test_suite.system_tests.n_state

39 """Class for testing various aspects specific to the N-state model.""" 40

41 - def check_vectors(self):

42 """Auxiliary method for checking the correct loading of bond vectors.""" 43 44 # The new order. 45 ds.order_new = array([ds.order_struct[ds.order_model[ds.order_model[0]]], 46 ds.order_struct[ds.order_model[ds.order_model[1]]], 47 ds.order_struct[ds.order_model[ds.order_model[2]]]]) 48 49 # The atom positions. 50 C_pos = [] 51 C_pos.append(array([6.250, 0.948, 1.968])) 52 C_pos.append(array([6.438, -0.139, 1.226])) 53 C_pos.append(array([6.108, -0.169, 0.378])) 54 55 H_pos = [] 56 H_pos.append(array([7.243, 0.580, 1.676])) 57 H_pos.append(array([7.271, -0.291, 0.525])) 58 H_pos.append(array([5.735, 0.003, -0.639])) 59 60 # The real vectors. 61 vect = [] 62 for i in range(3): 63 vect.append(H_pos[i] - C_pos[i]) 64 65 # Normalise. 66 for i in range(3): 67 vect[i] = vect[i] / norm(vect[i]) 68 69 # Print out. 70 print("Structure order: %s" % ds.order_struct) 71 print("Model order: %s" % ds.order_model) 72 print("New order: %s" % ds.order_new) 73 for i in range(3): 74 print("\ni = %i" % i) 75 print("The real vector: %s" % vect[i]) 76 print("The reordered vector: %s" % vect[ds.order_new[i]]) 77 print("The loaded vector: %s" % cdp.mol[0].res[0].spin[0].xh_vect[i]) 78 79 # Check. 80 for i in range(3): 81 self.assertAlmostEqual(norm(vect[ds.order_new[i]] - cdp.mol[0].res[0].spin[0].xh_vect[i]), 0.0) 82 for i in range(3): 83 self.assertAlmostEqual(norm(C_pos[ds.order_new[i]] - cdp.mol[0].res[0].spin[0].pos[i]), 0.0)

84 85

86 - def test_5_state_xz(self):

87 """A 5-state model in the xz-plane (no pivotting of alpha). 88 89 The 5 states correspond to the Euler angles (z-y-z notation): 90 - State 1: {0, pi/4, 0} 91 - State 2: {0, pi/8, 0} 92 - State 3: {0, 0, 0} 93 - State 4: {0, -pi/8, 0} 94 - State 5: {0, -pi/4, 0} 95 """ 96 97 # Execute the script. 98 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'5_state_xz.py') 99 100 # Test the optimised probabilities. 101 self.assertAlmostEqual(cdp.probs[0], 0.2) 102 self.assertAlmostEqual(cdp.probs[1], 0.2) 103 self.assertAlmostEqual(cdp.probs[2], 0.2) 104 self.assertAlmostEqual(cdp.probs[3], 0.2) 105 self.assertAlmostEqual(cdp.probs[4], 0.2) 106 107 # Test the optimised alpha Euler angles. 108 self.assertAlmostEqual(cdp.alpha[0], 0.0) 109 self.assertAlmostEqual(cdp.alpha[1], 0.0) 110 self.assertAlmostEqual(cdp.alpha[2], 0.0) 111 self.assertAlmostEqual(cdp.alpha[3], 0.0) 112 self.assertAlmostEqual(cdp.alpha[4], 0.0) 113 114 # Test the optimised beta Euler angles. 115 self.assertAlmostEqual(cdp.beta[0], pi/4) 116 self.assertAlmostEqual(cdp.beta[1], pi/8) 117 self.assertAlmostEqual(cdp.beta[2], 0.0) 118 self.assertAlmostEqual(cdp.beta[3], -pi/8) 119 self.assertAlmostEqual(cdp.beta[4], -pi/4) 120 121 # Test the optimised gamma Euler angles. 122 self.assertAlmostEqual(cdp.gamma[0], 0.0) 123 self.assertAlmostEqual(cdp.gamma[1], 0.0) 124 self.assertAlmostEqual(cdp.gamma[2], 0.0) 125 self.assertAlmostEqual(cdp.gamma[3], 0.0) 126 self.assertAlmostEqual(cdp.gamma[4], 0.0) 127 128 # Test the chi-squared. 129 self.assertAlmostEqual(cdp.chi2, 3.15009916529e-32)

