prompt.value

36 - def __init__(self, relax):

37 # Help. 38 self.__relax_help__ = \ 39 """Class for setting data values.""" 40 41 # Add the generic help string. 42 self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help 43 44 # Place relax in the class namespace. 45 self.__relax__ = relax

46 47

48 - def copy(self, run1=None, run2=None, param=None):

49 """Function for copying residue specific data values from run1 to run2. 50 51 Keyword Arguments 52 ~~~~~~~~~~~~~~~~~ 53 54 run1: The name of the run to copy from. 55 56 run2: The name of the run to copy to. 57 58 param: The parameter to copy. 59 60 61 Description 62 ~~~~~~~~~~~ 63 64 Only one parameter may be selected, therefore the 'param' argument should be a string. 65 66 If this function is used to change values of previously minimised runs, then the 67 minimisation statistics (chi-squared value, iteration count, function count, gradient count, 68 and Hessian count) will be reset to None. 69 70 71 Examples 72 ~~~~~~~~ 73 74 To copy the CSA values from the run 'm1' to 'm2', type: 75 76 relax> value.copy('m1', 'm2', 'CSA') 77 """ 78 79 # Function intro text. 80 if self.__relax__.interpreter.intro: 81 text = sys.ps3 + "value.copy(" 82 text = text + "run1=" + `run1` 83 text = text + ", run2=" + `run2` 84 text = text + ", param=" + `param` + ")" 85 print text 86 87 # The run1 argument. 88 if type(run1) != str: 89 raise RelaxStrError, ('run1', run1) 90 91 # The run2 argument. 92 if type(run2) != str: 93 raise RelaxStrError, ('run2', run2) 94 95 # The parameter. 96 if type(param) != str: 97 raise RelaxStrError, ('parameter', param) 98 99 # Execute the functional code. 100 self.__relax__.generic.value.copy(run1=run1, run2=run2, param=param)

101 102

103 - def display(self, run=None, param=None):

104 """Function for displaying residue specific data values. 105 106 Keyword Arguments 107 ~~~~~~~~~~~~~~~~~ 108 109 run: The name of the run. 110 111 param: The parameter to display. 112 113 114 Description 115 ~~~~~~~~~~~ 116 117 Only one parameter may be selected, therefore the 'param' argument should be a string. 118 119 120 Examples 121 ~~~~~~~~ 122 123 To show all CSA values for the run 'm1', type: 124 125 relax> value.display('m1', 'CSA') 126 """ 127 128 # Function intro text. 129 if self.__relax__.interpreter.intro: 130 text = sys.ps3 + "value.display(" 131 text = text + "run=" + `run` 132 text = text + ", param=" + `param` + ")" 133 print text 134 135 # The run name. 136 if type(run) != str: 137 raise RelaxStrError, ('run', run) 138 139 # The parameter. 140 if type(param) != str: 141 raise RelaxStrError, ('parameter', param) 142 143 # Execute the functional code. 144 self.__relax__.generic.value.display(run=run, param=param)

145 146

147 - def read(self, run=None, param=None, scaling=1.0, file=None, num_col=0, name_col=1, data_col=2, error_col=3, sep=None):

