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 check_read_results_1_3(self):

74 """Common code for the test_read_results_1_3*() tests.""" 75 76 # Path of the files. 77 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 78 79 # Read the equivalent 1.2 results file for the checks. 80 self.interpreter.pipe.create('1.2', 'mf') 81 self.interpreter.results.read(file='final_results_trunc_1.2', dir=path) 82 83 # Get the two data pipes. 84 pipe_12 = pipes.get_pipe('1.2') 85 pipe_13 = pipes.get_pipe('1.3') 86 87 # Test that the objects in the base pipes are the same. 88 print("Comparison of the objects of the base data pipe:") 89 self.object_comparison(obj1=pipe_12, obj2=pipe_13, skip=['mol', 'diff_tensor']) 90 91 # Test that the diffusion tensor data is the same. 92 print("Comparison of the objects of the diffusion tensor:") 93 self.object_comparison(obj1=pipe_12.diff_tensor, obj2=pipe_13.diff_tensor) 94 95 # Test the number of molecules. 96 self.assertEqual(len(pipe_12.mol), len(pipe_13.mol)) 97 98 # Loop over the molecules. 99 for i in xrange(len(pipe_12.mol)): 100 # Test the objects. 101 print("Comparison of the objects of the molecule:") 102 self.object_comparison(obj1=pipe_12.mol[i], obj2=pipe_13.mol[i], skip=['res']) 103 104 # Test the number of residues. 105 self.assertEqual(len(pipe_12.mol[i].res), len(pipe_13.mol[i].res)) 106 107 # Loop over the residues. 108 for j in xrange(len(pipe_12.mol[i].res)): 109 # Ok, really don't need to do a full comparison of all 162 residues for this test! 110 if j > 10: 111 break 112 113 # Test the objects. 114 print("Comparison of the objects of the residue:") 115 self.object_comparison(obj1=pipe_12.mol[i].res[j], obj2=pipe_13.mol[i].res[j], skip=['spin']) 116 117 # Test the number of spins. 118 self.assertEqual(len(pipe_12.mol[i].res[j].spin), len(pipe_13.mol[i].res[j].spin)) 119 120 # Loop over the spins. 121 for k in xrange(len(pipe_12.mol[i].res[j].spin)): 122 # Test the objects. 123 print("Comparison of the objects of the spin:") 124 self.object_comparison(obj1=pipe_12.mol[i].res[j].spin[k], obj2=pipe_13.mol[i].res[j].spin[k])

125 126

127 - def mesg_opt_debug(self, spin):

128 """Method for returning a string to help debug the minimisation. 129 130 @param spin: The SpinContainer of the optimised spin. 131 @type spin: SpinContainer instance 132 @return: The debugging string. 133 @rtype: str 134 """ 135 136 # Initialise the string. 137 string = 'Optimisation failure.\n\n' 138 139 # Create the string. 140 string = string + "%-18s%-25s\n" % ("System: ", SYSTEM) 141 string = string + "%-18s%-25s\n" % ("Release: ", RELEASE) 142 string = string + "%-18s%-25s\n" % ("Version: ", VERSION) 143 string = string + "%-18s%-25s\n" % ("Win32 version: ", (WIN32_VER[0] + " " + WIN32_VER[1] + " " + WIN32_VER[2] + " " + WIN32_VER[3])) 144 string = string + "%-18s%-25s\n" % ("Distribution: ", (DIST[0] + " " + DIST[1] + " " + DIST[2])) 145 string = string + "%-18s%-25s\n" % ("Architecture: ", (ARCH[0] + " " + ARCH[1])) 146 string = string + "%-18s%-25s\n" % ("Machine: ", MACH) 147 string = string + "%-18s%-25s\n" % ("Processor: ", PROC) 148 string = string + "%-18s%-25s\n" % ("Python version: ", PY_VER) 149 string = string + "%-18s%-25s\n" % ("Numpy version: ", NUMPY_VER) 150 string = string + "%-18s%-25s\n" % ("Libc version: ", (LIBC_VER[0] + " " + LIBC_VER[1])) 151 152 153 # Minimisation info. 154 string = string + '\n' 155 if spin.local_tm != None: 156 string = string + "%-15s %30.16g\n" % ('local_tm (ns):', spin.local_tm * 1e9) 157 if spin.s2 != None: 158 string = string + "%-15s %30.16g\n" % ('s2:', spin.s2) 159 if spin.s2f != None: 160 string = string + "%-15s %30.16g\n" % ('s2f:', spin.s2f) 161 if spin.s2s != None: 162 string = string + "%-15s %30.16g\n" % ('s2s:', spin.s2s) 163 if spin.te != None: 164 string = string + "%-15s %30.13g\n" % ('te (ps):', spin.te * 1e12) 165 if spin.tf != None: 166 string = string + "%-15s %30.13g\n" % ('tf (ps):', spin.tf * 1e12) 167 if spin.ts != None: 168 string = string + "%-15s %30.13g\n" % ('ts (ps):', spin.ts * 1e12) 169 if spin.rex != None: 170 string = string + "%-15s %30.17g\n" % ('rex:', spin.rex * (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2) 171 string = string + "%-15s %30.17g\n" % ('chi2:', spin.chi2) 172 string = string + "%-15s %30i\n" % ('iter:', spin.iter) 173 string = string + "%-15s %30i\n" % ('f_count:', spin.f_count) 174 string = string + "%-15s %30i\n" % ('g_count:', spin.g_count) 175 string = string + "%-15s %30i\n" % ('h_count:', spin.h_count) 176 string = string + "%-15s %30s\n" % ('warning:', spin.warning) 177 178 # Return the string. 179 return string

180 181

182 - def monte_carlo(self):

183 """Run Monte Carlo simulations for the optimised model-free model.""" 184 185 # Monte Carlo simulations. 186 self.interpreter.monte_carlo.setup(number=3) 187 self.interpreter.monte_carlo.create_data() 188 self.interpreter.monte_carlo.initial_values() 189 self.interpreter.minimise('newton') 190 #self.interpreter.eliminate() 191 self.interpreter.monte_carlo.error_analysis()

192 193

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

195 """Check if the contents of 2 objects are the same.""" 196 197 # The names are the same. 198 self.assertEqual(dir(obj1), dir(obj2)) 199 200 # Loop over the objects in the base objects. 201 for name in dir(obj1): 202 # Skip special objects. 203 if skip and name in skip: 204 continue 205 206 # Skip objects starting with '_'. 207 if search('^_', name): 208 continue 209 210 # Skip original class methods. 211 if name in list(obj1.__class__.__dict__.keys()): 212 continue 213 214 # Print out. 215 print(("\t" + name)) 216 217 # Get the sub-objects. 218 sub_obj1 = getattr(obj1, name) 219 sub_obj2 = getattr(obj2, name) 220 221 # Check that they are of the same type. 222 self.assertEqual(type(sub_obj1), type(sub_obj2)) 223 224 # Check that they are equal (converting to strings to avoid comparison nastiness). 225 self.assertEqual(str(sub_obj1), str(sub_obj2))

226 227

228 - def test_bug_14872_unicode_selection(self):

229 """Test catching bug #14872, the unicode string selection failure as submitted by Olivier Serve.""" 230 231 # Execute the script. 232 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_14872_unicode_selection.py')

233 234

235 - def test_bug_14941_local_tm_global_selection(self):

236 """Test catching bug #14941, the local tm global model selection problem as submitted by Mikaela Stewart (mikaela dot stewart att gmail dot com).""" 237 238 # Execute the script. 239 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_14941_local_tm_global_selection.py')

240 241

242 - def test_bug_15050(self):

243 """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).""" 244 245 # Execute the script. 246 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_15050.py')

247 248

249 - def test_bugs_12582_12591_12607(self):

250 """Test catching bugs #12582, #12591 and #12607 as submitted by Chris Brosey.""" 251 252 # Execute the script. 253 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bugs_12582_12591_12607.py') 254 255 # Test for bug #12607 (S2 changes because it is in the grid search when it should not be). 256 self.assertNotEqual(cdp.mol[0].res[1].spin[0].s2, 1.0)

257 258

259 - def test_bug_18790(self):

260 """Test catching bug #18790, the negative relaxation data RelaxError reported by Vitaly Vostrikov.""" 261 262 # Execute the script. 263 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_18790_negative_error.py')

264 265

266 - def test_create_m4(self):

267 """Creating model m4 with parameters {S2, te, Rex} using model_free.create_model().""" 268 269 # Execute the script. 270 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'create_m4.py') 271 272 # Test the model. 273 self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4') 274 self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['s2', 'te', 'rex'])

275 276

277 - def test_dauvergne_protocol(self):

278 """Check the execution of auto_analyses.dauvergne_protocol.""" 279 280 # Create a temporary directory for dumping files. 281 ds.tmpdir = mkdtemp() 282 283 # Execute the script. 284 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'dauvergne_protocol.py') 285 286 # Check the diffusion tensor. 287 self.assertEqual(cdp.diff_tensor.type, 'sphere') 288 self.assertAlmostEqual(cdp.diff_tensor.tm, 1e-8) 289 self.assertEqual(cdp.diff_tensor.fixed, True) 290 291 # The global minimisation info. 292 self.assertAlmostEqual(cdp.chi2, 4e-19) 293 294 # The spin ID info. 295 mol_names = ["sphere_mol1"] * 9 296 res_names = ["GLY"] * 9 297 res_nums = range(1, 10) 298 spin_names = ["N"] * 9 299 spin_nums = numpy.array(range(9)) * 2 + 1 300 301 # Check the spin data. 302 i = 0 303 for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 304 # The ID info. 305 self.assertEqual(mol_name, mol_names[i]) 306 self.assertEqual(res_name, res_names[i]) 307 self.assertEqual(res_num, res_nums[i]) 308 self.assertEqual(spin.name, spin_names[i]) 309 self.assertEqual(spin.num, spin_nums[i]) 310 311 # The data. 312 self.assertEqual(spin.select, True) 313 self.assertEqual(spin.fixed, False) 314 self.assertEqual(spin.proton_type, '1H') 315 self.assertEqual(spin.heteronuc_type, '15N') 316 self.assertEqual(spin.attached_proton, None) 317 self.assertAlmostEqual(spin.r, 1.02 * 1e-10) 318 self.assertAlmostEqual(spin.csa, -172e-6) 319 320 # The model-free data. 321 self.assertEqual(spin.model, 'm2') 322 self.assertEqual(spin.equation, 'mf_orig') 323 self.assertEqual(len(spin.params), 2) 324 self.assertEqual(spin.params[0], 's2') 325 self.assertEqual(spin.params[1], 'te') 326 self.assertAlmostEqual(spin.s2, 0.8) 327 self.assertEqual(spin.s2f, None) 328 self.assertEqual(spin.s2s, None) 329 self.assertEqual(spin.local_tm, None) 330 self.assertAlmostEqual(spin.te, 20e-12) 331 self.assertEqual(spin.tf, None) 332 self.assertEqual(spin.ts, None) 333 self.assertEqual(spin.rex, None) 334 335 # The spin minimisation info. 336 self.assertEqual(spin.chi2, None) 337 self.assertEqual(spin.iter, None) 338 self.assertEqual(spin.f_count, None) 339 self.assertEqual(spin.g_count, None) 340 self.assertEqual(spin.h_count, None) 341 self.assertEqual(spin.warning, None) 342 343 # Increment the index. 344 i += 1

