info

1 ############################################################################### 2 # # 3 # Copyright (C) 2001-2014,2016-2017 Edward d'Auvergne # 4 # Copyright (C) 2008 Sebastien Morin # 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 the introductory text container.""" 25 26 # Dependencies. 27 import dep_check 28 29 # Python module imports. 30 if dep_check.ctypes_module: 31 import ctypes 32 if hasattr(ctypes, 'windll'): 33 import ctypes.wintypes 34 else: 35 ctypes = None 36 if dep_check.ctypes_structure_module: 37 from ctypes import Structure 38 else: 39 Structure = object 40 from os import environ, pathsep, waitpid 41 import platform 42 from re import search, sub 43 PIPE, Popen = None, None 44 if dep_check.subprocess_module: 45 from subprocess import PIPE, Popen 46 import sys 47 from textwrap import wrap 48 49 # relax module imports. 50 from lib.compat import linux_distribution 51 from status import Status; status = Status() 52 from version import repo_head, repo_type, repo_url, version, version_full 53 54

55 -def print_sys_info():

56 """Print out the system information.""" 57 58 # Initialise the info box. 59 info = Info_box() 60 61 # Print all info. 62 print(info.sys_info())

63 64 65

66 -class Info_box(object):

67 """A container storing information about relax.""" 68 69 # Class variable for storing the class instance. 70 instance = None 71

72 - def __init__(self):

73 """Create the program introduction text stings. 74 75 This class generates a container with the following objects: 76 - title: The program title 'relax' 77 - version: For example 'repository commit' or '1.3.8'. 78 - desc: The short program description. 79 - copyright: A list of copyright statements. 80 - licence: Text pertaining to the licencing. 81 - errors: A list of import errors. 82 """ 83 84 # Program name and version. 85 self.title = "relax" 86 self.version = version 87 88 # The relax website. 89 self.website = "http://www.nmr-relax.com" 90 91 # Program description. 92 self.desc = "Molecular dynamics by NMR data analysis" 93 94 # Long description 95 self.desc_long = "The program relax is designed for the study of the dynamics of proteins or other macromolecules though the analysis of experimental NMR data. It is a community driven project created by NMR spectroscopists for NMR spectroscopists. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, and the Lipari and Szabo model-free analysis." 96 97 # Copyright printout. 98 self.copyright_final_year = 2024 99 self.copyright = [] 100 self.copyright.append("Copyright (C) 2001-2006 Edward d'Auvergne") 101 self.copyright.append("Copyright (C) 2006-%s the relax development team" % self.copyright_final_year) 102 self.copyright_short = "Copyright (C) 2001-%s the relax development team" % self.copyright_final_year 103 self.copyright_latex = r"Copyright \copyright\ 2001-%s the relax development team" % self.copyright_final_year 104 105 # Program licence and help. 106 self.licence = "This is free software which you are welcome to modify and redistribute under the conditions of the GNU General Public License (GPL), Version 3 or any later version published by the Free Software Foundation. This program, including all modules, is licensed under the GPL and comes with absolutely no warranty. For details type 'GPL' within the relax prompt." 107 108 # ImportErrors, if any. 109 self.errors = [] 110 if not dep_check.C_module_exp_fn: 111 self.errors.append(dep_check.C_module_exp_fn_mesg) 112 113 # References. 114 self._setup_references()

115 116

117 - def __new__(self, *args, **kargs):

118 """Replacement function for implementing the singleton design pattern.""" 119 120 # First initialisation. 121 if self.instance is None: 122 self.instance = object.__new__(self, *args, **kargs) 123 124 # Already initialised, so return the instance. 125 return self.instance

126 127

128 - def _setup_references(self):

129 """Build a dictionary of all references useful for relax.""" 130 131 # Initialise the dictionary. 132 self.bib = {} 133 134 # Place the containers into the dictionary. 135 self.bib['Bieri11'] = Bieri11() 136 self.bib['Clore90'] = Clore90() 137 self.bib['dAuvergne06'] = dAuvergne06() 138 self.bib['dAuvergneGooley03'] = dAuvergneGooley03() 139 self.bib['dAuvergneGooley06'] = dAuvergneGooley06() 140 self.bib['dAuvergneGooley07'] = dAuvergneGooley07() 141 self.bib['dAuvergneGooley08a'] = dAuvergneGooley08a() 142 self.bib['dAuvergneGooley08b'] = dAuvergneGooley08b() 143 self.bib['Delaglio95'] = Delaglio95() 144 self.bib['GoddardKneller'] = GoddardKneller() 145 self.bib['LipariSzabo82a'] = LipariSzabo82a() 146 self.bib['LipariSzabo82b'] = LipariSzabo82b()

147 148

149 - def centre(self, string, width=100):