130 131

132 - def test_A_to_chi(self):

133 """Test the conversion of the alignment tensor to the chi tensor.""" 134 135 # Execute the script. 136 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'A_to_chi.py') 137 138 # Test the optimised values. 139 for i in range(3): 140 self.assertAlmostEqual(cdp.chi[i, i] * 1e32, cdp.chi_ref[i] * 1e32, 2)

141 142

143 - def test_align_fit(self):

144 """Test the use of RDCs and PCSs to find the alignment tensor.""" 145 146 # Set the mode to use both RDCs and PCSs. 147 ds.mode = 'all' 148 tag = 'synth' 149 150 # Execute the script. 151 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py') 152 153 # Test the optimised values. 154 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.351261/2000) 155 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000) 156 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000) 157 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000) 158 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000) 159 self.assertAlmostEqual(cdp.chi2, 0.0) 160 self.assertAlmostEqual(cdp.q_rdc, 0.0) 161 self.assertAlmostEqual(cdp.q_pcs, 0.0) 162 163 # The spin data. 164 pcs = [1.0261275236, 0.75832284646, 0.65377417467, 0.88410306916, 0.83665620282, 1.887881182, 1.6564530832, 1.8489841033, -1.1143070855, -0.52863087918, -0.67600660991, -0.36996952054, -0.50720205688, -0.39889489474, -0.41237130008, -0.71313422816, -0.58642013802, -1.2160818959, -1.3990341569, -1.4084215541, -1.2007391713, -2.1392542193, -2.0165726596, -1.7623442985, -1.6437792517, -1.2415832517, -1.3008765368, -1.5872391105, -1.8060331465, -1.9063640494, -1.9817787999, -0.85264936663, -0.98332177588, -0.13370651687, -0.41762890604, -0.038212181921, -0.37986098085, 0.63582157322, 0.48346482178, 1.7566240094, 1.5694652222, 1.9914499872, 2.5316890107, 1.4559940851, 1.8661428328, 0.65003087965, 0.91690449156, 3.2096229388, 3.5547526651, 3.0579308183, 3.5933428117, 2.9062016872, 3.3750576279, 2.1848555929, 2.4769802024, 1.6466129291, 1.7719619979, 1.1373876736, 1.2182451528] 165 i = 0 166 for spin in spin_loop(): 167 # No PCS. 168 if not hasattr(spin, 'pcs'): 169 continue 170 171 # Check the value. 172 self.assertAlmostEqual(spin.pcs[tag], pcs[i]) 173 174 # Check the back-calculated value. 175 self.assertAlmostEqual(spin.pcs_bc[tag], pcs[i]) 176 177 # Increment the spin index. 178 i += 1 179 180 # Back calc. 181 self.interpreter.pcs.back_calc(tag) 182 183 # Check the spin data. 184 i = 0 185 for spin in spin_loop(): 186 # No PCS. 187 if not hasattr(spin, 'pcs'): 188 continue 189 190 # Check the back-calculated value. 191 self.assertAlmostEqual(spin.pcs_bc[tag], pcs[i]) 192 193 # Increment the spin index. 194 i += 1

195 196

197 - def test_align_fit_rand(self):