345 346

347 - def test_generate_ri(self):

348 """Back-calculate relaxation data.""" 349 350 # Execute the script. 351 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'generate_ri.py')

352 353

354 - def test_latex_table(self):

355 """Test the creation of a LaTeX table of model-free results, mimicking the latex_mf_table.py sample script.""" 356 357 # Execute the script. 358 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'latex_mf_table.py')

359 360

361 - def test_local_tm_10_S2_0_8_te_40(self):

362 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 363 364 # Setup the data pipe for optimisation. 365 self.script_exec(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') 366 367 # The proton frequencies in MHz. 368 frq = ['400', '500', '600', '700', '800', '900', '1000'] 369 370 # Load the relaxation data. 371 for i in range(len(frq)): 372 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) 373 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) 374 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) 375 376 # Set up the initial model-free parameter values (bypass the grid search for speed). 377 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 378 379 # Minimise. 380 self.interpreter.minimise('newton', 'gmw', 'back') 381 382 # Alias the relevent spin container. 383 spin = cdp.mol[0].res[0].spin[0] 384 385 # Check the values. 386 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

387 388

389 - def test_local_tm_10_S2_0_8_te_40_test2(self):

390 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 391 392 # Setup the data pipe for optimisation. 393 self.script_exec(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') 394 395 # The proton frequencies in MHz. 396 frq = ['400', '500', '600', '700', '800', '900', '1000'] 397 398 # Load the relaxation data. 399 for i in range(len(frq)): 400 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) 401 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) 402 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) 403 404 # Set up the initial model-free parameter values (bypass the grid search for speed). 405 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 406 407 # Minimise. 408 self.interpreter.minimise('newton', 'gmw', 'back') 409 410 # Alias the relevent spin container. 411 spin = cdp.mol[0].res[0].spin[0] 412 413 # Check the values. 414 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

415 416

417 - def test_local_tm_10_S2_0_8_te_40_test3(self):

418 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 419 420 # Setup the data pipe for optimisation. 421 self.script_exec(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') 422 423 # Load the relaxation data. 424 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) 425 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) 426 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) 427 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) 428 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) 429 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) 430 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) 431 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) 432 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) 433 434 # Set up the initial model-free parameter values (bypass the grid search for speed). 435 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 436 437 # Minimise. 438 self.interpreter.minimise('newton', 'gmw', 'back') 439 440 # Alias the relevent spin container. 441 spin = cdp.mol[0].res[0].spin[0] 442 443 # Check the values. 444 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

445 446

447 - def test_m0_grid(self):

448 """Test the optimisation of the m0 model-free model against the tm0 parameter grid.""" 449 450 # Initialise. 451 cdp._model = 'm0' 452 cdp._value_test = self.value_test 453 454 # Setup the data pipe for optimisation. 455 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

456 457

458 - def test_m0_grid_vs_m1(self):

459 """Test the optimisation of the m1 model-free model against the tm0 parameter grid.""" 460 461 # Initialise. 462 cdp._model = 'm1' 463 cdp._value_test = self.value_test 464 465 # Setup the data pipe for optimisation. 466 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

467 468

469 - def test_m0_grid_vs_m2(self):

470 """Test the optimisation of the m2 model-free model against the tm0 parameter grid.""" 471 472 # Initialise. 473 cdp._model = 'm2' 474 cdp._value_test = self.value_test 475 476 # Setup the data pipe for optimisation. 477 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

478 479

480 - def test_m0_grid_vs_m3(self):

481 """Test the optimisation of the m3 model-free model against the tm0 parameter grid.""" 482 483 # Initialise. 484 cdp._model = 'm3' 485 cdp._value_test = self.value_test 486 487 # Setup the data pipe for optimisation. 488 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

489 490

491 - def test_m0_grid_vs_m4(self):

492 """Test the optimisation of the m4 model-free model against the tm0 parameter grid.""" 493 494 # Initialise. 495 cdp._model = 'm4' 496 cdp._value_test = self.value_test 497 498 # Setup the data pipe for optimisation. 499 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

500 501

502 - def test_m1_grid(self):

503 """Test the optimisation of the m1 model-free model against the tm1 parameter grid.""" 504 505 # Initialise. 506 cdp._model = 'm1' 507 cdp._value_test = self.value_test 508 509 # Setup the data pipe for optimisation. 510 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm1_grid.py')

511 512

513 - def test_m2_grid(self):

514 """Test the optimisation of the m2 model-free model against the tm2 parameter grid.""" 515 516 # Initialise. 517 cdp._model = 'm2' 518 cdp._value_test = self.value_test 519 520 # Setup the data pipe for optimisation. 521 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

522 523

524 - def test_m2_grid_vs_m4(self):

525 """Test the optimisation of the m4 model-free model against the tm2 parameter grid.""" 526 527 # Initialise. 528 cdp._model = 'm4' 529 cdp._value_test = self.value_test 530 531 # Setup the data pipe for optimisation. 532 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

533 534

535 - def test_m3_grid(self):

536 """Test the optimisation of the m3 model-free model against the tm3 parameter grid.""" 537 538 # Initialise. 539 cdp._model = 'm3' 540 cdp._value_test = self.value_test 541 542 # Setup the data pipe for optimisation. 543 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm3_grid.py')

544 545

546 - def test_m4_grid(self):

547 """Test the optimisation of the m4 model-free model against the tm4 parameter grid.""" 548 549 # Initialise. 550 cdp._model = 'm4' 551 cdp._value_test = self.value_test 552 553 # Setup the data pipe for optimisation. 554 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm4_grid.py')

555 556

557 - def test_m5_grid(self):

558 """Test the optimisation of the m5 model-free model against the tm5 parameter grid.""" 559 560 # Initialise. 561 cdp._model = 'm5' 562 cdp._value_test = self.value_test 563 564 # Setup the data pipe for optimisation. 565 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm5_grid.py')

566 567

568 - def test_m6_grid(self):

569 """Test the optimisation of the m6 model-free model against the tm6 parameter grid.""" 570 571 # Initialise. 572 cdp._model = 'm6' 573 cdp._value_test = self.value_test 574 575 # Setup the data pipe for optimisation. 576 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm6_grid.py')

577 578

579 - def test_m7_grid(self):

580 """Test the optimisation of the m7 model-free model against the tm7 parameter grid.""" 581 582 # Initialise. 583 cdp._model = 'm7' 584 cdp._value_test = self.value_test 585 586 # Setup the data pipe for optimisation. 587 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm7_grid.py')

588 589

590 - def test_m8_grid(self):

591 """Test the optimisation of the m8 model-free model against the tm8 parameter grid.""" 592 593 # Initialise. 594 cdp._model = 'm8' 595 cdp._value_test = self.value_test 596 597 # Setup the data pipe for optimisation. 598 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm8_grid.py')

599 600

601 - def test_m9_grid(self):

602 """Test the optimisation of the m9 model-free model against the tm9 parameter grid.""" 603 604 # Initialise. 605 cdp._model = 'm9' 606 cdp._value_test = self.value_test 607 608 # Setup the data pipe for optimisation. 609 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm9_grid.py')

610 611

612 - def test_omp_analysis(self):

613 """Try a very minimal model-free analysis on the OMP relaxation data.""" 614 615 # Execute the script. 616 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'omp_model_free.py') 617 618 # Alias the final data pipe. 619 dp = pipes.get_pipe('final') 620 621 # Some checks. 622 self.assertEqual(dp.mol[0].res[0].spin[0].select_sim, [True, False, True]) 623 self.assertEqual(dp.mol[0].res[1].spin[0].select_sim, [True, True, False]) 624 self.assertEqual(dp.mol[0].res[2].spin[0].select_sim, [True, True, True]) 625 self.assert_(not hasattr(dp.mol[0].res[3].spin[0], 'select_sim'))

626 627

628 - def test_opendx_s2_te_rex(self):

629 """Mapping the {S2, te, Rex} chi2 space through the OpenDX user function dx.map().""" 630 631 # Execute the script. 632 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opendx_s2_te_rex.py')

633 634

635 - def test_opendx_theta_phi_da(self):

636 """Mapping the {theta, phi, Da} chi2 space through the OpenDX user function dx.map().""" 637 638 # Path of the files. 639 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 640 641 # Read the PDF file and set the vectors. 642 self.interpreter.structure.read_pdb(file='pdb', dir=path, read_model=1) 643 self.interpreter.structure.load_spins('@N') 644 self.interpreter.structure.vectors(attached='H') 645 646 # Read the relaxation data. 647 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) 648 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) 649 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) 650 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) 651 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) 652 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) 653 654 # Setup other values. 655 self.interpreter.diffusion_tensor.init((1.601 * 1e7, 1.34, 72.4, 90-77.9), param_types=4) 656 self.interpreter.value.set([N15_CSA, NH_BOND_LENGTH], ['csa', 'r']) 657 self.interpreter.value.set([0.8, 50 * 1e-12, 0.0], ['s2', 'te', 'rex']) 658 self.interpreter.value.set('15N', 'heteronuc_type') 659 self.interpreter.value.set('1H', 'proton_type') 660 661 # Select the model. 662 self.interpreter.model_free.select_model(model='m4') 663 664 # Map the space. 665 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')

666 667

668 - def test_opendx_tm_s2_te(self):

669 """Mapping the {local_tm, S2, te} chi2 space through the OpenDX user function dx.map().""" 670 671 # Path of the files. 672 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 673 674 # Read the sequence. 675 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 676 677 # Read the relaxation data. 678 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) 679 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) 680 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) 681 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) 682 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) 683 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) 684 685 # Setup other values. 686 self.interpreter.value.set([N15_CSA, NH_BOND_LENGTH], ['csa', 'r']) 687 self.interpreter.value.set('15N', 'heteronuc_type') 688 self.interpreter.value.set('1H', 'proton_type') 689 690 # Select the model. 691 self.interpreter.model_free.select_model(model='tm2') 692 693 # Map the space. 694 self.interpreter.dx.map(params=['local_tm', 's2', 'te'], spin_id=':2', inc=2, lower=[5e-9, 0.0, 0.0], file_prefix='devnull')

695 696

697 - def test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149(self):

