 * 2.0 * pi) 2176 self.assertEqual(cdp.diff_tensor.gamma, 42.15815798778408 / 360.0 * 2.0 * pi) 2177 2178 # Global relaxation data tests. 2179 self.assertEqual(cdp.ri_ids, ri_ids) 2180 for ri_id in ri_ids: 2181 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 2182 self.assertEqual(cdp.frq[ri_id], frq[ri_id]) 2183 2184 # Loop over the residues of the original data. 2185 for i in xrange(len(cdp.mol[0].res)): 2186 # Aliases 2187 res = cdp.mol[0].res[i] 2188 spin = cdp.mol[0].res[i].spin[0] 2189 2190 # Debugging print out. 2191 print(res) 2192 print(spin) 2193 2194 # Spin info tests. 2195 self.assertEqual(res.num, num[i]) 2196 self.assertEqual(res.name, name[i]) 2197 self.assertEqual(spin.num, None) 2198 self.assertEqual(spin.name, None) 2199 self.assertEqual(spin.select, select[i]) 2200 self.assertEqual(spin.fixed, False) 2201 2202 # Structural info. 2203 self.assertEqual(spin.heteronuc_type, '15N') 2204 self.assertEqual(spin.proton_type, '1H') 2205 self.assertEqual(spin.attached_proton, 'H') 2206 #FIXME 2207 #self.assertEqual(spin.nucleus, 'N') 2208 2209 # Model-free tests. 2210 self.assertEqual(spin.model, model[i]) 2211 self.assertEqual(spin.equation, eqi[i]) 2212 self.assertEqual(spin.params, params[i]) 2213 self.assertEqual(spin.s2, s2[i]) 2214 self.assertEqual(spin.s2f, s2f[i]) 2215 self.assertEqual(spin.s2s, s2s[i]) 2216 self.assertEqual(spin.local_tm, None) 2217 self.assertEqual(spin.te, te[i]) 2218 self.assertEqual(spin.tf, tf[i]) 2219 self.assertEqual(spin.ts, ts[i]) 2220 self.assertEqual(spin.rex, rex[i]) 2221 self.assertEqual(spin.r, r[i]) 2222 self.assertEqual(spin.csa, csa[i]) 2223 2224 # Minimisation statistic tests. 2225 self.assertEqual(spin.chi2, chi2[i]) 2226 self.assertEqual(spin.iter, iter[i]) 2227 self.assertEqual(spin.f_count, f_count[i]) 2228 self.assertEqual(spin.g_count, g_count[i]) 2229 self.assertEqual(spin.h_count, h_count[i]) 2230 self.assertEqual(spin.warning, None) 2231 2232 # Relaxation data tests. 2233 print ri_data 2234 if not ri_data[i].keys(): 2235 self.assertEqual(spin.ri_data, {}) 2236 self.assertEqual(spin.ri_data_err, {}) 2237 else: 2238 for ri_id in ri_ids: 2239 self.assertEqual(spin.ri_data[ri_id], ri_data[i][ri_id]) 2240 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[i][ri_id])

2241 2242

2243 - def test_read_results_1_3(self):

