generic_fns.palmer

36 - def __init__(self, relax):

37 """Class used to create and process input and output for the program Modelfree 4.""" 38 39 self.relax = relax

40 41

42 - def create(self, run, dir, force, binary, diff_search, sims, sim_type, trim, steps, constraints, nucleus, atom1, atom2):

43 """Function for creating the Modelfree4 input files. 44 45 The following files are created: 46 dir/mfin 47 dir/mfdata 48 dir/mfpar 49 dir/mfmodel 50 dir/run.sh 51 """ 52 53 # Test if the run exists. 54 if not run in self.relax.data.run_names: 55 raise RelaxNoRunError, run 56 57 # Test if sequence data is loaded. 58 if not self.relax.data.res.has_key(run): 59 raise RelaxNoSequenceError, run 60 61 # Test if the PDB file is loaded (for the spheroid and ellipsoid). 62 if not self.relax.data.diff[run].type == 'sphere' and not self.relax.data.pdb.has_key(run): 63 raise RelaxNoPdbError, run 64 65 # Test if the nucleus type has been set. 66 if not hasattr(self.relax.data, 'gx'): 67 raise RelaxNucleusError 68 69 # Directory creation. 70 if dir == None: 71 dir = run 72 self.relax.IO.mkdir(dir, print_flag=0) 73 74 # Place the arguments into 'self'. 75 self.run = run 76 self.dir = dir 77 self.force = force 78 self.binary = binary 79 self.diff_search = diff_search 80 self.sims = sims 81 self.sim_type = sim_type 82 self.trim = trim 83 self.steps = steps 84 self.constraints = constraints 85 self.nucleus = nucleus 86 self.atom1 = atom1 87 self.atom2 = atom2 88 89 # Number of field strengths and values. 90 self.num_frq = 0 91 self.frq = [] 92 for i in xrange(len(self.relax.data.res[self.run])): 93 if hasattr(self.relax.data.res[self.run][i], 'num_frq'): 94 if self.relax.data.res[self.run][i].num_frq > self.num_frq: 95 # Number of field strengths. 96 self.num_frq = self.relax.data.res[self.run][i].num_frq 97 98 # Field strength values. 99 for frq in self.relax.data.res[self.run][i].frq: 100 if frq not in self.frq: 101 self.frq.append(frq) 102 103 # The 'mfin' file. 104 mfin = self.open_file('mfin') 105 self.create_mfin(mfin) 106 mfin.close() 107 108 # Open the 'mfdata', 'mfmodel', and 'mfpar' files. 109 mfdata = self.open_file('mfdata') 110 mfmodel = self.open_file('mfmodel') 111 mfpar = self.open_file('mfpar') 112 113 # Loop over the sequence. 114 for i in xrange(len(self.relax.data.res[self.run])): 115 if hasattr(self.relax.data.res[self.run][i], 'num_frq'): 116 # The 'mfdata' file. 117 if not self.create_mfdata(i, mfdata): 118 continue 119 120 # The 'mfmodel' file. 121 self.create_mfmodel(i, mfmodel) 122 123 # The 'mfpar' file. 124 self.create_mfpar(i, mfpar) 125 126 # Close the 'mfdata', 'mfmodel', and 'mfpar' files. 127 mfdata.close() 128 mfmodel.close() 129 mfpar.close() 130 131 # The 'run.sh' script. 132 run = self.open_file('run.sh') 133 self.create_run(run) 134 run.close() 135 chmod(self.dir + '/run.sh', 0755)

136 137

138 - def create_mfdata(self, i, file):