148 """Function for reading residue specific data values from a file. 149 150 Keyword Arguments 151 ~~~~~~~~~~~~~~~~~ 152 153 run: The name of the run. 154 155 param: The parameter. 156 157 scaling: The factor to scale parameters by. 158 159 file: The name of the file containing the relaxation data. 160 161 num_col: The residue number column (the default is 0, ie the first column). 162 163 name_col: The residue name column (the default is 1). 164 165 data_col: The relaxation data column (the default is 2). 166 167 error_col: The experimental error column (the default is 3). 168 169 sep: The column separator (the default is white space). 170 171 172 Description 173 ~~~~~~~~~~~ 174 175 Only one parameter may be selected, therefore the 'param' argument should be a string. If 176 the file only contains values and no errors, set the error column argument to None. 177 178 If this function is used to change values of previously minimised runs, then the 179 minimisation statistics (chi-squared value, iteration count, function count, gradient count, 180 and Hessian count) will be reset to None. 181 182 183 Examples 184 ~~~~~~~~ 185 186 To load CSA values for the run 'm1' from the file 'csa_values' in the directory 'data', type 187 any of the following: 188 189 relax> value.read('m1', 'CSA', 'data/csa_value') 190 relax> value.read('m1', 'CSA', 'data/csa_value', 0, 1, 2, 3, None, 1) 191 relax> value.read(run='m1', param='CSA', file='data/csa_value', num_col=0, name_col=1, 192 data_col=2, error_col=3, sep=None) 193 """ 194 195 # Function intro text. 196 if self.__relax__.interpreter.intro: 197 text = sys.ps3 + "value.read(" 198 text = text + "run=" + `run` 199 text = text + ", param=" + `param` 200 text = text + ", scaling=" + `scaling` 201 text = text + ", file=" + `file` 202 text = text + ", num_col=" + `num_col` 203 text = text + ", name_col=" + `name_col` 204 text = text + ", data_col=" + `data_col` 205 text = text + ", error_col=" + `error_col` 206 text = text + ", sep=" + `sep` + ")" 207 print text 208 209 # The run name. 210 if type(run) != str: 211 raise RelaxStrError, ('run', run) 212 213 # The parameter. 214 if type(param) != str: 215 raise RelaxStrError, ('parameter', param) 216 217 # The scaling factor. 218 if type(scaling) != float: 219 raise RelaxFloatError, ('scaling', scaling) 220 221 # The file name. 222 if type(file) != str: 223 raise RelaxStrError, ('file', file) 224 225 # The number column. 226 if type(num_col) != int: 227 raise RelaxIntError, ('residue number column', num_col) 228 229 # The name column. 230 if name_col != None and type(name_col) != int: 231 raise RelaxNoneIntError, ('residue name column', name_col) 232 233 # The data column. 234 if type(data_col) != int: 235 raise RelaxIntError, ('data column', data_col) 236 237 # The error column. 238 if error_col != None and type(error_col) != int: 239 raise RelaxNoneIntError, ('error column', error_col) 240 241 # Column separator. 242 if sep != None and type(sep) != str: 243 raise RelaxNoneStrError, ('column separator', sep) 244 245 # Execute the functional code. 246 self.__relax__.generic.value.read(run=run, param=param, scaling=scaling, file=file, num_col=num_col, name_col=name_col, data_col=data_col, error_col=error_col, sep=sep)

247 248

249 - def set(self, run=None, value=None, param=None, res_num=None, res_name=None):