2244 """Read a relax 1.3 model-free results file using the user function results.read().""" 2245 2246 # Path of the files. 2247 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2248 2249 # Read the results file. 2250 self.interpreter.pipe.create('1.3', 'mf') 2251 self.interpreter.results.read(file='final_results_trunc_1.3', dir=path) 2252 2253 # Read the equivalent 1.2 results file for the checks. 2254 self.interpreter.pipe.create('1.2', 'mf') 2255 self.interpreter.results.read(file='final_results_trunc_1.2', dir=path) 2256 2257 # Get the two data pipes. 2258 pipe_12 = pipes.get_pipe('1.2') 2259 pipe_13 = pipes.get_pipe('1.3') 2260 2261 # Test that the objects in the base pipes are the same. 2262 print("Comparison of the objects of the base data pipe:") 2263 self.object_comparison(obj1=pipe_12, obj2=pipe_13, skip=['mol', 'diff_tensor']) 2264 2265 # Test that the diffusion tensor data is the same. 2266 print("Comparison of the objects of the diffusion tensor:") 2267 self.object_comparison(obj1=pipe_12.diff_tensor, obj2=pipe_13.diff_tensor) 2268 2269 # Test the number of molecules. 2270 self.assertEqual(len(pipe_12.mol), len(pipe_13.mol)) 2271 2272 # Loop over the molecules. 2273 for i in xrange(len(pipe_12.mol)): 2274 # Test the objects. 2275 print("Comparison of the objects of the molecule:") 2276 self.object_comparison(obj1=pipe_12.mol[i], obj2=pipe_13.mol[i], skip=['res']) 2277 2278 # Test the number of residues. 2279 self.assertEqual(len(pipe_12.mol[i].res), len(pipe_13.mol[i].res)) 2280 2281 # Loop over the residues. 2282 for j in xrange(len(pipe_12.mol[i].res)): 2283 # Ok, really don't need to do a full comparison of all 162 residues for this test! 2284 if j > 10: 2285 break 2286 2287 # Test the objects. 2288 print("Comparison of the objects of the residue:") 2289 self.object_comparison(obj1=pipe_12.mol[i].res[j], obj2=pipe_13.mol[i].res[j], skip=['spin']) 2290 2291 # Test the number of spins. 2292 self.assertEqual(len(pipe_12.mol[i].res[j].spin), len(pipe_13.mol[i].res[j].spin)) 2293 2294 # Loop over the spins. 2295 for k in xrange(len(pipe_12.mol[i].res[j].spin)): 2296 # Test the objects. 2297 print("Comparison of the objects of the spin:") 2298 self.object_comparison(obj1=pipe_12.mol[i].res[j].spin[k], obj2=pipe_13.mol[i].res[j].spin[k])

2299 2300 2301

2302 - def test_select_m4(self):

2303 """Selecting model m4 with parameters {S2, te, Rex} using model_free.select_model().""" 2304 2305 # Path of the files. 2306 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2307 2308 # Read the sequence. 2309 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2310 2311 # Select the model. 2312 self.interpreter.model_free.select_model(model='m4') 2313 2314 # Test the model. 2315 self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4') 2316 self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['s2', 'te', 'rex'])

2317 2318

2319 - def test_set_bond_length(self):

2320 """Setting the bond length through the user function value.set().""" 2321 2322 # Path of the files. 2323 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2324 2325 # Read the sequence. 2326 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2327 2328 # Set the CSA value. 2329 self.interpreter.value.set(NH_BOND_LENGTH, 'r') 2330 2331 # Test the value. 2332 self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)

2333 2334

2335 - def test_set_csa(self):

2336 """Setting the CSA value through the user function value.set().""" 2337 2338 # Path of the files. 2339 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2340 2341 # Read the sequence. 2342 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2343 2344 # Set the CSA value. 2345 self.interpreter.value.set(N15_CSA, 'csa') 2346 2347 # Test the value. 2348 self.assertEqual(cdp.mol[0].res[1].spin[0].csa, N15_CSA)

2349 2350

2351 - def test_set_csa_bond_length(self):

2352 """Setting both the CSA value and bond length through the user function value.set().""" 2353 2354 # Path of the files. 2355 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2356 2357 # Read the sequence. 2358 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2359 2360 # Set the CSA value and bond length simultaneously. 2361 self.interpreter.value.set([N15_CSA, NH_BOND_LENGTH], ['csa', 'r']) 2362 2363 # Test the values. 2364 self.assertEqual(cdp.mol[0].res[1].spin[0].csa, N15_CSA) 2365 self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)

2366 2367

2368 - def test_tm0_grid(self):

2369 """Test the optimisation of the tm0 model-free parameter grid.""" 2370 2371 # Initialise. 2372 cdp._model = 'tm0' 2373 cdp._value_test = self.value_test 2374 2375 # Setup the data pipe for optimisation. 2376 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

2377 2378

2379 - def test_tm1_grid(self):

2380 """Test the optimisation of the tm1 model-free parameter grid.""" 2381 2382 # Initialise. 2383 cdp._model = 'tm1' 2384 cdp._value_test = self.value_test 2385 2386 # Setup the data pipe for optimisation. 2387 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm1_grid.py')

2388 2389

2390 - def test_tm2_grid(self):