139 """Create the Modelfree4 input file 'mfmodel'.""" 140 141 # Spin title. 142 file.write("\nspin " + self.relax.data.res[self.run][i].name + "_" + `self.relax.data.res[self.run][i].num` + "\n") 143 144 # Data written flag. 145 written = 0 146 147 # Loop over the frequencies. 148 for j in xrange(self.num_frq): 149 # Set the data to None. 150 r1, r2, noe = None, None, None 151 152 # Loop over the relevant relaxation data. 153 for k in xrange(self.relax.data.res[self.run][i].num_ri): 154 if self.frq[j] != self.relax.data.res[self.run][i].frq[self.relax.data.res[self.run][i].remap_table[k]]: 155 continue 156 157 # Find the corresponding R1. 158 if self.relax.data.res[self.run][i].ri_labels[k] == 'R1': 159 r1 = self.relax.data.res[self.run][i].relax_data[k] 160 r1_err = self.relax.data.res[self.run][i].relax_error[k] 161 162 # Find the corresponding R2. 163 elif self.relax.data.res[self.run][i].ri_labels[k] == 'R2': 164 r2 = self.relax.data.res[self.run][i].relax_data[k] 165 r2_err = self.relax.data.res[self.run][i].relax_error[k] 166 167 # Find the corresponding NOE. 168 elif self.relax.data.res[self.run][i].ri_labels[k] == 'NOE': 169 noe = self.relax.data.res[self.run][i].relax_data[k] 170 noe_err = self.relax.data.res[self.run][i].relax_error[k] 171 172 # Test if the R1 exists for this frequency, otherwise skip the data. 173 if r1: 174 file.write('%-7s%-10.3f%20.15f%20.15f %-3i\n' % ('R1', self.frq[j]*1e-6, r1, r1_err, 1)) 175 else: 176 file.write('%-7s%-10.3f%20.15f%20.15f %-3i\n' % ('R1', self.frq[j]*1e-6, 0, 0, 0)) 177 178 # Test if the R2 exists for this frequency, otherwise skip the data. 179 if r2: 180 file.write('%-7s%-10.3f%20.15f%20.15f %-3i\n' % ('R2', self.frq[j]*1e-6, r2, r2_err, 1)) 181 else: 182 file.write('%-7s%-10.3f%20.15f%20.15f %-3i\n' % ('R2', self.frq[j]*1e-6, 0, 0, 0)) 183 184 # Test if the NOE exists for this frequency, otherwise skip the data. 185 if noe: 186 file.write('%-7s%-10.3f%20.15f%20.15f %-3i\n' % ('NOE', self.frq[j]*1e-6, noe, noe_err, 1)) 187 else: 188 file.write('%-7s%-10.3f%20.15f%20.15f %-3i\n' % ('NOE', self.frq[j]*1e-6, 0, 0, 0)) 189 190 written = 1 191 192 return written

193 194

195 - def create_mfin(self, file):

196 """Create the Modelfree4 input file 'mfin'.""" 197 198 # Set the diffusion tensor specific values. 199 if self.relax.data.diff[self.run].type == 'sphere': 200 diff = 'isotropic' 201 algorithm = 'brent' 202 tm = self.relax.data.diff[self.run].tm / 1e-9 203 dratio = 1 204 theta = 0 205 phi = 0 206 elif self.relax.data.diff[self.run].type == 'spheroid': 207 diff = 'axial' 208 algorithm = 'powell' 209 tm = self.relax.data.diff[self.run].tm / 1e-9 210 dratio = self.relax.data.diff[self.run].Dratio 211 theta = self.relax.data.diff[self.run].theta * 360.0 / (2.0 * pi) 212 phi = self.relax.data.diff[self.run].phi * 360.0 / (2.0 * pi) 213 elif self.relax.data.diff[self.run].type == 'ellipsoid': 214 diff = 'anisotropic' 215 algorithm = 'powell' 216 tm = self.relax.data.diff[self.run].tm / 1e-9 217 dratio = 0 218 theta = 0 219 phi = 0 220 221 # Add the main options. 222 file.write("optimization tval\n\n") 223 file.write("seed 0\n\n") 224 file.write("search grid\n\n") 225 226 # Diffusion type. 227 if self.relax.data.diff[self.run].fixed: 228 algorithm = 'fix' 229 230 file.write("diffusion " + diff + " " + self.diff_search + "\n\n") 231 file.write("algorithm " + algorithm + "\n\n") 232 233 # Monte Carlo simulations. 234 if self.sims: 235 file.write("simulations " + self.sim_type + " " + `self.sims` + " " + `self.trim` + "\n\n") 236 else: 237 file.write("simulations none\n\n") 238 239 selection = 'none' # To be changed. 240 file.write("selection " + selection + "\n\n") 241 file.write("sim_algorithm " + algorithm + "\n\n") 242 243 file.write("fields " + `self.num_frq`) 244 for frq in self.frq: 245 file.write(" " + `frq*1e-6`) 246 file.write("\n") 247 248 # tm. 249 file.write('%-7s' % 'tm') 250 file.write('%14.3f' % tm) 251 file.write('%2i' % 1) 252 file.write('%3i' % 0) 253 file.write('%5i' % 5) 254 file.write('%6i' % 15) 255 file.write('%4i\n' % 20) 256 257 # dratio. 258 file.write('%-7s' % 'Dratio') 259 file.write('%14s' % dratio) 260 file.write('%2i' % 1) 261 file.write('%3i' % 0) 262 file.write('%5i' % 0) 263 file.write('%6i' % 2) 264 file.write('%4i\n' % 5) 265 266 # theta. 267 file.write('%-7s' % 'Theta') 268 file.write('%14s' % theta) 269 file.write('%2i' % 1) 270 file.write('%3i' % 0) 271 file.write('%5i' % 0) 272 file.write('%6i' % 180) 273 file.write('%4i\n' % 10) 274 275 # phi. 276 file.write('%-7s' % 'Phi') 277 file.write('%14s' % phi) 278 file.write('%2i' % 1) 279 file.write('%3i' % 0) 280 file.write('%5i' % 0) 281 file.write('%6i' % 360) 282 file.write('%4i\n' % 10)