198 """Test the use of randomised RDCs and PCSs to find the alignment tensor.""" 199 200 # Set the mode to use both RDCs and PCSs. 201 ds.mode = 'all' 202 203 # Select the randomised data. 204 ds.rand = True 205 206 # Execute the script. 207 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py') 208 209 # The tag. 210 tag = 'synth' 211 212 # Loop a few times. 213 for i in range(4): 214 # Test the optimised values (these values are from relax, so are not 100% reliable as a check). 215 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.000189412096996) 216 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.000271130087923) 217 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.000264898401302) 218 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.000284115871058) 219 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.000152207413184) 220 self.assertAlmostEqual(cdp.chi2, 783.530808266) 221 self.assertAlmostEqual(cdp.q_pcs, 0.063345784112045375) 222 self.assertAlmostEqual(cdp.q_rdc, 0.084926009099013003) 223 224 # Get a spin to check. 225 spin = return_spin(':114@N') 226 227 # Check the RDC and PCS values. 228 self.assertAlmostEqual(spin.rdc[tag], -8.9193269604999994) 229 self.assertAlmostEqual(spin.rdc_bc[tag], -9.1030018792821394) 230 self.assertAlmostEqual(spin.pcs[tag], -0.41430390310999998) 231 self.assertAlmostEqual(spin.pcs_bc[tag], -0.39723010845807194) 232 233 # MC sims so next round can check if values change. 234 if i == 0: 235 # Set some errors. 236 for spin in spin_loop(): 237 spin.rdc_err = {tag: 1.0} 238 spin.pcs_err = {tag: 0.1} 239 240 # MC sims. 241 self.interpreter.monte_carlo.setup(number=3) 242 self.interpreter.monte_carlo.create_data() 243 self.interpreter.monte_carlo.initial_values() 244 self.interpreter.minimise('simplex', constraints=False, max_iter=5) 245 self.interpreter.monte_carlo.error_analysis() 246 247 # Back-calc so next round can check if values change. 248 if i == 2: 249 self.interpreter.rdc.back_calc(tag) 250 self.interpreter.pcs.back_calc(tag) 251 252 # Calc Q factors so next round can check if values change. 253 if i == 1: 254 self.interpreter.rdc.calc_q_factors() 255 self.interpreter.pcs.calc_q_factors()

256 257

258 - def test_align_fit_pcs(self):

259 """Test the use of PCSs to find the alignment tensor.""" 260 261 # Set the mode to use PCSs. 262 ds.mode = 'pcs' 263 264 # Execute the script. 265 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py') 266 267 # Test the optimised values. 268 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.351261/2000) 269 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000) 270 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000) 271 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000) 272 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000) 273 self.assertAlmostEqual(cdp.chi2, 0.0) 274 self.assertAlmostEqual(cdp.q_pcs, 0.0)

275 276

277 - def test_align_fit_pcs_rand(self):

278 """Test the use of randomised PCSs to find the alignment tensor.""" 279 280 # Set the mode to use PCSs. 281 ds.mode = 'pcs' 282 283 # Select the randomised data. 284 ds.rand = True 285 286 # Execute the script. 287 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py') 288 289 # Test the optimised values (these values are from relax, so are not 100% reliable as a check). 290 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.000189165581069) 291 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.000271897288335) 292 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.000264627388896) 293 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.000284180080857) 294 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.00015165641132) 295 self.assertAlmostEqual(cdp.chi2, 756.268087443) 296 self.assertAlmostEqual(cdp.q_pcs, 0.063341567973121266)

297 298

299 - def test_align_fit_rdc(self):

300 """Test the use of RDCs to find the alignment tensor.""" 301 302 # Set the mode to use RDCs. 303 ds.mode = 'rdc' 304 305 # Execute the script. 306 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py') 307 308 # Test the optimised values. 309 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.351261/2000) 310 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000) 311 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000) 312 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000) 313 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000) 314 self.assertAlmostEqual(cdp.chi2, 0.0) 315 self.assertAlmostEqual(cdp.q_rdc, 0.0)

316 317

318 - def test_align_fit_rdc_rand(self):

319 """Test the use of randomised RDCs to find the alignment tensor.""" 320 321 # Set the mode to use RDCs. 322 ds.mode = 'rdc' 323 324 # Select the randomised data. 325 ds.rand = True 326 327 # Execute the script. 328 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py') 329 330 # Test the optimised values (these are about ~10% different from Pales). 331 # Pales: S(zz) S(xx-yy) S(xy) S(xz) S(yz) 332 # Pales: -9.8124e-05 -5.2533e-04 -3.4446e-04 3.7369e-04 -1.8949e-04 333 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.00017045) 334 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.00024905) 335 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.00027502) 336 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.00029833) 337 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.00015125) 338 self.assertAlmostEqual(cdp.chi2, 23.5877482365) # Pales: 23.709 339 self.assertAlmostEqual(cdp.q_rdc, 0.078460000413257444) # Pales (Q Saupe): 0.079 340 self.assertAlmostEqual(cdp.q_rdc_norm2, 0.14049691097282743) # Pales (Q RDC_RMS): 0.141

