test_suite.system_tests.model

65 """TestCase class for the functional tests of model-free analysis.""" 66

67 - def setUp(self):

68 """Set up for all the functional tests.""" 69 70 # Create the data pipe. 71 self.interpreter.pipe.create('mf', 'mf')

72 73

74 - def check_read_results_1_3(self):

75 """Common code for the test_read_results_1_3*() tests.""" 76 77 # Path of the files. 78 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 79 80 # Read the equivalent 1.2 results file for the checks. 81 self.interpreter.pipe.create('1.2', 'mf') 82 self.interpreter.results.read(file='final_results_trunc_1.2', dir=path) 83 84 # Get the two data pipes. 85 pipe_12 = pipes.get_pipe('1.2') 86 pipe_13 = pipes.get_pipe('1.3') 87 88 # Test that the objects in the base pipes are the same. 89 print("Comparison of the objects of the base data pipe:") 90 self.object_comparison(obj1=pipe_12, obj2=pipe_13, skip=['mol', 'interatomic', 'diff_tensor']) 91 92 # Test that the diffusion tensor data is the same. 93 print("Comparison of the objects of the diffusion tensor:") 94 self.object_comparison(obj1=pipe_12.diff_tensor, obj2=pipe_13.diff_tensor) 95 96 # Test the number of molecules. 97 self.assertEqual(len(pipe_12.mol), len(pipe_13.mol)) 98 99 # Loop over the molecules. 100 for i in range(len(pipe_12.mol)): 101 # Test the objects. 102 print("Comparison of the objects of the molecule:") 103 self.object_comparison(obj1=pipe_12.mol[i], obj2=pipe_13.mol[i], skip=['res']) 104 105 # Test the number of residues. 106 self.assertEqual(len(pipe_12.mol[i].res), len(pipe_13.mol[i].res)) 107 108 # Loop over the residues. 109 for j in range(len(pipe_12.mol[i].res)): 110 # Ok, really don't need to do a full comparison of all 162 residues for this test! 111 if j > 10: 112 break 113 114 # Test the objects. 115 print("Comparison of the objects of the residue:") 116 self.object_comparison(obj1=pipe_12.mol[i].res[j], obj2=pipe_13.mol[i].res[j], skip=['spin']) 117 118 # Test the number of spins. 119 self.assertEqual(len(pipe_12.mol[i].res[j].spin), len(pipe_13.mol[i].res[j].spin)) 120 121 # Loop over the spins. 122 for k in range(len(pipe_12.mol[i].res[j].spin)): 123 # Test the objects. 124 print("Comparison of the objects of the spin:") 125 self.object_comparison(obj1=pipe_12.mol[i].res[j].spin[k], obj2=pipe_13.mol[i].res[j].spin[k]) 126 127 # Loop over the interatomic data containers. 128 for i in range(len(pipe_12.interatomic)): 129 # Test the objects. 130 print("Comparison of the objects of the molecule:") 131 self.object_comparison(obj1=pipe_12.interatomic[i], obj2=pipe_13.interatomic[i])

132 133

134 - def mesg_opt_debug(self, spin):

135 """Method for returning a string to help debug the minimisation. 136 137 @param spin: The SpinContainer of the optimised spin. 138 @type spin: SpinContainer instance 139 @return: The debugging string. 140 @rtype: str 141 """ 142 143 # Initialise the string. 144 string = 'Optimisation failure.\n\n' 145 146 # Create the string. 147 string = string + "%-18s%-25s\n" % ("System: ", SYSTEM) 148 string = string + "%-18s%-25s\n" % ("Release: ", RELEASE) 149 string = string + "%-18s%-25s\n" % ("Version: ", VERSION) 150 string = string + "%-18s%-25s\n" % ("Win32 version: ", (WIN32_VER[0] + " " + WIN32_VER[1] + " " + WIN32_VER[2] + " " + WIN32_VER[3])) 151 string = string + "%-18s%-25s\n" % ("Distribution: ", (DIST[0] + " " + DIST[1] + " " + DIST[2])) 152 string = string + "%-18s%-25s\n" % ("Architecture: ", (ARCH[0] + " " + ARCH[1])) 153 string = string + "%-18s%-25s\n" % ("Machine: ", MACH) 154 string = string + "%-18s%-25s\n" % ("Processor: ", PROC) 155 string = string + "%-18s%-25s\n" % ("Python version: ", PY_VER) 156 string = string + "%-18s%-25s\n" % ("Numpy version: ", NUMPY_VER) 157 string = string + "%-18s%-25s\n" % ("Libc version: ", (LIBC_VER[0] + " " + LIBC_VER[1])) 158 159 160 # Minimisation info. 161 string = string + '\n' 162 if spin.local_tm != None: 163 string = string + "%-15s %30.16g\n" % ('local_tm (ns):', spin.local_tm * 1e9) 164 if spin.s2 != None: 165 string = string + "%-15s %30.16g\n" % ('s2:', spin.s2) 166 if spin.s2f != None: 167 string = string + "%-15s %30.16g\n" % ('s2f:', spin.s2f) 168 if spin.s2s != None: 169 string = string + "%-15s %30.16g\n" % ('s2s:', spin.s2s) 170 if spin.te != None: 171 string = string + "%-15s %30.13g\n" % ('te (ps):', spin.te * 1e12) 172 if spin.tf != None: 173 string = string + "%-15s %30.13g\n" % ('tf (ps):', spin.tf * 1e12) 174 if spin.ts != None: 175 string = string + "%-15s %30.13g\n" % ('ts (ps):', spin.ts * 1e12) 176 if spin.rex != None: 177 string = string + "%-15s %30.17g\n" % ('rex:', spin.rex * (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2) 178 string = string + "%-15s %30.17g\n" % ('chi2:', spin.chi2) 179 string = string + "%-15s %30i\n" % ('iter:', spin.iter) 180 string = string + "%-15s %30i\n" % ('f_count:', spin.f_count) 181 string = string + "%-15s %30i\n" % ('g_count:', spin.g_count) 182 string = string + "%-15s %30i\n" % ('h_count:', spin.h_count) 183 string = string + "%-15s %30s\n" % ('warning:', spin.warning) 184 185 # Return the string. 186 return string

187 188

189 - def monte_carlo(self):

190 """Run Monte Carlo simulations for the optimised model-free model.""" 191 192 # Monte Carlo simulations. 193 self.interpreter.monte_carlo.setup(number=3) 194 self.interpreter.monte_carlo.create_data() 195 self.interpreter.monte_carlo.initial_values() 196 self.interpreter.minimise('newton') 197 #self.interpreter.eliminate() 198 self.interpreter.monte_carlo.error_analysis()

199 200

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

202 """Check if the contents of 2 objects are the same.""" 203 204 # The names are the same. 205 self.assertEqual(dir(obj1), dir(obj2)) 206 207 # Loop over the objects in the base objects. 208 for name in dir(obj1): 209 # Skip special objects. 210 if skip and name in skip: 211 continue 212 213 # Skip objects starting with '_'. 214 if search('^_', name): 215 continue 216 217 # Skip original class methods. 218 if name in list(obj1.__class__.__dict__.keys()): 219 continue 220 221 # Print out. 222 print("\t" + name) 223 224 # Get the sub-objects. 225 sub_obj1 = getattr(obj1, name) 226 sub_obj2 = getattr(obj2, name) 227 228 # Check that they are of the same type. 229 self.assertEqual(type(sub_obj1), type(sub_obj2)) 230 231 # Check that they are equal (converting to strings to avoid comparison nastiness). 232 if isinstance(sub_obj1, dict): 233 self.assertEqual(sub_obj1, sub_obj2) 234 else: 235 self.assertEqual(str(sub_obj1), str(sub_obj2))

236 237

238 - def test_bug_14872_unicode_selection(self):

239 """Test catching bug #14872, the unicode string selection failure as submitted by Olivier Serve.""" 240 241 # Execute the script. 242 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_14872_unicode_selection.py')

243 244

245 - def test_bug_14941_local_tm_global_selection(self):

246 """Test catching bug #14941, the local tm global model selection problem as submitted by Mikaela Stewart (mikaela dot stewart att gmail dot com).""" 247 248 # Execute the script. 249 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')

250 251

252 - def test_bug_15050(self):

253 """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).""" 254 255 # Execute the script. 256 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_15050.py')

257 258

259 - def test_bugs_12582_12591_12607(self):

260 """Test catching bugs #12582, #12591 and #12607 as submitted by Chris Brosey.""" 261 262 # Execute the script. 263 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bugs_12582_12591_12607.py') 264 265 # Test for bug #12607 (S2 changes because it is in the grid search when it should not be). 266 self.assertNotEqual(cdp.mol[0].res[1].spin[0].s2, 1.0)

267 268

269 - def test_bug_18790(self):

270 """Test catching bug #18790, the negative relaxation data RelaxError reported by Vitaly Vostrikov.""" 271 272 # Execute the script. 273 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_18790_negative_error.py')

274 275

276 - def test_bug_20213_asn_sidechain(self):

277 """Bug #20213 catch, the model selection failure due to the presence of Asp and Gln sidechain N spins.""" 278 279 # Create a temporary directory for dumping files. 280 ds.tmpdir = mkdtemp() 281 282 # Execute the script. 283 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_20213_asn_sidechain.py')

284 285

286 - def test_create_m4(self):

287 """Creating model m4 with parameters {S2, te, Rex} using model_free.create_model().""" 288 289 # Execute the script. 290 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'create_m4.py') 291 292 # Test the model. 293 self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4') 294 self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['s2', 'te', 'rex'])

295 296

297 - def test_dauvergne_protocol(self):

298 """Check the execution of auto_analyses.dauvergne_protocol.""" 299 300 # Create a temporary directory for dumping files. 301 ds.tmpdir = mkdtemp() 302 303 # Execute the script. 304 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'dauvergne_protocol.py') 305 306 # Check the diffusion tensor. 307 self.assertEqual(cdp.diff_tensor.type, 'sphere') 308 self.assertAlmostEqual(cdp.diff_tensor.tm, 1e-8) 309 self.assertEqual(cdp.diff_tensor.fixed, True) 310 311 # The global minimisation info. 312 self.assertAlmostEqual(cdp.chi2, 4e-19) 313 314 # The spin info. 315 mol_names = ["sphere_mol1"] * 20 316 res_names = ["GLY"] * 20 317 res_nums = [] 318 for i in range(1, 10): 319 res_nums.append(i) 320 res_nums.append(i) 321 res_nums.append(i) 322 res_nums.append(i) 323 spin_names = ["N", "H"] * 9 + ["NE1", "HE1"] 324 spin_nums = list(range(1, 21)) 325 isotopes = ["15N", "1H"] * 10 326 csa = [-172e-6, None] * 10 327 select = [True, False] * 10 328 fixed = [False, False] * 10 329 s2 = [0.8, None] * 10 330 te = [20e-12, None] * 10 331 332 # Check the spin data. 333 i = 0 334 for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 335 # The ID info. 336 self.assertEqual(mol_name, mol_names[i]) 337 self.assertEqual(res_name, res_names[i]) 338 self.assertEqual(res_num, res_nums[i]) 339 self.assertEqual(spin.name, spin_names[i]) 340 self.assertEqual(spin.num, spin_nums[i]) 341 342 # The data. 343 self.assertEqual(spin.select, select[i]) 344 self.assertEqual(spin.fixed, fixed[i]) 345 self.assertEqual(spin.isotope, isotopes[i]) 346 if csa[i] == None: 347 self.assertEqual(spin.csa, None) 348 else: 349 self.assertAlmostEqual(spin.csa, csa[i]) 350 351 # The model-free data. 352 self.assertEqual(spin.model, 'm2') 353 self.assertEqual(spin.equation, 'mf_orig') 354 self.assertEqual(len(spin.params), 2) 355 self.assertEqual(spin.params[0], 's2') 356 self.assertEqual(spin.params[1], 'te') 357 if s2[i] == None: 358 self.assertEqual(spin.s2, None) 359 else: 360 self.assertAlmostEqual(spin.s2, 0.8) 361 self.assertEqual(spin.s2f, None) 362 self.assertEqual(spin.s2s, None) 363 self.assertEqual(spin.local_tm, None) 364 if te[i] == None: 365 self.assertEqual(spin.te, None) 366 else: 367 self.assertAlmostEqual(spin.te, 20e-12) 368 self.assertEqual(spin.tf, None) 369 self.assertEqual(spin.ts, None) 370 self.assertEqual(spin.rex, None) 371 372 # The spin minimisation info. 373 self.assertEqual(spin.chi2, None) 374 self.assertEqual(spin.iter, None) 375 self.assertEqual(spin.f_count, None) 376 self.assertEqual(spin.g_count, None) 377 self.assertEqual(spin.h_count, None) 378 self.assertEqual(spin.warning, None) 379 380 # Increment the index. 381 i += 1 382 383 # Check the interatomic data. 384 i = 0 385 for interatom in interatomic_loop(): 386 self.assertAlmostEqual(interatom.r, 1.02 * 1e-10)

