palmer

8 - def __init__(self, mf):

9 "Class used to create and process input and output for the program Modelfree 4." 10 11 self.mf = mf 12 13 print "Model-free analysis based on " + self.mf.usr_param.method + " model selection." 14 self.ask_stage() 15 title = "<<< Stage " + self.mf.data.stage + " - " 16 title = title + self.mf.usr_param.method + " model selection >>>\n\n\n" 17 18 if self.mf.debug: 19 self.mf.file_ops.init_log_file(title) 20 21 self.update_data() 22 self.extract_relax_data() 23 24 if self.mf.debug: 25 self.log_input_info() 26 27 if match('^AIC$', self.mf.usr_param.method) or match('^AICc$', self.mf.usr_param.method): 28 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5'] 29 self.model_selection = self.mf.modsel.asymptotic 30 elif match('^BIC$', self.mf.usr_param.method): 31 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5'] 32 self.model_selection = self.mf.modsel.asymptotic 33 elif match('^Bootstrap$', self.mf.usr_param.method): 34 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5'] 35 self.model_selection = self.mf.modsel.bootstrap 36 elif match('^CV$', self.mf.usr_param.method): 37 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5'] 38 self.model_selection = self.mf.modsel.cv 39 elif match('^Expect$', self.mf.usr_param.method): 40 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5'] 41 self.model_selection = self.mf.modsel.exp_overall_disc 42 elif match('^Farrow$', self.mf.usr_param.method): 43 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5'] 44 self.model_selection = self.mf.modsel.farrow 45 elif match('^Palmer$', self.mf.usr_param.method): 46 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5', 'f-m1m2', 'f-m1m3'] 47 if self.mf.data.num_data_sets > 3: 48 self.mf.data.runs.append('f-m2m4') 49 self.mf.data.runs.append('f-m2m5') 50 self.mf.data.runs.append('f-m3m4') 51 self.model_selection = self.mf.modsel.palmer 52 elif match('^Overall$', self.mf.usr_param.method): 53 message = "See the file 'modsel/overall_disc.py' for details.\n" 54 self.mf.file_ops.read_file('op_data', message) 55 self.mf.data.overall_disc.op_data = self.mf.file_ops.open_file(file_name='op_data') 56 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5'] 57 #self.mf.modsel.overall_disc(self.mf) 58 else: 59 raise NameError, "The model-free analysis method is not set correctly. Check self.method in the file 'usr_param.py', quitting program." 60 61 self.mf.data.mfin.default_data() 62 self.goto_stage()

63 64

65 - def ask_stage(self):

66 "User input of stage number." 67 68 print "\n[ Select the stage for model-free analysis ]\n" 69 print "The stages are:" 70 print " Stage 1 (1): Creation of the files for the model-free calculations for models 1 to 5." 71 print " Stage 2 (2): Model selection and creation of a final run." 72 print " Stage 3 (3): Extraction of the data." 73 74 while 1: 75 input = raw_input('> ') 76 valid_stages = ['1', '2', '3'] 77 if input in valid_stages: 78 self.mf.data.stage = input 79 break 80 else: 81 print "Invalid stage number. Choose either 1, 2, or 3." 82 if match('2', self.mf.data.stage): 83 while 1: 84 print "Stage 2 has the following two options for the final run:" 85 print " (a): No optimization of the diffusion tensor." 86 print " (b): Optimization of the diffusion tensor." 87 input = raw_input('> ') 88 valid_stages = ['a', 'b'] 89 if input in valid_stages: 90 self.mf.data.stage = self.mf.data.stage + input 91 break 92 else: 93 print "Invalid option, choose either a or b." 94 95 print "The stage chosen is " + self.mf.data.stage + "\n"

96 97

98 - def close_mf_files(self, dir):

99 "Close the mfin, mfdata, mfmodel, mfpar, and run files, and make the run file executable." 100 101 self.mf.mfin.close() 102 self.mf.mfdata.close() 103 self.mf.mfmodel.close() 104 self.mf.mfpar.close() 105 self.mf.run.close() 106 chmod(dir + '/run', 0777)

107 108

109 - def create_mfdata(self, res, flag='1'):