341 342

343 - def test_lactose_n_state_fixed(self):

344 """The 4-state model analysis of lactose using RDCs and PCSs.""" 345 346 # The model. 347 ds.model = 'fixed' 348 349 # Execute the script. 350 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'lactose_n_state.py')

351 352

353 - def test_lactose_n_state_population(self):

354 """The 4-state model analysis of lactose using RDCs and PCSs.""" 355 356 # The model. 357 ds.model = 'population' 358 359 # Execute the script. 360 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'lactose_n_state.py')

361 362

363 - def test_metal_pos_opt(self):

364 """Test a certain algorithm for the optimisation of the lanthanide position using RDCs and PCSs (with missing data).""" 365 366 # Execute the script. 367 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'metal_pos_opt.py') 368 369 # Check the metal position. 370 self.assertAlmostEqual(cdp.paramagnetic_centre[0], -14.845) 371 self.assertAlmostEqual(cdp.paramagnetic_centre[1], 0.969) 372 self.assertAlmostEqual(cdp.paramagnetic_centre[2], 0.265) 373 374 # The actual tensors. 375 A_5D = [] 376 A_5D.append([1.42219822168827662867e-04, -1.44543001566521341940e-04, -7.07796211648713973798e-04, -6.01619494082773244303e-04, 2.02008007072950861996e-04]) 377 A_5D.append([3.56720663040924505435e-04, -2.68385787902088840916e-04, -1.69361406642305853832e-04, 1.71873715515064501074e-04, -3.05790155096090983822e-04]) 378 A_5D.append([2.32088908680377300801e-07, 2.08076808579168379617e-06, -2.21735465435989729223e-06, -3.74311563209448033818e-06, -2.40784858070560310370e-06]) 379 A_5D.append([-2.62495279588228071048e-04, 7.35617367964106275147e-04, 6.39754192258981332648e-05, 6.27880171180572523460e-05, 2.01197582457700226708e-04]) 380 381 # Check the tensors. 382 for i in range(len(A_5D)): 383 self.assertAlmostEqual(cdp.align_tensors[i].Axx, A_5D[i][0]) 384 self.assertAlmostEqual(cdp.align_tensors[i].Ayy, A_5D[i][1]) 385 self.assertAlmostEqual(cdp.align_tensors[i].Axy, A_5D[i][2]) 386 self.assertAlmostEqual(cdp.align_tensors[i].Axz, A_5D[i][3]) 387 self.assertAlmostEqual(cdp.align_tensors[i].Ayz, A_5D[i][4]) 388 389 # Test the optimised values. 390 self.assertAlmostEqual(cdp.chi2, 0.0) 391 self.assertAlmostEqual(cdp.q_rdc, 0.0) 392 self.assertAlmostEqual(cdp.q_pcs, 0.0)

393 394

395 - def test_missing_data(self):

396 """Test the use of RDCs and PCSs to find the alignment tensor with missing data.""" 397 398 # Execute the script. 399 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'missing_data_test.py') 400 401 # The actual tensors. 402 A_5D = [] 403 A_5D.append([1.42219822168827662867e-04, -1.44543001566521341940e-04, -7.07796211648713973798e-04, -6.01619494082773244303e-04, 2.02008007072950861996e-04]) 404 A_5D.append([3.56720663040924505435e-04, -2.68385787902088840916e-04, -1.69361406642305853832e-04, 1.71873715515064501074e-04, -3.05790155096090983822e-04]) 405 A_5D.append([2.32088908680377300801e-07, 2.08076808579168379617e-06, -2.21735465435989729223e-06, -3.74311563209448033818e-06, -2.40784858070560310370e-06]) 406 A_5D.append([-2.62495279588228071048e-04, 7.35617367964106275147e-04, 6.39754192258981332648e-05, 6.27880171180572523460e-05, 2.01197582457700226708e-04]) 407 408 # Check the tensors. 409 for i in range(len(A_5D)): 410 self.assertAlmostEqual(cdp.align_tensors[i].Axx, A_5D[i][0]) 411 self.assertAlmostEqual(cdp.align_tensors[i].Ayy, A_5D[i][1]) 412 self.assertAlmostEqual(cdp.align_tensors[i].Axy, A_5D[i][2]) 413 self.assertAlmostEqual(cdp.align_tensors[i].Axz, A_5D[i][3]) 414 self.assertAlmostEqual(cdp.align_tensors[i].Ayz, A_5D[i][4]) 415 416 # Test the optimised values. 417 self.assertAlmostEqual(cdp.chi2, 0.0) 418 self.assertAlmostEqual(cdp.q_rdc, 0.0) 419 self.assertAlmostEqual(cdp.q_pcs, 0.0)