387 388

389 - def test_generate_ri(self):

390 """Back-calculate relaxation data.""" 391 392 # Execute the script. 393 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'generate_ri.py')

394 395

396 - def test_latex_table(self):

397 """Test the creation of a LaTeX table of model-free results, mimicking the latex_mf_table.py sample script.""" 398 399 # Execute the script. 400 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'latex_mf_table.py')

401 402

403 - def test_local_tm_10_S2_0_8_te_40(self):

404 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 405 406 # Setup the data pipe for optimisation. 407 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') 408 409 # The proton frequencies in MHz. 410 frq = ['400', '500', '600', '700', '800', '900', '1000'] 411 412 # Load the relaxation data. 413 for i in range(len(frq)): 414 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, spin_id='@N') 415 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, spin_id='@N') 416 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, spin_id='@N') 417 418 # Set up the initial model-free parameter values (bypass the grid search for speed). 419 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 420 421 # Minimise. 422 self.interpreter.minimise('newton', 'gmw', 'back') 423 424 # Alias the relevent spin container. 425 spin = cdp.mol[0].res[0].spin[0] 426 427 # Check the values. 428 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

429 430

431 - def test_local_tm_10_S2_0_8_te_40_test2(self):

432 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 433 434 # Setup the data pipe for optimisation. 435 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') 436 437 # The proton frequencies in MHz. 438 frq = ['400', '500', '600', '700', '800', '900', '1000'] 439 440 # Load the relaxation data. 441 for i in range(len(frq)): 442 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, spin_id='@N') 443 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, spin_id='@N') 444 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, spin_id='@N') 445 446 # Set up the initial model-free parameter values (bypass the grid search for speed). 447 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 448 449 # Minimise. 450 self.interpreter.minimise('newton', 'gmw', 'back') 451 452 # Alias the relevent spin container. 453 spin = cdp.mol[0].res[0].spin[0] 454 455 # Check the values. 456 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

457 458

459 - def test_local_tm_10_S2_0_8_te_40_test3(self):

460 """Test the optimisation of the test set {tm=10, S2=0.8, te=40}.""" 461 462 # Setup the data pipe for optimisation. 463 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') 464 465 # Load the relaxation data. 466 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, spin_id='@N') 467 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, spin_id='@N') 468 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, spin_id='@N') 469 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, spin_id='@N') 470 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, spin_id='@N') 471 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, spin_id='@N') 472 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, spin_id='@N') 473 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, spin_id='@N') 474 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, spin_id='@N') 475 476 # Set up the initial model-free parameter values (bypass the grid search for speed). 477 self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2', 'te']) 478 479 # Minimise. 480 self.interpreter.minimise('newton', 'gmw', 'back') 481 482 # Alias the relevent spin container. 483 spin = cdp.mol[0].res[0].spin[0] 484 485 # Check the values. 486 self.value_test(spin, local_tm=10, s2=0.8, te=40, chi2=0.0)

487 488

489 - def test_m0_grid(self):

490 """Test the optimisation of the m0 model-free model against the tm0 parameter grid.""" 491 492 # Initialise. 493 cdp._model = 'm0' 494 cdp._value_test = self.value_test 495 496 # Setup the data pipe for optimisation. 497 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

498 499

500 - def test_m0_grid_vs_m1(self):

501 """Test the optimisation of the m1 model-free model against the tm0 parameter grid.""" 502 503 # Initialise. 504 cdp._model = 'm1' 505 cdp._value_test = self.value_test 506 507 # Setup the data pipe for optimisation. 508 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

509 510

511 - def test_m0_grid_vs_m2(self):

512 """Test the optimisation of the m2 model-free model against the tm0 parameter grid.""" 513 514 # Initialise. 515 cdp._model = 'm2' 516 cdp._value_test = self.value_test 517 518 # Setup the data pipe for optimisation. 519 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

520 521

522 - def test_m0_grid_vs_m3(self):

523 """Test the optimisation of the m3 model-free model against the tm0 parameter grid.""" 524 525 # Initialise. 526 cdp._model = 'm3' 527 cdp._value_test = self.value_test 528 529 # Setup the data pipe for optimisation. 530 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

531 532

533 - def test_m0_grid_vs_m4(self):

534 """Test the optimisation of the m4 model-free model against the tm0 parameter grid.""" 535 536 # Initialise. 537 cdp._model = 'm4' 538 cdp._value_test = self.value_test 539 540 # Setup the data pipe for optimisation. 541 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

542 543

544 - def test_m1_grid(self):

545 """Test the optimisation of the m1 model-free model against the tm1 parameter grid.""" 546 547 # Initialise. 548 cdp._model = 'm1' 549 cdp._value_test = self.value_test 550 551 # Setup the data pipe for optimisation. 552 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm1_grid.py')

553 554

555 - def test_m2_grid(self):

556 """Test the optimisation of the m2 model-free model against the tm2 parameter grid.""" 557 558 # Initialise. 559 cdp._model = 'm2' 560 cdp._value_test = self.value_test 561 562 # Setup the data pipe for optimisation. 563 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

564 565

566 - def test_m2_grid_vs_m4(self):

567 """Test the optimisation of the m4 model-free model against the tm2 parameter grid.""" 568 569 # Initialise. 570 cdp._model = 'm4' 571 cdp._value_test = self.value_test 572 573 # Setup the data pipe for optimisation. 574 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

575 576

577 - def test_m3_grid(self):

578 """Test the optimisation of the m3 model-free model against the tm3 parameter grid.""" 579 580 # Initialise. 581 cdp._model = 'm3' 582 cdp._value_test = self.value_test 583 584 # Setup the data pipe for optimisation. 585 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm3_grid.py')

586 587

588 - def test_m4_grid(self):

589 """Test the optimisation of the m4 model-free model against the tm4 parameter grid.""" 590 591 # Initialise. 592 cdp._model = 'm4' 593 cdp._value_test = self.value_test 594 595 # Setup the data pipe for optimisation. 596 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm4_grid.py')

597 598

599 - def test_m5_grid(self):

600 """Test the optimisation of the m5 model-free model against the tm5 parameter grid.""" 601 602 # Initialise. 603 cdp._model = 'm5' 604 cdp._value_test = self.value_test 605 606 # Setup the data pipe for optimisation. 607 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm5_grid.py')

608 609

610 - def test_m6_grid(self):

611 """Test the optimisation of the m6 model-free model against the tm6 parameter grid.""" 612 613 # Initialise. 614 cdp._model = 'm6' 615 cdp._value_test = self.value_test 616 617 # Setup the data pipe for optimisation. 618 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm6_grid.py')

619 620

621 - def test_m7_grid(self):

622 """Test the optimisation of the m7 model-free model against the tm7 parameter grid.""" 623 624 # Initialise. 625 cdp._model = 'm7' 626 cdp._value_test = self.value_test 627 628 # Setup the data pipe for optimisation. 629 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm7_grid.py')

630 631

632 - def test_m8_grid(self):

633 """Test the optimisation of the m8 model-free model against the tm8 parameter grid.""" 634 635 # Initialise. 636 cdp._model = 'm8' 637 cdp._value_test = self.value_test 638 639 # Setup the data pipe for optimisation. 640 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm8_grid.py')

641 642

643 - def test_m9_grid(self):

644 """Test the optimisation of the m9 model-free model against the tm9 parameter grid.""" 645 646 # Initialise. 647 cdp._model = 'm9' 648 cdp._value_test = self.value_test 649 650 # Setup the data pipe for optimisation. 651 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm9_grid.py')

652 653

654 - def test_omp_analysis(self):

655 """Try a very minimal model-free analysis on the OMP relaxation data.""" 656 657 # Execute the script. 658 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'omp_model_free.py') 659 660 # Alias the final data pipe. 661 dp = pipes.get_pipe('final') 662 663 # Some checks. 664 self.assertEqual(dp.mol[0].res[0].spin[0].select_sim, [True, False, True]) 665 self.assertEqual(dp.mol[0].res[1].spin[0].select_sim, [True, True, False]) 666 self.assertEqual(dp.mol[0].res[2].spin[0].select_sim, [True, True, True]) 667 self.assert_(not hasattr(dp.mol[0].res[3].spin[0], 'select_sim'))

668 669

670 - def test_opendx_s2_te_rex(self):

671 """Mapping the {S2, te, Rex} chi2 space through the OpenDX user function dx.map().""" 672 673 # Execute the script. 674 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opendx_s2_te_rex.py')

675 676

677 - def test_opendx_theta_phi_da(self):

678 """Mapping the {theta, phi, Da} chi2 space through the OpenDX user function dx.map().""" 679 680 # Path of the files. 681 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 682 683 # Read the PDF file and set the vectors. 684 self.interpreter.structure.read_pdb(file='pdb', dir=path, read_model=1) 685 686 # Load all N spins. 687 self.interpreter.structure.load_spins('@N') 688 689 # Read the relaxation data. 690 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) 691 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) 692 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) 693 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) 694 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) 695 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) 696 697 # Set up the diffusion tensor. 698 self.interpreter.diffusion_tensor.init((1.601 * 1e7, 1.34, 72.4, 90-77.9), param_types=4) 699 700 # Define the magnetic dipole-dipole relaxation interaction. 701 self.interpreter.structure.load_spins('@H') 702 self.interpreter.dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True) 703 self.interpreter.dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10) 704 self.interpreter.dipole_pair.unit_vectors() 705 706 # Set up the spin parameters. 707 self.interpreter.value.set(N15_CSA, 'csa') 708 self.interpreter.value.set([0.8, 50 * 1e-12, 0.0], ['s2', 'te', 'rex']) 709 710 # Set the spin information. 711 self.interpreter.spin.isotope('15N', spin_id='@N') 712 self.interpreter.spin.isotope('1H', spin_id='@H') 713 714 # Select the model. 715 self.interpreter.model_free.select_model(model='m4') 716 717 # Map the space. 718 self.interpreter.dx.map(params=['theta', 'phi', 'Da'], spin_id='#pdb_mol1:2@N', inc=2, lower=[0, 0, -0.5*1e7], upper=[pi, 2.0*pi, 1.0*1e7], file_prefix='devnull')

719 720

721 - def test_opendx_tm_s2_te(self):

722 """Mapping the {local_tm, S2, te} chi2 space through the OpenDX user function dx.map().""" 723 724 # Path of the files. 725 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 726 727 # Read the sequence. 728 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 729 730 # Read the relaxation data. 731 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) 732 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) 733 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) 734 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) 735 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) 736 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) 737 738 # Name the spins and set the element type. 739 self.interpreter.spin.name('N') 740 self.interpreter.spin.element('N') 741 742 # Create all attached protons. 743 self.interpreter.sequence.attach_protons() 744 745 # Define the magnetic dipole-dipole relaxation interaction. 746 self.interpreter.dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True) 747 self.interpreter.dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10) 748 749 # Set up the CSA value. 750 self.interpreter.value.set(N15_CSA, 'csa') 751 752 # Set the spin information. 753 self.interpreter.spin.isotope('15N', spin_id='@N') 754 self.interpreter.spin.isotope('1H', spin_id='@H') 755 756 # Select the model. 757 self.interpreter.model_free.select_model(model='tm2') 758 759 # Map the space. 760 self.interpreter.dx.map(params=['local_tm', 's2', 'te'], spin_id=':2@N', inc=2, lower=[5e-9, 0.0, 0.0], file_prefix='devnull')