698 """Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 699 700 The optimisation options are: 701 - BFGS optimisation. 702 - Backtracking line search. 703 - Constrained. 704 705 The true data set is: 706 - S2 = 0.970 707 - te = 2048 ps 708 - Rex = 0.149 s^-1 709 """ 710 711 # Setup the data pipe for optimisation. 712 self.script_exec(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') 713 714 # Set up the initial model-free parameter values (bypass the grid search for speed). 715 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 716 717 # Minimise. 718 self.interpreter.minimise('bfgs', 'back') 719 720 # Alias the relevent spin container. 721 spin = cdp.mol[0].res[1].spin[0] 722 723 # Optimisation differences. 724 ########################### 725 726 # 32-bit Linux. 727 # iter: 203 728 # f_count: 955 729 # g_count: 209 730 731 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-devel/2009-05/msg00003.html). 732 # System: Linux 733 # Release: 2.6.28-gentoo-r5 734 # Version: #1 SMP Sat Apr 25 13:31:51 EDT 2009 735 # Win32 version: 736 # Distribution: 737 # Architecture: 32bit ELF 738 # Machine: i686 739 # Processor: Intel(R) Pentium(R) M processor 1.80GHz 740 # Python version: 2.5.4 741 # numpy version: 1.2.1 742 # 743 # s2: 0.9700000000012307 744 # te: 2048.0000002299716 745 # rex: 0.14899999997647859 746 # chi2: 1.9223825944220359e-20 747 # iter: 157 748 # f_count: 722 749 # g_count: 164 750 # h_count: 0 751 # warning: None 752 753 # 32-bit i686 Linux. 754 # System: Linux 755 # Release: 2.6.33.7-desktop-2mnb 756 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 757 # Win32 version: 758 # Distribution: mandrake 2010.2 Official 759 # Architecture: 32bit ELF 760 # Machine: i686 761 # Processor: i686 762 # Python version: 2.6.5 763 # Numpy version: 1.4.1 764 # Libc version: glibc 2.0 765 # 766 # s2: 0.9700000000016741 767 # te (ps): 2048.000000312 768 # rex: 0.14899999996808433 769 # chi2: 3.5466670276032307e-20 770 # iter: 158 771 # f_count: 744 772 # g_count: 165 773 # h_count: 0 774 # warning: None 775 776 # 32-bit i686 Linux. 777 # System: Linux 778 # Release: 2.6.33.7-desktop-2mnb 779 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 780 # Win32 version: 781 # Distribution: mandrake 2010.2 Official 782 # Architecture: 32bit ELF 783 # Machine: i686 784 # Processor: i686 785 # Python version: 2.6.5 786 # Numpy version: 1.4.1 787 # Libc version: glibc 2.0 788 # 789 # s2: 0.9700000000016741 790 # te: 2048.000000312 791 # rex: 0.14899999996808433 792 # chi2: 3.5466670276032307e-20 793 # iter: 158 794 # f_count: 744 795 # g_count: 165 796 # h_count: 0 797 # warning: None 798 799 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-users/2011-01/msg00029.html). 800 # System: Linux 801 # Release: 2.6.28-17-generic 802 # Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 803 # Win32 version: 804 # Distribution: Ubuntu 9.04 jaunty 805 # Architecture: 32bit ELF 806 # Machine: i686 807 # Processor: 808 # Python version: 2.6.2 809 # Numpy version: 1.2.1 810 # Libc version: glibc 2.4 811 # 812 # s2: 0.970000000000951 813 # te (ps): 2048.000000178 814 # rex: 0.14899999998189395 815 # chi2: 1.1498599057727952e-20 816 # iter: 154 817 # f_count: 598 818 # g_count: 161 819 # h_count: 0 820 # warning: None 821 822 # 64-bit x86_64 Linux. 823 # System: Linux 824 # Release: 2.6.24.7-server-2mnb 825 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 826 # Win32 version: 827 # Distribution: mandriva 2008.1 Official 828 # Architecture: 64bit ELF 829 # Machine: x86_64 830 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 831 # Python version: 2.5.2 832 # Numpy version: 1.2.0 833 # Libc version: glibc 2.2.5 834 # 835 # s2: 0.9699999999999785 836 # te: 2047.9999999962433 837 # rex: 0.14900000000039709 838 # chi2: 5.2479491342506911e-24 839 # iter: 162 840 # f_count: 758 841 # g_count: 169 842 # h_count: 0 843 # warning: None 844 845 # 32-bit Windows. 846 # iter: 156 847 # f_count: 701 848 # g_count: 163 849 850 # 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). 851 # System: Darwin 852 # Release: 9.5.0 853 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; root:xnu-1228.7.58~1/RELEASE_PPC 854 # Win32 version: 855 # Distribution: 856 # Architecture: 32bit 857 # Machine: Power Macintosh 858 # Processor: powerpc 859 # Python version: 2.5.2 860 # numpy version: 1.1.1 861 # 862 # s2: 0.9699999999999861 863 # te: 2047.9999999978033 864 # rex: 0.14900000000028032 865 # chi2: 1.8533903598853284e-24 866 # iter: 156 867 # f_count: 695 868 # g_count: 162 869 # h_count: 0 870 # warning: None 871 872 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14173). 873 # System: Darwin 874 # Release: 9.8.0 875 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 876 # Win32 version: 877 # Distribution: 878 # Architecture: 32bit 879 # Machine: i386 880 # Processor: i386 881 # Python version: 2.6.2 882 # numpy version: 1.3.0 883 # 884 # s2: 0.9700000000009170 885 # te: 2048.0000001751678 886 # rex: 0.14899999998256069 887 # chi2: 1.1151721805269898e-20 888 # iter: 175 889 # f_count: 735 890 # g_count: 182 891 # h_count: 0 892 # warning: None 893 894 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14173). 895 # System: Darwin 896 # Release: 9.8.0 897 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 898 # Win32 version: 899 # Distribution: 900 # Architecture: 64bit 901 # Machine: i386 902 # Processor: i386 903 # Python version: 2.6.2 904 # numpy version: 1.3.0 905 # 906 # s2: 0.9699999999999785 907 # te: 2047.9999999962433 908 # rex: 0.14900000000039709 909 # chi2: 5.2479491342506911e-24 910 # iter: 162 911 # f_count: 758 912 # g_count: 169 913 # h_count: 0 914 # warning: None 915 916 # Optimisation values. 917 select = True 918 s2 = 0.9699999999999995 919 te = 2048.000000000022283 920 rex = 0.14900000000000566 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 921 chi2 = 3.1024517431117421e-27 922 iter = [154, 156, 157, 158, 162, 175, 203] 923 f_count = [598, 695, 701, 722, 735, 744, 758, 955] 924 g_count = [161, 162, 163, 164, 165, 169, 182, 209] 925 h_count = 0 926 warning = None 927 928 # Test the values. 929 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 930 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

931 932

933 - def test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149(self):

934 """Constrained BFGS opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 935 936 The optimisation options are: 937 - BFGS optimisation. 938 - More and Thuente line search. 939 - Constrained. 940 941 The true data set is: 942 - S2 = 0.970 943 - te = 2048 ps 944 - Rex = 0.149 s^-1 945 """ 946 947 # Setup the data pipe for optimisation. 948 self.script_exec(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') 949 950 # Set up the initial model-free parameter values (bypass the grid search for speed). 951 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 952 953 # Minimise. 954 self.interpreter.minimise('bfgs', 'mt') 955 956 # Alias the relevent spin container. 957 spin = cdp.mol[0].res[1].spin[0] 958 959 # Optimisation differences. 960 ########################### 961 962 # 32-bit Linux. 963 # f_count: 388 964 # g_count: 388 965 966 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-devel/2009-05/msg00003.html). 967 # System: Linux 968 # Release: 2.6.28-gentoo-r5 969 # Version: #1 SMP Sat Apr 25 13:31:51 EDT 2009 970 # Win32 version: 971 # Distribution: 972 # Architecture: 32bit ELF 973 # Machine: i686 974 # Processor: Intel(R) Pentium(R) M processor 1.80GHz 975 # Python version: 2.5.4 976 # numpy version: 1.2.1 977 # 978 # s2: 0.9700000000000604 979 # te: 2048.0000000114946 980 # rex: 0.14899999999885985 981 # chi2: 4.762657780645096e-23 982 # iter: 120 983 # f_count: 386 984 # g_count: 386 985 # h_count: 0 986 # warning: None 987 988 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-users/2011-01/msg00029.html). 989 # System: Linux 990 # Release: 2.6.28-17-generic 991 # Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 992 # Win32 version: 993 # Distribution: Ubuntu 9.04 jaunty 994 # Architecture: 32bit ELF 995 # Machine: i686 996 # Processor: 997 # Python version: 2.6.2 998 # Numpy version: 1.2.1 999 # Libc version: glibc 2.4 1000 # 1001 # s2: 0.9700000000000614 1002 # te (ps): 2048.000000012 1003 # rex: 0.14899999999883881 1004 # chi2: 4.9272178768519757e-23 1005 # iter: 120 1006 # f_count: 381 1007 # g_count: 381 1008 # h_count: 0 1009 # warning: None 1010 1011 # 64-bit x86_64 Linux. 1012 # System: Linux 1013 # Release: 2.6.24.7-server-2mnb 1014 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1015 # Win32 version: 1016 # Distribution: mandriva 2008.1 Official 1017 # Architecture: 64bit ELF 1018 # Machine: x86_64 1019 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1020 # Python version: 2.5.2 1021 # Numpy version: 1.2.0 1022 # Libc version: glibc 2.2.5 1023 # 1024 # s2: 0.9700000000000603 1025 # te: 2048.0000000114601 1026 # rex: 0.14899999999886163 1027 # chi2: 4.7289676642197204e-23 1028 # iter: 120 1029 # f_count: 384 1030 # g_count: 384 1031 # h_count: 0 1032 # warning: None 1033 1034 # 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). 1035 # System: Darwin 1036 # Release: 9.5.0 1037 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1038 # root:xnu-1228.7.58~1/RELEASE_PPC 1039 # Win32 version: 1040 # Distribution: 1041 # Architecture: 32bit 1042 # Machine: Power Macintosh 1043 # Processor: powerpc 1044 # Python version: 2.5.2 1045 # numpy version: 1.1.1 1046 # 1047 # s2: 0.9700000000000607 1048 # te: 2048.0000000115510 1049 # rex: 0.14899999999885080 1050 # chi2: 4.8056261450870388e-23 1051 # iter: 120 1052 # f_count: 377 1053 # g_count: 377 1054 # h_count: 0 1055 # warning: None 1056 1057 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14174). 1058 # System: Darwin 1059 # Release: 9.8.0 1060 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1061 # Win32 version: 1062 # Distribution: 1063 # Architecture: 32bit 1064 # Machine: i386 1065 # Processor: i386 1066 # Python version: 2.6.2 1067 # numpy version: 1.3.0 1068 # 1069 # s2: 0.9700000000000604 1070 # te: 2048.0000000114997 1071 # rex: 0.14899999999886168 1072 # chi2: 4.7647467884964078e-23 1073 # iter: 120 1074 # f_count: 386 1075 # g_count: 386 1076 # h_count: 0 1077 # warning: None 1078 1079 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14174). 1080 # System: Darwin 1081 # Release: 9.8.0 1082 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1083 # Win32 version: 1084 # Distribution: 1085 # Architecture: 64bit 1086 # Machine: i386 1087 # Processor: i386 1088 # Python version: 2.6.2 1089 # numpy version: 1.3.0 1090 # 1091 # s2: 0.9700000000000603 1092 # te: 2048.0000000114601 1093 # rex: 0.14899999999886163 1094 # chi2: 4.7289676642197204e-23 1095 # iter: 120 1096 # f_count: 384 1097 # g_count: 384 1098 # h_count: 0 1099 # warning: None 1100 1101 # Optimisation values. 1102 select = True 1103 s2 = 0.9700000000000580 1104 te = 2048.000000011044449 1105 rex = 0.148999999998904 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1106 chi2 = 4.3978813282102374e-23 1107 iter = 120 1108 f_count = [377, 381, 384, 386, 388] 1109 g_count = [377, 381, 384, 386, 388] 1110 h_count = 0 1111 warning = None 1112 1113 # Test the values. 1114 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1115 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1116 1117

1118 - def test_opt_constr_cd_back_S2_0_970_te_2048_Rex_0_149(self):