110 """Create the Modelfree input file mfdata. 111 112 This function is run once for each residue. If the flag variable is set to 0, all data 113 for this residue will be excluded. If the exclude_set variable is given, the data flag 114 corresponding to that set will be set to 0 (Used by the cross-validation method). 115 """ 116 117 mfdata = self.mf.mfdata 118 119 mfdata.write("\nspin " + self.mf.data.relax_data[0][res][1] + "_" + self.mf.data.relax_data[0][res][0] + "\n") 120 for i in range(self.mf.data.num_ri): 121 mfdata.write('%-7s' % self.mf.data.data_types[i]) 122 mfdata.write('%-10s' % self.mf.data.frq_label[self.mf.data.remap_table[i]]) 123 mfdata.write('%20s' % self.mf.data.relax_data[i][res][2]) 124 mfdata.write('%20s' % self.mf.data.relax_data[i][res][3]) 125 mfdata.write(' %-3s\n' % flag)

126 127

128 - def create_mfin(self):

129 "Create the Modelfree input file mfin" 130 131 mfin = self.mf.mfin 132 133 mfin.write("optimization tval\n\n") 134 mfin.write("seed 0\n\n") 135 mfin.write("search grid\n\n") 136 mfin.write("diffusion " + self.mf.data.mfin.diff + " " + self.mf.data.mfin.diff_search + "\n\n") 137 mfin.write("algorithm " + self.mf.data.mfin.algorithm + "\n\n") 138 if match('y', self.mf.data.mfin.sims): 139 mfin.write("simulations " + self.mf.data.mfin.sim_type + " " + self.mf.data.mfin.num_sim) 140 mfin.write(" " + self.mf.data.mfin.trim + "\n\n") 141 elif match('n', self.mf.data.mfin.sims): 142 mfin.write("simulations none\n\n") 143 mfin.write("selection " + self.mf.data.mfin.selection + "\n\n") 144 mfin.write("sim_algorithm " + self.mf.data.mfin.algorithm + "\n\n") 145 mfin.write("fields " + `self.mf.data.num_frq`) 146 for frq in range(self.mf.data.num_frq): 147 mfin.write(" " + `self.mf.data.frq[frq]*1e-6`) 148 mfin.write("\n") 149 # tm. 150 mfin.write('%-7s' % 'tm') 151 mfin.write('%14s' % self.mf.usr_param.tm['val']) 152 mfin.write('%2s' % self.mf.usr_param.tm['flag']) 153 mfin.write('%3s' % self.mf.usr_param.tm['bound']) 154 mfin.write('%5s' % self.mf.usr_param.tm['lower']) 155 mfin.write('%6s' % self.mf.usr_param.tm['upper']) 156 mfin.write('%4s\n' % self.mf.usr_param.tm['steps']) 157 # dratio. 158 mfin.write('%-7s' % 'Dratio') 159 mfin.write('%14s' % self.mf.usr_param.dratio['val']) 160 mfin.write('%2s' % self.mf.usr_param.dratio['flag']) 161 mfin.write('%3s' % self.mf.usr_param.dratio['bound']) 162 mfin.write('%5s' % self.mf.usr_param.dratio['lower']) 163 mfin.write('%6s' % self.mf.usr_param.dratio['upper']) 164 mfin.write('%4s\n' % self.mf.usr_param.dratio['steps']) 165 # theta. 166 mfin.write('%-7s' % 'Theta') 167 mfin.write('%14s' % self.mf.usr_param.theta['val']) 168 mfin.write('%2s' % self.mf.usr_param.theta['flag']) 169 mfin.write('%3s' % self.mf.usr_param.theta['bound']) 170 mfin.write('%5s' % self.mf.usr_param.theta['lower']) 171 mfin.write('%6s' % self.mf.usr_param.theta['upper']) 172 mfin.write('%4s\n' % self.mf.usr_param.theta['steps']) 173 # phi. 174 mfin.write('%-7s' % 'Phi') 175 mfin.write('%14s' % self.mf.usr_param.phi['val']) 176 mfin.write('%2s' % self.mf.usr_param.phi['flag']) 177 mfin.write('%3s' % self.mf.usr_param.phi['bound']) 178 mfin.write('%5s' % self.mf.usr_param.phi['lower']) 179 mfin.write('%6s' % self.mf.usr_param.phi['upper']) 180 mfin.write('%4s\n' % self.mf.usr_param.phi['steps'])

