Source Code for Module lib.errors

   1  ############################################################################### 
   2  #                                                                             # 
   3  # Copyright (C) 2003-2013 Edward d'Auvergne                                   # 
   4  # Copyright (C) 2014 Troels E. Linnet                                         # 
   5  #                                                                             # 
   6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
   7  #                                                                             # 
   8  # This program is free software: you can redistribute it and/or modify        # 
   9  # it under the terms of the GNU General Public License as published by        # 
  10  # the Free Software Foundation, either version 3 of the License, or           # 
  11  # (at your option) any later version.                                         # 
  12  #                                                                             # 
  13  # This program is distributed in the hope that it will be useful,             # 
  14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
  15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
  16  # GNU General Public License for more details.                                # 
  17  #                                                                             # 
  18  # You should have received a copy of the GNU General Public License           # 
  19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
  20  #                                                                             # 
  21  ############################################################################### 
  22   
  23  # Module docstring. 
  24  """Module containing all of the RelaxError objects.""" 
  25   
  26   
  27  # Python module imports. 
  28  try: 
  29      from bz2 import BZ2File 
  30      bz2 = True 
  31  except ImportError: 
  32      bz2 = False 
  33  from re import match 
  34  import sys 
  35  import time 
  36   
  37  # relax module imports. 
  38  from compat import pickle 
  39  from lib import ansi 
  40   
  41   
  42  # Text variables. 
  43  BIN = 'a binary number (0 or 1)' 
  44  BOOL = 'a Boolean (True or False)' 
  45  INT = 'an integer' 
  46  FILE = 'a file object' 
  47  FLOAT = 'a floating point number' 
  48  FUNC = 'a function' 
  49  LIST = 'a list' 
  50  LIST_FLOAT = 'a list of floating point numbers' 
  51  LIST_INT = 'a list of integers' 
  52  LIST_NUM = 'a list of numbers' 
  53  LIST_STR = 'a list of strings' 
  54  LIST_VAL = 'a list of values' 
  55  MATRIX_FLOAT = 'a matrix of floating point numbers' 
  56  NONE = 'None' 
  57  NUM = 'a number' 
  58  TUPLE = 'a tuple' 
  59  TUPLE_FLOAT = 'a tuple of floating point numbers' 
  60  TUPLE_INT = 'a tuple of integers' 
  61  TUPLE_NUM = 'a tuple of numbers' 
  62  TUPLE_STR = 'a tuple of strings' 
  63  STR = 'a string' 
  64  VAL = 'a value' 
  65   
  66   
  67 -def save_state(): 
  68      """Save the program state, for debugging purposes.""" 
  69   
  70      # relax data store singleton import.  Must be done here! 
  71      try: 
  72          from data_store import Relax_data_store; ds = Relax_data_store() 
  73   
  74      # Ok, this is not relax so don't do anything! 
  75      except ImportError: 
  76          return 
  77   
  78      # Append the date and time to the save file. 
  79      now = time.localtime() 
  80      file_name = "relax_state_%i%02i%02i_%02i%02i%02i" % (now[0], now[1], now[2], now[3], now[4], now[5]) 
  81   
  82      # Open the file for writing. 
  83      if bz2: 
  84          sys.stderr.write("\n\nStoring the relax state in the file '%s.bz2'.\n\n\n" % file_name) 
  85          file = BZ2File(file_name+'.bz2', 'w') 
  86      else: 
  87          sys.stderr.write("\n\nStoring the relax state in the file '%s'.\n\n\n" % file_name) 
  88          file = open(file_name, 'w') 
  89   
  90      # Pickle the data class and write it to file 
  91      pickle.dump(ds, file, 1) 
  92   
  93      # Close the file. 
  94      file.close() 
  95   
  96   
  97 -def list_to_text(data): 
  98      """Convert the given Python list to a text representation. 
  99   
 100      @param data:    The list of Python objects. 
 101      @type data:     list 
 102      @return:        The English text version of the list. 
 103      @rtype:         str 
 104      """ 
 105   
 106      # Initialise. 
 107      text = '' 
 108   
 109      # Loop over the elements, adding the to the list. 
 110      for i in range(len(data)): 
 111          # Add the text. 
 112          text += repr(data[i]) 
 113   
 114          # Comma separators. 
 115          if i < len(data) - 2: 
 116              text += ', ' 
 117   
 118          # Last separator. 
 119          if i == len(data) - 2: 
 120              text += ' and ' 
 121   
 122      # Return the text. 
 123      return text 
 124   
 125   
 126  # Base class for all errors. 
 127  ############################ 
 128   
 129 -class BaseError(Exception): 
 130      """The base class for all RelaxErrors.""" 
 131   
 132 -    def __str__(self): 
 133          """Modify the behaviour of the error system.""" 
 134   
 135          # Save the state if the escalate flag is turned on. 
 136          from status import Status; status = Status() 
 137          if status.escalate: 
 138              save_state() 
 139   
 140          # Modify the error message to include 'RelaxError' at the start (using coloured text if a TTY). 
 141          if ansi.enable_control_chars(stream=2): 
 142              return ("%sRelaxError: %s%s\n" % (ansi.relax_error, self.text, ansi.end)) 
 143          else: 
 144              return ("RelaxError: %s\n" % self.text) 
 145   
 146   
 147 -class BaseArgError(BaseError): 
 148      """The base class for all the argument related RelaxErrors.""" 
 149   
 150      # The allowed simple types. 
 151      simple_types = [] 
 152   
 153      # The allowed list types (anything with a size). 