761 762

763 - def test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149(self):

764 """Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 765 766 The optimisation options are: 767 - BFGS optimisation. 768 - Backtracking line search. 769 - Constrained. 770 771 The true data set is: 772 - S2 = 0.970 773 - te = 2048 ps 774 - Rex = 0.149 s^-1 775 """ 776 777 # Setup the data pipe for optimisation. 778 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') 779 780 # Set up the initial model-free parameter values (bypass the grid search for speed). 781 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 782 783 # Minimise. 784 self.interpreter.minimise('bfgs', 'back') 785 786 # Alias the relevent spin container. 787 spin = cdp.mol[0].res[1].spin[0] 788 789 # Optimisation differences. 790 ########################### 791 792 # 32-bit Linux. 793 # iter: 203 794 # f_count: 955 795 # g_count: 209 796 797 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-devel/2009-05/msg00003.html). 798 # System: Linux 799 # Release: 2.6.28-gentoo-r5 800 # Version: #1 SMP Sat Apr 25 13:31:51 EDT 2009 801 # Win32 version: 802 # Distribution: 803 # Architecture: 32bit ELF 804 # Machine: i686 805 # Processor: Intel(R) Pentium(R) M processor 1.80GHz 806 # Python version: 2.5.4 807 # numpy version: 1.2.1 808 # 809 # s2: 0.9700000000012307 810 # te: 2048.0000002299716 811 # rex: 0.14899999997647859 812 # chi2: 1.9223825944220359e-20 813 # iter: 157 814 # f_count: 722 815 # g_count: 164 816 # h_count: 0 817 # warning: None 818 819 # 32-bit i686 Linux. 820 # System: Linux 821 # Release: 2.6.33.7-desktop-2mnb 822 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 823 # Win32 version: 824 # Distribution: mandrake 2010.2 Official 825 # Architecture: 32bit ELF 826 # Machine: i686 827 # Processor: i686 828 # Python version: 2.6.5 829 # Numpy version: 1.4.1 830 # Libc version: glibc 2.0 831 # 832 # s2: 0.9700000000016741 833 # te (ps): 2048.000000312 834 # rex: 0.14899999996808433 835 # chi2: 3.5466670276032307e-20 836 # iter: 158 837 # f_count: 744 838 # g_count: 165 839 # h_count: 0 840 # warning: None 841 842 # 32-bit i686 Linux. 843 # System: Linux 844 # Release: 2.6.33.7-desktop-2mnb 845 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 846 # Win32 version: 847 # Distribution: mandrake 2010.2 Official 848 # Architecture: 32bit ELF 849 # Machine: i686 850 # Processor: i686 851 # Python version: 2.6.5 852 # Numpy version: 1.4.1 853 # Libc version: glibc 2.0 854 # 855 # s2: 0.9700000000016741 856 # te: 2048.000000312 857 # rex: 0.14899999996808433 858 # chi2: 3.5466670276032307e-20 859 # iter: 158 860 # f_count: 744 861 # g_count: 165 862 # h_count: 0 863 # warning: None 864 865 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-users/2011-01/msg00029.html). 866 # System: Linux 867 # Release: 2.6.28-17-generic 868 # Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 869 # Win32 version: 870 # Distribution: Ubuntu 9.04 jaunty 871 # Architecture: 32bit ELF 872 # Machine: i686 873 # Processor: 874 # Python version: 2.6.2 875 # Numpy version: 1.2.1 876 # Libc version: glibc 2.4 877 # 878 # s2: 0.970000000000951 879 # te (ps): 2048.000000178 880 # rex: 0.14899999998189395 881 # chi2: 1.1498599057727952e-20 882 # iter: 154 883 # f_count: 598 884 # g_count: 161 885 # h_count: 0 886 # warning: None 887 888 # 64-bit x86_64 Linux. 889 # System: Linux 890 # Release: 2.6.24.7-server-2mnb 891 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 892 # Win32 version: 893 # Distribution: mandriva 2008.1 Official 894 # Architecture: 64bit ELF 895 # Machine: x86_64 896 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 897 # Python version: 2.5.2 898 # Numpy version: 1.2.0 899 # Libc version: glibc 2.2.5 900 # 901 # s2: 0.9699999999999785 902 # te: 2047.9999999962433 903 # rex: 0.14900000000039709 904 # chi2: 5.2479491342506911e-24 905 # iter: 162 906 # f_count: 758 907 # g_count: 169 908 # h_count: 0 909 # warning: None 910 911 # 32-bit Windows. 912 # iter: 156 913 # f_count: 701 914 # g_count: 163 915 916 # 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). 917 # System: Darwin 918 # Release: 9.5.0 919 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; root:xnu-1228.7.58~1/RELEASE_PPC 920 # Win32 version: 921 # Distribution: 922 # Architecture: 32bit 923 # Machine: Power Macintosh 924 # Processor: powerpc 925 # Python version: 2.5.2 926 # numpy version: 1.1.1 927 # 928 # s2: 0.9699999999999861 929 # te: 2047.9999999978033 930 # rex: 0.14900000000028032 931 # chi2: 1.8533903598853284e-24 932 # iter: 156 933 # f_count: 695 934 # g_count: 162 935 # h_count: 0 936 # warning: None 937 938 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14173). 939 # System: Darwin 940 # Release: 9.8.0 941 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 942 # Win32 version: 943 # Distribution: 944 # Architecture: 32bit 945 # Machine: i386 946 # Processor: i386 947 # Python version: 2.6.2 948 # numpy version: 1.3.0 949 # 950 # s2: 0.9700000000009170 951 # te: 2048.0000001751678 952 # rex: 0.14899999998256069 953 # chi2: 1.1151721805269898e-20 954 # iter: 175 955 # f_count: 735 956 # g_count: 182 957 # h_count: 0 958 # warning: None 959 960 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14173). 961 # System: Darwin 962 # Release: 9.8.0 963 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 964 # Win32 version: 965 # Distribution: 966 # Architecture: 64bit 967 # Machine: i386 968 # Processor: i386 969 # Python version: 2.6.2 970 # numpy version: 1.3.0 971 # 972 # s2: 0.9699999999999785 973 # te: 2047.9999999962433 974 # rex: 0.14900000000039709 975 # chi2: 5.2479491342506911e-24 976 # iter: 162 977 # f_count: 758 978 # g_count: 169 979 # h_count: 0 980 # warning: None 981 982 # Optimisation values. 983 select = True 984 s2 = 0.9699999999999995 985 te = 2048.000000000022283 986 rex = 0.14900000000000566 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 987 chi2 = 3.1024517431117421e-27 988 iter = [154, 156, 157, 158, 162, 175, 203] 989 f_count = [598, 695, 701, 722, 735, 744, 758, 955] 990 g_count = [161, 162, 163, 164, 165, 169, 182, 209] 991 h_count = 0 992 warning = None 993 994 # Test the values. 995 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 996 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

997 998

999 - def test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149(self):

1000 """Constrained BFGS opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1001 1002 The optimisation options are: 1003 - BFGS optimisation. 1004 - More and Thuente line search. 1005 - Constrained. 1006 1007 The true data set is: 1008 - S2 = 0.970 1009 - te = 2048 ps 1010 - Rex = 0.149 s^-1 1011 """ 1012 1013 # Setup the data pipe for optimisation. 1014 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') 1015 1016 # Set up the initial model-free parameter values (bypass the grid search for speed). 1017 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1018 1019 # Minimise. 1020 self.interpreter.minimise('bfgs', 'mt') 1021 1022 # Alias the relevent spin container. 1023 spin = cdp.mol[0].res[1].spin[0] 1024 1025 # Optimisation differences. 1026 ########################### 1027 1028 # 32-bit Linux. 1029 # f_count: 388 1030 # g_count: 388 1031 1032 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-devel/2009-05/msg00003.html). 1033 # System: Linux 1034 # Release: 2.6.28-gentoo-r5 1035 # Version: #1 SMP Sat Apr 25 13:31:51 EDT 2009 1036 # Win32 version: 1037 # Distribution: 1038 # Architecture: 32bit ELF 1039 # Machine: i686 1040 # Processor: Intel(R) Pentium(R) M processor 1.80GHz 1041 # Python version: 2.5.4 1042 # numpy version: 1.2.1 1043 # 1044 # s2: 0.9700000000000604 1045 # te: 2048.0000000114946 1046 # rex: 0.14899999999885985 1047 # chi2: 4.762657780645096e-23 1048 # iter: 120 1049 # f_count: 386 1050 # g_count: 386 1051 # h_count: 0 1052 # warning: None 1053 1054 # 32-bit i686 Linux (http://www.nmr-relax.com/mail.gna.org/public/relax-users/2011-01/msg00029.html). 1055 # System: Linux 1056 # Release: 2.6.28-17-generic 1057 # Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 1058 # Win32 version: 1059 # Distribution: Ubuntu 9.04 jaunty 1060 # Architecture: 32bit ELF 1061 # Machine: i686 1062 # Processor: 1063 # Python version: 2.6.2 1064 # Numpy version: 1.2.1 1065 # Libc version: glibc 2.4 1066 # 1067 # s2: 0.9700000000000614 1068 # te (ps): 2048.000000012 1069 # rex: 0.14899999999883881 1070 # chi2: 4.9272178768519757e-23 1071 # iter: 120 1072 # f_count: 381 1073 # g_count: 381 1074 # h_count: 0 1075 # warning: None 1076 1077 # 64-bit x86_64 Linux. 1078 # System: Linux 1079 # Release: 2.6.24.7-server-2mnb 1080 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1081 # Win32 version: 1082 # Distribution: mandriva 2008.1 Official 1083 # Architecture: 64bit ELF 1084 # Machine: x86_64 1085 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1086 # Python version: 2.5.2 1087 # Numpy version: 1.2.0 1088 # Libc version: glibc 2.2.5 1089 # 1090 # s2: 0.9700000000000603 1091 # te: 2048.0000000114601 1092 # rex: 0.14899999999886163 1093 # chi2: 4.7289676642197204e-23 1094 # iter: 120 1095 # f_count: 384 1096 # g_count: 384 1097 # h_count: 0 1098 # warning: None 1099 1100 # 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). 1101 # System: Darwin 1102 # Release: 9.5.0 1103 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1104 # root:xnu-1228.7.58~1/RELEASE_PPC 1105 # Win32 version: 1106 # Distribution: 1107 # Architecture: 32bit 1108 # Machine: Power Macintosh 1109 # Processor: powerpc 1110 # Python version: 2.5.2 1111 # numpy version: 1.1.1 1112 # 1113 # s2: 0.9700000000000607 1114 # te: 2048.0000000115510 1115 # rex: 0.14899999999885080 1116 # chi2: 4.8056261450870388e-23 1117 # iter: 120 1118 # f_count: 377 1119 # g_count: 377 1120 # h_count: 0 1121 # warning: None 1122 1123 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14174). 1124 # System: Darwin 1125 # Release: 9.8.0 1126 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1127 # Win32 version: 1128 # Distribution: 1129 # Architecture: 32bit 1130 # Machine: i386 1131 # Processor: i386 1132 # Python version: 2.6.2 1133 # numpy version: 1.3.0 1134 # 1135 # s2: 0.9700000000000604 1136 # te: 2048.0000000114997 1137 # rex: 0.14899999999886168 1138 # chi2: 4.7647467884964078e-23 1139 # iter: 120 1140 # f_count: 386 1141 # g_count: 386 1142 # h_count: 0 1143 # warning: None 1144 1145 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14174). 1146 # System: Darwin 1147 # Release: 9.8.0 1148 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1149 # Win32 version: 1150 # Distribution: 1151 # Architecture: 64bit 1152 # Machine: i386 1153 # Processor: i386 1154 # Python version: 2.6.2 1155 # numpy version: 1.3.0 1156 # 1157 # s2: 0.9700000000000603 1158 # te: 2048.0000000114601 1159 # rex: 0.14899999999886163 1160 # chi2: 4.7289676642197204e-23 1161 # iter: 120 1162 # f_count: 384 1163 # g_count: 384 1164 # h_count: 0 1165 # warning: None 1166 1167 # Optimisation values. 1168 select = True 1169 s2 = 0.9700000000000580 1170 te = 2048.000000011044449 1171 rex = 0.148999999998904 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1172 chi2 = 4.3978813282102374e-23 1173 iter = 120 1174 f_count = [377, 381, 384, 386, 388] 1175 g_count = [377, 381, 384, 386, 388] 1176 h_count = 0 1177 warning = None 1178 1179 # Test the values. 1180 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1181 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1182 1183