283 284

285 - def create_mfmodel(self, i, file):

286 """Create the Modelfree4 input file 'mfmodel'.""" 287 288 # Spin title. 289 file.write("\nspin " + self.relax.data.res[self.run][i].name + "_" + `self.relax.data.res[self.run][i].num` + "\n") 290 291 # tloc. 292 file.write('%-3s%-6s%-6.1f' % ('M1', 'tloc', 0)) 293 if 'tm' in self.relax.data.res[self.run][i].params: 294 file.write('%-4i' % 1) 295 else: 296 file.write('%-4i' % 0) 297 298 if self.constraints: 299 file.write('%-2i' % 2) 300 else: 301 file.write('%-2i' % 0) 302 303 file.write('%11.3f%12.3f %-4s\n' % (0, 20, self.steps)) 304 305 # Theta. 306 file.write('%-3s%-6s%-6.1f' % ('M1', 'Theta', 0)) 307 file.write('%-4i' % 0) 308 309 if self.constraints: 310 file.write('%-2i' % 2) 311 else: 312 file.write('%-2i' % 0) 313 314 file.write('%11.3f%12.3f %-4s\n' % (0, 90, self.steps)) 315 316 # S2f. 317 file.write('%-3s%-6s%-6.1f' % ('M1', 'Sf2', 1)) 318 if 'S2f' in self.relax.data.res[self.run][i].params: 319 file.write('%-4i' % 1) 320 else: 321 file.write('%-4i' % 0) 322 323 if self.constraints: 324 file.write('%-2i' % 2) 325 else: 326 file.write('%-2i' % 0) 327 328 file.write('%11.3f%12.3f %-4s\n' % (0, 1, self.steps)) 329 330 # S2s. 331 file.write('%-3s%-6s%-6.1f' % ('M1', 'Ss2', 1)) 332 if 'S2s' in self.relax.data.res[self.run][i].params or 'S2' in self.relax.data.res[self.run][i].params: 333 file.write('%-4i' % 1) 334 else: 335 file.write('%-4i' % 0) 336 337 if self.constraints: 338 file.write('%-2i' % 2) 339 else: 340 file.write('%-2i' % 0) 341 342 file.write('%11.3f%12.3f %-4s\n' % (0, 1, self.steps)) 343 344 # te. 345 file.write('%-3s%-6s%-6.1f' % ('M1', 'te', 0)) 346 if 'te' in self.relax.data.res[self.run][i].params or 'ts' in self.relax.data.res[self.run][i].params: 347 file.write('%-4i' % 1) 348 else: 349 file.write('%-4i' % 0) 350 351 if self.constraints: 352 file.write('%-2i' % 2) 353 else: 354 file.write('%-2i' % 0) 355 356 file.write('%11.3f%12.3f %-4s\n' % (0, 10000, self.steps)) 357 358 # Rex. 359 file.write('%-3s%-6s%-6.1f' % ('M1', 'Rex', 0)) 360 if 'Rex' in self.relax.data.res[self.run][i].params: 361 file.write('%-4i' % 1) 362 else: 363 file.write('%-4i' % 0) 364 365 if self.constraints: 366 file.write('%-2i' % -1) 367 else: 368 file.write('%-2i' % 0) 369 370 file.write('%11.3f%12.3f %-4s\n' % (0, 20, self.steps))