250 """Function for setting residue specific data values. 251 252 Keyword arguments 253 ~~~~~~~~~~~~~~~~~ 254 255 run: The run to assign the values to. 256 257 value: The value(s). 258 259 param: The parameter(s). 260 261 res_num: The residue number. 262 263 res_name: The residue name. 264 265 266 Description 267 ~~~~~~~~~~~ 268 269 If this function is used to change values of previously minimised runs, then the 270 minimisation statistics (chi-squared value, iteration count, function count, gradient count, 271 and Hessian count) will be reset to None. 272 273 274 The value argument can be None, a single value, or an array of values while the parameter 275 argument can be None, a string, or array of strings. The choice of which combination 276 determines the behaviour of this function. The following table describes what occurs in 277 each instance. The Value column refers to the 'value' argument while the Param column refers 278 to the 'param' argument. In these columns, 'None' corresponds to None, '1' corresponds 279 to either a single value or single string, and 'n' corresponds to either an array of values 280 or an array of strings. 281 282 ____________________________________________________________________________________________ 283 | | | | 284 | Value | Param | Description | 285 |_______|_______|__________________________________________________________________________| 286 | | | | 287 | None | None | This case is used to set the model parameters prior to minimisation or | 288 | | | calculation. The model parameters are set to the default values. | 289 | | | | 290 | 1 | None | Invalid combination. | 291 | | | | 292 | n | None | This case is used to set the model parameters prior to minimisation or | 293 | | | calculation. The length of the value array must be equal to the number | 294 | | | of model parameters for an individual residue. The parameters will be | 295 | | | set to the corresponding number. | 296 | | | | 297 | None | 1 | The parameter matching the string will be set to the default value. | 298 | | | | 299 | 1 | 1 | The parameter matching the string will be set to the supplied number. | 300 | | | | 301 | n | 1 | Invalid combination. | 302 | | | | 303 | None | n | Each parameter matching the strings will be set to the default values. | 304 | | | | 305 | 1 | n | Each parameter matching the strings will be set to the supplied number. | 306 | | | | 307 | n | n | Each parameter matching the strings will be set to the corresponding | 308 | | | number. Both arrays must be of equal length. | 309 |_______|_______|__________________________________________________________________________| 310 311 312 Residue number and name argument 313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 314 315 If the 'res_num' and 'res_name' arguments are left as the defaults of None, then the 316 function will be applied to all residues. Otherwise the residue number can be set to either 317 an integer for selecting a single residue or a python regular expression string for 318 selecting multiple residues. The residue name argument must be a string and can use regular 319 expression as well. If the data is global non-residue specific data, such as diffusion 320 tensor parameters, supplying the residue number and name will terminate the program with an 321 error. 322 323 324 Examples 325 ~~~~~~~~ 326 327 To set the parameter values for the run 'test' to the default values, for all residues, 328 type: 329 330 relax> value.set('test') 331 332 333 To set the parameter values of residue 10, which is the model-free run 'm4' and has the 334 parameters {S2, te, Rex}, the following can be used. Rex term is the value for the first 335 given field strength. 336 337 relax> value.set('m4', [0.97, 2.048*1e-9, 0.149], res_num=10) 338 relax> value.set('m4', value=[0.97, 2.048*1e-9, 0.149], res_num=10) 339 340 341 To set the CSA value for the model-free run 'tm3' to the default value, type: 342 343 relax> value.set('tm3', param='csa') 344 345 346 To set the CSA value of all residues in the reduced spectral density mapping run '600MHz' to 347 -172 ppm, type: 348 349 relax> value.set('600MHz', -172 * 1e-6, 'csa') 350 relax> value.set('600MHz', value=-172 * 1e-6, param='csa') 351 352 353 To set the NH bond length of all residues in the model-free run 'm5' to 1.02 Angstroms, 354 type: 355 356 relax> value.set('m5', 1.02 * 1e-10, 'bond_length') 357 relax> value.set('m5', value=1.02 * 1e-10, param='r') 358 359 360 To set both the bond length and the CSA value for the run 'new' to the default values, type: 361 362 relax> value.set('new', param=['bond length', 'csa']) 363 364 365 To set both tf and ts in the model-free run 'm6' to 100 ps, type: 366 367 relax> value.set('m6', 100e-12, ['tf', 'ts']) 368 relax> value.set('m6', value=100e-12, param=['tf', 'ts']) 369 370 371 To set the S2 and te parameter values for model-free run 'm4' which has the parameters 372 {S2, te, Rex} to 0.56 and 13 ps, type: 373 374 relax> value.set('m4', [0.56, 13e-12], ['S2', 'te'], 10) 375 relax> value.set('m4', value=[0.56, 13e-12], param=['S2', 'te'], res_num=10) 376 relax> value.set(run='m4', value=[0.56, 13e-12], param=['S2', 'te'], res_num=10) 377 """ 378 379 # Function intro text. 380 if self.__relax__.interpreter.intro: 381 text = sys.ps3 + "value.set(" 382 text = text + "run=" + `run` 383 text = text + ", value=" + `value` 384 text = text + ", param=" + `param` 385 text = text + ", res_num=" + `res_num` 386 text = text + ", res_name=" + `res_name` + ")" 387 print text 388 389 # The run name. 390 if type(run) != str: 391 raise RelaxStrError, ('run', run) 392 393 # The value. 394 if value != None and type(value) != float and type(value) != int and type(value) != list: 395 raise RelaxNoneFloatListError, ('value', value) 396 if type(value) == list: 397 for i in xrange(len(value)): 398 if type(value[i]) != float and type(value[i]) != int: 399 raise RelaxListFloatError, ('value', value) 400 401 # The parameter. 402 if param != None and type(param) != str and type(param) != list: 403 raise RelaxNoneStrListError, ('parameter', param) 404 if type(param) == list: 405 for i in xrange(len(param)): 406 if type(param[i]) != str: 407 raise RelaxListStrError, ('parameter', param) 408 409 # The invalid combination of a single value and no param argument. 410 if (type(value) == float or type(value) == int) and param == None: 411 raise RelaxError, "Invalid value and parameter argument combination, for details by type 'help(value.set)'" 412 413 # The invalid combination of an array of values and a single param string. 414 if type(value) == list and type(param) == str: 415 raise RelaxError, "Invalid value and parameter argument combination, for details by type 'help(value.set)'" 416 417 # Value array and parameter array of equal length. 418 if type(value) == list and type(param) == list and len(value) != len(param): 419 raise RelaxError, "Both the value array and parameter array must be of equal length." 420 421 # Residue number. 422 if res_num != None and type(res_num) != int and type(res_num) != str: 423 raise RelaxNoneIntStrError, ('residue number', res_num) 424 425 # Residue name. 426 if res_name != None and type(res_name) != str: 427 raise RelaxNoneStrError, ('residue name', res_name) 428 429 # Execute the functional code. 430 self.__relax__.generic.value.set(run=run, value=value, param=param, res_num=res_num, res_name=res_name)