1184 - def test_opt_constr_cd_back_S2_0_970_te_2048_Rex_0_149(self):

1185 """Constrained coordinate descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1186 1187 The optimisation options are: 1188 - Coordinate descent optimisation. 1189 - Backtracking line search. 1190 - Constrained. 1191 1192 The true data set is: 1193 - S2 = 0.970 1194 - te = 2048 ps 1195 - Rex = 0.149 s^-1 1196 """ 1197 1198 # Setup the data pipe for optimisation. 1199 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') 1200 1201 # Set up the initial model-free parameter values (bypass the grid search for speed). 1202 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1203 1204 # Minimise. 1205 self.interpreter.minimise('cd', 'back', max_iter=50) 1206 1207 # Alias the relevent spin container. 1208 spin = cdp.mol[0].res[1].spin[0] 1209 1210 # Optimisation differences. 1211 ########################### 1212 1213 # 64-bit x86_64 Linux. 1214 # System: Linux 1215 # Release: 2.6.24.7-server-2mnb 1216 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1217 # Win32 version: 1218 # Distribution: mandriva 2008.1 Official 1219 # Architecture: 64bit ELF 1220 # Machine: x86_64 1221 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1222 # Python version: 2.5.2 1223 # Numpy version: 1.2.0 1224 # Libc version: glibc 2.2.5 1225 # 1226 # s2: 0.9097900390625000 1227 # te: 25.0000000000000 1228 # rex: 1.24017333984375000 1229 # chi2: 53.476155463267176 1230 # iter: 50 1231 # f_count: 131 1232 # g_count: 51 1233 # h_count: 0 1234 # warning: Maximum number of iterations reached 1235 1236 # Optimisation values. 1237 select = True 1238 s2 = 0.9097900390625 1239 te = 25.00000000000000 1240 rex = 1.24017333984375 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1241 chi2 = 53.476155463267176 1242 iter = 50 1243 f_count = 131 1244 g_count = 51 1245 h_count = 0 1246 warning = 'Maximum number of iterations reached' 1247 1248 # Test the values. 1249 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1250 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1251 1252

1253 - def test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149(self):

1254 """Constrained coordinate descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1255 1256 The optimisation options are: 1257 - Coordinate descent optimisation. 1258 - More and Thuente line search. 1259 - Constrained. 1260 1261 The true data set is: 1262 - S2 = 0.970 1263 - te = 2048 ps 1264 - Rex = 0.149 s^-1 1265 """ 1266 1267 # Setup the data pipe for optimisation. 1268 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') 1269 1270 # Set up the initial model-free parameter values (bypass the grid search for speed). 1271 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1272 1273 # Minimise. 1274 self.interpreter.minimise('cd', 'mt') 1275 1276 # Alias the relevent spin container. 1277 spin = cdp.mol[0].res[1].spin[0] 1278 1279 # Optimisation differences. 1280 ########################### 1281 1282 # 32-bit Linux. 1283 # f_count: 738 1284 # g_count: 738 1285 1286 # 32-bit i686 Linux. 1287 # System: Linux 1288 # Release: 2.6.33.7-desktop-2mnb 1289 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1290 # Win32 version: 1291 # Distribution: mandrake 2010.2 Official 1292 # Architecture: 32bit ELF 1293 # Machine: i686 1294 # Processor: i686 1295 # Python version: 2.6.5 1296 # Numpy version: 1.4.1 1297 # Libc version: glibc 2.0 1298 # 1299 # s2: 0.9700000000219662 1300 # te: 2048.000001534 1301 # rex: 0.14899999946980566 1302 # chi2: 2.3474910055938013e-18 1303 # iter: 200 1304 # f_count: 874 1305 # g_count: 874 1306 # h_count: 0 1307 # warning: None 1308 1309 # 64-bit x86_64 Linux. 1310 # System: Linux 1311 # Release: 2.6.24.7-server-2mnb 1312 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1313 # Win32 version: 1314 # Distribution: mandriva 2008.1 Official 1315 # Architecture: 64bit ELF 1316 # Machine: x86_64 1317 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1318 # Python version: 2.5.2 1319 # Numpy version: 1.2.0 1320 # Libc version: glibc 2.2.5 1321 # 1322 # s2: 0.9700000000219674 1323 # te: 2048.0000015341870 1324 # rex: 0.14899999946977982 1325 # chi2: 2.3477234248531005e-18 1326 # iter: 198 1327 # f_count: 757 1328 # g_count: 757 1329 # h_count: 0 1330 # warning: None 1331 1332 # 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). 1333 # System: Darwin 1334 # Release: 9.5.0 1335 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1336 # root:xnu-1228.7.58~1/RELEASE_PPC 1337 # Win32 version: 1338 # Distribution: 1339 # Architecture: 32bit 1340 # Machine: Power Macintosh 1341 # Processor: powerpc 1342 # Python version: 2.5.2 1343 # numpy version: 1.1.1 1344 # 1345 # s2: 0.9700000000219674 1346 # te: 2048.0000015341870 1347 # rex: 0.14899999946977982 1348 # chi2: 2.3477234248531005e-18 1349 # iter: 198 1350 # f_count: 757 1351 # g_count: 757 1352 # h_count: 0 1353 # warning: None 1354 1355 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14175). 1356 # System: Darwin 1357 # Release: 9.8.0 1358 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1359 # Win32 version: 1360 # Distribution: 1361 # Architecture: 64bit 1362 # Machine: i386 1363 # Processor: i386 1364 # Python version: 2.6.2 1365 # numpy version: 1.3.0 1366 # 1367 # s2: 0.9700000000219674 1368 # te: 2048.0000015341870 1369 # rex: 0.14899999946977982 1370 # chi2: 2.3477234248531005e-18 1371 # iter: 198 1372 # f_count: 757 1373 # g_count: 757 1374 # h_count: 0 1375 # warning: None 1376 1377 # Optimisation values. 1378 select = True 1379 s2 = 0.9700000000219674 1380 te = 2048.000001534187049 1381 rex = 0.14899999946977982 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1382 chi2 = 2.3477234248531005e-18 1383 iter = [198, 200] 1384 f_count = [738, 757, 874] 1385 g_count = [738, 757, 874] 1386 h_count = 0 1387 warning = None 1388 1389 # Test the values. 1390 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1391 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1392 1393

1394 - def test_opt_constr_newton_gmw_back_S2_0_970_te_2048_Rex_0_149(self):

1395 """Constrained Newton opt, GMW Hessian mod, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1396 1397 The optimisation options are: 1398 - Newton optimisation. 1399 - GMW Hessian modification. 1400 - Backtracking line search. 1401 - Constrained. 1402 1403 The true data set is: 1404 - S2 = 0.970 1405 - te = 2048 ps 1406 - Rex = 0.149 s^-1 1407 """ 1408 1409 # Setup the data pipe for optimisation. 1410 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') 1411 1412 # Set up the initial model-free parameter values (bypass the grid search for speed). 1413 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1414 1415 # Minimise. 1416 self.interpreter.minimise('newton', 'gmw', 'back') 1417 1418 # Alias the relevent spin container. 1419 spin = cdp.mol[0].res[1].spin[0] 1420 1421 # Optimisation differences. 1422 ########################### 1423 1424 # 32-bit Linux. 1425 # f_count: 55 1426 # g_count: 23 1427 1428 # 32-bit i686 Linux. 1429 # System: Linux 1430 # Release: 2.6.33.7-desktop-2mnb 1431 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1432 # Win32 version: 1433 # Distribution: mandrake 2010.2 Official 1434 # Architecture: 32bit ELF 1435 # Machine: i686 1436 # Processor: i686 1437 # Python version: 2.6.5 1438 # Numpy version: 1.4.1 1439 # Libc version: glibc 2.0 1440 # 1441 # s2: 0.9699999999999992 1442 # te: 2048 1443 # rex: 0.14900000000002034 1444 # chi2: 1.1701970207791308e-27 1445 # iter: 18 1446 # f_count: 57 1447 # g_count: 23 1448 # h_count: 18 1449 # warning: None 1450 1451 # 64-bit x86_64 Linux. 1452 # System: Linux 1453 # Release: 2.6.24.7-server-2mnb 1454 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1455 # Win32 version: 1456 # Distribution: mandriva 2008.1 Official 1457 # Architecture: 64bit ELF 1458 # Machine: x86_64 1459 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1460 # Python version: 2.5.2 1461 # Numpy version: 1.2.0 1462 # Libc version: glibc 2.2.5 1463 # 1464 # s2: 0.9699999999999995 1465 # te: 2048.0000000000473 1466 # rex: 0.14900000000001926 1467 # chi2: 7.9357208397255696e-28 1468 # iter: 18 1469 # f_count: 55 1470 # g_count: 23 1471 # h_count: 18 1472 # warning: None 1473 1474 # 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). 1475 # System: Darwin 1476 # Release: 9.5.0 1477 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1478 # root:xnu-1228.7.58~1/RELEASE_PPC 1479 # Win32 version: 1480 # Distribution: 1481 # Architecture: 32bit 1482 # Machine: Power Macintosh 1483 # Processor: powerpc 1484 # Python version: 2.5.2 1485 # numpy version: 1.1.1 1486 # 1487 # s2: 0.9699999999999993 1488 # te: 2048.0000000000427 1489 # rex: 0.14900000000002098 1490 # chi2: 5.7085251917483392e-28 1491 # iter: 18 1492 # f_count: 94 1493 # g_count: 23 1494 # h_count: 18 1495 # warning: None 1496 1497 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14177). 1498 # System: Darwin 1499 # Release: 9.8.0 1500 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1501 # Win32 version: 1502 # Distribution: 1503 # Architecture: 32bit 1504 # Machine: i386 1505 # Processor: i386 1506 # Python version: 2.6.2 1507 # numpy version: 1.3.0 1508 # 1509 # s2: 0.9699999999999994 1510 # te: 2048.0000000000455 1511 # rex: 0.14900000000001823 1512 # chi2: 7.3040158179665562e-28 1513 # iter: 18 1514 # f_count: 55 1515 # g_count: 23 1516 # h_count: 18 1517 # warning: None 1518 1519 # Optimisation values. 1520 select = True 1521 s2 = 0.9699999999999994 1522 te = 2048.000000000045020 1523 rex = 0.14900000000001817 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1524 chi2 = 7.3040158179665562e-28 1525 iter = 18 1526 f_count = [55, 57, 94] 1527 g_count = [23] 1528 h_count = 18 1529 warning = None 1530 1531 # Test the values. 1532 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1533 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1534 1535

1536 - def test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149(self):