371 372

373 - def create_mfpar(self, i, file):

374 """Create the Modelfree4 input file 'mfpar'.""" 375 376 # Spin title. 377 file.write("\nspin " + self.relax.data.res[self.run][i].name + "_" + `self.relax.data.res[self.run][i].num` + "\n") 378 379 file.write('%-14s' % "constants") 380 file.write('%-6i' % self.relax.data.res[self.run][i].num) 381 file.write('%-7s' % self.nucleus) 382 file.write('%-8.3f' % (self.relax.data.gx / 1e7)) 383 file.write('%-8.3f' % (self.relax.data.res[self.run][i].r * 1e10)) 384 file.write('%-8.3f\n' % (self.relax.data.res[self.run][i].csa * 1e6)) 385 386 file.write('%-10s' % "vector") 387 file.write('%-4s' % self.atom1) 388 file.write('%-4s\n' % self.atom2)

389 390

391 - def create_run(self, file):

392 """Create the script 'run.sh' for the execution of Modelfree4.""" 393 394 file.write("#! /bin/sh\n") 395 file.write(self.binary + " -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out") 396 if self.relax.data.diff[self.run].type != 'sphere': 397 # Copy the pdb file to the model directory so there are no problems with the existance of *.rotate files. 398 system('cp ' + self.relax.data.pdb[self.run].file_name + ' ' + self.dir) 399 file.write(" -s " + self.relax.data.pdb[self.run].file_name.split('/')[-1]) 400 file.write("\n")

401 402

403 - def execute(self, run, dir, force, binary):

404 """Function for executing Modelfree4. 405 406 BUG: Control-C during execution causes the cwd to stay as dir. 407 """ 408 409 # Arguments. 410 self.run = run 411 self.dir = dir 412 self.force = force 413 self.binary = binary 414 415 # The current directory. 416 orig_dir = getcwd() 417 418 # The directory. 419 if dir == None: 420 dir = run 421 if not access(dir, F_OK): 422 raise RelaxDirError, ('Modelfree4', dir) 423 424 # Change to this directory. 425 chdir(dir) 426 427 # Catch failures and return to the correct directory. 428 try: 429 # Test if the 'mfin' input file exists. 430 if not access('mfin', F_OK): 431 raise RelaxFileError, ('mfin input', 'mfin') 432 433 # Test if the 'mfdata' input file exists. 434 if not access('mfdata', F_OK): 435 raise RelaxFileError, ('mfdata input', 'mfdata') 436 437 # Test if the 'mfmodel' input file exists. 438 if not access('mfmodel', F_OK): 439 raise RelaxFileError, ('mfmodel input', 'mfmodel') 440 441 # Test if the 'mfpar' input file exists. 442 if not access('mfpar', F_OK): 443 raise RelaxFileError, ('mfpar input', 'mfpar') 444 445 # Test if the 'PDB' input file exists. 446 if self.relax.data.diff[run].type != 'sphere': 447 pdb = self.relax.data.pdb[self.run].file_name.split('/')[-1] 448 if not access(pdb, F_OK): 449 raise RelaxFileError, ('PDB', pdb) 450 else: 451 pdb = None 452 453 # Remove the file 'mfout' and '*.out' if the force flag is set. 454 if force: 455 for file in listdir(getcwd()): 456 if search('out$', file) or search('rotate$', file): 457 remove(file) 458 459 # Test the binary file string corresponds to a valid executable. 460 self.relax.IO.test_binary(self.binary) 461 462 # Execute Modelfree4 (inputting a PDB file). 463 if pdb: 464 status = spawnlp(P_WAIT, self.binary, self.binary, '-i', 'mfin', '-d', 'mfdata', '-p', 'mfpar', '-m', 'mfmodel', '-o', 'mfout', '-e', 'out', '-s', pdb) 465 if status: 466 raise RelaxProgFailError, 'Modelfree4' 467 468 469 # Execute Modelfree4 (without a PDB file). 470 else: 471 status = spawnlp(P_WAIT, self.binary, self.binary, '-i', 'mfin', '-d', 'mfdata', '-p', 'mfpar', '-m', 'mfmodel', '-o', 'mfout', '-e', 'out') 472 if status: 473 raise RelaxProgFailError, 'Modelfree4' 474 475 # Failure. 476 except: 477 # Change back to the original directory. 478 chdir(orig_dir) 479 480 # Reraise the error. 481 raise 482 483 # Change back to the original directory. 484 chdir(orig_dir)