181 182

183 - def create_mfmodel(self, res, md, type='M1'):

184 "Create the M1 or M2 section of the Modelfree input file mfmodel" 185 186 mfmodel = self.mf.mfmodel 187 188 if match('M1', type): 189 mfmodel.write("\nspin " + self.mf.data.relax_data[0][res][1] + "_" + self.mf.data.relax_data[0][res][0] + "\n") 190 else: 191 mfmodel.write("\n") 192 193 # tloc. 194 mfmodel.write('%-3s' % type) 195 mfmodel.write('%-6s' % 'tloc') 196 mfmodel.write('%-6s' % md['tloc']['start']) 197 mfmodel.write('%-4s' % md['tloc']['flag']) 198 mfmodel.write('%-2s' % md['tloc']['bound']) 199 mfmodel.write('%11s' % md['tloc']['lower']) 200 mfmodel.write('%12s' % md['tloc']['upper']) 201 mfmodel.write(' %-4s\n' % md['tloc']['steps']) 202 # Theta. 203 mfmodel.write('%-3s' % type) 204 mfmodel.write('%-6s' % 'Theta') 205 mfmodel.write('%-6s' % md['theta']['start']) 206 mfmodel.write('%-4s' % md['theta']['flag']) 207 mfmodel.write('%-2s' % md['theta']['bound']) 208 mfmodel.write('%11s' % md['theta']['lower']) 209 mfmodel.write('%12s' % md['theta']['upper']) 210 mfmodel.write(' %-4s\n' % md['theta']['steps']) 211 # S2f. 212 mfmodel.write('%-3s' % type) 213 mfmodel.write('%-6s' % 'Sf2') 214 mfmodel.write('%-6s' % md['sf2']['start']) 215 mfmodel.write('%-4s' % md['sf2']['flag']) 216 mfmodel.write('%-2s' % md['sf2']['bound']) 217 mfmodel.write('%11s' % md['sf2']['lower']) 218 mfmodel.write('%12s' % md['sf2']['upper']) 219 mfmodel.write(' %-4s\n' % md['sf2']['steps']) 220 # S2s. 221 mfmodel.write('%-3s' % type) 222 mfmodel.write('%-6s' % 'Ss2') 223 mfmodel.write('%-6s' % md['ss2']['start']) 224 mfmodel.write('%-4s' % md['ss2']['flag']) 225 mfmodel.write('%-2s' % md['ss2']['bound']) 226 mfmodel.write('%11s' % md['ss2']['lower']) 227 mfmodel.write('%12s' % md['ss2']['upper']) 228 mfmodel.write(' %-4s\n' % md['ss2']['steps']) 229 # te. 230 mfmodel.write('%-3s' % type) 231 mfmodel.write('%-6s' % 'te') 232 mfmodel.write('%-6s' % md['te']['start']) 233 mfmodel.write('%-4s' % md['te']['flag']) 234 mfmodel.write('%-2s' % md['te']['bound']) 235 mfmodel.write('%11s' % md['te']['lower']) 236 mfmodel.write('%12s' % md['te']['upper']) 237 mfmodel.write(' %-4s\n' % md['te']['steps']) 238 # Rex. 239 mfmodel.write('%-3s' % type) 240 mfmodel.write('%-6s' % 'Rex') 241 mfmodel.write('%-6s' % md['rex']['start']) 242 mfmodel.write('%-4s' % md['rex']['flag']) 243 mfmodel.write('%-2s' % md['rex']['bound']) 244 mfmodel.write('%11s' % md['rex']['lower']) 245 mfmodel.write('%12s' % md['rex']['upper']) 246 mfmodel.write(' %-4s\n' % md['rex']['steps'])

247 248

249 - def create_mfpar(self, res):