431 432

433 - def write(self, run=None, param=None, file=None, dir=None, force=0):

434 """Function for writing residue specific data values to a file. 435 436 Keyword Arguments 437 ~~~~~~~~~~~~~~~~~ 438 439 run: The name of the run. 440 441 param: The parameter. 442 443 file: The name of the file. 444 445 dir: The directory name. 446 447 force: A flag which, if set to 1, will cause the file to be overwritten. 448 449 450 Description 451 ~~~~~~~~~~~ 452 453 If no directory name is given, the file will be placed in the current working directory. 454 455 The parameter argument should be a string. 456 457 458 Examples 459 ~~~~~~~~ 460 461 To write the CSA values for the run 'm1' to the file 'csa.txt', type: 462 463 relax> value.write('m1', 'CSA', 'csa.txt') 464 relax> value.write(run='m1', param='CSA', file='csa.txt') 465 466 467 To write the NOE values from the run 'noe' to the file 'noe', type: 468 469 relax> value.write('noe', 'noe', 'noe.out') 470 relax> value.write('noe', param='noe', file='noe.out') 471 relax> value.write(run='noe', param='noe', file='noe.out') 472 relax> value.write(run='noe', param='noe', file='noe.out', force=1) 473 """ 474 475 # Function intro text. 476 if self.__relax__.interpreter.intro: 477 text = sys.ps3 + "value.write(" 478 text = text + "run=" + `run` 479 text = text + ", param=" + `param` 480 text = text + ", file=" + `file` 481 text = text + ", dir=" + `dir` 482 text = text + ", force=" + `force` + ")" 483 print text 484 485 # The run name. 486 if type(run) != str: 487 raise RelaxStrError, ('run', run) 488 489 # The parameter. 490 if type(param) != str: 491 raise RelaxStrError, ('parameter', param) 492 493 # File. 494 if type(file) != str: 495 raise RelaxStrError, ('file name', file) 496 497 # Directory. 498 if dir != None and type(dir) != str: 499 raise RelaxNoneStrError, ('directory name', dir) 500 501 # The force flag. 502 if type(force) != int or (force != 0 and force != 1): 503 raise RelaxBinError, ('force flag', force) 504 505 # Execute the functional code. 506 self.__relax__.generic.value.write(run=run, param=param, file=file, dir=dir, force=force)