1537 """Constrained Newton opt, GMW Hessian mod, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1538 1539 The optimisation options are: 1540 - Newton optimisation. 1541 - GMW Hessian modification. 1542 - More and Thuente line search. 1543 - Constrained. 1544 1545 The true data set is: 1546 - S2 = 0.970 1547 - te = 2048 ps 1548 - Rex = 0.149 s^-1 1549 """ 1550 1551 # Setup the data pipe for optimisation. 1552 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') 1553 1554 # Set up the initial model-free parameter values (bypass the grid search for speed). 1555 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1556 1557 # Minimise. 1558 self.interpreter.minimise('newton', 'gmw', 'mt') 1559 1560 # Monte Carlo simulations. 1561 self.monte_carlo() 1562 1563 # Alias the relevent spin container. 1564 spin = cdp.mol[0].res[1].spin[0] 1565 1566 # Optimisation differences. 1567 ########################### 1568 1569 # 32-bit Linux. 1570 # f_count: 159, 95 1571 # g_count: 159 1572 1573 # 32-bit i686 Linux. 1574 # System: Linux 1575 # Release: 2.6.33.7-desktop-2mnb 1576 # Version: #1 SMP Mon Sep 20 19:00:25 UTC 2010 1577 # Win32 version: 1578 # Distribution: mandrake 2010.2 Official 1579 # Architecture: 32bit ELF 1580 # Machine: i686 1581 # Processor: i686 1582 # Python version: 2.6.5 1583 # Numpy version: 1.4.1 1584 # Libc version: glibc 2.0 1585 # 1586 # s2: 0.9699999999999994 1587 # te: 2048 1588 # rex: 0.14900000000002014 1589 # chi2: 7.9326439528899843e-28 1590 # iter: 22 1591 # f_count: 95 1592 # g_count: 95 1593 # h_count: 22 1594 # warning: None 1595 1596 # 64-bit x86_64 Linux. 1597 # System: Linux 1598 # Release: 2.6.24.7-server-2mnb 1599 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1600 # Win32 version: 1601 # Distribution: mandriva 2008.1 Official 1602 # Architecture: 64bit ELF 1603 # Machine: x86_64 1604 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1605 # Python version: 2.5.2 1606 # Numpy version: 1.2.0 1607 # Libc version: glibc 2.2.5 1608 # 1609 # s2: 0.9699999999999994 1610 # te: 2048.0000000000446 1611 # rex: 0.14900000000001615 1612 # chi2: 8.3312601381368332e-28 1613 # iter: 22 1614 # f_count: 91 1615 # g_count: 91 1616 # h_count: 22 1617 # warning: None 1618 1619 # 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). 1620 # f_count: 153 1621 # g_count: 153 1622 1623 # 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). 1624 # System: Darwin 1625 # Release: 9.5.0 1626 # Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; 1627 # root:xnu-1228.7.58~1/RELEASE_PPC 1628 # Win32 version: 1629 # Distribution: 1630 # Architecture: 32bit 1631 # Machine: Power Macintosh 1632 # Processor: powerpc 1633 # Python version: 2.5.2 1634 # numpy version: 1.1.1 1635 # 1636 # s2: 0.9699999999999993 1637 # te: 2048.0000000000409 1638 # rex: 0.14900000000002178 1639 # chi2: 6.8756889983348349e-28 1640 # iter: 22 1641 # f_count: 160 1642 # g_count: 160 1643 # h_count: 22 1644 # warning: None 1645 1646 # 32-bit Windows. 1647 # f_count: 165 1648 # g_count: 165 1649 1650 # 32-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14176). 1651 # System: Darwin 1652 # Release: 9.8.0 1653 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1654 # Win32 version: 1655 # Distribution: 1656 # Architecture: 32bit 1657 # Machine: i386 1658 # Processor: i386 1659 # Python version: 2.6.2 1660 # numpy version: 1.3.0 1661 # 1662 # s2: 0.9699999999999994 1663 # te: 2048.0000000000446 1664 # rex: 0.14900000000001609 1665 # chi2: 8.3312601381368332e-28 1666 # iter: 22 1667 # f_count: 91 1668 # g_count: 91 1669 # h_count: 22 1670 # warning: None 1671 1672 # 64-bit i386 Darwin (https://web.archive.org/web/https://gna.org/bugs/?14176). 1673 # System: Darwin 1674 # Release: 9.8.0 1675 # Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 1676 # Win32 version: 1677 # Distribution: 1678 # Architecture: 64bit 1679 # Machine: i386 1680 # Processor: i386 1681 # Python version: 2.6.2 1682 # numpy version: 1.3.0 1683 # 1684 # s2: 0.9699999999999994 1685 # te: 2048.0000000000446 1686 # rex: 0.14900000000001609 1687 # chi2: 8.3312601381368332e-28 1688 # iter: 22 1689 # f_count: 91 1690 # g_count: 91 1691 # h_count: 22 1692 # warning: None 1693 1694 # Optimisation values. 1695 select = True 1696 s2 = 0.9699999999999993 1697 te = 2048.000000000041837 1698 rex = 0.14900000000002225 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1699 chi2 = 6.8756889983348349e-28 1700 iter = 22 1701 f_count = [91, 95, 153, 159, 160, 165] 1702 g_count = [91, 95, 153, 159, 160, 165] 1703 h_count = 22 1704 warning = None 1705 1706 # Test the values. 1707 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1708 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1709 1710

1711 - def test_opt_constr_sd_back_S2_0_970_te_2048_Rex_0_149(self):

1712 """Constrained steepest descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} 1713 1714 The optimisation options are: 1715 - Steepest descent optimisation. 1716 - Backtracking line search. 1717 - Constrained. 1718 1719 The true data set is: 1720 - S2 = 0.970 1721 - te = 2048 ps 1722 - Rex = 0.149 s^-1 1723 """ 1724 1725 # Setup the data pipe for optimisation. 1726 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') 1727 1728 # Set up the initial model-free parameter values (bypass the grid search for speed). 1729 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1730 1731 # Minimise. 1732 self.interpreter.minimise('sd', 'back', max_iter=50) 1733 1734 # Alias the relevent spin container. 1735 spin = cdp.mol[0].res[1].spin[0] 1736 1737 # Optimisation differences. 1738 ########################### 1739 1740 # 64-bit x86_64 Linux. 1741 # System: Linux 1742 # Release: 2.6.24.7-server-2mnb 1743 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1744 # Win32 version: 1745 # Distribution: mandriva 2008.1 Official 1746 # Architecture: 64bit ELF 1747 # Machine: x86_64 1748 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1749 # Python version: 2.5.2 1750 # Numpy version: 1.2.0 1751 # Libc version: glibc 2.2.5 1752 # 1753 # s2: 0.9157922083468916 1754 # te: 0.3056865872253 1755 # rex: 0.34008409798064831 1756 # chi2: 68.321956795340569 1757 # iter: 50 1758 # f_count: 134 1759 # g_count: 51 1760 # h_count: 0 1761 # warning: Maximum number of iterations reached 1762 1763 # Optimisation values. 1764 select = True 1765 s2 = 0.91579220834688024 1766 te = 0.30568658722531733 1767 rex = 0.34008409798366124 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1768 chi2 = 68.321956795264342 1769 iter = 50 1770 f_count = 134 1771 g_count = 51 1772 h_count = 0 1773 warning = 'Maximum number of iterations reached' 1774 1775 # Test the values. 1776 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1777 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1778 1779

1780 - def test_opt_constr_sd_mt_S2_0_970_te_2048_Rex_0_149(self):

1781 """Constrained steepest descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} 1782 1783 The optimisation options are: 1784 - Steepest descent optimisation. 1785 - More and Thuente line search. 1786 - Constrained. 1787 1788 The true data set is: 1789 - S2 = 0.970 1790 - te = 2048 ps 1791 - Rex = 0.149 s^-1 1792 """ 1793 1794 # Setup the data pipe for optimisation. 1795 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') 1796 1797 # Set up the initial model-free parameter values (bypass the grid search for speed). 1798 self.interpreter.value.set([1.0, 0.0, 0.0], ['s2', 'te', 'rex']) 1799 1800 # Minimise. 1801 self.interpreter.minimise('sd', 'mt', max_iter=50) 1802 1803 # Alias the relevent spin container. 1804 spin = cdp.mol[0].res[1].spin[0] 1805 1806 # Optimisation differences. 1807 ########################### 1808 1809 # 64-bit x86_64 Linux. 1810 # System: Linux 1811 # Release: 2.6.24.7-server-2mnb 1812 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1813 # Win32 version: 1814 # Distribution: mandriva 2008.1 Official 1815 # Architecture: 64bit ELF 1816 # Machine: x86_64 1817 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1818 # Python version: 2.5.2 1819 # Numpy version: 1.2.0 1820 # Libc version: glibc 2.2.5 1821 # 1822 # s2: 0.9161999495781851 1823 # te: 0.1231968757090 1824 # rex: 0.16249110939079675 1825 # chi2: 73.843613548025075 1826 # iter: 50 1827 # f_count: 108 1828 # g_count: 108 1829 # h_count: 0 1830 # warning: Maximum number of iterations reached 1831 1832 # Optimisation values. 1833 select = True 1834 s2 = 0.91619994957822126 1835 te = 0.12319687570987945 1836 rex = 0.16249110942961512 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 1837 chi2 = 73.843613546506191 1838 iter = 50 1839 f_count = 108 1840 g_count = 108 1841 h_count = 0 1842 warning = 'Maximum number of iterations reached' 1843 1844 # Test the values. 1845 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1846 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1847 1848

1849 - def test_opt_grid_search_S2_0_970_te_2048_Rex_0_149(self):

1850 """Constrained grid search {S2=0.970, te=2048, Rex=0.149}. 1851 1852 The optimisation options are: 1853 - Constrained grid search. 1854 1855 The true data set is: 1856 - S2 = 0.970 1857 - te = 2048 ps 1858 - Rex = 0.149 s^-1 1859 """ 1860 1861 # Setup the data pipe for optimisation. 1862 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') 1863 1864 # Grid search. 1865 self.interpreter.grid_search(inc=11) 1866 1867 # Alias the relevent spin container. 1868 spin = cdp.mol[0].res[1].spin[0] 1869 1870 # Optimisation differences. 1871 ########################### 1872 1873 # 64-bit x86_64 Linux. 1874 # System: Linux 1875 # Release: 2.6.24.7-server-2mnb 1876 # Version: #1 SMP Thu Oct 30 14:50:37 EDT 2008 1877 # Win32 version: 1878 # Distribution: mandriva 2008.1 Official 1879 # Architecture: 64bit ELF 1880 # Machine: x86_64 1881 # Processor: Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz 1882 # Python version: 2.5.2 1883 # Numpy version: 1.2.0 1884 # Libc version: glibc 2.2.5 1885 # 1886 # s2: 1 1887 # te: 0 1888 # rex: 0 1889 # chi2: 3.9844117908982288 1890 # iter: 1331 1891 # f_count: 1331 1892 # g_count: 0 1893 # h_count: 0 1894 # warning: None 1895 1896 # Optimisation values. 1897 select = True 1898 s2 = 1.0 1899 te = 0.0 1900 rex = 0.0 1901 chi2 = 3.9844117908982288 1902 iter = 1331 1903 f_count = 1331 1904 g_count = 0 1905 h_count = 0 1906 warning = None 1907 1908 # Test the values. 1909 self.assertEqual(cdp.mol[0].res[0].spin[0].select, False) 1910 self.value_test(spin, select=select, s2=s2, te=te, rex=rex, chi2=chi2)

1911 1912

1913 - def test_read_relax_data(self):

1914 """Reading of relaxation data using the user function relax_data.read().""" 1915 1916 # Path of the files. 1917 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 1918 1919 # Read the sequence. 1920 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 1921 1922 # Read the relaxation data. 1923 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) 1924 1925 # Test the data and error. 1926 self.assertEqual(cdp.mol[0].res[1].spin[0].ri_data['R1_600'], 1.3874977659397683) 1927 self.assertEqual(cdp.mol[0].res[1].spin[0].ri_data_err['R1_600'], 0.027749955318795365)

1928 1929

1930 - def test_read_results_1_2(self):