1119 """Constrained coordinate descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1120 1121 The optimisation options are: 1122 - Coordinate descent optimisation. 1123 - Backtracking line search. 1124 - Constrained. 1125 1126 The true data set is: 1127 - S2 = 0.970 1128 - te = 2048 ps 1129 - Rex = 0.149 s^-1 1130 """ 1131 1132 # Setup the data pipe for optimisation. 1133 self.script_exec(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') 1134 1135 # Set up the initial model-free parameter values (bypass the grid search for speed). 1136 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1137 1138 # Minimise. 1139 self.interpreter.minimise('cd', 'back', max_iter=50) 1140 1141 # Alias the relevent spin container. 1142 spin = cdp.mol[0].res[1].spin[0] 1143 1144 # Optimisation differences. 1145 ########################### 1146 1147 # 64-bit x86_64 Linux. 1148 # System: Linux 1149 # Release: 2.6.24.7-server-2mnb 1150 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1151 # Win32 version: 1152 # Distribution: mandriva 2008.1 Official 1153 # Architecture: 64bit ELF 1154 # Machine: x86_64 1155 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1156 # Python version: 2.5.2 1157 # Numpy version: 1.2.0 1158 # Libc version: glibc 2.2.5 1159 # 1160 # s2: 0.9097900390625000 1161 # te: 25.0000000000000 1162 # rex: 1.24017333984375000 1163 # chi2: 53.476155463267176 1164 # iter: 50 1165 # f_count: 131 1166 # g_count: 51 1167 # h_count: 0 1168 # warning: Maximum number of iterations reached 1169 1170 # Optimisation values. 1171 select = True 1172 s2 = 0.9097900390625 1173 te = 25.00000000000000 1174 rex = 1.24017333984375 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1175 chi2 = 53.476155463267176 1176 iter = 50 1177 f_count = 131 1178 g_count = 51 1179 h_count = 0 1180 warning = 'Maximum number of iterations reached' 1181 1182 # Test the values. 1183 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1184 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1185 1186

1187 - def test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149(self):

1188 """Constrained coordinate descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1189 1190 The optimisation options are: 1191 - Coordinate descent optimisation. 1192 - More and Thuente line search. 1193 - Constrained. 1194 1195 The true data set is: 1196 - S2 = 0.970 1197 - te = 2048 ps 1198 - Rex = 0.149 s^-1 1199 """ 1200 1201 # Setup the data pipe for optimisation. 1202 self.script_exec(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') 1203 1204 # Set up the initial model-free parameter values (bypass the grid search for speed). 1205 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1206 1207 # Minimise. 1208 self.interpreter.minimise('cd', 'mt') 1209 1210 # Alias the relevent spin container. 1211 spin = cdp.mol[0].res[1].spin[0] 1212 1213 # Optimisation differences. 1214 ########################### 1215 1216 # 32-bit Linux. 1217 # f_count: 738 1218 # g_count: 738 1219 1220 # 32-bit i686 Linux. 1221 # System: Linux 1222 # Release: 2.6.33.7-desktop-2mnb 1223 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1224 # Win32 version: 1225 # Distribution: mandrake 2010.2 Official 1226 # Architecture: 32bit ELF 1227 # Machine: i686 1228 # Processor: i686 1229 # Python version: 2.6.5 1230 # Numpy version: 1.4.1 1231 # Libc version: glibc 2.0 1232 # 1233 # s2: 0.9700000000219662 1234 # te: 2048.000001534 1235 # rex: 0.14899999946980566 1236 # chi2: 2.3474910055938013e-18 1237 # iter: 200 1238 # f_count: 874 1239 # g_count: 874 1240 # h_count: 0 1241 # warning: None 1242 1243 # 64-bit x86_64 Linux. 1244 # System: Linux 1245 # Release: 2.6.24.7-server-2mnb 1246 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1247 # Win32 version: 1248 # Distribution: mandriva 2008.1 Official 1249 # Architecture: 64bit ELF 1250 # Machine: x86_64 1251 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1252 # Python version: 2.5.2 1253 # Numpy version: 1.2.0 1254 # Libc version: glibc 2.2.5 1255 # 1256 # s2: 0.9700000000219674 1257 # te: 2048.0000015341870 1258 # rex: 0.14899999946977982 1259 # chi2: 2.3477234248531005e-18 1260 # iter: 198 1261 # f_count: 757 1262 # g_count: 757 1263 # h_count: 0 1264 # warning: None 1265 1266 # 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). 1267 # System: Darwin 1268 # Release: 9.5.0 1269 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1270 # root:xnu-1228.7.58~1/RELEASE_PPC 1271 # Win32 version: 1272 # Distribution: 1273 # Architecture: 32bit 1274 # Machine: Power Macintosh 1275 # Processor: powerpc 1276 # Python version: 2.5.2 1277 # numpy version: 1.1.1 1278 # 1279 # s2: 0.9700000000219674 1280 # te: 2048.0000015341870 1281 # rex: 0.14899999946977982 1282 # chi2: 2.3477234248531005e-18 1283 # iter: 198 1284 # f_count: 757 1285 # g_count: 757 1286 # h_count: 0 1287 # warning: None 1288 1289 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14175). 1290 # System: Darwin 1291 # Release: 9.8.0 1292 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1293 # Win32 version: 1294 # Distribution: 1295 # Architecture: 64bit 1296 # Machine: i386 1297 # Processor: i386 1298 # Python version: 2.6.2 1299 # numpy version: 1.3.0 1300 # 1301 # s2: 0.9700000000219674 1302 # te: 2048.0000015341870 1303 # rex: 0.14899999946977982 1304 # chi2: 2.3477234248531005e-18 1305 # iter: 198 1306 # f_count: 757 1307 # g_count: 757 1308 # h_count: 0 1309 # warning: None 1310 1311 # Optimisation values. 1312 select = True 1313 s2 = 0.9700000000219674 1314 te = 2048.000001534187049 1315 rex = 0.14899999946977982 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1316 chi2 = 2.3477234248531005e-18 1317 iter = [198, 200] 1318 f_count = [738, 757, 874] 1319 g_count = [738, 757, 874] 1320 h_count = 0 1321 warning = None 1322 1323 # Test the values. 1324 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1325 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1326 1327

1328 - def test_opt_constr_newton_gmw_back_S2_0_970_te_2048_Rex_0_149(self):

1329 """Constrained Newton opt, GMW Hessian mod, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1330 1331 The optimisation options are: 1332 - Newton optimisation. 1333 - GMW Hessian modification. 1334 - Backtracking line search. 1335 - Constrained. 1336 1337 The true data set is: 1338 - S2 = 0.970 1339 - te = 2048 ps 1340 - Rex = 0.149 s^-1 1341 """ 1342 1343 # Setup the data pipe for optimisation. 1344 self.script_exec(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') 1345 1346 # Set up the initial model-free parameter values (bypass the grid search for speed). 1347 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1348 1349 # Minimise. 1350 self.interpreter.minimise('newton', 'gmw', 'back') 1351 1352 # Alias the relevent spin container. 1353 spin = cdp.mol[0].res[1].spin[0] 1354 1355 # Optimisation differences. 1356 ########################### 1357 1358 # 32-bit Linux. 1359 # f_count: 55 1360 # g_count: 23 1361 1362 # 32-bit i686 Linux. 1363 # System: Linux 1364 # Release: 2.6.33.7-desktop-2mnb 1365 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1366 # Win32 version: 1367 # Distribution: mandrake 2010.2 Official 1368 # Architecture: 32bit ELF 1369 # Machine: i686 1370 # Processor: i686 1371 # Python version: 2.6.5 1372 # Numpy version: 1.4.1 1373 # Libc version: glibc 2.0 1374 # 1375 # s2: 0.9699999999999992 1376 # te: 2048 1377 # rex: 0.14900000000002034 1378 # chi2: 1.1701970207791308e-27 1379 # iter: 18 1380 # f_count: 57 1381 # g_count: 23 1382 # h_count: 18 1383 # warning: None 1384 1385 # 64-bit x86_64 Linux. 1386 # System: Linux 1387 # Release: 2.6.24.7-server-2mnb 1388 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1389 # Win32 version: 1390 # Distribution: mandriva 2008.1 Official 1391 # Architecture: 64bit ELF 1392 # Machine: x86_64 1393 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1394 # Python version: 2.5.2 1395 # Numpy version: 1.2.0 1396 # Libc version: glibc 2.2.5 1397 # 1398 # s2: 0.9699999999999995 1399 # te: 2048.0000000000473 1400 # rex: 0.14900000000001926 1401 # chi2: 7.9357208397255696e-28 1402 # iter: 18 1403 # f_count: 55 1404 # g_count: 23 1405 # h_count: 18 1406 # warning: None 1407 1408 # 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). 1409 # System: Darwin 1410 # Release: 9.5.0 1411 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1412 # root:xnu-1228.7.58~1/RELEASE_PPC 1413 # Win32 version: 1414 # Distribution: 1415 # Architecture: 32bit 1416 # Machine: Power Macintosh 1417 # Processor: powerpc 1418 # Python version: 2.5.2 1419 # numpy version: 1.1.1 1420 # 1421 # s2: 0.9699999999999993 1422 # te: 2048.0000000000427 1423 # rex: 0.14900000000002098 1424 # chi2: 5.7085251917483392e-28 1425 # iter: 18 1426 # f_count: 94 1427 # g_count: 23 1428 # h_count: 18 1429 # warning: None 1430 1431 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14177). 1432 # System: Darwin 1433 # Release: 9.8.0 1434 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1435 # Win32 version: 1436 # Distribution: 1437 # Architecture: 32bit 1438 # Machine: i386 1439 # Processor: i386 1440 # Python version: 2.6.2 1441 # numpy version: 1.3.0 1442 # 1443 # s2: 0.9699999999999994 1444 # te: 2048.0000000000455 1445 # rex: 0.14900000000001823 1446 # chi2: 7.3040158179665562e-28 1447 # iter: 18 1448 # f_count: 55 1449 # g_count: 23 1450 # h_count: 18 1451 # warning: None 1452 1453 # Optimisation values. 1454 select = True 1455 s2 = 0.9699999999999994 1456 te = 2048.000000000045020 1457 rex = 0.14900000000001817 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1458 chi2 = 7.3040158179665562e-28 1459 iter = 18 1460 f_count = [55, 57, 94] 1461 g_count = [23] 1462 h_count = 18 1463 warning = None 1464 1465 # Test the values. 1466 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1467 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1468 1469

1470 - def test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149(self):