485 486

487 - def extract(self, run, dir):

488 """Function for extracting the Modelfree4 results out of the 'mfout' file.""" 489 490 # Arguments. 491 self.run = run 492 493 # Test if sequence data is loaded. 494 if not self.relax.data.res.has_key(self.run): 495 raise RelaxNoSequenceError, self.run 496 497 # The directory. 498 if dir == None: 499 dir = run 500 if not access(dir, F_OK): 501 raise RelaxDirError, ('Modelfree4', dir) 502 503 # Test if the file exists. 504 if not access(dir + "/mfout", F_OK): 505 raise RelaxFileError, ('Modelfree4', dir + "/mfout") 506 507 # Open the file. 508 mfout_file = open(dir + "/mfout", 'r') 509 self.mfout_lines = mfout_file.readlines() 510 mfout_file.close() 511 512 # Get the section line positions of the mfout file. 513 self.line_positions() 514 515 516 # Find out if simulations were carried out. 517 sims = 0 518 for i in xrange(len(self.mfout_lines)): 519 if search('_iterations', self.mfout_lines[i]): 520 row = split(self.mfout_lines[i]) 521 sims = int(row[1]) 522 523 # Loop over the sequence. 524 pos = 0 525 for i in xrange(len(self.relax.data.res[self.run])): 526 # Reassign the data structure. 527 data = self.relax.data.res[self.run][i] 528 529 # Skip unselected residues. 530 if not data.select: 531 continue 532 533 # Missing data sets. 534 if not hasattr(data, 'model'): 535 continue 536 537 # No relaxation data. 538 if not hasattr(data, 'num_frq'): 539 continue 540 541 # Get the S2 data. 542 if 'S2' in data.params: 543 data.s2, data.s2_err = self.get_mf_data(self.mfout_S2_pos + pos) 544 545 # Get the S2f data. 546 if 'S2f' in data.params or 'S2s' in data.params: 547 data.s2f, data.s2f_err = self.get_mf_data(self.mfout_S2f_pos + pos) 548 549 # Get the S2s data. 550 if 'S2f' in data.params or 'S2s' in data.params: 551 data.s2s, data.s2s_err = self.get_mf_data(self.mfout_S2s_pos + pos) 552 553 # Get the te data. 554 if 'te' in data.params: 555 data.te, data.te_err = self.get_mf_data(self.mfout_te_pos + pos) 556 data.te = data.te / 1e12 557 data.te_err = data.te_err / 1e12 558 559 # Get the ts data. 560 if 'ts' in data.params: 561 data.ts, data.ts_err = self.get_mf_data(self.mfout_te_pos + pos) 562 data.ts = data.ts / 1e12 563 data.ts_err = data.ts_err / 1e12 564 565 # Get the Rex data. 566 if 'Rex' in data.params: 567 data.rex, data.rex_err = self.get_mf_data(self.mfout_Rex_pos + pos) 568 data.rex = data.rex / (2.0 * pi * data.frq[0])**2 569 data.rex_err = data.rex_err / (2.0 * pi * data.frq[0])**2 570 571 # Get the chi-squared data. 572 if not sims: 573 row = split(self.mfout_lines[self.mfout_chi2_pos + pos]) 574 data.chi2 = float(row[1]) 575 else: 576 # The mfout chi2 position (with no sims) plus 2 (for the extra XML) plus the residue position times 22 (because of the simulated SSE rows). 577 row = split(self.mfout_lines[self.mfout_chi2_pos + 2 + 22*pos]) 578 data.chi2 = float(row[1]) 579 580 # Increment the residue position. 581 pos = pos + 1

582 583

584 - def get_mf_data(self, pos):