420 421

422 - def test_monte_carlo_sims(self):

423 """Test the Monte Carlo simulation data of fitting RDCs and PCSs.""" 424 425 # Execute the script. 426 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'monte_carlo_testing.py') 427 428 # Test the optimised values. 429 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.351261/2000) 430 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000) 431 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000) 432 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000) 433 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000) 434 self.assertAlmostEqual(cdp.chi2 / 1e6, 1745860.0485368515 / 1e6) 435 self.assertAlmostEqual(cdp.q_rdc, 0.0) 436 self.assertAlmostEqual(cdp.q_pcs, 0.0) 437 438 # The tensor key. 439 key = 'synth' 440 441 # The spin data. 442 for spin in spin_loop(): 443 # Print out. 444 print(spin) 445 446 # Check for simulation data. 447 if spin.name == 'N': 448 self.assert_(hasattr(spin, 'rdc_sim')) 449 self.assert_(spin.rdc_sim.has_key(key)) 450 self.assert_(hasattr(spin, 'pcs_sim')) 451 self.assert_(spin.pcs_sim.has_key(key)) 452 453 # Check the values of the simulated data. 454 for i in range(cdp.sim_number): 455 if spin.name == 'N': 456 self.assertAlmostEqual(spin.rdc[key], spin.rdc_sim[key][i], 5) 457 self.assertAlmostEqual(spin.pcs[key], spin.pcs_sim[key][i]) 458 459 # Test the optimised simluation values. 460 for i in range(cdp.sim_number): 461 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.351261/2000) 462 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000) 463 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000) 464 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000) 465 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000) 466 self.assertAlmostEqual(cdp.chi2 / 1e6, 1745860.0485368515 / 1e6) 467 468 # Test the tensor error values. 469 self.assertAlmostEqual(cdp.align_tensors[0].Axx_err, 0.0) 470 self.assertAlmostEqual(cdp.align_tensors[0].Ayy_err, 0.0) 471 self.assertAlmostEqual(cdp.align_tensors[0].Axy_err, 0.0) 472 self.assertAlmostEqual(cdp.align_tensors[0].Axz_err, 0.0) 473 self.assertAlmostEqual(cdp.align_tensors[0].Ayz_err, 0.0)

474 475

476 - def test_paramag_centre_fit(self):

477 """Test the use of RDCs and PCSs to find the alignment tensor.""" 478 479 # Set the mode to use both RDCs and PCSs. 480 ds.mode = 'all' 481 482 # Execute the script. 483 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'paramag_centre_fit.py') 484 485 # Check the paramagnetic centre position. 486 self.assertAlmostEqual(cdp.paramagnetic_centre[0], 32.555, 1) 487 self.assertAlmostEqual(cdp.paramagnetic_centre[1], -19.130, 1) 488 self.assertAlmostEqual(cdp.paramagnetic_centre[2], 27.775, 1) 489 490 # Test the optimised values. 491 self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.351261/2000, 5) 492 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000, 5) 493 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000, 5) 494 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000, 5) 495 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000, 5) 496 self.assertAlmostEqual(cdp.chi2, 0.0, 2) 497 self.assertAlmostEqual(cdp.q_rdc, 0.0, 2) 498 self.assertAlmostEqual(cdp.q_pcs, 0.0, 2)

499 500

501 - def test_pcs_back_calc(self):

502 """Test the back-calculation of PCSs for ubiquitin.""" 503 504 # Execute the script. 505 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'pcs_back_calc.py') 506 507 # Test the optimised values. 508 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].pcs_bc['A'], 0.061941887563792014) 509 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].pcs_bc['A'], -0.077886567972081502) 510 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].pcs_bc['A'], -0.13928519099517916)