 154      list_types = [] 
 155   
 156   
 157 -    def __init__(self, name, value, size=None): 
 158          """A default initialisation and error message formatting method.""" 
 159   
 160          # The initial part of the message. 
 161          self.text = "The %s argument '%s' must be " % (name, value) 
 162   
 163          # Append the fixed size to the list types. 
 164          if size != None: 
 165              for i in range(len(self.list_types)): 
 166                  self.list_types[i] = self.list_types[i] + " of size %s" % repr(size) 
 167   
 168          # Combine all elements. 
 169          all_types = self.simple_types + self.list_types 
 170   
 171          # Multiple elements. 
 172          if len(all_types) > 1: 
 173              self.text = self.text + "either " 
 174   
 175          # Generate the list string. 
 176          for i in range(len(all_types)): 
 177              # Separators. 
 178              if i > 0: 
 179                  # Or. 
 180                  if i == len(all_types)-1: 
 181                      self.text = self.text + ", or " 
 182   
 183                  # Commas. 
 184                  else: 
 185                      self.text = self.text + ", " 
 186   
 187              # Append the text. 
 188              self.text = self.text + all_types[i] 
 189   
 190          # The end. 
 191          self.text = self.text + "." 
 192   
 193   
 194  # Standard errors. 
 195  ################## 
 196   
 197 -class RelaxError(BaseError): 
 198 -    def __init__(self, text): 
 199          self.text = text 
 200   
 201   
 202  # Module import errors. 
 203  ####################### 
 204   
 205 -class RelaxNoModuleInstallError(BaseError): 
 206 -    def __init__(self, desc, name): 
 207          self.text = "The %s module '%s' cannot be found.  Please check that it is installed." % (desc, name) 
 208   
 209   
 210  # Fault. 
 211  ######## 
 212   
 213 -class RelaxFault(BaseError): 
 214 -    def __init__(self): 
 215          self.text = "Impossible to be here, please re-run relax with the '--debug' flag and summit a bug report at https://web.archive.org/web/https://gna.org/projects/relax/." 
 216   
 217 -    def __str__(self): 
 218          # Save the program state, no matter what. 
 219          save_state() 
 220   
 221          # Modify the error message to include 'RelaxError' at the start. 
 222          return ("RelaxError: " + self.text + "\n") 
 223   
 224   
 225  # Code implementation errors. 
 226  ############################# 
 227   
 228  # Not implemented yet. 
 229 -class RelaxImplementError(BaseError): 
 230 -    def __init__(self, fn_name=None): 
 231          if fn_name: 
 232              self.text = "The %s function has not yet been implemented for the current data pipe." % fn_name 
 233          else: 
 234              self.text = "This has not yet been implemented for the current data pipe." 
 235   
 236   
 237  # Program errors. 
 238  ################# 
 239   
 240  # Cannot locate the program. 
 241 -class RelaxProgError(BaseError): 
 242 -    def __init__(self, name): 
 243          self.text = "The program " + repr(name) + " cannot be found." 
 244   
 245   
 246  # The binary executable file does not exist (full path has been given!). 
 247 -class RelaxMissingBinaryError(BaseError): 
 248 -    def __init__(self, name): 
 249          self.text = "The binary executable file " + repr(name) + " does not exist." 
 250   
 251   
 252  # The binary executable file is not executable. 
 253 -class RelaxNonExecError(BaseError): 
 254 -    def __init__(self, name): 
 255          self.text = "The binary executable file " + repr(name) + " is not executable." 
 256   
 257   
 258  # The binary executable file is not located within the system path. 
 259 -class RelaxNoInPathError(BaseError): 
 260 -    def __init__(self, name): 
 261          self.text = "The binary executable file " + repr(name) + " is not located within the system path." 
 262   
 263   
 264  # Program execution failure. 
 265 -class RelaxProgFailError(BaseError): 
 266 -    def __init__(self, name): 
 267          self.text = "Execution of the program " + name + " has failed." 
 268   
 269   
 270  # PDB errors. 
 271  ############# 
 272   
 273  # PDB data corresponding to the data pipe already exists. 
 274 -class RelaxPdbError(BaseError): 
 275 -    def __init__(self, pipe=None): 
 276          if pipe != None: 
 277              self.text = "PDB data corresponding to the data pipe " + repr(pipe) + " already exists." 
 278          else: 
 279              self.text = "PDB data already exists." 
 280   
 281  # No PDB loaded. 
 282 -class RelaxNoPdbError(BaseError): 
 283 -    def __init__(self, pipe=None): 
 284          if pipe != None: 
 285              self.text = "No PDB file has been loaded for the data pipe " + repr(pipe) + "." 
 286          else: 
 287              self.text = "No PDB file has been loaded." 
 288   
 289  # Loading error. 
 290 -class RelaxPdbLoadError(BaseError): 
 291 -    def __init__(self, name): 
 292          self.text = "The PDB file " + repr(name) + " could not be loaded properly, no molecular chains could be extracted." 
 293   
 294  # Multiple unit vectors. 
 295 -class RelaxMultiVectorError(BaseError): 
 296 -    def __init__(self, spin_id=None): 
 297          if spin_id != None: 
 298              self.text = "The multiple unit XH bond vectors for the spin '%s' - this is not supported by the current data pipe type." % spin_id 
 299          else: 
 300              self.text = "The multiple unit XH bond vectors per spin - this is not supported by the current data pipe type." 
 301   
 302  # No unit vectors. 