1931 """Read a relax 1.2 model-free results file using the user function results.read().""" 1932 1933 # Read the results. 1934 self.interpreter.results.read(file='results_1.2', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 1935 1936 # Debugging printout. 1937 print(cdp) 1938 1939 # The spin specific data. 1940 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] 1941 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] 1942 model = ['m6', 'm8', 'm6', 'm6', 'm5', 'm5', 'm6', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm5', 'm8'] 1943 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']] 1944 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] 1945 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] 1946 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] 1947 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] 1948 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] 1949 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] 1950 1951 # Relaxation data. 1952 ri_ids = ['R1_500', 'R2_500', 'NOE_500', 'R1_600', 'R2_600', 'NOE_600', 'R1_750', 'R2_750', 'NOE_750'] 1953 types_list = ['R1', 'R2', 'NOE', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 1954 frqs_list = [500000000.0] * 3 + [600000000.0] * 3 + [750000000.0] * 3 1955 ri_type = {} 1956 frqs = {} 1957 for i in range(len(ri_ids)): 1958 ri_type[ri_ids[i]] = types_list[i] 1959 frqs[ri_ids[i]] = frqs_list[i] 1960 1961 ri_data = {} 1962 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] 1963 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] 1964 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] 1965 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] 1966 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] 1967 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] 1968 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] 1969 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] 1970 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] 1971 1972 ri_data_err = {} 1973 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] 1974 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] 1975 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] 1976 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] 1977 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] 1978 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] 1979 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] 1980 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] 1981 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] 1982 1983 # Misc tests. 1984 self.assertEqual(cdp.pipe_type, 'mf') 1985 self.assertEqual(cdp.hybrid_pipes, []) 1986 1987 # Diffusion tensor tests. 1988 self.assertEqual(cdp.diff_tensor.type, 'sphere') 1989 self.assertEqual(cdp.diff_tensor.tm, 6.2029050826362826e-09) 1990 1991 # Global minimisation statistic tests. 1992 self.assertEqual(cdp.chi2, 88.0888600975) 1993 self.assertEqual(cdp.iter, 1) 1994 self.assertEqual(cdp.f_count, 20) 1995 self.assertEqual(cdp.g_count, 2) 1996 self.assertEqual(cdp.h_count, 1) 1997 self.assertEqual(cdp.warning, None) 1998 1999 # Global relaxation data tests. 2000 self.assertEqual(cdp.ri_ids, ri_ids) 2001 for ri_id in ri_ids: 2002 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 2003 self.assertEqual(cdp.frq[ri_id], frqs[ri_id]) 2004 2005 # Loop over the residues of the original data. 2006 j = 0 2007 for i in range(len(cdp.mol[0].res)): 2008 # Aliases 2009 res = cdp.mol[0].res[i] 2010 spin = cdp.mol[0].res[i].spin[0] 2011 h_spin = None 2012 if len(cdp.mol[0].res[i].spin) > 1: 2013 h_spin = cdp.mol[0].res[i].spin[1] 2014 2015 # Debugging printout. 2016 print(res) 2017 print(spin) 2018 2019 # Spin info tests. 2020 self.assertEqual(res.num, num[i]) 2021 self.assertEqual(res.name, 'XXX') 2022 self.assertEqual(spin.num, None) 2023 if select[i]: 2024 self.assertEqual(spin.name, 'N') 2025 self.assertEqual(spin.fixed, False) 2026 else: 2027 self.assertEqual(spin.name, None) 2028 self.assertEqual(spin.select, select[i]) 2029 if h_spin: 2030 self.assertEqual(h_spin.num, None) 2031 self.assertEqual(h_spin.name, 'H') 2032 self.assertEqual(h_spin.select, False) 2033 2034 # Skip deselected spins. 2035 if not select[i]: 2036 continue 2037 2038 # Nuclear isotope info. 2039 self.assertEqual(spin.isotope, '15N') 2040 self.assertEqual(h_spin.isotope, '1H') 2041 2042 # Model-free tests. 2043 self.assertEqual(spin.model, model[j]) 2044 self.assertEqual(spin.equation, 'mf_ext') 2045 self.assertEqual(spin.params, params[j]) 2046 self.assertEqual(spin.s2, s2[j]) 2047 self.assertEqual(spin.s2f, s2f[j]) 2048 self.assertEqual(spin.s2s, s2s[j]) 2049 self.assertEqual(spin.local_tm, None) 2050 self.assertEqual(spin.te, None) 2051 if tf[j] != None: 2052 tf[j] = tf[j]*1e-12 2053 self.assertEqual(spin.tf, tf[j]) 2054 self.assertEqual(spin.ts, ts[j]*1e-12) 2055 if rex[j] != None: 2056 rex[j] = rex[j]/(2.0*pi*500000000.0)**2 2057 self.assertEqual(spin.rex, rex[j]) 2058 self.assertEqual(spin.csa, -0.00016999999999999999) 2059 2060 # Minimisation statistic tests. 2061 self.assertEqual(spin.chi2, None) 2062 self.assertEqual(spin.iter, None) 2063 self.assertEqual(spin.f_count, None) 2064 self.assertEqual(spin.g_count, None) 2065 self.assertEqual(spin.h_count, None) 2066 self.assertEqual(spin.warning, None) 2067 2068 # Relaxation data tests. 2069 for ri_id in cdp.ri_ids: 2070 print(ri_id) 2071 self.assertEqual(spin.ri_data[ri_id], ri_data[ri_id][j]) 2072 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[ri_id][j]) 2073 2074 # Secondary index. 2075 j = j + 1 2076 2077 # The interatomic data tests. 2078 for i in range(len(cdp.interatomic)): 2079 self.assertEqual(cdp.interatomic[i].r, 1.0200000000000001e-10)

2080 2081

2082 - def test_read_results_1_2_pse4(self):

2083 """Read the truncated relax 1.2 model-free results file for PSE-4.""" 2084 2085 # Read the results. 2086 self.interpreter.results.read(file='pse4_trunc', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 2087 2088 # Debugging printout. 2089 print(cdp) 2090 2091 # The spin specific data. 2092 num = [24, 27] 2093 name = ['ser', 'gln'] 2094 eqi = [None, 'mf_ext'] 2095 select = [False, True] 2096 model = [None, 'm5'] 2097 params = [[], ['s2f', 's2', 'ts']] 2098 s2 = [None, 0.86578779694713515] 2099 s2f = [None, 0.88618694421409949] 2100 s2s = [None, 0.97698098871784322] 2101 s2s_sim = [[None, None, None], 2102 [0.95852080081635382, 0.97574415413309512, 0.97293450506144197]] 2103 tf = [None, None] 2104 ts = [None, 598.8142249659868e-12] 2105 rex = [None, None] 2106 csa = [None, -0.00017199999999999998] 2107 ri_ids = ['R1_800', 'NOE_800', 'R1_600', 'R2_600', 'NOE_600', 'R1_500', 'R2_500', 'NOE_500'] 2108 ri_type_list = ['R1', 'NOE', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 2109 frq_list = [799744000.0]*2 + [599737000.0]*3 + [499719000.0]*3 2110 ri_data_list = [[], 2111 [0.6835, 0.81850000000000001, 0.98409999999999997, 16.5107, 0.79796699999999998, 1.3174999999999999, 15.381500000000001, 0.73046900000000003]] 2112 ri_data_err_list = [[], 2113 [0.026957200000000001, 0.025881000000000001, 0.0243073, 0.497137, 0.028663000000000001, 0.038550000000000001, 0.40883999999999998, 0.022016299999999999]] 2114 ri_type = {} 2115 frq = {} 2116 ri_data = [{}, {}] 2117 ri_data_err = [{}, {}] 2118 for i in range(len(ri_ids)): 2119 ri_type[ri_ids[i]] = ri_type_list[i] 2120 frq[ri_ids[i]] = frq_list[i] 2121 ri_data[1][ri_ids[i]] = ri_data_list[1][i] 2122 ri_data_err[1][ri_ids[i]] = ri_data_err_list[1][i] 2123 2124 # The interatomic data. 2125 r = [None, 1.0200000000000001e-10] 2126 2127 # Misc tests. 2128 self.assertEqual(cdp.pipe_type, 'mf') 2129 self.assertEqual(cdp.hybrid_pipes, []) 2130 2131 # Diffusion tensor tests. 2132 self.assertEqual(cdp.diff_tensor.type, 'ellipsoid') 2133 self.assertEqual(cdp.diff_tensor.tm, 1.2682770910095516e-08) 2134 self.assertEqual(cdp.diff_tensor.tm_err, 2.4053909822304126e-11) 2135 self.assertEqual(cdp.diff_tensor.tm_sim[0], 1.2666656725867738e-08) 2136 self.assertEqual(cdp.diff_tensor.tm_sim[1], 1.2689812011679408e-08) 2137 self.assertEqual(cdp.diff_tensor.tm_sim[2], 1.2698266641804573e-08) 2138 2139 # Global minimisation statistic tests. 2140 self.assertEqual(cdp.chi2, 935.13348627485448) 2141 self.assertEqual(cdp.chi2_sim[0], 898.0981500197106) 2142 self.assertEqual(cdp.chi2_sim[1], 904.11113814725172) 2143 self.assertEqual(cdp.chi2_sim[2], 902.03890817023728) 2144 self.assertEqual(cdp.iter, 1) 2145 self.assertEqual(cdp.iter_sim[0], 23) 2146 self.assertEqual(cdp.iter_sim[1], 30) 2147 self.assertEqual(cdp.iter_sim[2], 16) 2148 self.assertEqual(cdp.f_count, 21) 2149 self.assertEqual(cdp.f_count_sim[0], 61) 2150 self.assertEqual(cdp.f_count_sim[1], 501) 2151 self.assertEqual(cdp.f_count_sim[2], 59) 2152 self.assertEqual(cdp.g_count, 2) 2153 self.assertEqual(cdp.g_count_sim[0], 27) 2154 self.assertEqual(cdp.g_count_sim[1], 34) 2155 self.assertEqual(cdp.g_count_sim[2], 20) 2156 self.assertEqual(cdp.h_count, 1) 2157 self.assertEqual(cdp.h_count_sim[0], 23) 2158 self.assertEqual(cdp.h_count_sim[1], 30) 2159 self.assertEqual(cdp.h_count_sim[2], 16) 2160 self.assertEqual(cdp.warning, None) 2161 self.assertEqual(cdp.warning_sim[0], None) 2162 self.assertEqual(cdp.warning_sim[1], None) 2163 self.assertEqual(cdp.warning_sim[2], None) 2164 2165 # Global relaxation data tests. 2166 self.assertEqual(cdp.ri_ids, ri_ids) 2167 for ri_id in ri_ids: 2168 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 2169 self.assertEqual(cdp.frq[ri_id], frq[ri_id]) 2170 2171 # Loop over the residues of the original data. 2172 for i in range(len(cdp.mol[0].res)): 2173 # Aliases 2174 res = cdp.mol[0].res[i] 2175 spin = cdp.mol[0].res[i].spin[0] 2176 h_spin = cdp.mol[0].res[i].spin[1] 2177 2178 # Debugging printout. 2179 print(res) 2180 print(spin) 2181 2182 # Spin info tests. 2183 self.assertEqual(res.num, num[i]) 2184 self.assertEqual(res.name, name[i]) 2185 self.assertEqual(spin.num, None) 2186 self.assertEqual(spin.name, 'N') 2187 self.assertEqual(spin.select, select[i]) 2188 self.assertEqual(spin.fixed, False) 2189 self.assertEqual(h_spin.num, None) 2190 self.assertEqual(h_spin.name, 'H') 2191 self.assertEqual(h_spin.select, False) 2192 2193 # Nuclear isotope info. 2194 self.assertEqual(spin.isotope, '15N') 2195 self.assertEqual(h_spin.isotope, '1H') 2196 2197 # Model-free tests. 2198 self.assertEqual(spin.model, model[i]) 2199 self.assertEqual(spin.equation, eqi[i]) 2200 self.assertEqual(spin.params, params[i]) 2201 self.assertEqual(spin.s2, s2[i]) 2202 self.assertEqual(spin.s2f, s2f[i]) 2203 self.assertEqual(spin.s2s, s2s[i]) 2204 self.assertEqual(spin.local_tm, None) 2205 self.assertEqual(spin.te, None) 2206 self.assertEqual(spin.tf, tf[i]) 2207 self.assertEqual(spin.ts, ts[i]) 2208 self.assertEqual(spin.rex, rex[i]) 2209 self.assertEqual(spin.csa, csa[i]) 2210 for j in range(3): 2211 self.assertEqual(spin.s2s_sim[j], s2s_sim[i][j]) 2212 2213 # Minimisation statistic tests. 2214 self.assertEqual(spin.chi2, None) 2215 self.assertEqual(spin.iter, None) 2216 self.assertEqual(spin.f_count, None) 2217 self.assertEqual(spin.g_count, None) 2218 self.assertEqual(spin.h_count, None) 2219 self.assertEqual(spin.warning, None) 2220 2221 # Relaxation data tests. 2222 if i == 0: 2223 self.assertEqual(spin.ri_data, {}) 2224 self.assertEqual(spin.ri_data_err, {}) 2225 else: 2226 for ri_id in ri_ids: 2227 self.assertEqual(spin.ri_data[ri_id], ri_data[i][ri_id]) 2228 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[i][ri_id]) 2229 2230 # The interatomic data tests. 2231 for i in range(len(cdp.interatomic)): 2232 self.assertEqual(cdp.interatomic[i].r, r[i])