511 512

513 - def test_pcs_fit_true_pos(self):

514 """Test the fit of DNA PCSs at the true Ln3+ position.""" 515 516 # Set the Ln3+ position. 517 ds.para_centre = 'true' 518 519 # Execute the script. 520 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'dna_pcs_fit.py') 521 522 # Test the optimised values. 523 self.assertAlmostEqual(cdp.align_tensors[0].Axx, 1.42219822168827662867e-04) 524 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, -1.44543001566521341940e-04) 525 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -7.07796211648713973798e-04) 526 self.assertAlmostEqual(cdp.align_tensors[0].Axz, -6.01619494082773244303e-04) 527 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, 2.02008007072950861996e-04) 528 self.assertAlmostEqual(cdp.chi2, 0.0) 529 self.assertAlmostEqual(cdp.q_pcs, 0.0)

530 531

532 - def test_pcs_fit_zero_pos(self):

533 """Test the fit of DNA PCSs at a Ln3+ position of [0, 0, 0].""" 534 535 # Set the Ln3+ position. 536 ds.para_centre = 'zero' 537 538 # Execute the script. 539 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'dna_pcs_fit.py') 540 541 # Test the optimised values. 542 self.assertAlmostEqual(cdp.align_tensors[0].Axx, 9.739588118243e-07) 543 self.assertAlmostEqual(cdp.align_tensors[0].Ayy, -1.077401299806e-05) 544 self.assertAlmostEqual(cdp.align_tensors[0].Axy, -2.321033328910e-06) 545 self.assertAlmostEqual(cdp.align_tensors[0].Axz, 5.105903556692e-07) 546 self.assertAlmostEqual(cdp.align_tensors[0].Ayz, 1.676638764825e-05) 547 self.assertAlmostEqual(cdp.chi2, 2125.9562247877066) 548 self.assertAlmostEqual(cdp.q_pcs, 0.76065986767333704) 549 550 # The chi tensor. 551 chi_diag = calc_chi_tensor(cdp.align_tensors[0].A_diag, 799.75376122 * 1e6, 298) 552 chi_diag = chi_diag * 1e33 553 self.assertAlmostEqual((chi_diag[2, 2] - (chi_diag[0, 0] + chi_diag[1, 1])/2.0), -6.726159808496, 5) 554 self.assertAlmostEqual((chi_diag[0, 0] - chi_diag[1, 1]), -3.960936794864, 6)

555 556

557 - def test_pcs_to_rdc(self):

558 """Test the back-calculation of RDCs from a PCS derived tensor.""" 559 560 # Execute the script. 561 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'pcs_to_rdc.py') 562 563 # Test the values. 564 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].rdc_bc['A'], 4.1319413321530014) 565 self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].rdc_bc['A'], -9.5802642470087989) 566 self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].rdc_bc['A'], -16.244078605100817)

567 568

569 - def test_rdc_tensor(self):

570 """Test the calculation of an alignment tensor from RDC data.""" 571 572 # Execute the script. 573 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'rdc_tensor.py')

574 575

576 - def test_stereochem_analysis(self):

577 """The full relative stereochemistry analysis.""" 578 579 # Create a temporary directory for all result files. 580 ds.tmpdir = mkdtemp() 581 582 # Execute the script. 583 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'stereochem_analysis.py') 584 585 # Check the base directory files. 586 files = listdir(ds.tmpdir) 587 for file in files: 588 print("Checking file %s." % file) 589 self.assert_(file in ['NOE_viol_S_sorted', 'ensembles_superimposed', 'RDC_PAN_dist.agr', 'Q_factors_S', 'NOE_viol_curve.agr', 'NOE_viol_dist.agr', 'RDC_PAN_curve.agr', 'NOE_viol_S', 'Q_factors_R_sorted', 'NOE_results', 'Q_factors_R', 'NOE_viol_R_sorted', 'logs', 'NOE_viol_R', 'Q_factors_S_sorted', 'RDC_PAN_results', 'correlation_plot.agr', 'correlation_plot_scaled.agr']) 590 591 # Check the sub-directory files. 592 subdirs = ['ensembles_superimposed', 'logs', 'NOE_results', 'RDC_PAN_results'] 593 files = [['S0.pdb', 'S2.pdb', 'R0.pdb', 'R1.pdb', 'S1.pdb', 'R2.pdb'], 594 ['RDC_PAN_analysis.log', 'NOE_viol.log'], 595 ['S_results_0.bz2', 'S_results_1.bz2', 'R_results_2.bz2', 'R_results_0.bz2', 'S_results_2.bz2', 'R_results_1.bz2'], 596 ['S_results_0.bz2', 'S_results_1.bz2', 'R_results_2.bz2', 'R_results_0.bz2', 'S_results_2.bz2', 'R_results_1.bz2']] 597 for i in range(len(subdirs)): 598 for file in listdir(ds.tmpdir + sep + subdirs[i]): 599 print("Checking file %s." % file) 600 self.assert_(file in files[i])