 303 -class RelaxNoVectorsError(BaseError): 
 304 -    def __init__(self, pipe=None): 
 305          if pipe: 
 306              self.text = "No unit vectors have been calculated for the data pipe '%s'" % pipe 
 307          else: 
 308              self.text = "No unit vectors have been calculated." 
 309   
 310  # No chains within the PDB file. 
 311 -class RelaxNoPdbChainError(BaseError): 
 312 -    def __init__(self): 
 313          self.text = "No peptide or nucleotide chains can be found within the PDB file." 
 314   
 315   
 316  # Nuclear errors. 
 317  ################# 
 318   
 319  # Nucleus not set. 
 320 -class RelaxNucleusError(BaseError): 
 321 -    def __init__(self, spin_id=None): 
 322          if spin_id != None: 
 323              self.text = "The type of nucleus for the spin '%s' has not yet been set." % spin_id 
 324          else: 
 325              self.text = "The type of nucleus has not yet been set." 
 326   
 327  # Spin type not set. 
 328 -class RelaxSpinTypeError(BaseError): 
 329 -    def __init__(self, spin_id=None): 
 330          if spin_id != None: 
 331              self.text = "The nuclear isotope type for the spin '%s' has not yet been set.  Please use the spin.isotope user function to set the type." % spin_id 
 332          else: 
 333              self.text = "The nuclear isotope type has not yet been set.  Please use the spin.isotope user function to set the type." 
 334   
 335   
 336  # Argument errors. 
 337  ################## 
 338   
 339   
 340  # Misc. 
 341  #~~~~~~ 
 342   
 343  # Invalid argument. 
 344 -class RelaxInvalidError(BaseArgError): 
 345 -    def __init__(self, name, value): 
 346          self.text = "The " + name + " argument " + repr(value) + " is invalid." 
 347   
 348  # Argument not in the list. 
 349 -class RelaxArgNotInListError(BaseArgError): 
 350 -    def __init__(self, name, value, list): 
 351          self.text = "The " + name + " argument " + repr(value) + " is neither " 
 352          for i in range(len(list)-1): 
 353              self.text = self.text + repr(list[i]) + ', ' 
 354          self.text = self.text + 'nor ' + repr(list[-1]) + "." 
 355   
 356  # Length of the list. 
 357 -class RelaxLenError(BaseArgError): 
 358 -    def __init__(self, name, len): 
 359          self.text = "The " + name + " argument must be of length " + repr(len) + "." 
 360   
 361  # None. 
 362 -class RelaxNoneError(BaseArgError): 
 363 -    def __init__(self, name): 
 364          self.text = "The " + name + " argument has not been supplied." 
 365   
 366  # Not None. 
 367 -class RelaxArgNotNoneError(BaseArgError): 
 368 -    def __init__(self, name, value): 
 369          self.text = "The %s argument of '%s' must be None." 
 370   
 371   
 372  # Simple types. 
 373  #~~~~~~~~~~~~~~ 
 374   
 375  # Boolean - the values True and False. 
 376 -class RelaxBoolError(BaseArgError): 
 377      simple_types = [BOOL] 
 378   
 379  # Binary - integers 0 and 1. 
 380 -class RelaxBinError(BaseArgError): 
 381      simple_types = [BIN] 
 382   
 383  # Float. 
 384 -class RelaxFloatError(BaseArgError): 
 385      simple_types = [FLOAT] 
 386   
 387 -class RelaxNoneFloatError(BaseArgError): 
 388      simple_types = [NONE, FLOAT] 
 389   
 390  # Number. 
 391 -class RelaxNumError(BaseArgError): 
 392      simple_types = [NUM] 
 393   
 394 -class RelaxNoneNumError(BaseArgError): 
 395      simple_types = [NONE, NUM] 
 396   
 397  # Function. 
 398 -class RelaxFunctionError(BaseArgError): 
 399      simple_types = [FUNC] 
 400   
 401 -class RelaxNoneFunctionError(BaseArgError): 
 402      simple_types = [NONE, FUNC] 
 403   
 404  # Integer. 
 405 -class RelaxIntError(BaseArgError): 
 406      simple_types = [INT] 
 407   
 408 -class RelaxNoneIntError(BaseArgError): 
 409      simple_types = [NONE, INT] 
 410   
 411  # String. 
 412 -class RelaxStrError(BaseArgError): 
 413      simple_types = [STR] 
 414   
 415 -class RelaxNoneStrError(BaseArgError): 
 416      simple_types = [NONE, STR] 
 417   
 418   
 419  # Simple mixes. 
 420  #~~~~~~~~~~~~~~ 
 421   
 422  # Integer or string. 
 423 -class RelaxIntStrError(BaseArgError): 
 424      simple_types = [INT, STR] 
 425   
 426 -class RelaxNoneIntStrError(BaseArgError): 
 427      simple_types = [NONE, INT, STR] 
 428   
 429  # String or file descriptor. 
 430 -class RelaxStrFileError(BaseArgError): 
 431      simple_types = [STR, FILE] 
 432   
 433 -class RelaxNoneStrFileError(BaseArgError): 
 434      simple_types = [NONE, STR, FILE] 
 435   
 436   
 437  # List types. 
 438  #~~~~~~~~~~~~ 
 439   
 440   
 441  # List. 
 442 -class RelaxListError(BaseArgError): 
 443      list_types = [LIST] 
 444   
 445 -class RelaxNoneListError(BaseArgError): 
 446      simple_types = [NONE] 
 447      list_types = [LIST] 
 448   
 449  # List of floating point numbers. 