2233 2234

2235 - def test_read_results_1_2_tem1(self):

2236 """Read the truncated relax 1.2 model-free results file for TEM-1.""" 2237 2238 # Read the results. 2239 self.interpreter.results.read(file='tem1_trunc', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free') 2240 2241 # Debugging printout. 2242 print(cdp) 2243 2244 # The spin specific data. 2245 num = [26, 27, 29, 30, 31, 32, 33, 34] 2246 name = ['His', 'Pro', 'Thr', 'Leu', 'Val', 'Lys', 'Val', 'Lys'] 2247 eqi = [None, None, None, 'mf_ext', 'mf_orig', 'mf_orig', None, 'mf_orig'] 2248 select = [False, False, False, True, True, True, False, True] 2249 model = [None, None, None, 'm5', 'm2', 'm1', None, 'm1'] 2250 params = [None, None, None, ['s2f', 's2', 'ts'], ['s2', 'te'], ['s2'], None, ['s2']] 2251 s2 = [None, None, None, 0.85674161305142216, 0.89462664243726608, 0.90201790111143165, None, 0.92099297347361675] 2252 s2f = [None, None, None, 0.88220054271390302, None, None, None, None] 2253 s2s = [None, None, None, 0.97114156200339452, None, None, None, None] 2254 te = [None, None, None, None, 43.262426916926735*1e-12, None, None, None] 2255 tf = [None, None, None, None, None, None, None, None] 2256 ts = [None, None, None, 2385.912514843546*1e-12, None, None, None, None] 2257 rex = [None, None, None, None, None, None, None, None] 2258 csa = [None, None, None, -0.00017199999999999998, -0.00017199999999999998, -0.00017199999999999998, None, -0.00017199999999999998] 2259 ri_ids = ['R1_800', 'R2_800', 'R1_600', 'R2_600', 'NOE_600', 'R1_500', 'R2_500', 'NOE_500'] 2260 ri_type_list = ['R1', 'R2', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'] 2261 frq_list = [799812000.0]*2 + [599739000.0]*3 + [499827000.0]*3 2262 ri_data_list = [[], 2263 [], 2264 [], 2265 [0.75680000000000003, 18.797999999999998, 1.0747, 16.477, 0.86873100000000003, 1.2625999999999999, 15.3367, 0.77803197999999996], 2266 [0.75019999999999998, 19.201599999999999, 1.0617000000000001, 17.652899999999999, 0.73757200000000001, 1.3165, 15.949, 0.72442474000000001], 2267 [0.75860000000000005, 19.303799999999999, 1.0605, 16.593699999999998, 0.79137500000000005, 1.3425, 15.327199999999999, 0.83449132000000004], 2268 [], 2269 [0.71919999999999995, 20.165400000000002, 1.0729, 17.291899999999998, 0.80444599999999999, 1.2971999999999999, 15.9963, 0.73164684999999996]] 2270 ri_data_err_list = [[], 2271 [], 2272 [], 2273 [0.028001600000000001, 0.21729999999999999, 0.031166300000000001, 0.44487900000000002, 0.043210699999999998, 0.054291800000000001, 0.69015199999999999, 0.038901600000000001], 2274 [0.028899999999999999, 0.25640000000000002, 0.030789299999999999, 0.476628, 0.036686799999999999, 0.0566095, 0.71770500000000004, 0.036221200000000002], 2275 [0.033399999999999999, 0.2233, 0.030754500000000001, 0.44802999999999998, 0.039363000000000002, 0.057727500000000001, 0.689724, 0.041724600000000001], 2276 [], 2277 [0.027699999999999999, 0.52810000000000001, 0.031399999999999997, 0.46688099999999999, 0.040013100000000003, 0.055779599999999999, 0.71983399999999997, 0.036582299999999998]] 2278 ri_type = {} 2279 frq = {} 2280 ri_data = [] 2281 ri_data_err = [] 2282 for i in range(len(ri_data_list)): 2283 ri_data.append({}) 2284 ri_data_err.append({}) 2285 2286 for i in range(len(ri_ids)): 2287 ri_type[ri_ids[i]] = ri_type_list[i] 2288 frq[ri_ids[i]] = frq_list[i] 2289 for j in range(len(ri_data_list)): 2290 if len(ri_data_list[j]): 2291 ri_data[j][ri_ids[i]] = ri_data_list[j][i] 2292 ri_data_err[j][ri_ids[i]] = ri_data_err_list[j][i] 2293 2294 chi2 = [None, None, None, 7.9383923597292441, 10.93852890925343, 3.1931459495488084, None, 8.3598891989018611] 2295 iter = [None, None, None, 55, 10, 3, None, 3] 2296 f_count = [None, None, None, 170, 148, 10, None, 10] 2297 g_count = [None, None, None, 60, 14, 6, None, 6] 2298 h_count = [None, None, None, 55, 10, 3, None, 3] 2299 2300 # The interatomic data. 2301 r = [None, None, None, 1.0200000000000001e-10, 1.0200000000000001e-10, 1.0200000000000001e-10, None, 1.0200000000000001e-10] 2302 2303 # Misc tests. 2304 self.assertEqual(cdp.pipe_type, 'mf') 2305 self.assertEqual(cdp.hybrid_pipes, []) 2306 2307 # Diffusion tensor tests. 2308 self.assertEqual(cdp.diff_tensor.type, 'ellipsoid') 2309 self.assertEqual(cdp.diff_tensor.tm, 1.2526607261882971e-08) 2310 self.assertEqual(cdp.diff_tensor.Da, 2784606.8835473624) 2311 self.assertEqual(cdp.diff_tensor.Dr, 0.097243698709517518) 2312 self.assertEqual(cdp.diff_tensor.alpha, 48.852555276419558 / 360.0 * 2.0 * pi) 2313 self.assertEqual(cdp.diff_tensor.beta, 9.7876096346750447 / 360.0 * 2.0 * pi) 2314 self.assertEqual(cdp.diff_tensor.gamma, 42.15815798778408 / 360.0 * 2.0 * pi) 2315 2316 # Global relaxation data tests. 2317 self.assertEqual(cdp.ri_ids, ri_ids) 2318 for ri_id in ri_ids: 2319 self.assertEqual(cdp.ri_type[ri_id], ri_type[ri_id]) 2320 self.assertEqual(cdp.frq[ri_id], frq[ri_id]) 2321 2322 # Loop over the residues of the original data. 2323 for i in range(len(cdp.mol[0].res)): 2324 # Aliases 2325 res = cdp.mol[0].res[i] 2326 spin = cdp.mol[0].res[i].spin[0] 2327 h_spin = cdp.mol[0].res[i].spin[1] 2328 2329 # Debugging printout. 2330 print(res) 2331 print(spin) 2332 2333 # Spin info tests. 2334 self.assertEqual(res.num, num[i]) 2335 self.assertEqual(res.name, name[i]) 2336 self.assertEqual(spin.num, None) 2337 self.assertEqual(spin.name, 'N') 2338 self.assertEqual(spin.select, select[i]) 2339 self.assertEqual(spin.fixed, False) 2340 self.assertEqual(h_spin.num, None) 2341 self.assertEqual(h_spin.name, 'H') 2342 self.assertEqual(h_spin.select, False) 2343 2344 # Nuclear isotope info. 2345 self.assertEqual(spin.isotope, '15N') 2346 self.assertEqual(h_spin.isotope, '1H') 2347 2348 # Model-free tests. 2349 self.assertEqual(spin.model, model[i]) 2350 self.assertEqual(spin.equation, eqi[i]) 2351 self.assertEqual(spin.params, params[i]) 2352 self.assertEqual(spin.s2, s2[i]) 2353 self.assertEqual(spin.s2f, s2f[i]) 2354 self.assertEqual(spin.s2s, s2s[i]) 2355 self.assertEqual(spin.local_tm, None) 2356 self.assertEqual(spin.te, te[i]) 2357 self.assertEqual(spin.tf, tf[i]) 2358 self.assertEqual(spin.ts, ts[i]) 2359 self.assertEqual(spin.rex, rex[i]) 2360 self.assertEqual(spin.csa, csa[i]) 2361 2362 # Minimisation statistic tests. 2363 self.assertEqual(spin.chi2, chi2[i]) 2364 self.assertEqual(spin.iter, iter[i]) 2365 self.assertEqual(spin.f_count, f_count[i]) 2366 self.assertEqual(spin.g_count, g_count[i]) 2367 self.assertEqual(spin.h_count, h_count[i]) 2368 self.assertEqual(spin.warning, None) 2369 2370 # Relaxation data tests. 2371 if not ri_data[i].keys(): 2372 self.assertEqual(spin.ri_data, {}) 2373 self.assertEqual(spin.ri_data_err, {}) 2374 else: 2375 for ri_id in ri_ids: 2376 self.assertEqual(spin.ri_data[ri_id], ri_data[i][ri_id]) 2377 self.assertEqual(spin.ri_data_err[ri_id], ri_data_err[i][ri_id]) 2378 2379 # The interatomic data tests. 2380 for i in range(len(cdp.interatomic)): 2381 self.assertEqual(cdp.interatomic[i].r, r[i])

2382 2383

2384 - def test_read_results_1_3_v1(self):

2385 """Read a 1.3 model-free results file (relax XML version 1).""" 2386 2387 # Path of the files. 2388 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2389 2390 # Read the results file. 2391 self.interpreter.pipe.create('1.3', 'mf') 2392 self.interpreter.results.read(file='final_results_trunc_1.3_v1', dir=path) 2393 2394 # The shared part of the test. 2395 self.check_read_results_1_3()

2396 2397

2398 - def test_read_results_1_3_pre_py273_v1(self):

2399 """Read a 1.3 model-free results file (pre-Python 2.7.3, relax XML version 1).""" 2400 2401 # Path of the files. 2402 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2403 2404 # Read the results file. 2405 self.interpreter.pipe.create('1.3', 'mf') 2406 self.interpreter.results.read(file='final_results_trunc_1.3_pre_py2.7.3_v1', dir=path) 2407 2408 # The shared part of the test. 2409 self.check_read_results_1_3()

2410 2411

2412 - def test_read_results_1_3_v2(self):

2413 """Read a 1.3 model-free results file (relax XML version 2).""" 2414 2415 # Path of the files. 2416 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2417 2418 # Read the results file. 2419 self.interpreter.pipe.create('1.3', 'mf') 2420 self.interpreter.results.read(file='final_results_trunc_1.3_v2', dir=path) 2421 2422 # The shared part of the test. 2423 self.check_read_results_1_3()

2424 2425

2426 - def test_read_results_1_3_v2_broken(self):