150 """Format the string to be centred to a certain number of spaces. 151 152 @param string: The string to centre. 153 @type string: str 154 @keyword width: The number of characters to centre to. 155 @type width: int 156 @return: The centred string with leading whitespace added. 157 @rtype: str 158 """ 159 160 # Calculate the number of spaces needed. 161 spaces = int((width - len(string)) / 2) 162 163 # The new string. 164 string = spaces * ' ' + string 165 166 # Return the new string. 167 return string

168 169

170 - def file_type(self, path):

171 """Return a string representation of the file type. 172 173 @param path: The full path of the file to return information about. 174 @type path: str 175 @return: The single line file type information string. 176 @rtype: str 177 """ 178 179 # Python 2.3 and earlier. 180 if Popen == None: 181 return '' 182 183 # Test if the 'file' program is installed. 184 pipe = Popen('file --help', shell=True, stdout=PIPE, stderr=PIPE, close_fds=False) 185 err = pipe.stderr.readlines() 186 if err: 187 return '' 188 189 # The command. 190 cmd = "file -b '%s'" % path 191 192 # Execute. 193 pipe = Popen(cmd, shell=True, stdout=PIPE, close_fds=False) 194 if not hasattr(ctypes, 'windll'): 195 waitpid(pipe.pid, 0) 196 197 # The STDOUT data. 198 data = pipe.stdout.readlines() 199 200 # Mac OS X 3-way binary. 201 if data[0][:-1] == 'Mach-O universal binary with 3 architectures': 202 # Arch. 203 arch = [None, None, None] 204 for i in range(3): 205 row = data[i+1].split('\t') 206 arch[i] = row[1][:-1] 207 arch.sort() 208 209 # The full file type printout. 210 if arch == ['Mach-O 64-bit executable x86_64', 'Mach-O executable i386', 'Mach-O executable ppc']: 211 file_type = '3-way exec (i386, ppc, x86_64)' 212 elif arch == ['Mach-O 64-bit bundle x86_64', 'Mach-O bundle i386', 'Mach-O bundle ppc']: 213 file_type = '3-way bundle (i386, ppc, x86_64)' 214 elif arch == ['Mach-O 64-bit dynamically linked shared library x86_64', 'Mach-O dynamically linked shared library i386', 'Mach-O dynamically linked shared library ppc']: 215 file_type = '3-way lib (i386, ppc, x86_64)' 216 elif arch == ['Mach-O 64-bit object x86_64', 'Mach-O object i386', 'Mach-O object ppc']: 217 file_type = '3-way obj (i386, ppc, x86_64)' 218 else: 219 file_type = '3-way %s' % arch 220 221 # Mac OS X 2-way binary. 222 elif data[0][:-1] == 'Mach-O universal binary with 2 architectures': 223 # Arch. 224 arch = [None, None] 225 for i in range(2): 226 row = data[i+1].split('\t') 227 arch[i] = row[1][:-1] 228 arch.sort() 229 230 # The full file type printout. 231 if arch == ['Mach-O executable i386', 'Mach-O executable ppc']: 232 file_type = '2-way exec (i386, ppc)' 233 elif arch == ['Mach-O bundle i386', 'Mach-O bundle ppc']: 234 file_type = '2-way bundle (i386, ppc)' 235 elif arch == ['Mach-O dynamically linked shared library i386', 'Mach-O dynamically linked shared library ppc']: 236 file_type = '2-way lib (i386, ppc)' 237 elif arch == ['Mach-O object i386', 'Mach-O object ppc']: 238 file_type = '2-way obj (i386, ppc)' 239 else: 240 file_type = '2-way %s' % arch 241 242 # Default to all info. 243 else: 244 file_type = data[0][:-1] 245 if hasattr(file_type, 'decode'): 246 file_type = file_type.decode() 247 for i in range(1, len(data)): 248 row = data[i].split('\t') 249 arch[i] = row[1][:-1] 250 file_type += " %s" % arch 251 252 # Return a string value. 253 if file_type == None: 254 return '' 255 return file_type

256 257

258 - def format_max_width(self, data):

259 """Return the text formatting width for the given data. 260 261 @param data: The list of things to print out. 262 @type data: list 263 @return: The maximum width of the elements in the list. 264 @rtype: int 265 """ 266 267 # Init. 268 width = 0 269 270 # Loop over the data. 271 for i in range(len(data)): 272 # The string representation size. 273 size = len(str(data[i])) 274 275 # Find the max size. 276 if size > width: 277 width = size 278 279 # Return the max width. 280 return width

281 282

283 - def intro_text(self):