 450 -class RelaxListFloatError(BaseArgError): 
 451      list_types = [LIST_FLOAT] 
 452   
 453 -class RelaxNoneListFloatError(BaseArgError): 
 454      list_types = [LIST_FLOAT] 
 455   
 456  # List of floating point numbers or strings. 
 457 -class RelaxListFloatStrError(BaseArgError): 
 458      list_types = [LIST_FLOAT, LIST_STR] 
 459   
 460  # List of integers. 
 461 -class RelaxListIntError(BaseArgError): 
 462      list_types = [LIST_INT] 
 463   
 464  # List of integers. 
 465 -class RelaxNoneListIntError(BaseArgError): 
 466      simple_types = [NONE] 
 467      list_types = [LIST_INT] 
 468   
 469  # List of numbers. 
 470 -class RelaxListNumError(BaseArgError): 
 471      list_types = [LIST_NUM] 
 472   
 473 -class RelaxNoneListNumError(BaseArgError): 
 474      simple_types = [NONE] 
 475      list_types = [LIST_NUM] 
 476   
 477  # List of strings. 
 478 -class RelaxListStrError(BaseArgError): 
 479      list_types = [LIST_STR] 
 480   
 481 -class RelaxNoneListStrError(BaseArgError): 
 482      simple_types = [NONE] 
 483      list_types = [LIST_STR] 
 484   
 485   
 486  # Simple or list types. 
 487  #~~~~~~~~~~~~~~~~~~~~~~ 
 488   
 489  # Float or list. 
 490 -class RelaxNoneFloatListError(BaseArgError): 
 491      simple_types = [NONE, FLOAT] 
 492      list_types = [LIST] 
 493   
 494  # Float, str, or list. 
 495 -class RelaxNoneFloatStrListError(BaseArgError): 
 496      simple_types = [NONE, FLOAT, STR] 
 497      list_types = [LIST] 
 498   
 499  # Integer or list of integers. 
 500 -class RelaxIntListIntError(BaseArgError): 
 501      simple_types = [INT] 
 502      list_types = [LIST_INT] 
 503   
 504 -class RelaxNoneIntListIntError(BaseArgError): 
 505      simple_types = [NONE, INT] 
 506      list_types = [LIST_INT] 
 507   
 508  # Number, string, or list of numbers or strings. 
 509 -class RelaxNumStrListNumStrError(BaseArgError): 
 510      simple_types = [NUM, STR] 
 511      list_types = [LIST_NUM, LIST_STR] 
 512   
 513 -class RelaxNoneNumStrListNumStrError(BaseArgError): 
 514      simple_types = [NONE, NUM, STR] 
 515      list_types = [LIST_NUM, LIST_STR] 
 516   
 517  # String or list. 
 518 -class RelaxNoneStrListError(BaseArgError): 
 519      simple_types = [NONE, STR] 
 520      list_types = [LIST] 
 521   
 522  # String or list of numbers. 
 523 -class RelaxStrListNumError(BaseArgError): 
 524      simple_types = [STR] 
 525      list_types = [LIST_NUM] 
 526   
 527 -class RelaxNoneStrListNumError(BaseArgError): 
 528      simple_types = [NONE, STR] 
 529      list_types = [LIST_NUM] 
 530   
 531  # String or list of strings. 
 532 -class RelaxStrListStrError(BaseArgError): 
 533      simple_types = [STR] 
 534      list_types = [LIST_STR] 
 535   
 536 -class RelaxNoneStrListStrError(BaseArgError): 
 537      simple_types = [NONE, STR] 
 538      list_types = [LIST_STR] 
 539   
 540  # Value or list of values. 
 541 -class RelaxValListValError(BaseArgError): 
 542      simple_types = [VAL] 
 543      list_types = [LIST_VAL] 
 544   
 545 -class RelaxNoneValListValError(BaseArgError): 
 546      simple_types = [NONE, VAL] 
 547      list_types = [LIST_VAL] 
 548   
 549   
 550  # Tuple types. 
 551  #~~~~~~~~~~~~~ 
 552   
 553  # Tuple. 
 554 -class RelaxTupleError(BaseArgError): 
 555      list_types = [TUPLE] 
 556   
 557 -class RelaxNoneTupleError(BaseArgError): 
 558      simple_types = [NONE] 
 559      list_types = [TUPLE] 
 560   
 561  # Tuple of numbers. 
 562 -class RelaxTupleNumError(BaseArgError): 
 563      list_types = [TUPLE_NUM] 
 564   
 565   
 566  # Simple or tuple types. 
 567  #~~~~~~~~~~~~~~~~~~~~~~~ 
 568   
 569  # Number or tuple. 
 570 -class RelaxNumTupleError(BaseArgError): 
 571      simple_types = [NUM] 
 572      list_types = [TUPLE] 
 573   
 574  # Number or tuple of numbers. 
 575 -class RelaxNumTupleNumError(BaseArgError): 
 576      simple_types = [NUM] 
 577      list_types = [TUPLE_NUM] 
 578   
 579 -class RelaxNoneNumTupleNumError(BaseArgError): 
 580      simple_types = [NONE, NUM] 
 581      list_types = [TUPLE_NUM] 
 582   
 583   
 584  # Matrix types. 
 585  #~~~~~~~~~~~~~~ 
 586   
 587  # Matrix of floating point numbers. 