2427 """Read a 1.3 model-free results file (relax XML version 2) with corrupted floats. 2428 2429 The floats are deliberately mangled to test the IEEE-754 reading. 2430 """ 2431 2432 # Path of the files. 2433 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2434 2435 # Read the results file. 2436 self.interpreter.pipe.create('1.3', 'mf') 2437 self.interpreter.results.read(file='final_results_trunc_1.3_v2_broken', dir=path) 2438 2439 # The shared part of the test. 2440 self.check_read_results_1_3()

2441 2442

2443 - def test_read_results_1_3_pre_py273_v2(self):

2444 """Read a 1.3 model-free results file (pre-Python 2.7.3, relax XML version 2).""" 2445 2446 # Path of the files. 2447 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2448 2449 # Read the results file. 2450 self.interpreter.pipe.create('1.3', 'mf') 2451 self.interpreter.results.read(file='final_results_trunc_1.3_pre_py2.7.3_v2', dir=path) 2452 2453 # The shared part of the test. 2454 self.check_read_results_1_3()

2455 2456

2457 - def test_select_m4(self):

2458 """Selecting model m4 with parameters {S2, te, Rex} using model_free.select_model().""" 2459 2460 # Path of the files. 2461 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2462 2463 # Read the sequence. 2464 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2465 2466 # Select the model. 2467 self.interpreter.model_free.select_model(model='m4') 2468 2469 # Test the model. 2470 self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4') 2471 self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['s2', 'te', 'rex'])

2472 2473

2474 - def test_set_csa(self):

2475 """Setting the CSA value through the user function value.set().""" 2476 2477 # Path of the files. 2478 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 2479 2480 # Read the sequence. 2481 self.interpreter.sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2) 2482 2483 # Set the CSA value. 2484 self.interpreter.value.set(N15_CSA, 'csa') 2485 2486 # Test the value. 2487 self.assertEqual(cdp.mol[0].res[1].spin[0].csa, N15_CSA)

2488 2489

2490 - def test_tm0_grid(self):

2491 """Test the optimisation of the tm0 model-free parameter grid.""" 2492 2493 # Initialise. 2494 cdp._model = 'tm0' 2495 cdp._value_test = self.value_test 2496 2497 # Setup the data pipe for optimisation. 2498 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm0_grid.py')

2499 2500

2501 - def test_tm1_grid(self):

2502 """Test the optimisation of the tm1 model-free parameter grid.""" 2503 2504 # Initialise. 2505 cdp._model = 'tm1' 2506 cdp._value_test = self.value_test 2507 2508 # Setup the data pipe for optimisation. 2509 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm1_grid.py')

2510 2511

2512 - def test_tm2_grid(self):

2513 """Test the optimisation of the tm2 model-free parameter grid.""" 2514 2515 # Initialise. 2516 cdp._model = 'tm2' 2517 cdp._value_test = self.value_test 2518 2519 # Setup the data pipe for optimisation. 2520 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')

2521 2522

2523 - def test_tm3_grid(self):

2524 """Test the optimisation of the tm3 model-free parameter grid.""" 2525 2526 # Initialise. 2527 cdp._model = 'tm3' 2528 cdp._value_test = self.value_test 2529 2530 # Setup the data pipe for optimisation. 2531 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm3_grid.py')

2532 2533

2534 - def test_tm4_grid(self):

2535 """Test the optimisation of the tm4 model-free parameter grid.""" 2536 2537 # Initialise. 2538 cdp._model = 'tm4' 2539 cdp._value_test = self.value_test 2540 2541 # Setup the data pipe for optimisation. 2542 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm4_grid.py')

2543 2544

2545 - def test_tm5_grid(self):

2546 """Test the optimisation of the tm5 model-free parameter grid.""" 2547 2548 # Initialise. 2549 cdp._model = 'tm5' 2550 cdp._value_test = self.value_test 2551 2552 # Setup the data pipe for optimisation. 2553 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm5_grid.py')

2554 2555

2556 - def test_tm6_grid(self):

2557 """Test the optimisation of the tm6 model-free parameter grid.""" 2558 2559 # Initialise. 2560 cdp._model = 'tm6' 2561 cdp._value_test = self.value_test 2562 2563 # Setup the data pipe for optimisation. 2564 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm6_grid.py')

2565 2566

2567 - def test_tm7_grid(self):

2568 """Test the optimisation of the tm7 model-free parameter grid.""" 2569 2570 # Initialise. 2571 cdp._model = 'tm7' 2572 cdp._value_test = self.value_test 2573 2574 # Setup the data pipe for optimisation. 2575 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm7_grid.py')

2576 2577

2578 - def test_tm8_grid(self):

2579 """Test the optimisation of the tm8 model-free parameter grid.""" 2580 2581 # Initialise. 2582 cdp._model = 'tm8' 2583 cdp._value_test = self.value_test 2584 2585 # Setup the data pipe for optimisation. 2586 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm8_grid.py')

2587 2588

2589 - def test_tm9_grid(self):

2590 """Test the optimisation of the tm9 model-free parameter grid.""" 2591 2592 # Initialise. 2593 cdp._model = 'tm9' 2594 cdp._value_test = self.value_test 2595 2596 # Setup the data pipe for optimisation. 2597 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm9_grid.py')

2598 2599

2600 - def test_tylers_peptide(self):

2601 """Try a component of model-free analysis on Tyler Reddy's peptide data (truncated).""" 2602 2603 # Execute the script. 2604 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'tylers_peptide.py')

2605 2606

2607 - def test_write_results(self):

2608 """Writing of model-free results using the user function results.write().""" 2609 2610 # Path of the files. 2611 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP' 2612 2613 # Read the results file. 2614 self.interpreter.results.read(file='final_results_trunc_1.2', dir=path) 2615 2616 # A dummy file object for catching the results.write() output. 2617 file = DummyFileObject() 2618 2619 # Write the results file into a dummy file. 2620 self.interpreter.results.write(file=file, dir=path) 2621 2622 # Now, get the contents of that file, and then 'close' that file. 2623 test_lines = file.readlines() 2624 file.close() 2625 2626 # Read the results file for Python 3.2+. 2627 if sys.version_info[0] >= 3 and sys.version_info[1] >= 2: 2628 file = open_read_file(file_name='final_results_trunc_2.1_py3', dir=path) 2629 2630 # Read the results file for Python 3.1. 2631 elif sys.version_info[0] >= 3 and sys.version_info[1] == 1: 2632 file = open_read_file(file_name='final_results_trunc_1.3_pre_py2.7.3_v2', dir=path) 2633 2634 # Read the results file for Python 2.7.3+ (excluding Python 3). 2635 elif dep_check.xml_type == 'internal' and sys.version_info[0] >= 2 and sys.version_info[1] >= 7 and sys.version_info[2] >= 3: 2636 file = open_read_file(file_name='final_results_trunc_1.3_v2', dir=path) 2637 2638 # Read the results file for pre Python 2.7.3 versions. 2639 else: 2640 file = open_read_file(file_name='final_results_trunc_1.3_pre_py2.7.3_v2', dir=path) 2641 2642 # Extract the data, then close the results file. 2643 true_lines = file.readlines() 2644 file.close() 2645 2646 # Test the rest of the lines. 2647 for i in range(len(test_lines)): 2648 # Skip the second line, as it contains the date and hence should not be the same. 2649 # Also skip the third line, as the pipe names are different. 2650 if i == 1 or i == 2: 2651 continue 2652 2653 # Alias the lines. 2654 test = test_lines[i] 2655 true = true_lines[i] 2656 2657 # Try to convert the test line into a python object (for cross-platform support). 2658 try: 2659 # Process the post 2.7.3 Python XML. 2660 if search('<value>', test): 2661 test = test.lstrip() 2662 test = test.replace('<value>', '') 2663 test = test.replace('</value>', '') 2664 if search('<ieee_754_byte_array>', test): 2665 test = test.lstrip() 2666 test = test.replace('<ieee_754_byte_array>', '') 2667 test = test.replace('</ieee_754_byte_array>', '') 2668 2669 test = eval(test) 2670 except: 2671 pass 2672 2673 # Try to convert the true line into a python object (for cross-platform support). 2674 try: 2675 # Process the post 2.7.3 Python XML. 2676 if search('<value>', true): 2677 true = true.lstrip() 2678 true = true.replace('<value>', '') 2679 true = true.replace('</value>', '') 2680 if search('<ieee_754_byte_array>', true): 2681 true = true.lstrip() 2682 true = true.replace('<ieee_754_byte_array>', '') 2683 true = true.replace('</ieee_754_byte_array>', '') 2684 2685 true = eval(true) 2686 except: 2687 pass 2688 2689 # Test that the line is the same. 2690 self.assertEqual(test, true)

2691 2692

2693 - 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):

2694 """Test the optimisation values.""" 2695 2696 # Get the debugging message. 2697 mesg = self.mesg_opt_debug(spin) 2698 2699 # Convert to lists. 2700 if iter != None and not isinstance(iter, list): 2701 iter = [iter] 2702 if f_count != None and not isinstance(f_count, list): 2703 f_count = [f_count] 2704 if g_count != None and not isinstance(g_count, list): 2705 g_count = [g_count] 2706 if h_count != None and not isinstance(h_count, list): 2707 h_count = [h_count] 2708 2709 # Test all the values. 2710 ###################### 2711 2712 # Spin selection. 2713 self.assertEqual(spin.select, select, msg=mesg) 2714 2715 # The local tm correlation time. 2716 if local_tm != None: 2717 self.assertAlmostEqual(spin.local_tm / 1e-9, local_tm, msg=mesg) 2718 else: 2719 self.assertEqual(spin.local_tm, None, msg=mesg) 2720 2721 # S2 order parameter. 2722 if s2 != None: 2723 self.assertAlmostEqual(spin.s2, s2, msg=mesg) 2724 else: 2725 self.assertEqual(spin.s2, None, msg=mesg) 2726 2727 # S2f order parameter. 2728 if s2f != None: 2729 self.assertAlmostEqual(spin.s2f, s2f, 5, msg=mesg) 2730 else: 2731 self.assertEqual(spin.s2f, None, msg=mesg) 2732 2733 # S2s order parameter. 2734 if s2s != None: 2735 self.assertAlmostEqual(spin.s2s, s2s, 5, msg=mesg) 2736 else: 2737 self.assertEqual(spin.s2s, None, msg=mesg) 2738 2739 # te correlation time. 2740 if isinstance(te, float): 2741 self.assertAlmostEqual(spin.te / 1e-12, te, 5, msg=mesg) 2742 elif te == None: 2743 self.assertEqual(spin.te, None, msg=mesg) 2744 2745 # tf correlation time. 2746 if isinstance(tf, float): 2747 self.assertAlmostEqual(spin.tf / 1e-12, tf, 4, msg=mesg) 2748 elif tf == None: 2749 self.assertEqual(spin.tf, None, msg=mesg) 2750 2751 # ts correlation time. 2752 if isinstance(ts, float): 2753 self.assertAlmostEqual(spin.ts / 1e-12, ts, 4, msg=mesg) 2754 elif ts == None: 2755 self.assertEqual(spin.ts, None, msg=mesg) 2756 2757 # Chemical exchange. 2758 if isinstance(rex, float): 2759 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) 2760 elif rex == None: 2761 self.assertEqual(spin.rex, None, msg=mesg) 2762 2763 # The optimisation stats. 2764 if chi2 != None: 2765 self.assertAlmostEqual(spin.chi2, chi2, msg=mesg) 2766 if iter != None: 2767 self.assert_(spin.iter in iter, msg=mesg) 2768 if f_count != None: 2769 self.assert_(spin.f_count in f_count, msg=mesg) 2770 if g_count != None: 2771 self.assert_(spin.g_count in g_count, msg=mesg) 2772 if h_count != None: 2773 self.assert_(spin.h_count in h_count, msg=mesg) 2774 if warning != None: 2775 self.assertEqual(spin.warning, warning, msg=mesg)

Source Code for Module test_suite.system_tests.model_free