507 508 509 # Docstring modification. 510 ######################### 511 512 # Copy function. 513 copy.__doc__ = copy.__doc__ + "\n\n" + regexp_doc() + "\n" 514 copy.__doc__ = copy.__doc__ + Consistency_tests.set.__doc__ + "\n" 515 copy.__doc__ = copy.__doc__ + Consistency_tests.return_data_name.__doc__ + "\n" 516 copy.__doc__ = copy.__doc__ + Model_free.set_doc.__doc__ + "\n\n" 517 copy.__doc__ = copy.__doc__ + Model_free.return_data_name.__doc__ + "\n" 518 copy.__doc__ = copy.__doc__ + Jw_mapping.set.__doc__ + "\n" 519 copy.__doc__ = copy.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n" 520 copy.__doc__ = copy.__doc__ + Relax_fit.set_doc.__doc__ + "\n" 521 copy.__doc__ = copy.__doc__ + Relax_fit.return_data_name.__doc__ + "\n" 522 523 # Display function. 524 display.__doc__ = display.__doc__ + "\n\n" + regexp_doc() + "\n" 525 display.__doc__ = display.__doc__ + Consistency_tests.return_data_name.__doc__ + "\n" 526 display.__doc__ = display.__doc__ + Model_free.return_data_name.__doc__ + "\n\n" 527 display.__doc__ = display.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n" 528 display.__doc__ = display.__doc__ + Relax_fit.return_data_name.__doc__ + "\n" 529 530 # Read function. 531 read.__doc__ = read.__doc__ + "\n\n" + regexp_doc() + "\n" 532 read.__doc__ = read.__doc__ + Consistency_tests.set.__doc__ + "\n" 533 read.__doc__ = read.__doc__ + Consistency_tests.return_data_name.__doc__ + "\n" 534 read.__doc__ = read.__doc__ + Model_free.set_doc.__doc__ + "\n\n" 535 read.__doc__ = read.__doc__ + Model_free.return_data_name.__doc__ + "\n" 536 read.__doc__ = read.__doc__ + Jw_mapping.set.__doc__ + "\n" 537 read.__doc__ = read.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n" 538 read.__doc__ = read.__doc__ + Relax_fit.set_doc.__doc__ + "\n" 539 read.__doc__ = read.__doc__ + Relax_fit.return_data_name.__doc__ + "\n" 540 541 # Set function. 542 set.__doc__ = set.__doc__ + "\n\n" + regexp_doc() + "\n" 543 set.__doc__ = set.__doc__ + Consistency_tests.set.__doc__ + "\n" 544 set.__doc__ = set.__doc__ + Consistency_tests.return_data_name.__doc__ + "\n" 545 set.__doc__ = set.__doc__ + Consistency_tests.default_value.__doc__ + "\n" 546 set.__doc__ = set.__doc__ + Model_free.set_doc.__doc__ + "\n" 547 set.__doc__ = set.__doc__ + Model_free.return_data_name.__doc__ + "\n" 548 set.__doc__ = set.__doc__ + Model_free.default_value.__doc__ + "\n\n" 549 set.__doc__ = set.__doc__ + Jw_mapping.set.__doc__ + "\n" 550 set.__doc__ = set.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n" 551 set.__doc__ = set.__doc__ + Jw_mapping.default_value.__doc__ + "\n" 552 set.__doc__ = set.__doc__ + Diffusion_tensor.set.__doc__ + "\n" 553 set.__doc__ = set.__doc__ + Diffusion_tensor.return_data_name.__doc__ + "\n" 554 set.__doc__ = set.__doc__ + Diffusion_tensor.default_value.__doc__ + "\n\n" 555 set.__doc__ = set.__doc__ + Relax_fit.set_doc.__doc__ + "\n" 556 set.__doc__ = set.__doc__ + Relax_fit.return_data_name.__doc__ + "\n" 557 set.__doc__ = set.__doc__ + Relax_fit.default_value.__doc__ + "\n\n" 558 559 # Write function. 560 write.__doc__ = write.__doc__ + "\n\n" + regexp_doc() + "\n" 561 write.__doc__ = write.__doc__ + Consistency_tests.return_data_name.__doc__ + "\n\n" 562 write.__doc__ = write.__doc__ + Model_free.return_data_name.__doc__ + "\n\n" 563 write.__doc__ = write.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n\n" 564 write.__doc__ = write.__doc__ + Noe.return_data_name.__doc__ + "\n" 565 write.__doc__ = write.__doc__ + Relax_fit.return_data_name.__doc__ + "\n"

Source Code for Module prompt.value