 588 -class RelaxMatrixFloatError(BaseArgError): 
 589      list_types = [MATRIX_FLOAT] 
 590   
 591 -class RelaxNoneMatrixFloatError(BaseArgError): 
 592      list_types = [MATRIX_FLOAT] 
 593   
 594   
 595   
 596  # Sequence errors. 
 597  ################## 
 598   
 599  # No sequence loaded. 
 600 -class RelaxNoSequenceError(BaseError): 
 601 -    def __init__(self, pipe=None): 
 602          if pipe == None: 
 603              self.text = "The sequence data does not exist." 
 604          else: 
 605              self.text = "The sequence data for the data pipe " + repr(pipe) + " does not exist." 
 606   
 607  # The sequence already exists. 
 608 -class RelaxSequenceError(BaseError): 
 609 -    def __init__(self, pipe=None): 
 610          if pipe == None: 
 611              self.text = "The sequence data already exists." 
 612          else: 
 613              self.text = "The sequence data for the data pipe " + repr(pipe) + " already exists." 
 614   
 615  # The two sequences are different. 
 616 -class RelaxDiffSeqError(BaseError): 
 617 -    def __init__(self, pipe1, pipe2): 
 618          self.text = "The sequences for the data pipes " + repr(pipe1) + " and " + repr(pipe2) + " are not the same." 
 619   
 620  # The number of molecules are different. 
 621 -class RelaxDiffMolNumError(BaseError): 
 622 -    def __init__(self, pipe1, pipe2): 
 623          self.text = "The number of molecules do not match between pipes '%s' and '%s'." % (pipe1, pipe2) 
 624   
 625  # The number of residues are different. 
 626 -class RelaxDiffResNumError(BaseError): 
 627 -    def __init__(self, pipe1, pipe2): 
 628          self.text = "The number of residues do not match between pipes '%s' and '%s'." % (pipe1, pipe2) 
 629   
 630  # The number of spins are different. 
 631 -class RelaxDiffSpinNumError(BaseError): 
 632 -    def __init__(self, pipe1, pipe2): 
 633          self.text = "The number of spins do not match between pipes '%s' and '%s'." % (pipe1, pipe2) 
 634   
 635  # Multiple spins matching the ID. 
 636 -class RelaxMultiMolIDError(BaseError): 
 637 -    def __init__(self, id): 
 638          if id == '': 
 639              self.text = "The empty molecule ID corresponds to more than a single molecule in the current data pipe." 
 640          else: 
 641              self.text = "The molecule ID '%s' corresponds to more than a single molecule in the current data pipe." % id 
 642   
 643  # Multiple spins matching the ID. 
 644 -class RelaxMultiResIDError(BaseError): 
 645 -    def __init__(self, id): 
 646          if id == '': 
 647              self.text = "The empty residue ID corresponds to more than a single residue in the current data pipe." 
 648          else: 
 649              self.text = "The residue ID '%s' corresponds to more than a single residue in the current data pipe." % id 
 650   
 651  # Multiple spins matching the ID. 
 652 -class RelaxMultiSpinIDError(BaseError): 
 653 -    def __init__(self, id, id_list=None): 
 654          if id_list != None and id == '': 
 655              self.text = "The empty spin ID corresponds to multiple spins, including %s." % list_to_text(id_list) 
 656          elif id_list == None and id == '': 
 657              self.text = "The empty spin ID corresponds to more than a single spin in the current data pipe." 
 658          elif id_list != None: 
 659              self.text = "The spin ID '%s' corresponds to multiple spins, including %s." % (id, list_to_text(id_list)) 
 660          else: 
 661              self.text = "The spin ID '%s' corresponds to more than a single spin in the current data pipe." % id 
 662   
 663  # Cannot find the residue in the sequence. 
 664 -class RelaxNoResError(BaseError): 
 665 -    def __init__(self, number, name=None): 
 666          if name == None: 
 667              self.text = "The residue '" + repr(number) + "' cannot be found in the sequence." 
 668          else: 
 669              self.text = "The residue '" + repr(number) + " " + name + "' cannot be found in the sequence." 
 670   
 671  # Cannot find the spin in the sequence. 
 672 -class RelaxNoSpinError(BaseError): 
 673 -    def __init__(self, id, pipe=None): 
 674          if pipe == None: 
 675              self.text = "The spin '%s' does not exist." % id 
 676          else: 
 677              self.text = "The spin '%s' does not exist in the '%s' data pipe." % (id, pipe) 
 678   
 679  # The sequence data is not valid. 
 680 -class RelaxInvalidSeqError(BaseError): 
 681 -    def __init__(self, line, problem=None): 
 682          if problem == None: 
 683              self.text = "The sequence data in the line %s is invalid." % line 
 684          else: 
 685              self.text = "The sequence data in the line %s is invalid, %s." % (line, problem) 
 686   
 687  # The spins have not been loaded 
 688 -class RelaxSpinsNotLoadedError(BaseError): 
 689 -    def __init__(self, spin_id): 
 690          self.text = "The spin information for the spin " + repr(spin_id) + " has not yet been loaded, please use the structure.load_spins user function." 
 691   
 692   
 693  # Interatomic data errors. 
 694  ########################## 
 695   
 696  # No interatomic data. 
 697 -class RelaxNoInteratomError(BaseError): 
 698 -    def __init__(self, spin_id1=None, spin_id2=None, pipe=None): 
 699          if spin_id1 and pipe: 
 700              self.text = "The interatomic data between the spins '%s' and '%s' for the data pipe '%s' does not exist." % (spin_id1, spin_id2, pipe) 
 701          elif spin_id1: 
 702              self.text = "The interatomic data between the spins '%s' and '%s' does not exist." % (spin_id1, spin_id2) 
 703          elif pipe: 
 704              self.text = "The interatomic data for the data pipe '%s' does not exist." % pipe 
 705          else: 
 706              self.text = "The interatomic data does not exist." 