2391 """Test the optimisation of the tm2 model-free parameter grid.""" 2392 2393 # Initialise. 2394 cdp._model = 'tm2' 2395 cdp._value_test = self.value_test 2396 2397 # Setup the data pipe for optimisation. 2398 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

2399 2400

2401 - def test_tm3_grid(self):

2402 """Test the optimisation of the tm3 model-free parameter grid.""" 2403 2404 # Initialise. 2405 cdp._model = 'tm3' 2406 cdp._value_test = self.value_test 2407 2408 # Setup the data pipe for optimisation. 2409 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm3_grid.py')

2410 2411

2412 - def test_tm4_grid(self):

2413 """Test the optimisation of the tm4 model-free parameter grid.""" 2414 2415 # Initialise. 2416 cdp._model = 'tm4' 2417 cdp._value_test = self.value_test 2418 2419 # Setup the data pipe for optimisation. 2420 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm4_grid.py')

2421 2422

2423 - def test_tm5_grid(self):

2424 """Test the optimisation of the tm5 model-free parameter grid.""" 2425 2426 # Initialise. 2427 cdp._model = 'tm5' 2428 cdp._value_test = self.value_test 2429 2430 # Setup the data pipe for optimisation. 2431 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm5_grid.py')

2432 2433

2434 - def test_tm6_grid(self):

2435 """Test the optimisation of the tm6 model-free parameter grid.""" 2436 2437 # Initialise. 2438 cdp._model = 'tm6' 2439 cdp._value_test = self.value_test 2440 2441 # Setup the data pipe for optimisation. 2442 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm6_grid.py')

2443 2444

2445 - def test_tm7_grid(self):

2446 """Test the optimisation of the tm7 model-free parameter grid.""" 2447 2448 # Initialise. 2449 cdp._model = 'tm7' 2450 cdp._value_test = self.value_test 2451 2452 # Setup the data pipe for optimisation. 2453 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm7_grid.py')

2454 2455

2456 - def test_tm8_grid(self):

2457 """Test the optimisation of the tm8 model-free parameter grid.""" 2458 2459 # Initialise. 2460 cdp._model = 'tm8' 2461 cdp._value_test = self.value_test 2462 2463 # Setup the data pipe for optimisation. 2464 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm8_grid.py')

2465 2466

2467 - def test_tm9_grid(self):

2468 """Test the optimisation of the tm9 model-free parameter grid.""" 2469 2470 # Initialise. 2471 cdp._model = 'tm9' 2472 cdp._value_test = self.value_test 2473 2474 # Setup the data pipe for optimisation. 2475 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm9_grid.py')

2476 2477

2478 - def test_tylers_peptide(self):

2479 """Try a component of model-free analysis on Tyler Reddy's peptide data (truncated).""" 2480 2481 # Execute the script. 2482 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'tylers_peptide.py')

2483 2484

2485 - def test_write_results(self):

2486 """Writing of model-free results using the user function results.write().""" 2487 2488 # Path of the files. 2489 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2490 2491 # Read the results file. 2492 self.interpreter.results.read(file='final_results_trunc_1.2', dir=path) 2493 2494 # A dummy file object for catching the results.write() output. 2495 file = DummyFileObject() 2496 2497 # Write the results file into a dummy file. 2498 self.interpreter.results.write(file=file, dir=path) 2499 2500 # Now, get the contents of that file, and then 'close' that file. 2501 test_lines = file.readlines() 2502 file.close() 2503 2504 # Read the 1.3 results file, extract the data, then close it again. 2505 a, b, c = platform.python_version_tuple() 2506 if dep_check.xml_type == 'internal' and int(a) >= 2 and int(b) >= 7 and int(c) >= 3: 2507 file = open_read_file(file_name='final_results_trunc_1.3_new', dir=path) 2508 else: 2509 file = open_read_file(file_name='final_results_trunc_1.3', dir=path) 2510 true_lines = file.readlines() 2511 file.close() 2512 2513 # Test the rest of the lines. 2514 for i in xrange(len(test_lines)): 2515 # Skip the second line, as it contains the date and hence should not be the same. 2516 # Also skip the third line, as the pipe names are different. 2517 if i == 1 or i == 2: 2518 continue 2519 2520 # Try to convert the test line into a python object (for cross-platform support). 2521 try: 2522 test_line = eval(test_lines[i]) 2523 except: 2524 test_line = test_lines[i] 2525 2526 # Try to convert the true line into a python object (for cross-platform support). 2527 try: 2528 true_line = eval(true_lines[i]) 2529 except: 2530 true_line = true_lines[i] 2531 2532 # Test that the line is the same. 2533 self.assertEqual(test_line, true_line)