1471 """Constrained Newton opt, GMW Hessian mod, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1472 1473 The optimisation options are: 1474 - Newton optimisation. 1475 - GMW Hessian modification. 1476 - More and Thuente line search. 1477 - Constrained. 1478 1479 The true data set is: 1480 - S2 = 0.970 1481 - te = 2048 ps 1482 - Rex = 0.149 s^-1 1483 """ 1484 1485 # Setup the data pipe for optimisation. 1486 self.script_exec(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') 1487 1488 # Set up the initial model-free parameter values (bypass the grid search for speed). 1489 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1490 1491 # Minimise. 1492 self.interpreter.minimise('newton', 'gmw', 'mt') 1493 1494 # Monte Carlo simulations. 1495 self.monte_carlo() 1496 1497 # Alias the relevent spin container. 1498 spin = cdp.mol[0].res[1].spin[0] 1499 1500 # Optimisation differences. 1501 ########################### 1502 1503 # 32-bit Linux. 1504 # f_count: 159, 95 1505 # g_count: 159 1506 1507 # 32-bit i686 Linux. 1508 # System: Linux 1509 # Release: 2.6.33.7-desktop-2mnb 1510 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1511 # Win32 version: 1512 # Distribution: mandrake 2010.2 Official 1513 # Architecture: 32bit ELF 1514 # Machine: i686 1515 # Processor: i686 1516 # Python version: 2.6.5 1517 # Numpy version: 1.4.1 1518 # Libc version: glibc 2.0 1519 # 1520 # s2: 0.9699999999999994 1521 # te: 2048 1522 # rex: 0.14900000000002014 1523 # chi2: 7.9326439528899843e-28 1524 # iter: 22 1525 # f_count: 95 1526 # g_count: 95 1527 # h_count: 22 1528 # warning: None 1529 1530 # 64-bit x86_64 Linux. 1531 # System: Linux 1532 # Release: 2.6.24.7-server-2mnb 1533 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1534 # Win32 version: 1535 # Distribution: mandriva 2008.1 Official 1536 # Architecture: 64bit ELF 1537 # Machine: x86_64 1538 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1539 # Python version: 2.5.2 1540 # Numpy version: 1.2.0 1541 # Libc version: glibc 2.2.5 1542 # 1543 # s2: 0.9699999999999994 1544 # te: 2048.0000000000446 1545 # rex: 0.14900000000001615 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 x86_64 Linux (Not sure why there is a difference here, maybe this is gcc or blas/lapack - Python and numpy versions are identical). 1554 # f_count: 153 1555 # g_count: 153 1556 1557 # 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). 1558 # System: Darwin 1559 # Release: 9.5.0 1560 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1561 # root:xnu-1228.7.58~1/RELEASE_PPC 1562 # Win32 version: 1563 # Distribution: 1564 # Architecture: 32bit 1565 # Machine: Power Macintosh 1566 # Processor: powerpc 1567 # Python version: 2.5.2 1568 # numpy version: 1.1.1 1569 # 1570 # s2: 0.9699999999999993 1571 # te: 2048.0000000000409 1572 # rex: 0.14900000000002178 1573 # chi2: 6.8756889983348349e-28 1574 # iter: 22 1575 # f_count: 160 1576 # g_count: 160 1577 # h_count: 22 1578 # warning: None 1579 1580 # 32-bit Windows. 1581 # f_count: 165 1582 # g_count: 165 1583 1584 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14176). 1585 # System: Darwin 1586 # Release: 9.8.0 1587 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1588 # Win32 version: 1589 # Distribution: 1590 # Architecture: 32bit 1591 # Machine: i386 1592 # Processor: i386 1593 # Python version: 2.6.2 1594 # numpy version: 1.3.0 1595 # 1596 # s2: 0.9699999999999994 1597 # te: 2048.0000000000446 1598 # rex: 0.14900000000001609 1599 # chi2: 8.3312601381368332e-28 1600 # iter: 22 1601 # f_count: 91 1602 # g_count: 91 1603 # h_count: 22 1604 # warning: None 1605 1606 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14176). 1607 # System: Darwin 1608 # Release: 9.8.0 1609 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1610 # Win32 version: 1611 # Distribution: 1612 # Architecture: 64bit 1613 # Machine: i386 1614 # Processor: i386 1615 # Python version: 2.6.2 1616 # numpy version: 1.3.0 1617 # 1618 # s2: 0.9699999999999994 1619 # te: 2048.0000000000446 1620 # rex: 0.14900000000001609 1621 # chi2: 8.3312601381368332e-28 1622 # iter: 22 1623 # f_count: 91 1624 # g_count: 91 1625 # h_count: 22 1626 # warning: None 1627 1628 # Optimisation values. 1629 select = True 1630 s2 = 0.9699999999999993 1631 te = 2048.000000000041837 1632 rex = 0.14900000000002225 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1633 chi2 = 6.8756889983348349e-28 1634 iter = 22 1635 f_count = [91, 95, 153, 159, 160, 165] 1636 g_count = [91, 95, 153, 159, 160, 165] 1637 h_count = 22 1638 warning = None 1639 1640 # Test the values. 1641 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1642 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1643 1644

1645 - def test_opt_constr_sd_back_S2_0_970_te_2048_Rex_0_149(self):

1646 """Constrained steepest descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1647 1648 The optimisation options are: 1649 - Steepest descent optimisation. 1650 - Backtracking line search. 1651 - Constrained. 1652 1653 The true data set is: 1654 - S2 = 0.970 1655 - te = 2048 ps 1656 - Rex = 0.149 s^-1 1657 """ 1658 1659 # Setup the data pipe for optimisation. 1660 self.script_exec(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') 1661 1662 # Set up the initial model-free parameter values (bypass the grid search for speed). 1663 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1664 1665 # Minimise. 1666 self.interpreter.minimise('sd', 'back', max_iter=50) 1667 1668 # Alias the relevent spin container. 1669 spin = cdp.mol[0].res[1].spin[0] 1670 1671 # Optimisation differences. 1672 ########################### 1673 1674 # 64-bit x86_64 Linux. 1675 # System: Linux 1676 # Release: 2.6.24.7-server-2mnb 1677 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1678 # Win32 version: 1679 # Distribution: mandriva 2008.1 Official 1680 # Architecture: 64bit ELF 1681 # Machine: x86_64 1682 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1683 # Python version: 2.5.2 1684 # Numpy version: 1.2.0 1685 # Libc version: glibc 2.2.5 1686 # 1687 # s2: 0.9157922083468916 1688 # te: 0.3056865872253 1689 # rex: 0.34008409798064831 1690 # chi2: 68.321956795340569 1691 # iter: 50 1692 # f_count: 134 1693 # g_count: 51 1694 # h_count: 0 1695 # warning: Maximum number of iterations reached 1696 1697 # Optimisation values. 1698 select = True 1699 s2 = 0.91579220834688024 1700 te = 0.30568658722531733 1701 rex = 0.34008409798366124 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1702 chi2 = 68.321956795264342 1703 iter = 50 1704 f_count = 134 1705 g_count = 51 1706 h_count = 0 1707 warning = 'Maximum number of iterations reached' 1708 1709 # Test the values. 1710 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1711 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1712 1713

1714 - def test_opt_constr_sd_mt_S2_0_970_te_2048_Rex_0_149(self):

1715 """Constrained steepest descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1716 1717 The optimisation options are: 1718 - Steepest descent optimisation. 1719 - More and Thuente line search. 1720 - Constrained. 1721 1722 The true data set is: 1723 - S2 = 0.970 1724 - te = 2048 ps 1725 - Rex = 0.149 s^-1 1726 """ 1727 1728 # Setup the data pipe for optimisation. 1729 self.script_exec(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') 1730 1731 # Set up the initial model-free parameter values (bypass the grid search for speed). 1732 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1733 1734 # Minimise. 1735 self.interpreter.minimise('sd', 'mt', max_iter=50) 1736 1737 # Alias the relevent spin container. 1738 spin = cdp.mol[0].res[1].spin[0] 1739 1740 # Optimisation differences. 1741 ########################### 1742 1743 # 64-bit x86_64 Linux. 1744 # System: Linux 1745 # Release: 2.6.24.7-server-2mnb 1746 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1747 # Win32 version: 1748 # Distribution: mandriva 2008.1 Official 1749 # Architecture: 64bit ELF 1750 # Machine: x86_64 1751 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1752 # Python version: 2.5.2 1753 # Numpy version: 1.2.0 1754 # Libc version: glibc 2.2.5 1755 # 1756 # s2: 0.9161999495781851 1757 # te: 0.1231968757090 1758 # rex: 0.16249110939079675 1759 # chi2: 73.843613548025075 1760 # iter: 50 1761 # f_count: 108 1762 # g_count: 108 1763 # h_count: 0 1764 # warning: Maximum number of iterations reached 1765 1766 # Optimisation values. 1767 select = True 1768 s2 = 0.91619994957822126 1769 te = 0.12319687570987945 1770 rex = 0.16249110942961512 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1771 chi2 = 73.843613546506191 1772 iter = 50 1773 f_count = 108 1774 g_count = 108 1775 h_count = 0 1776 warning = 'Maximum number of iterations reached' 1777 1778 # Test the values. 1779 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1780 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1781 1782

1783 - def test_opt_grid_search_S2_0_970_te_2048_Rex_0_149(self):

1784 """Constrained grid search {S2=0.970, te=2048, Rex=0.149}. 1785 1786 The optimisation options are: 1787 - Constrained grid search. 1788 1789 The true data set is: 1790 - S2 = 0.970 1791 - te = 2048 ps 1792 - Rex = 0.149 s^-1 1793 """ 1794 1795 # Setup the data pipe for optimisation. 1796 self.script_exec(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') 1797 1798 # Grid search. 1799 self.interpreter.grid_search(inc=11) 1800 1801 # Alias the relevent spin container. 1802 spin = cdp.mol[0].res[1].spin[0] 1803 1804 # Optimisation differences. 1805 ########################### 1806 1807 # 64-bit x86_64 Linux. 1808 # System: Linux 1809 # Release: 2.6.24.7-server-2mnb 1810 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1811 # Win32 version: 1812 # Distribution: mandriva 2008.1 Official 1813 # Architecture: 64bit ELF 1814 # Machine: x86_64 1815 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1816 # Python version: 2.5.2 1817 # Numpy version: 1.2.0 1818 # Libc version: glibc 2.2.5 1819 # 1820 # s2: 1 1821 # te: 0 1822 # rex: 0 1823 # chi2: 3.9844117908982288 1824 # iter: 1331 1825 # f_count: 1331 1826 # g_count: 0 1827 # h_count: 0 1828 # warning: None 1829 1830 # Optimisation values. 1831 select = True 1832 s2 = 1.0 1833 te = 0.0 1834 rex = 0.0 1835 chi2 = 3.9844117908982288 1836 iter = 1331 1837 f_count = 1331 1838 g_count = 0 1839 h_count = 0 1840 warning = None 1841 1842 # Test the values. 1843 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1844 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1845 1846

1847 - def test_read_relax_data(self):

1848 """Reading of relaxation data using the user function relax_data.read().""" 1849 1850 # Path of the files. 1851 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 1852 1853 # Read the sequence. 1854 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 1855 1856 # Read the relaxation data. 1857 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) 1858 1859 # Test the data and error. 1860 self.assertEqual(cdp.mol[0].res[1].spin[0].ri_data['R1_600'], 1.3874977659397683) 1861 self.assertEqual(cdp.mol[0].res[1].spin[0].ri_data_err['R1_600'], 0.027749955318795365)

1862 1863

1864 - def test_read_results_1_2(self):