 707   
 708  # The interatomic data already exists. 
 709 -class RelaxInteratomError(BaseError): 
 710 -    def __init__(self, pipe=None): 
 711          if pipe == None: 
 712              self.text = "The interatomic data already exists." 
 713          else: 
 714              self.text = "The interatomic data for the data pipe " + repr(pipe) + " already exists." 
 715   
 716  # Inconsistency in the interatomic data. 
 717 -class RelaxInteratomInconsistentError(BaseError): 
 718 -    def __init__(self, pipe1, pipe2): 
 719          self.text = "The interatomic data is inconsistent between the data pipes '%s' and '%s'." % (pipe1, pipe2) 
 720   
 721   
 722   
 723  # Domain errors. 
 724  ################ 
 725   
 726  # No domain defined. 
 727 -class RelaxNoDomainError(BaseError): 
 728 -    def __init__(self, id=None): 
 729          if id == None: 
 730              self.text = "No domains are defined." 
 731          else: 
 732              self.text = "The domain '%s' is not defined." % id 
 733   
 734   
 735   
 736  # Spectrometer information errors. 
 737  ################################## 
 738   
 739  # No frequency information. 
 740 -class RelaxNoFrqError(BaseError): 
 741 -    def __init__(self, pipe_name=None, id=None): 
 742          self.text = "No spectrometer frequency information" 
 743          if id != None: 
 744              self.text += " for the '%s' experiment ID" % id 
 745          self.text += " is present" 
 746          if pipe_name != None: 
 747              self.text += " in the '%s' data pipe" % pipe_name 
 748          self.text += "." 
 749   
 750   
 751   
 752  # Spectral data errors. 
 753  ####################### 
 754   
 755  # No peak intensity data. 
 756 -class RelaxNoPeakIntensityError(BaseError): 
 757 -    def __init__(self, spectrum_id=None): 
 758          if spectrum_id == None: 
 759              self.text = "No peak intensity data has been loaded." 
 760          else: 
 761              self.text = "Peak intensity data for the '%s' spectrum ID does not exist." 
 762   
 763  # No spectral data. 
 764 -class RelaxNoSpectraError(BaseError): 
 765 -    def __init__(self, spectrum_id): 
 766          self.text = "Spectral data corresponding to the ID string '%s' does not exist." % spectrum_id 
 767   
 768  # Spectral data already exists. 
 769 -class RelaxSpectraError(BaseError): 
 770 -    def __init__(self, spectrum_id): 
 771          self.text = "Spectral data corresponding to the ID string '%s' already exists." % spectrum_id 
 772   
 773   
 774  # Relaxation data errors. 
 775  ######################### 
 776   
 777  # No relaxation data. 
 778 -class RelaxNoRiError(BaseError): 
 779 -    def __init__(self, ri_id): 
 780          self.text = "Relaxation data corresponding to the ID string '%s' does not exist." % ri_id 
 781   
 782  # Relaxation data already exists. 
 783 -class RelaxRiError(BaseError): 
 784 -    def __init__(self, ri_id): 
 785          self.text = "Relaxation data corresponding to the ID string '%s' already exists." % ri_id 
 786   
 787   
 788  # J coupling errors. 
 789  #################### 
 790   
 791  # No J data. 
 792 -class RelaxNoJError(BaseError): 
 793 -    def __init__(self): 
 794          self.text = "No J coupling data exists." 
 795   
 796  # J data already exists. 
 797 -class RelaxJError(BaseError): 
 798 -    def __init__(self): 
 799          self.text = "J coupling data already exists." 
 800   
 801   
 802  # RDC and PCS data errors. 
 803  ########################## 
 804   
 805  # No alignment data. 
 806 -class RelaxNoAlignError(BaseError): 
 807 -    def __init__(self, align_id, pipe=None): 
 808          if pipe != None: 
 809              self.text = "The alignment ID string '%s' is missing from the data pipe '%s'." % (align_id, pipe) 
 810          else: 
 811              self.text = "The alignment ID string '%s' is missing." % align_id 
 812   
 813  # Alignment data already exists. 
 814 -class RelaxAlignError(BaseError): 
 815 -    def __init__(self, align_id): 
 816          self.text = "Alignment data corresponding to the ID string '%s' already exists." % align_id 
 817   
 818  # No RDC data. 
 819 -class RelaxNoRDCError(BaseError): 
 820 -    def __init__(self, id=None): 
 821          if id: 
 822              self.text = "RDC data corresponding to the identification string " + repr(id) + " does not exist." 
 823          else: 
 824              self.text = "No RDC data exists." 
 825   
 826  # RDC data already exists. 
 827 -class RelaxRDCError(BaseError): 
 828 -    def __init__(self, id): 
 829          self.text = "RDC data corresponding to the identification string " + repr(id) + " already exists." 
 830   
 831  # No PCS data. 
 832 -class RelaxNoPCSError(BaseError): 
 833 -    def __init__(self, id=None): 
 834          if id: 
 835              self.text = "PCS data corresponding to the identification string " + repr(id) + " does not exist." 
 836          else: 
 837              self.text = "No PCS data exists." 
 838   
 839  # PCS data already exists. 