2534 2535

2536 - def value_test(self, spin, select=True, local_tm=None, s2=None, s2f=None, s2s=None, te=None, tf=None, ts=None, rex=None, chi2=None, iter=None, f_count=None, g_count=None, h_count=None, warning=None):

2537 """Test the optimisation values.""" 2538 2539 # Get the debugging message. 2540 mesg = self.mesg_opt_debug(spin) 2541 2542 # Convert to lists. 2543 if iter != None and not isinstance(iter, list): 2544 iter = [iter] 2545 if f_count != None and not isinstance(f_count, list): 2546 f_count = [f_count] 2547 if g_count != None and not isinstance(g_count, list): 2548 g_count = [g_count] 2549 if h_count != None and not isinstance(h_count, list): 2550 h_count = [h_count] 2551 2552 # Test all the values. 2553 ###################### 2554 2555 # Spin selection. 2556 self.assertEqual(spin.select, select, msg=mesg) 2557 2558 # The local tm correlation time. 2559 if local_tm != None: 2560 self.assertAlmostEqual(spin.local_tm / 1e-9, local_tm, msg=mesg) 2561 else: 2562 self.assertEqual(spin.local_tm, None, msg=mesg) 2563 2564 # S2 order parameter. 2565 if s2 != None: 2566 self.assertAlmostEqual(spin.s2, s2, msg=mesg) 2567 else: 2568 self.assertEqual(spin.s2, None, msg=mesg) 2569 2570 # S2f order parameter. 2571 if s2f != None: 2572 self.assertAlmostEqual(spin.s2f, s2f, 5, msg=mesg) 2573 else: 2574 self.assertEqual(spin.s2f, None, msg=mesg) 2575 2576 # S2s order parameter. 2577 if s2s != None: 2578 self.assertAlmostEqual(spin.s2s, s2s, 5, msg=mesg) 2579 else: 2580 self.assertEqual(spin.s2s, None, msg=mesg) 2581 2582 # te correlation time. 2583 if isinstance(te, float): 2584 self.assertAlmostEqual(spin.te / 1e-12, te, 5, msg=mesg) 2585 elif te == None: 2586 self.assertEqual(spin.te, None, msg=mesg) 2587 2588 # tf correlation time. 2589 if isinstance(tf, float): 2590 self.assertAlmostEqual(spin.tf / 1e-12, tf, 4, msg=mesg) 2591 elif tf == None: 2592 self.assertEqual(spin.tf, None, msg=mesg) 2593 2594 # ts correlation time. 2595 if isinstance(ts, float): 2596 self.assertAlmostEqual(spin.ts / 1e-12, ts, 4, msg=mesg) 2597 elif ts == None: 2598 self.assertEqual(spin.ts, None, msg=mesg) 2599 2600 # Chemical exchange. 2601 if isinstance(rex, float): 2602 self.assertAlmostEqual(spin.rex * (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2, rex * (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2, msg=mesg) 2603 elif rex == None: 2604 self.assertEqual(spin.rex, None, msg=mesg) 2605 2606 # The optimisation stats. 2607 if chi2 != None: 2608 self.assertAlmostEqual(spin.chi2, chi2, msg=mesg) 2609 if iter != None: 2610 self.assert_(spin.iter in iter, msg=mesg) 2611 if f_count != None: 2612 self.assert_(spin.f_count in f_count, msg=mesg) 2613 if g_count != None: 2614 self.assert_(spin.g_count in g_count, msg=mesg) 2615 if h_count != None: 2616 self.assert_(spin.h_count in h_count, msg=mesg) 2617 if warning != None: 2618 self.assertEqual(spin.warning, warning, msg=mesg)

Source Code for Module test_suite.system_tests.model_free