1865 """Read a relax 1.2 model-free results file using the user function results.read().""" 1866 1867 # Read the results. 1868 self.interpreter.results.read(file='results_1.2', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 1869 1870 # Debugging printout. 1871 print(cdp) 1872 1873 # The spin specific data. 1874 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] 1875 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] 1876 model = ['m6', 'm8', 'm6', 'm6', 'm5', 'm5', 'm6', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm8'] 1877 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']] 1878 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] 1879 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] 1880 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] 1881 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] 1882 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] 1883 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] 1884 1885 # Relaxation data. 1886 ri_ids = ['R1_500', 'R2_500', 'NOE_500', 'R1_600', 'R2_600', 'NOE_600', 'R1_750', 'R2_750', 'NOE_750'] 1887 types_list = ['R1', 'R2', 'NOE', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 1888 frqs_list = [500000000.0] * 3 + [600000000.0] * 3 + [750000000.0] * 3 1889 ri_type = {} 1890 frqs = {} 1891 for i in range(len(ri_ids)): 1892 ri_type[ri_ids[i]] = types_list[i] 1893 frqs[ri_ids[i]] = frqs_list[i] 1894 1895 ri_data = {} 1896 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] 1897 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] 1898 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] 1899 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] 1900 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] 1901 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] 1902 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] 1903 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] 1904 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] 1905 1906 ri_data_err = {} 1907 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] 1908 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] 1909 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] 1910 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] 1911 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] 1912 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] 1913 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] 1914 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] 1915 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] 1916 1917 # Misc tests. 1918 self.assertEqual(cdp.pipe_type, 'mf') 1919 self.assertEqual(cdp.hybrid_pipes, []) 1920 1921 # Diffusion tensor tests. 1922 self.assertEqual(cdp.diff_tensor.type, 'sphere') 1923 self.assertEqual(cdp.diff_tensor.tm, 6.2029050826362826e-09) 1924 1925 # Global minimisation statistic tests. 1926 self.assertEqual(cdp.chi2, 88.0888600975) 1927 self.assertEqual(cdp.iter, 1) 1928 self.assertEqual(cdp.f_count, 20) 1929 self.assertEqual(cdp.g_count, 2) 1930 self.assertEqual(cdp.h_count, 1) 1931 self.assertEqual(cdp.warning, None) 1932 1933 # Global relaxation data tests. 1934 self.assertEqual(cdp.ri_ids, ri_ids) 1935 for ri_id in ri_ids: 1936 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 1937 self.assertEqual(cdp.frq[ri_id], frqs[ri_id]) 1938 1939 # Loop over the residues of the original data. 1940 j = 0 1941 for i in xrange(len(cdp.mol[0].res)): 1942 # Aliases 1943 res = cdp.mol[0].res[i] 1944 spin = cdp.mol[0].res[i].spin[0] 1945 1946 # Debugging printout. 1947 print(res) 1948 print(spin) 1949 1950 # Spin info tests. 1951 self.assertEqual(res.num, num[i]) 1952 self.assertEqual(res.name, 'XXX') 1953 self.assertEqual(spin.num, None) 1954 self.assertEqual(spin.name, None) 1955 self.assertEqual(spin.select, select[i]) 1956 self.assertEqual(spin.fixed, False) 1957 1958 # Skip deselected spins. 1959 if not select[i]: 1960 continue 1961 1962 # Structural info. 1963 self.assertEqual(spin.heteronuc_type, '15N') 1964 self.assertEqual(spin.proton_type, '1H') 1965 self.assertEqual(spin.attached_proton, None) 1966 1967 # Model-free tests. 1968 self.assertEqual(spin.model, model[j]) 1969 self.assertEqual(spin.equation, 'mf_ext') 1970 self.assertEqual(spin.params, params[j]) 1971 self.assertEqual(spin.s2, s2[j]) 1972 self.assertEqual(spin.s2f, s2f[j]) 1973 self.assertEqual(spin.s2s, s2s[j]) 1974 self.assertEqual(spin.local_tm, None) 1975 self.assertEqual(spin.te, None) 1976 if tf[j] != None: 1977 tf[j] = tf[j]*1e-12 1978 self.assertEqual(spin.tf, tf[j]) 1979 self.assertEqual(spin.ts, ts[j]*1e-12) 1980 if rex[j] != None: 1981 rex[j] = rex[j]/(2.0*pi*500000000.0)**2 1982 self.assertEqual(spin.rex, rex[j]) 1983 self.assertEqual(spin.r, 1.0200000000000001e-10) 1984 self.assertEqual(spin.csa, -0.00016999999999999999) 1985 1986 # Minimisation statistic tests. 1987 self.assertEqual(spin.chi2, None) 1988 self.assertEqual(spin.iter, None) 1989 self.assertEqual(spin.f_count, None) 1990 self.assertEqual(spin.g_count, None) 1991 self.assertEqual(spin.h_count, None) 1992 self.assertEqual(spin.warning, None) 1993 1994 # Relaxation data tests. 1995 for ri_id in cdp.ri_ids: 1996 print(ri_id) 1997 self.assertEqual(spin.ri_data[ri_id], ri_data[ri_id][j]) 1998 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[ri_id][j]) 1999 2000 # Secondary index. 2001 j = j + 1

2002 2003

2004 - def test_read_results_1_2_pse4(self):

2005 """Read the truncated relax 1.2 model-free results file for PSE-4.""" 2006 2007 # Read the results. 2008 self.interpreter.results.read(file='pse4_trunc', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 2009 2010 # Debugging printout. 2011 print(cdp) 2012 2013 # The spin specific data. 2014 num = [24, 27] 2015 name = ['ser', 'gln'] 2016 eqi = [None, 'mf_ext'] 2017 select = [False, True] 2018 model = [None, 'm5'] 2019 params = [[], ['s2f', 's2', 'ts']] 2020 s2 = [None, 0.86578779694713515] 2021 s2f = [None, 0.88618694421409949] 2022 s2s = [None, 0.97698098871784322] 2023 s2s_sim = [[None, None, None], 2024 [0.95852080081635382, 0.97574415413309512, 0.97293450506144197]] 2025 tf = [None, None] 2026 ts = [None, 598.8142249659868e-12] 2027 rex = [None, None] 2028 r = [None, 1.0200000000000001e-10] 2029 csa = [None, -0.00017199999999999998] 2030 ri_ids = ['R1_800', 'NOE_800', 'R1_600', 'R2_600', 'NOE_600', 'R1_500', 'R2_500', 'NOE_500'] 2031 ri_type_list = ['R1', 'NOE', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 2032 frq_list = [799744000.0]*2 + [599737000.0]*3 + [499719000.0]*3 2033 ri_data_list = [[], 2034 [0.6835, 0.81850000000000001, 0.98409999999999997, 16.5107, 0.79796699999999998, 1.3174999999999999, 15.381500000000001, 0.73046900000000003]] 2035 ri_data_err_list = [[], 2036 [0.026957200000000001, 0.025881000000000001, 0.0243073, 0.497137, 0.028663000000000001, 0.038550000000000001, 0.40883999999999998, 0.022016299999999999]] 2037 ri_type = {} 2038 frq = {} 2039 ri_data = [{}, {}] 2040 ri_data_err = [{}, {}] 2041 for i in range(len(ri_ids)): 2042 ri_type[ri_ids[i]] = ri_type_list[i] 2043 frq[ri_ids[i]] = frq_list[i] 2044 ri_data[1][ri_ids[i]] = ri_data_list[1][i] 2045 ri_data_err[1][ri_ids[i]] = ri_data_err_list[1][i] 2046 2047 # Misc tests. 2048 self.assertEqual(cdp.pipe_type, 'mf') 2049 self.assertEqual(cdp.hybrid_pipes, []) 2050 2051 # Diffusion tensor tests. 2052 self.assertEqual(cdp.diff_tensor.type, 'ellipsoid') 2053 self.assertEqual(cdp.diff_tensor.tm, 1.2682770910095516e-08) 2054 self.assertEqual(cdp.diff_tensor.tm_err, 2.4053909822304126e-11) 2055 self.assertEqual(cdp.diff_tensor.tm_sim[0], 1.2666656725867738e-08) 2056 self.assertEqual(cdp.diff_tensor.tm_sim[1], 1.2689812011679408e-08) 2057 self.assertEqual(cdp.diff_tensor.tm_sim[2], 1.2698266641804573e-08) 2058 2059 # Global minimisation statistic tests. 2060 self.assertEqual(cdp.chi2, 935.13348627485448) 2061 self.assertEqual(cdp.chi2_sim[0], 898.0981500197106) 2062 self.assertEqual(cdp.chi2_sim[1], 904.11113814725172) 2063 self.assertEqual(cdp.chi2_sim[2], 902.03890817023728) 2064 self.assertEqual(cdp.iter, 1) 2065 self.assertEqual(cdp.iter_sim[0], 23) 2066 self.assertEqual(cdp.iter_sim[1], 30) 2067 self.assertEqual(cdp.iter_sim[2], 16) 2068 self.assertEqual(cdp.f_count, 21) 2069 self.assertEqual(cdp.f_count_sim[0], 61) 2070 self.assertEqual(cdp.f_count_sim[1], 501) 2071 self.assertEqual(cdp.f_count_sim[2], 59) 2072 self.assertEqual(cdp.g_count, 2) 2073 self.assertEqual(cdp.g_count_sim[0], 27) 2074 self.assertEqual(cdp.g_count_sim[1], 34) 2075 self.assertEqual(cdp.g_count_sim[2], 20) 2076 self.assertEqual(cdp.h_count, 1) 2077 self.assertEqual(cdp.h_count_sim[0], 23) 2078 self.assertEqual(cdp.h_count_sim[1], 30) 2079 self.assertEqual(cdp.h_count_sim[2], 16) 2080 self.assertEqual(cdp.warning, None) 2081 self.assertEqual(cdp.warning_sim[0], None) 2082 self.assertEqual(cdp.warning_sim[1], None) 2083 self.assertEqual(cdp.warning_sim[2], None) 2084 2085 # Global relaxation data tests. 2086 self.assertEqual(cdp.ri_ids, ri_ids) 2087 for ri_id in ri_ids: 2088 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 2089 self.assertEqual(cdp.frq[ri_id], frq[ri_id]) 2090 2091 # Loop over the residues of the original data. 2092 for i in xrange(len(cdp.mol[0].res)): 2093 # Aliases 2094 res = cdp.mol[0].res[i] 2095 spin = cdp.mol[0].res[i].spin[0] 2096 2097 # Debugging printout. 2098 print(res) 2099 print(spin) 2100 2101 # Spin info tests. 2102 self.assertEqual(res.num, num[i]) 2103 self.assertEqual(res.name, name[i]) 2104 self.assertEqual(spin.num, None) 2105 self.assertEqual(spin.name, None) 2106 self.assertEqual(spin.select, select[i]) 2107 self.assertEqual(spin.fixed, False) 2108 2109 # Structural info. 2110 self.assertEqual(spin.heteronuc_type, '15N') 2111 self.assertEqual(spin.proton_type, '1H') 2112 self.assertEqual(spin.attached_proton, 'H') 2113 #FIXME 2114 #self.assertEqual(spin.nucleus, 'N') 2115 2116 # Model-free tests. 2117 self.assertEqual(spin.model, model[i]) 2118 self.assertEqual(spin.equation, eqi[i]) 2119 self.assertEqual(spin.params, params[i]) 2120 self.assertEqual(spin.s2, s2[i]) 2121 self.assertEqual(spin.s2f, s2f[i]) 2122 self.assertEqual(spin.s2s, s2s[i]) 2123 self.assertEqual(spin.local_tm, None) 2124 self.assertEqual(spin.te, None) 2125 self.assertEqual(spin.tf, tf[i]) 2126 self.assertEqual(spin.ts, ts[i]) 2127 self.assertEqual(spin.rex, rex[i]) 2128 self.assertEqual(spin.r, r[i]) 2129 self.assertEqual(spin.csa, csa[i]) 2130 for j in range(3): 2131 self.assertEqual(spin.s2s_sim[j], s2s_sim[i][j]) 2132 2133 # Minimisation statistic tests. 2134 self.assertEqual(spin.chi2, None) 2135 self.assertEqual(spin.iter, None) 2136 self.assertEqual(spin.f_count, None) 2137 self.assertEqual(spin.g_count, None) 2138 self.assertEqual(spin.h_count, None) 2139 self.assertEqual(spin.warning, None) 2140 2141 # Relaxation data tests. 2142 if i == 0: 2143 self.assertEqual(spin.ri_data, {}) 2144 self.assertEqual(spin.ri_data_err, {}) 2145 else: 2146 for ri_id in ri_ids: 2147 self.assertEqual(spin.ri_data[ri_id], ri_data[i][ri_id]) 2148 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[i][ri_id])