 840 -class RelaxPCSError(BaseError): 
 841 -    def __init__(self, id): 
 842          self.text = "PCS data corresponding to the identification string " + repr(id) + " already exists." 
 843   
 844   
 845  # Model-free errors. 
 846  #################### 
 847   
 848  # Model-free data already exists. 
 849 -class RelaxMfError(BaseError): 
 850 -    def __init__(self, pipe): 
 851          self.text = "Model-free data corresponding to the data pipe " + repr(pipe) + " already exists." 
 852   
 853   
 854  # Tensor errors. 
 855  ################ 
 856   
 857  # Tensor data corresponding to the data pipe already exists. 
 858 -class RelaxTensorError(BaseError): 
 859 -    def __init__(self, tensor_type): 
 860          self.text = "The " + tensor_type + " tensor data already exists." 
 861   
 862  # No tensor data exists. 
 863 -class RelaxNoTensorError(BaseError): 
 864 -    def __init__(self, tensor_type, tensor_label=None): 
 865          if not tensor_label: 
 866              self.text = "No " + tensor_type + " tensor data exists." 
 867          else: 
 868              self.text = "No " + tensor_type + " tensor data exists for the tensor " + repr(tensor_label) + "." 
 869   
 870   
 871  # File errors. 
 872  ############## 
 873   
 874  # No directory. 
 875 -class RelaxDirError(BaseError): 
 876 -    def __init__(self, name, dir): 
 877          if name == None: 
 878              self.text = "The directory " + repr(dir) + " does not exist." 
 879          else: 
 880              self.text = "The " + name + " directory " + repr(dir) + " does not exist." 
 881   
 882  # No file. 
 883 -class RelaxFileError(BaseError): 
 884 -    def __init__(self, name, file_name=None): 
 885          if file_name == None: 
 886              self.text = "The file " + repr(name) + " does not exist." 
 887          else: 
 888              self.text = "The " + name + " file " + repr(file_name) + " does not exist." 
 889   
 890  # No data in file. 
 891 -class RelaxFileEmptyError(BaseError): 
 892 -    def __init__(self): 
 893          self.text = "The file contains no data." 
 894   
 895  # Overwrite file. 
 896 -class RelaxFileOverwriteError(BaseError): 
 897 -    def __init__(self, file_name, flag): 
 898          self.text = "The file " + repr(file_name) + " already exists.  Set the " + flag + " to True to overwrite." 
 899   
 900  # Invalid data format. 
 901 -class RelaxInvalidDataError(BaseError): 
 902 -    def __init__(self): 
 903          self.text = "The format of the data is invalid." 
 904   
 905   
 906  # Data pipe errors. 
 907  ################### 
 908   
 909  # The data pipe bundle already exists. 
 910 -class RelaxBundleError(BaseError): 
 911 -    def __init__(self, bundle): 
 912          self.text = "The data pipe bundle '%s' already exists." % bundle 
 913   
 914  # No data pipe bundles exist. 
 915 -class RelaxNoBundleError(BaseError): 
 916 -    def __init__(self, bundle=None): 
 917          if bundle != None: 
 918              self.text = "The data pipe bundle '%s' has not been created yet." % bundle 
 919          else: 
 920              self.text = "No data pipe bundles currently exist.  Please use the pipe.bundle user function first." 
 921   
 922  # The data pipe already exists. 
 923 -class RelaxPipeError(BaseError): 
 924 -    def __init__(self, pipe): 
 925          self.text = "The data pipe " + repr(pipe) + " already exists." 
 926   
 927  # No data pipe exists. 
 928 -class RelaxNoPipeError(BaseError): 
 929 -    def __init__(self, pipe=None): 
 930          if pipe != None: 
 931              self.text = "The data pipe " + repr(pipe) + " has not been created yet." 
 932          else: 
 933              self.text = "No data pipes currently exist.  Please use the pipe.create user function first." 
 934   
 935   
 936  # Spin-Residue-Molecule errors. 
 937  ############################### 
 938   
 939  # Disallow molecule selection. 
 940 -class RelaxMolSelectDisallowError(BaseError): 
 941 -    def __init__(self): 
 942          self.text = "The selection of molecules is not allowed." 
 943   
 944  # Disallow residue selection. 
 945 -class RelaxResSelectDisallowError(BaseError): 
 946 -    def __init__(self): 
 947          self.text = "The selection of residues is not allowed." 
 948   
 949  # Disallow spin selection. 
 950 -class RelaxSpinSelectDisallowError(BaseError): 
 951 -    def __init__(self): 
 952          self.text = "The selection of spin systems is not allowed." 
 953   
 954  # The spin must be specified. 
 955 -class RelaxNoSpinSpecError(BaseError): 
 956 -    def __init__(self): 
 957          self.text = "The spin system must be specified." 
 958   
 959   
 960   
 961  # Setup errors. 
 962  ############### 
 963   
 964  # Cannot setup the functions. 
 965 -class RelaxFuncSetupError(BaseError): 
 966 -    def __init__(self, string): 
 967          self.text = "This function is not available for " + string + "." 
 968   
 969  # The model already exists. 
 970 -class RelaxModelError(BaseError): 
 971 -    def __init__(self, name=None): 
 972          if name != None: 
 973              self.text = "The " + name + " model already exists." 
 974          else: 
 975              self.text = "The model already exists." 
 976   
 977   
 978  # The model has not been setup. 
 979 -class RelaxNoModelError(BaseError): 
 980 -    def __init__(self, name=None): 
 981          if name != None: 
 982              self.text = "The specific " + name + " model has not been selected or set up." 