250 "Create the Modelfree input file mfpar" 251 252 mfpar = self.mf.mfpar 253 254 mfpar.write("\nspin " + self.mf.data.relax_data[0][res][1] + "_" + self.mf.data.relax_data[0][res][0] + "\n") 255 256 mfpar.write('%-14s' % "constants") 257 mfpar.write('%-6s' % self.mf.data.relax_data[0][res][0]) 258 mfpar.write('%-7s' % self.mf.usr_param.const['nucleus']) 259 mfpar.write('%-8s' % self.mf.usr_param.const['gamma']) 260 mfpar.write('%-8s' % `self.mf.usr_param.const['rxh']*1e10`) 261 mfpar.write('%-8s\n' % `self.mf.usr_param.const['csa']*1e6`) 262 263 mfpar.write('%-10s' % "vector") 264 mfpar.write('%-4s' % self.mf.usr_param.vector['atom1']) 265 mfpar.write('%-4s\n' % self.mf.usr_param.vector['atom2'])

266 267

268 - def create_run(self, dir):

269 "Create the file 'run' to execute the model-free run" 270 271 self.mf.run.write("modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out") 272 if self.mf.usr_param.diff == 'axial': 273 # Copy the pdb file to the model directory so there are no problems with the *.rotate 274 # file already existing. 275 cmd = 'cp ' + self.mf.usr_param.pdb_full + ' ' + dir 276 system(cmd) 277 self.mf.run.write(" -s " + self.mf.usr_param.pdb_file) 278 self.mf.run.write("\n")

279 280

281 - def extract_mf_data(self):

282 "Extract the model-free results." 283 284 for model in self.mf.data.runs: 285 mfout = self.mf.file_ops.read_file(model + '/mfout') 286 mfout_lines = mfout.readlines() 287 mfout.close() 288 print "Extracting model-free data from " + model + "/mfout." 289 num_res = len(self.mf.data.relax_data[0]) 290 if match('^m', model): 291 self.mf.data.model = self.mf.star.extract(mfout_lines, num_res, self.mf.usr_param.chi2_lim, self.mf.usr_param.ftest_lim, ftest='n') 292 if match('^f', model): 293 self.mf.data.model = self.mf.star.extract(mfout_lines, num_res, self.mf.usr_param.chi2_lim, self.mf.usr_param.ftest_lim, ftest='y')

294 295

296 - def final_run(self):

297 "Creation of the final run. Files are placed in the directory 'final'." 298 299 self.mf.file_ops.mkdir('final') 300 open_mf_files(dir='final') 301 self.create_mfin() 302 303 self.create_run(dir='final') 304 for res in range(len(self.mf.data.relax_data[0])): 305 if match('0', self.mf.data.results[res]['model']): 306 model = 'none' 307 elif match('2+3', self.mf.data.results[res]['model']): 308 model = 'none' 309 elif match('4+5', self.mf.data.results[res]['model']): 310 model = 'none' 311 elif match('^1', self.mf.data.results[res]['model']): 312 model = "m1" 313 else: 314 model = 'm' + self.mf.data.results[res]['model'] 315 self.set_run_flags(model) 316 # Mfdata. 317 if match('none', model): 318 self.create_mfdata(res, flag='0') 319 else: 320 self.create_mfdata(res, flag='1') 321 # Mfmodel. 322 self.create_mfmodel(res, self.mf.usr_param.md1, type='M1') 323 # Mfpar. 324 self.create_mfpar(res) 325 self.close_mf_files(dir='final')

326 327

328 - def goto_stage(self):

329 if match('1', self.mf.data.stage): 330 print "\n[ Stage 1 ]\n" 331 self.set_vars_stage_initial() 332 if match('^CV$', self.mf.usr_param.method): 333 self.stage_initial_cv() 334 else: 335 self.stage_initial() 336 print "\n[ End of stage 1 ]\n\n" 337 338 if match('^2', self.mf.data.stage): 339 print "\n[ Stage 2 ]\n" 340 self.set_vars_stage_selection() 341 self.stage_selection() 342 if match('2a', self.mf.data.stage): 343 self.final_run() 344 if match('2b', self.mf.data.stage): 345 if match('isotropic', self.mf.data.mfin.diff): 346 self.mf.data.mfin.algorithm = 'brent' 347 self.mf.data.mfin.diff_search = 'grid' 348 elif match('axial', self.mf.data.mfin.diff): 349 self.mf.data.mfin.algorithm = 'powell' 350 self.final_run() 351 print "\n[ End of stage 2 ]\n\n" 352 353 if match('3', self.mf.data.stage): 354 print "\n[ Stage 3 ]\n" 355 self.stage_final() 356 print "\n[ End of stage 3 ]\n\n"