585 """Extract the model-free data from the given position of the mfout file. 586 587 This method is designed to catch a number of bugs in Modelfree4's mfout file. 588 589 The first bug is the presence of a series of '*' characters causing a fusion of two columns. 590 This is handled by splitting by the '*' char and then returning the first element. 591 592 The second bug is when the floating point number is too big to fit into Modelfree4's string 593 format limit of 15.3f. This results in a results line such as: 594 595 246 10000.00019682363392.000 1 0.000 0.000 0.000 0.000 596 597 This is caught by scanning for two '.' characters in the column, and handled by assuming 598 that every floating point number will have three decimal characters. 599 600 @param pos: The mfout line position. 601 @type pos: int 602 @return: The value and error. 603 @rtype: tuple of 2 floats 604 """ 605 606 # Split the line up. 607 row = split(self.mfout_lines[pos]) 608 609 # The value and error, assuming a bug free mfout file. 610 val = row[1] 611 err = row[4] 612 613 # The Modelfree4 '*' column fusion bug. 614 if search('\*', val) or search('\*', err): 615 # Split by the '*' character. 616 val_row = split(val, '*') 617 err_row = split(err, '*') 618 619 # The value and error (the first elements). 620 val = val_row[0] 621 err = err_row[0] 622 623 # The Modelfree4 large float column fusion bug. 624 new_row = [] 625 fused = False 626 for element in row: 627 # Count the number of '.' characters. 628 num = count(element, '.') 629 630 # Catch two or more '.' characters. 631 if num > 1: 632 # Set the fused flag. 633 fused = True 634 635 # Loop over each fused number. 636 for i in xrange(num): 637 # Find the index of the first '.'. 638 index = find(element, '.') 639 640 # The first number (index + decimal point + 3 decimal chars). 641 new_row.append(element[0:index+4]) 642 643 # Strip the first number from the element for the next loop iteration. 644 element = element[index+4:] 645 646 # Otherwise the column element is fine. 647 else: 648 new_row.append(element) 649 650 # Bug has been caught. 651 if fused: 652 val = new_row[1] 653 err = new_row[4] 654 655 # Return the value and error, as floats. 656 return float(val), float(err)

657 658

659 - def line_positions(self):

660 """Function for getting the section positions (line number) of the mfout file.""" 661 662 # Loop over the file. 663 i = 0 664 while i < len(self.mfout_lines): 665 # Model-free data. 666 if match('data_model_1', self.mfout_lines[i]): 667 # Shift down two lines (to avoid the lines not starting with a space).. 668 i = i + 2 669 670 # Walk through all the data. 671 while 1: 672 # Break once the end of the data section is reached. 673 if not self.mfout_lines[i] == '\n' and not search('^ ', self.mfout_lines[i]): 674 break 675 676 # Split the line up. 677 row = split(self.mfout_lines[i]) 678 679 # S2 position (skip the heading and move to the first residue). 680 if len(row) == 2 and row[0] == 'S2': 681 self.mfout_S2_pos = i + 1 682 683 # S2f position (skip the heading and move to the first residue). 684 if len(row) == 2 and row[0] == 'S2f': 685 self.mfout_S2f_pos = i + 1 686 687 # S2s position (skip the heading and move to the first residue). 688 if len(row) == 2 and row[0] == 'S2s': 689 self.mfout_S2s_pos = i + 1 690 691 # te position (skip the heading and move to the first residue). 692 if len(row) == 2 and row[0] == 'te': 693 self.mfout_te_pos = i + 1 694 695 # Rex position (skip the heading and move to the first residue). 696 if len(row) == 2 and row[0] == 'Rex': 697 self.mfout_Rex_pos = i + 1 698 699 # Move to the next line number. 700 i = i + 1 701 702 # Chi-squared values. 703 if match('data_sse', self.mfout_lines[i]): 704 self.mfout_chi2_pos = i + 3 705 706 # Move to the next line number. 707 i = i + 1

708 709

710 - def open_file(self, file_name):

711 """Function for opening a file to write to.""" 712 713 file_name = self.dir + "/" + file_name 714 if access(file_name, F_OK) and not self.force: 715 raise RelaxFileOverwriteError, (file_name, 'force flag') 716 return open(file_name, 'w')

Source Code for Module generic_fns.palmer