 983          else: 
 984              self.text = "The specific model has not been selected or set up." 
 985   
 986   
 987  # Regular expression errors. 
 988  ############################ 
 989   
 990  # Bad regular expression. 
 991 -class RelaxRegExpError(BaseError): 
 992 -    def __init__(self, name, value): 
 993          self.text = "The " + name + " argument " + repr(value) + " is not valid regular expression." 
 994   
 995   
 996  # Data type errors. 
 997  ################### 
 998   
 999  # Parameter cannot be set. 
1000 -class RelaxParamSetError(BaseError): 
1001 -    def __init__(self, name, param_type=None): 
1002          if param_type != None: 
1003              self.text = "The " + name + " parameter, " + repr(param_type) + ", cannot be set." 
1004          else: 
1005              self.text = "The " + name + " parameter cannot be set." 
1006   
1007  # Value already exists. 
1008 -class RelaxValueError(BaseError): 
1009 -    def __init__(self, data_type, pipe=None): 
1010          if pipe != None: 
1011              self.text = "The data type " + repr(data_type) + " already exists for the data pipe " + repr(pipe) + "." 
1012          else: 
1013              self.text = "The data type " + repr(data_type) + " already exists." 
1014   
1015  # No data value. 
1016 -class RelaxNoValueError(BaseError): 
1017 -    def __init__(self, name, spin_id=None, spin_id2=None): 
1018          if spin_id2 != None: 
1019              self.text = "The %s value has not yet been set for spins '%s' and '%s'." % (name, spin_id, spin_id2) 
1020          elif spin_id != None: 
1021              self.text = "The %s value has not yet been set for spin '%s'." % (name, spin_id) 
1022          else: 
1023              self.text = "The " + repr(name) + " value has not yet been set." 
1024   
1025  # Unknown data type. 
1026 -class RelaxUnknownDataTypeError(BaseError): 
1027 -    def __init__(self, name): 
1028          self.text = "The data type " + repr(name) + " is unknown." 
1029   
1030  # Unknown parameter. 
1031 -class RelaxUnknownParamError(BaseError): 
1032 -    def __init__(self, name, param_type=None): 
1033          if param_type != None: 
1034              self.text = "The " + name + " parameter, " + repr(param_type) + ", is unknown." 
1035          else: 
1036              self.text = "The " + name + " parameter is unknown." 
1037   
1038  # Unknown parameter combination. 
1039 -class RelaxUnknownParamCombError(BaseError): 
1040 -    def __init__(self, name, data): 
1041          self.text = "The " + repr(name) + " argument " + repr(data) + " represents an unknown parameter combination." 
1042   
1043   
1044  # Simulation errors. 
1045  #################### 
1046   
1047  # No simulations. 
1048 -class RelaxNoSimError(BaseError): 
1049 -    def __init__(self, pipe=None): 
1050          if pipe: 
1051              self.text = "Simulations for the data pipe " + repr(pipe) + " have not been setup." 
1052          else: 
1053              self.text = "Simulations have not been setup." 
1054   
1055   
1056  # Style errors. 
1057  ############### 
1058   
1059  # Unknown style. 
1060 -class RelaxStyleError(BaseError): 
1061 -    def __init__(self, style): 
1062          self.text = "The style " + repr(style) + " is unknown." 
1063   
1064   
1065  # Colour errors. 
1066  ################ 
1067   
1068  # Invalid colour. 
1069 -class RelaxInvalidColourError(BaseError): 
1070 -    def __init__(self, colour): 
1071          self.text = "The colour " + repr(colour) + " is invalid." 
1072   
1073   
1074  # Value errors. 
1075  ############### 
1076   
1077  # Infinity. 
1078 -class RelaxInfError(BaseError): 
1079 -    def __init__(self, name): 
1080          self.text = "The invalid " + name + " floating point value of infinity has occurred." 
1081   
1082  # NaN (Not a Number). 
1083 -class RelaxNaNError(BaseError): 
1084 -    def __init__(self, name): 
1085          self.text = "The invalid " + name + " floating point value of NaN (Not a Number) has occurred." 
1086   
1087   
1088  # XML errors. 
1089  ############# 
1090   
1091  # Cannot recreate from the XML - the structure is not empty. 
1092 -class RelaxFromXMLNotEmptyError(BaseError): 
1093 -    def __init__(self, name): 
1094          self.text = "The " + name + " data structure cannot be recreated from the XML elements as the structure is not empty." 
1095   
1096   
1097   
1098  # An object of all the RelaxErrors. 
1099  ################################### 
1100   
1101  # Function for setting up the AllRelaxErrors object. 
1102 -def all_errors(names): 
1103      """Function for returning all the RelaxErrors to allow the AllRelaxError object to be created.""" 
1104   
1105      # Empty list. 
1106      list = [] 
1107   
1108      # Loop over all objects of this module. 
1109      for name in names: 
1110          # Get the object. 
1111          object = globals()[name] 
1112   
1113          # Skip over all non error class objects. 
1114          if not (isinstance(object, type(RelaxError)) or isinstance(object, type(type))) or not match('Relax', name): 
1115              continue 
1116   
1117          # Append to the list. 
1118          list.append(object) 
1119   
1120      # Return the list of RelaxErrors 
1121      return list 
1122   
1123  # Initialise the AllRelaxErrors structure, as a tuple for the except statements, so it can be imported. 
1124  AllRelaxErrors = tuple(all_errors(dir())) 
1125