357 358

359 - def open_mf_files(self, dir):

360 "Open the mfin, mfdata, mfmodel, mfpar, and run files for writing." 361 362 self.mf.mfin = open(dir + '/mfin', 'w') 363 self.mf.mfdata = open(dir + '/mfdata', 'w') 364 self.mf.mfmodel = open(dir + '/mfmodel', 'w') 365 self.mf.mfpar = open(dir + '/mfpar', 'w') 366 self.mf.run = open(dir + '/run', 'w')

367 368

369 - def set_run_flags(self, model):

370 "Reset, and then set the flags in self.mf.usr_param.md1 and md2." 371 372 self.mf.usr_param.md1['sf2']['flag'] = '0' 373 self.mf.usr_param.md1['ss2']['flag'] = '0' 374 self.mf.usr_param.md1['te']['flag'] = '0' 375 self.mf.usr_param.md1['rex']['flag'] = '0' 376 377 self.mf.usr_param.md2['sf2']['flag'] = '0' 378 self.mf.usr_param.md2['ss2']['flag'] = '0' 379 self.mf.usr_param.md2['te']['flag'] = '0' 380 self.mf.usr_param.md2['rex']['flag'] = '0' 381 382 # Normal runs. 383 if model == "m1": 384 self.mf.usr_param.md1['ss2']['flag'] = '1' 385 if model == "m2": 386 self.mf.usr_param.md1['ss2']['flag'] = '1' 387 self.mf.usr_param.md1['te']['flag'] = '1' 388 if model == "m3": 389 self.mf.usr_param.md1['ss2']['flag'] = '1' 390 self.mf.usr_param.md1['rex']['flag'] = '1' 391 if model == "m4": 392 self.mf.usr_param.md1['ss2']['flag'] = '1' 393 self.mf.usr_param.md1['te']['flag'] = '1' 394 self.mf.usr_param.md1['rex']['flag'] = '1' 395 if model == "m5": 396 self.mf.usr_param.md1['sf2']['flag'] = '1' 397 self.mf.usr_param.md1['ss2']['flag'] = '1' 398 self.mf.usr_param.md1['te']['flag'] = '1' 399 400 # F-tests. 401 if model == "f-m1m2": 402 self.mf.usr_param.md1['ss2']['flag'] = '1' 403 self.mf.usr_param.md2['ss2']['flag'] = '1' 404 self.mf.usr_param.md2['te']['flag'] = '1' 405 if model == "f-m1m3": 406 self.mf.usr_param.md1['ss2']['flag'] = '1' 407 self.mf.usr_param.md2['ss2']['flag'] = '1' 408 self.mf.usr_param.md2['rex']['flag'] = '1' 409 if model == "f-m1m4": 410 self.mf.usr_param.md1['ss2']['flag'] = '1' 411 self.mf.usr_param.md2['ss2']['flag'] = '1' 412 self.mf.usr_param.md2['te']['flag'] = '1' 413 self.mf.usr_param.md2['rex']['flag'] = '1' 414 if model == "f-m1m5": 415 self.mf.usr_param.md1['ss2']['flag'] = '1' 416 self.mf.usr_param.md2['ss2']['flag'] = '1' 417 self.mf.usr_param.md2['sf2']['flag'] = '1' 418 self.mf.usr_param.md2['te']['flag'] = '1' 419 if model == "f-m2m4": 420 self.mf.usr_param.md1['ss2']['flag'] = '1' 421 self.mf.usr_param.md1['te']['flag'] = '1' 422 self.mf.usr_param.md2['ss2']['flag'] = '1' 423 self.mf.usr_param.md2['te']['flag'] = '1' 424 self.mf.usr_param.md2['rex']['flag'] = '1' 425 if model == "f-m2m5": 426 self.mf.usr_param.md1['ss2']['flag'] = '1' 427 self.mf.usr_param.md1['te']['flag'] = '1' 428 self.mf.usr_param.md2['ss2']['flag'] = '1' 429 self.mf.usr_param.md2['sf2']['flag'] = '1' 430 self.mf.usr_param.md2['te']['flag'] = '1' 431 if model == "f-m3m4": 432 self.mf.usr_param.md1['ss2']['flag'] = '1' 433 self.mf.usr_param.md1['rex']['flag'] = '1' 434 self.mf.usr_param.md2['ss2']['flag'] = '1' 435 self.mf.usr_param.md2['te']['flag'] = '1' 436 self.mf.usr_param.md2['rex']['flag'] = '1'