2149 2150

2151 - def test_read_results_1_2_tem1(self):

2152 """Read the truncated relax 1.2 model-free results file for TEM-1.""" 2153 2154 # Read the results. 2155 self.interpreter.results.read(file='tem1_trunc', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 2156 2157 # Debugging printout. 2158 print(cdp) 2159 2160 # The spin specific data. 2161 num = [26, 27, 29, 30, 31, 32, 33, 34] 2162 name = ['His', 'Pro', 'Thr', 'Leu', 'Val', 'Lys', 'Val', 'Lys'] 2163 eqi = [None, None, None, 'mf_ext', 'mf_orig', 'mf_orig', None, 'mf_orig'] 2164 select = [False, False, False, True, True, True, False, True] 2165 model = [None, None, None, 'm5', 'm2', 'm1', None, 'm1'] 2166 params = [None, None, None, ['s2f', 's2', 'ts'], ['s2', 'te'], ['s2'], None, ['s2']] 2167 s2 = [None, None, None, 0.85674161305142216, 0.89462664243726608, 0.90201790111143165, None, 0.92099297347361675] 2168 s2f = [None, None, None, 0.88220054271390302, None, None, None, None] 2169 s2s = [None, None, None, 0.97114156200339452, None, None, None, None] 2170 te = [None, None, None, None, 43.262426916926735*1e-12, None, None, None] 2171 tf = [None, None, None, None, None, None, None, None] 2172 ts = [None, None, None, 2385.912514843546*1e-12, None, None, None, None] 2173 rex = [None, None, None, None, None, None, None, None] 2174 r = [None, None, None, 1.0200000000000001e-10, 1.0200000000000001e-10, 1.0200000000000001e-10, None, 1.0200000000000001e-10] 2175 csa = [None, None, None, -0.00017199999999999998, -0.00017199999999999998, -0.00017199999999999998, None, -0.00017199999999999998] 2176 ri_ids = ['R1_800', 'R2_800', 'R1_600', 'R2_600', 'NOE_600', 'R1_500', 'R2_500', 'NOE_500'] 2177 ri_type_list = ['R1', 'R2', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 2178 frq_list = [799812000.0]*2 + [599739000.0]*3 + [499827000.0]*3 2179 ri_data_list = [[], 2180 [], 2181 [], 2182 [0.75680000000000003, 18.797999999999998, 1.0747, 16.477, 0.86873100000000003, 1.2625999999999999, 15.3367, 0.77803197999999996], 2183 [0.75019999999999998, 19.201599999999999, 1.0617000000000001, 17.652899999999999, 0.73757200000000001, 1.3165, 15.949, 0.72442474000000001], 2184 [0.75860000000000005, 19.303799999999999, 1.0605, 16.593699999999998, 0.79137500000000005, 1.3425, 15.327199999999999, 0.83449132000000004], 2185 [], 2186 [0.71919999999999995, 20.165400000000002, 1.0729, 17.291899999999998, 0.80444599999999999, 1.2971999999999999, 15.9963, 0.73164684999999996]] 2187 ri_data_err_list = [[], 2188 [], 2189 [], 2190 [0.028001600000000001, 0.21729999999999999, 0.031166300000000001, 0.44487900000000002, 0.043210699999999998, 0.054291800000000001, 0.69015199999999999, 0.038901600000000001], 2191 [0.028899999999999999, 0.25640000000000002, 0.030789299999999999, 0.476628, 0.036686799999999999, 0.0566095, 0.71770500000000004, 0.036221200000000002], 2192 [0.033399999999999999, 0.2233, 0.030754500000000001, 0.44802999999999998, 0.039363000000000002, 0.057727500000000001, 0.689724, 0.041724600000000001], 2193 [], 2194 [0.027699999999999999, 0.52810000000000001, 0.031399999999999997, 0.46688099999999999, 0.040013100000000003, 0.055779599999999999, 0.71983399999999997, 0.036582299999999998]] 2195 ri_type = {} 2196 frq = {} 2197 ri_data = [] 2198 ri_data_err = [] 2199 for i in range(len(ri_data_list)): 2200 ri_data.append({}) 2201 ri_data_err.append({}) 2202 2203 for i in range(len(ri_ids)): 2204 ri_type[ri_ids[i]] = ri_type_list[i] 2205 frq[ri_ids[i]] = frq_list[i] 2206 for j in range(len(ri_data_list)): 2207 if len(ri_data_list[j]): 2208 ri_data[j][ri_ids[i]] = ri_data_list[j][i] 2209 ri_data_err[j][ri_ids[i]] = ri_data_err_list[j][i] 2210 2211 chi2 = [None, None, None, 7.9383923597292441, 10.93852890925343, 3.1931459495488084, None, 8.3598891989018611] 2212 iter = [None, None, None, 55, 10, 3, None, 3] 2213 f_count = [None, None, None, 170, 148, 10, None, 10] 2214 g_count = [None, None, None, 60, 14, 6, None, 6] 2215 h_count = [None, None, None, 55, 10, 3, None, 3] 2216 2217 # Misc tests. 2218 self.assertEqual(cdp.pipe_type, 'mf') 2219 self.assertEqual(cdp.hybrid_pipes, []) 2220 2221 # Diffusion tensor tests. 2222 self.assertEqual(cdp.diff_tensor.type, 'ellipsoid') 2223 self.assertEqual(cdp.diff_tensor.tm, 1.2526607261882971e-08) 2224 self.assertEqual(cdp.diff_tensor.Da, 2784606.8835473624) 2225 self.assertEqual(cdp.diff_tensor.Dr, 0.097243698709517518) 2226 self.assertEqual(cdp.diff_tensor.alpha, 48.852555276419558 / 360.0 * 2.0 * pi) 2227 self.assertEqual(cdp.diff_tensor.beta, 9.7876096346750447 / 360.0 * 2.0 * pi) 2228 self.assertEqual(cdp.diff_tensor.gamma, 42.15815798778408 / 360.0 * 2.0 * pi) 2229 2230 # Global relaxation data tests. 2231 self.assertEqual(cdp.ri_ids, ri_ids) 2232 for ri_id in ri_ids: 2233 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 2234 self.assertEqual(cdp.frq[ri_id], frq[ri_id]) 2235 2236 # Loop over the residues of the original data. 2237 for i in xrange(len(cdp.mol[0].res)): 2238 # Aliases 2239 res = cdp.mol[0].res[i] 2240 spin = cdp.mol[0].res[i].spin[0] 2241 2242 # Debugging printout. 2243 print(res) 2244 print(spin) 2245 2246 # Spin info tests. 2247 self.assertEqual(res.num, num[i]) 2248 self.assertEqual(res.name, name[i]) 2249 self.assertEqual(spin.num, None) 2250 self.assertEqual(spin.name, None) 2251 self.assertEqual(spin.select, select[i]) 2252 self.assertEqual(spin.fixed, False) 2253 2254 # Structural info. 2255 self.assertEqual(spin.heteronuc_type, '15N') 2256 self.assertEqual(spin.proton_type, '1H') 2257 self.assertEqual(spin.attached_proton, 'H') 2258 #FIXME 2259 #self.assertEqual(spin.nucleus, 'N') 2260 2261 # Model-free tests. 2262 self.assertEqual(spin.model, model[i]) 2263 self.assertEqual(spin.equation, eqi[i]) 2264 self.assertEqual(spin.params, params[i]) 2265 self.assertEqual(spin.s2, s2[i]) 2266 self.assertEqual(spin.s2f, s2f[i]) 2267 self.assertEqual(spin.s2s, s2s[i]) 2268 self.assertEqual(spin.local_tm, None) 2269 self.assertEqual(spin.te, te[i]) 2270 self.assertEqual(spin.tf, tf[i]) 2271 self.assertEqual(spin.ts, ts[i]) 2272 self.assertEqual(spin.rex, rex[i]) 2273 self.assertEqual(spin.r, r[i]) 2274 self.assertEqual(spin.csa, csa[i]) 2275 2276 # Minimisation statistic tests. 2277 self.assertEqual(spin.chi2, chi2[i]) 2278 self.assertEqual(spin.iter, iter[i]) 2279 self.assertEqual(spin.f_count, f_count[i]) 2280 self.assertEqual(spin.g_count, g_count[i]) 2281 self.assertEqual(spin.h_count, h_count[i]) 2282 self.assertEqual(spin.warning, None) 2283 2284 # Relaxation data tests. 2285 if not ri_data[i].keys(): 2286 self.assertEqual(spin.ri_data, {}) 2287 self.assertEqual(spin.ri_data_err, {}) 2288 else: 2289 for ri_id in ri_ids: 2290 self.assertEqual(spin.ri_data[ri_id], ri_data[i][ri_id]) 2291 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[i][ri_id])

2292 2293

2294 - def test_read_results_1_3_v1(self):

2295 """Read a 1.3 model-free results file (relax XML version 1).""" 2296 2297 # Path of the files. 2298 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2299 2300 # Read the results file. 2301 self.interpreter.pipe.create('1.3', 'mf') 2302 self.interpreter.results.read(file='final_results_trunc_1.3_v1', dir=path) 2303 2304 # The shared part of the test. 2305 self.check_read_results_1_3()

2306 2307

2308 - def test_read_results_1_3_pre_py273_v1(self):

2309 """Read a 1.3 model-free results file (pre-Python 2.7.3, relax XML version 1).""" 2310 2311 # Path of the files. 2312 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2313 2314 # Read the results file. 2315 self.interpreter.pipe.create('1.3', 'mf') 2316 self.interpreter.results.read(file='final_results_trunc_1.3_pre_py2.7.3_v1', dir=path) 2317 2318 # The shared part of the test. 2319 self.check_read_results_1_3()

2320 2321

2322 - def test_read_results_1_3_v2(self):

2323 """Read a 1.3 model-free results file (relax XML version 2).""" 2324 2325 # Path of the files. 2326 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2327 2328 # Read the results file. 2329 self.interpreter.pipe.create('1.3', 'mf') 2330 self.interpreter.results.read(file='final_results_trunc_1.3_v2', dir=path) 2331 2332 # The shared part of the test. 2333 self.check_read_results_1_3()

2334 2335

2336 - def test_read_results_1_3_v2_broken(self):