601 602

603 - def test_populations(self):

604 """Test the 'population' N-state model optimisation using RDCs and PCSs (with missing data).""" 605 606 # Execute the script. 607 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'populations.py') 608 609 # The actual tensors. 610 A_5D = [] 611 A_5D.append([1.42219822168827662867e-04, -1.44543001566521341940e-04, -7.07796211648713973798e-04, -6.01619494082773244303e-04, 2.02008007072950861996e-04]) 612 A_5D.append([3.56720663040924505435e-04, -2.68385787902088840916e-04, -1.69361406642305853832e-04, 1.71873715515064501074e-04, -3.05790155096090983822e-04]) 613 A_5D.append([2.32088908680377300801e-07, 2.08076808579168379617e-06, -2.21735465435989729223e-06, -3.74311563209448033818e-06, -2.40784858070560310370e-06]) 614 A_5D.append([-2.62495279588228071048e-04, 7.35617367964106275147e-04, 6.39754192258981332648e-05, 6.27880171180572523460e-05, 2.01197582457700226708e-04]) 615 616 # Check the tensors. 617 for i in range(len(A_5D)): 618 self.assertAlmostEqual(cdp.align_tensors[i].Axx, A_5D[i][0]) 619 self.assertAlmostEqual(cdp.align_tensors[i].Ayy, A_5D[i][1]) 620 self.assertAlmostEqual(cdp.align_tensors[i].Axy, A_5D[i][2]) 621 self.assertAlmostEqual(cdp.align_tensors[i].Axz, A_5D[i][3]) 622 self.assertAlmostEqual(cdp.align_tensors[i].Ayz, A_5D[i][4]) 623 624 # Check the populations. 625 self.assertEqual(len(cdp.probs), 3) 626 self.assertAlmostEqual(cdp.probs[0], 0.3) 627 self.assertAlmostEqual(cdp.probs[1], 0.6) 628 self.assertAlmostEqual(cdp.probs[2], 0.1) 629 630 # Test the optimised values. 631 self.assertAlmostEqual(cdp.chi2, 0.0) 632 self.assertAlmostEqual(cdp.q_rdc, 0.0) 633 self.assertAlmostEqual(cdp.q_pcs, 0.0)

634 635

636 - def test_vector_loading1(self):

637 """Test the loading of inter-atomic vectors in the 'population' N-state model.""" 638 639 # Order. 640 ds.order_struct = [1, 2, 0] 641 ds.order_model = [0, 1, 2] 642 643 # Execute the script. 644 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'vector_loading.py') 645 646 # Check the vectors. 647 self.check_vectors()

648 649

650 - def test_vector_loading2(self):

651 """Test the loading of inter-atomic vectors in the 'population' N-state model.""" 652 653 # Order. 654 ds.order_struct = [0, 1, 2] 655 ds.order_model = [2, 0, 1] 656 657 # Execute the script. 658 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'vector_loading.py') 659 660 # Check the vectors. 661 self.check_vectors()

662 663

664 - def test_vector_loading3(self):

665 """Test the loading of inter-atomic vectors in the 'population' N-state model.""" 666 667 # Order. 668 ds.order_struct = [1, 0, 2] 669 ds.order_model = [2, 0, 1] 670 671 # Execute the script. 672 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'vector_loading.py') 673 674 # Check the vectors. 675 self.check_vectors()

Source Code for Module test_suite.system_tests.n_state_model