437 438

439 - def stage_final(self):

440 raise NameError, "Stage 3 not implemented yet.\n"

441 442

443 - def stage_initial(self):

444 "Creation of the files for the Modelfree calculations for the models in self.mf.data.runs." 445 446 for model in self.mf.data.runs: 447 if match('^m', model): 448 print "Creating input files for model " + model 449 if self.mf.debug: 450 self.mf.log.write("\n\n<<< Model " + model + " >>>\n\n") 451 elif match('^f', model): 452 print "Creating input files for the F-test " + model 453 if self.mf.debug: 454 self.mf.log.write("\n\n<<< F-test " + model + " >>>\n\n") 455 else: 456 raise NameError, "The run '" + model + "'does not start with an m or f, quitting program!\n\n" 457 self.mf.file_ops.mkdir(dir=model) 458 self.open_mf_files(dir=model) 459 self.set_run_flags(model) 460 461 if self.mf.debug: 462 self.log_params('M1', self.mf.usr_param.md1) 463 self.log_params('M2', self.mf.usr_param.md2) 464 465 if match('^m', model): 466 self.mf.data.mfin.selection = 'none' 467 self.create_mfin() 468 elif match('^f', model): 469 self.mf.data.mfin.selection = 'ftest' 470 self.create_mfin() 471 self.create_run(dir=model) 472 for res in range(len(self.mf.data.relax_data[0])): 473 # Mfdata. 474 self.create_mfdata(res) 475 # Mfmodel. 476 self.create_mfmodel(res, self.mf.usr_param.md1, type='M1') 477 if match('^f', model): 478 self.create_mfmodel(res, self.mf.usr_param.md2, type='M2') 479 # Mfpar. 480 self.create_mfpar(res) 481 self.close_mf_files(dir=model)

482 483

484 - def stage_initial_cv(self):

485 "Creation of the files for the Modelfree calculations for the models in self.mf.data.runs." 486 487 for model in self.mf.data.runs: 488 print "Creating input files for model " + model 489 490 if self.mf.debug: 491 self.mf.log.write("\n\n<<< Model " + model + " >>>\n\n") 492 493 self.mf.file_ops.mkdir(dir=model) 494 self.set_run_flags(model) 495 496 if self.mf.debug: 497 self.log_params('M1', self.mf.usr_param.md1) 498 self.log_params('M2', self.mf.usr_param.md2) 499 500 for i in range(self.mf.data.num_ri): 501 cv_dir = model + "/" + model + "-" + self.mf.data.frq_label[self.mf.data.remap_table[i]] + "_" + self.mf.data.data_types[i] 502 self.mf.file_ops.mkdir(dir=cv_dir) 503 open_mf_files(dir=cv_dir) 504 self.mf.data.mfin.selection = 'none' 505 self.create_mfin() 506 self.create_run(dir=model) 507 for res in range(len(self.mf.data.relax_data[0])): 508 # Mfdata. 509 self.create_mfdata(res, i) 510 # Mfmodel. 511 self.create_mfmodel(res, self.mf.usr_param.md1, type='M1') 512 # Mfpar. 513 self.create_mfpar(res) 514 self.close_mf_files(dir=cv_dir)

515 516

517 - def set_vars_stage_initial(self):

518 "Set the options for the initial runs." 519 520 self.mf.data.mfin.sims = 'n'

521 522

523 - def set_vars_stage_selection(self):

524 "Set the options for the final run." 525 526 self.mf.data.mfin.sims = 'y'

Source Code for Module palmer