2337 """Read a 1.3 model-free results file (relax XML version 2) with corrupted floats. 2338 2339 The floats are deliberately mangled to test the IEEE-754 reading. 2340 """ 2341 2342 # Path of the files. 2343 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2344 2345 # Read the results file. 2346 self.interpreter.pipe.create('1.3', 'mf') 2347 self.interpreter.results.read(file='final_results_trunc_1.3_v2_broken', dir=path) 2348 2349 # The shared part of the test. 2350 self.check_read_results_1_3()

2351 2352

2353 - def test_read_results_1_3_pre_py273_v2(self):

2354 """Read a 1.3 model-free results file (pre-Python 2.7.3, relax XML version 2).""" 2355 2356 # Path of the files. 2357 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2358 2359 # Read the results file. 2360 self.interpreter.pipe.create('1.3', 'mf') 2361 self.interpreter.results.read(file='final_results_trunc_1.3_pre_py2.7.3_v2', dir=path) 2362 2363 # The shared part of the test. 2364 self.check_read_results_1_3()

2365 2366

2367 - def test_select_m4(self):

2368 """Selecting model m4 with parameters {S2, te, Rex} using model_free.select_model().""" 2369 2370 # Path of the files. 2371 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2372 2373 # Read the sequence. 2374 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2375 2376 # Select the model. 2377 self.interpreter.model_free.select_model(model='m4') 2378 2379 # Test the model. 2380 self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4') 2381 self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['s2', 'te', 'rex'])

2382 2383

2384 - def test_set_bond_length(self):

2385 """Setting the bond length through the user function value.set().""" 2386 2387 # Path of the files. 2388 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2389 2390 # Read the sequence. 2391 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2392 2393 # Set the CSA value. 2394 self.interpreter.value.set(NH_BOND_LENGTH, 'r') 2395 2396 # Test the value. 2397 self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)

2398 2399

2400 - def test_set_csa(self):

2401 """Setting the CSA value through the user function value.set().""" 2402 2403 # Path of the files. 2404 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2405 2406 # Read the sequence. 2407 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2408 2409 # Set the CSA value. 2410 self.interpreter.value.set(N15_CSA, 'csa') 2411 2412 # Test the value. 2413 self.assertEqual(cdp.mol[0].res[1].spin[0].csa, N15_CSA)

2414 2415

2416 - def test_set_csa_bond_length(self):

2417 """Setting both the CSA value and bond length through the user function value.set().""" 2418 2419 # Path of the files. 2420 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2421 2422 # Read the sequence. 2423 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2424 2425 # Set the CSA value and bond length simultaneously. 2426 self.interpreter.value.set([N15_CSA, NH_BOND_LENGTH], ['csa', 'r']) 2427 2428 # Test the values. 2429 self.assertEqual(cdp.mol[0].res[1].spin[0].csa, N15_CSA) 2430 self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)

2431 2432

2433 - def test_tm0_grid(self):

2434 """Test the optimisation of the tm0 model-free parameter grid.""" 2435 2436 # Initialise. 2437 cdp._model = 'tm0' 2438 cdp._value_test = self.value_test 2439 2440 # Setup the data pipe for optimisation. 2441 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

2442 2443

2444 - def test_tm1_grid(self):

2445 """Test the optimisation of the tm1 model-free parameter grid.""" 2446 2447 # Initialise. 2448 cdp._model = 'tm1' 2449 cdp._value_test = self.value_test 2450 2451 # Setup the data pipe for optimisation. 2452 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm1_grid.py')

2453 2454

2455 - def test_tm2_grid(self):

2456 """Test the optimisation of the tm2 model-free parameter grid.""" 2457 2458 # Initialise. 2459 cdp._model = 'tm2' 2460 cdp._value_test = self.value_test 2461 2462 # Setup the data pipe for optimisation. 2463 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

2464 2465

2466 - def test_tm3_grid(self):

2467 """Test the optimisation of the tm3 model-free parameter grid.""" 2468 2469 # Initialise. 2470 cdp._model = 'tm3' 2471 cdp._value_test = self.value_test 2472 2473 # Setup the data pipe for optimisation. 2474 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm3_grid.py')

2475 2476

2477 - def test_tm4_grid(self):

2478 """Test the optimisation of the tm4 model-free parameter grid.""" 2479 2480 # Initialise. 2481 cdp._model = 'tm4' 2482 cdp._value_test = self.value_test 2483 2484 # Setup the data pipe for optimisation. 2485 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm4_grid.py')

2486 2487

2488 - def test_tm5_grid(self):

2489 """Test the optimisation of the tm5 model-free parameter grid.""" 2490 2491 # Initialise. 2492 cdp._model = 'tm5' 2493 cdp._value_test = self.value_test 2494 2495 # Setup the data pipe for optimisation. 2496 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm5_grid.py')

2497 2498

2499 - def test_tm6_grid(self):

2500 """Test the optimisation of the tm6 model-free parameter grid.""" 2501 2502 # Initialise. 2503 cdp._model = 'tm6' 2504 cdp._value_test = self.value_test 2505 2506 # Setup the data pipe for optimisation. 2507 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm6_grid.py')

2508 2509

2510 - def test_tm7_grid(self):

2511 """Test the optimisation of the tm7 model-free parameter grid.""" 2512 2513 # Initialise. 2514 cdp._model = 'tm7' 2515 cdp._value_test = self.value_test 2516 2517 # Setup the data pipe for optimisation. 2518 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm7_grid.py')

2519 2520

2521 - def test_tm8_grid(self):

2522 """Test the optimisation of the tm8 model-free parameter grid.""" 2523 2524 # Initialise. 2525 cdp._model = 'tm8' 2526 cdp._value_test = self.value_test 2527 2528 # Setup the data pipe for optimisation. 2529 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm8_grid.py')

2530 2531

2532 - def test_tm9_grid(self):

2533 """Test the optimisation of the tm9 model-free parameter grid.""" 2534 2535 # Initialise. 2536 cdp._model = 'tm9' 2537 cdp._value_test = self.value_test 2538 2539 # Setup the data pipe for optimisation. 2540 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm9_grid.py')

2541 2542

2543 - def test_tylers_peptide(self):

2544 """Try a component of model-free analysis on Tyler Reddy's peptide data (truncated).""" 2545 2546 # Execute the script. 2547 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'tylers_peptide.py')

2548 2549

2550 - def test_write_results(self):

2551 """Writing of model-free results using the user function results.write().""" 2552 2553 # Path of the files. 2554 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2555 2556 # Read the results file. 2557 self.interpreter.results.read(file='final_results_trunc_1.2', dir=path) 2558 2559 # A dummy file object for catching the results.write() output. 2560 file = DummyFileObject() 2561 2562 # Write the results file into a dummy file. 2563 self.interpreter.results.write(file=file, dir=path) 2564 2565 # Now, get the contents of that file, and then 'close' that file. 2566 test_lines = file.readlines() 2567 file.close() 2568 2569 # Read the 1.3 results file, extract the data, then close it again. 2570 a, b, c = platform.python_version_tuple() 2571 if dep_check.xml_type == 'internal' and int(a) >= 2 and int(b) >= 7 and int(c) >= 3: 2572 file = open_read_file(file_name='final_results_trunc_1.3_v2', dir=path) 2573 else: 2574 file = open_read_file(file_name='final_results_trunc_1.3_pre_py2.7.3_v2', dir=path) 2575 true_lines = file.readlines() 2576 file.close() 2577 2578 # Test the rest of the lines. 2579 for i in xrange(len(test_lines)): 2580 # Skip the second line, as it contains the date and hence should not be the same. 2581 # Also skip the third line, as the pipe names are different. 2582 if i == 1 or i == 2: 2583 continue 2584 2585 # Try to convert the test line into a python object (for cross-platform support). 2586 try: 2587 test_line = eval(test_lines[i]) 2588 except: 2589 test_line = test_lines[i] 2590 2591 # Try to convert the true line into a python object (for cross-platform support). 2592 try: 2593 true_line = eval(true_lines[i]) 2594 except: 2595 true_line = true_lines[i] 2596 2597 # Test that the line is the same. 2598 self.assertEqual(test_line, true_line)

2599 2600

2601 - 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):

2602 """Test the optimisation values.""" 2603 2604 # Get the debugging message. 2605 mesg = self.mesg_opt_debug(spin) 2606 2607 # Convert to lists. 2608 if iter != None and not isinstance(iter, list): 2609 iter = [iter] 2610 if f_count != None and not isinstance(f_count, list): 2611 f_count = [f_count] 2612 if g_count != None and not isinstance(g_count, list): 2613 g_count = [g_count] 2614 if h_count != None and not isinstance(h_count, list): 2615 h_count = [h_count] 2616 2617 # Test all the values. 2618 ###################### 2619 2620 # Spin selection. 2621 self.assertEqual(spin.select, select, msg=mesg) 2622 2623 # The local tm correlation time. 2624 if local_tm != None: 2625 self.assertAlmostEqual(spin.local_tm / 1e-9, local_tm, msg=mesg) 2626 else: 2627 self.assertEqual(spin.local_tm, None, msg=mesg) 2628 2629 # S2 order parameter. 2630 if s2 != None: 2631 self.assertAlmostEqual(spin.s2, s2, msg=mesg) 2632 else: 2633 self.assertEqual(spin.s2, None, msg=mesg) 2634 2635 # S2f order parameter. 2636 if s2f != None: 2637 self.assertAlmostEqual(spin.s2f, s2f, 5, msg=mesg) 2638 else: 2639 self.assertEqual(spin.s2f, None, msg=mesg) 2640 2641 # S2s order parameter. 2642 if s2s != None: 2643 self.assertAlmostEqual(spin.s2s, s2s, 5, msg=mesg) 2644 else: 2645 self.assertEqual(spin.s2s, None, msg=mesg) 2646 2647 # te correlation time. 2648 if isinstance(te, float): 2649 self.assertAlmostEqual(spin.te / 1e-12, te, 5, msg=mesg) 2650 elif te == None: 2651 self.assertEqual(spin.te, None, msg=mesg) 2652 2653 # tf correlation time. 2654 if isinstance(tf, float): 2655 self.assertAlmostEqual(spin.tf / 1e-12, tf, 4, msg=mesg) 2656 elif tf == None: 2657 self.assertEqual(spin.tf, None, msg=mesg) 2658 2659 # ts correlation time. 2660 if isinstance(ts, float): 2661 self.assertAlmostEqual(spin.ts / 1e-12, ts, 4, msg=mesg) 2662 elif ts == None: 2663 self.assertEqual(spin.ts, None, msg=mesg) 2664 2665 # Chemical exchange. 2666 if isinstance(rex, float): 2667 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) 2668 elif rex == None: 2669 self.assertEqual(spin.rex, None, msg=mesg) 2670 2671 # The optimisation stats. 2672 if chi2 != None: 2673 self.assertAlmostEqual(spin.chi2, chi2, msg=mesg) 2674 if iter != None: 2675 self.assert_(spin.iter in iter, msg=mesg) 2676 if f_count != None: 2677 self.assert_(spin.f_count in f_count, msg=mesg) 2678 if g_count != None: 2679 self.assert_(spin.g_count in g_count, msg=mesg) 2680 if h_count != None: 2681 self.assert_(spin.h_count in h_count, msg=mesg) 2682 if warning != None: 2683 self.assertEqual(spin.warning, warning, msg=mesg)

Source Code for Module test_suite.system_tests.model_free