284 """Create the introductory string for STDOUT printing. 285 286 This text is word-wrapped to a fixed width of 100 characters (or 80 on MS Windows). 287 288 289 @return: The introductory string. 290 @rtype: str 291 """ 292 293 # Some new lines. 294 intro_string = '\n\n\n' 295 296 # Program name and version - subversion code. 297 if version == 'repository commit': 298 if repo_type == 'git': 299 text = "%s %s" % (self.title, self.version) 300 text2 = "%s" % repo_head 301 else: 302 text = "%s %s r%s" % (self.title, self.version, repo_head) 303 text2 = "%s" % repo_url 304 intro_string += self.centre(text, status.text_width) + '\n' + self.centre(text2, status.text_width) + '\n' 305 if repo_type == 'git': 306 for url in repo_url.split('\n'): 307 intro_string += self.centre(url, status.text_width) + '\n' 308 intro_string += '\n' 309 310 # Program name and version - official releases. 311 else: 312 text = "%s %s" % (self.title, self.version) 313 intro_string = intro_string + self.centre(text, status.text_width) + '\n\n' 314 315 # Program description. 316 intro_string = intro_string + self.centre(self.desc, status.text_width) + '\n\n' 317 318 # Copyright printout. 319 for i in range(len(self.copyright)): 320 intro_string = intro_string + self.centre(self.copyright[i], status.text_width) + '\n' 321 intro_string = intro_string + '\n' 322 323 # Program licence and help (wrapped). 324 for line in wrap(self.licence, status.text_width): 325 intro_string = intro_string + line + '\n' 326 intro_string = intro_string + '\n' 327 328 # Help message. 329 help = "Assistance in using the relax prompt and scripting interface can be accessed by typing 'help' within the prompt." 330 for line in wrap(help, status.text_width): 331 intro_string = intro_string + line + '\n' 332 333 # ImportErrors, if any. 334 for i in range(len(self.errors)): 335 intro_string = intro_string + '\n' + self.errors[i] + '\n' 336 intro_string = intro_string + '\n' 337 338 # The multi-processor message, if it exists. 339 if hasattr(self, 'multi_processor_string'): 340 for line in wrap('Processor fabric: %s\n' % self.multi_processor_string, status.text_width): 341 intro_string = intro_string + line + '\n' 342 343 # Return the formatted text. 344 return intro_string

345 346

347 - def package_info(self):

348 """Return a string for printing to STDOUT with info from the Python packages used by relax. 349 350 @return: The info string. 351 @rtype: str 352 """ 353 354 # Init. 355 text = '' 356 package = [] 357 status = [] 358 version = [] 359 path = [] 360 361 # Intro. 362 text = text + ("\nPython packages and modules (most are optional):\n\n") 363 364 # Header. 365 package.append("Name") 366 status.append("Installed") 367 version.append("Version") 368 path.append("Path") 369 370 # minfx. 371 package.append('minfx') 372 status.append(True) 373 if hasattr(dep_check.minfx, '__version__'): 374 version.append(dep_check.minfx.__version__) 375 else: 376 version.append('Unknown') 377 path.append(dep_check.minfx.__path__[0]) 378 379 # bmrblib. 380 package.append('bmrblib') 381 status.append(dep_check.bmrblib_module) 382 try: 383 if hasattr(dep_check.bmrblib, '__version__'): 384 version.append(dep_check.bmrblib.__version__) 385 else: 386 version.append('Unknown') 387 except: 388 version.append('') 389 try: 390 path.append(dep_check.bmrblib.__path__[0]) 391 except: 392 path.append('') 393 394 # numpy. 395 package.append('numpy') 396 status.append(True) 397 try: 398 version.append(dep_check.numpy.version.version) 399 path.append(dep_check.numpy.__path__[0]) 400 except: 401 version.append('') 402 path.append('') 403 404 # scipy. 405 package.append('scipy') 406 status.append(dep_check.scipy_module) 407 try: 408 version.append(dep_check.scipy.version.version) 409 path.append(dep_check.scipy.__path__[0]) 410 except: 411 version.append('') 412 path.append('') 413 414 # wxPython. 415 package.append('wxPython') 416 status.append(dep_check.wx_module) 417 try: 418 version.append(dep_check.wx.version()) 419 path.append(dep_check.wx.__path__[0]) 420 except: 421 version.append('') 422 path.append('') 423 424 # matplotlib. 425 package.append('matplotlib') 426 status.append(dep_check.matplotlib_module) 427 try: 428 version.append(dep_check.matplotlib.__version__) 429 path.append(dep_check.matplotlib.__path__[0]) 430 except: 431 version.append('') 432 path.append('') 433 434 # mpi4py. 435 package.append('mpi4py') 436 status.append(dep_check.mpi4py_module) 437 try: 438 version.append(dep_check.mpi4py.__version__) 439 path.append(dep_check.mpi4py.__path__[0]) 440 441 # MPI version. 442 try: 443 import mpi4py.MPI 444 vendor = mpi4py.MPI.get_vendor() 445 version[-1] += (" (%s %s.%s.%s)" % (vendor[0], vendor[1][0], vendor[1][1], vendor[1][2])) 446 except: 447 pass 448 449 except: 450 version.append('') 451 path.append('') 452 453 # epydoc. 454 package.append('epydoc') 455 status.append(dep_check.epydoc_module) 456 try: 457 version.append(dep_check.epydoc.__version__) 458 path.append(dep_check.epydoc.__path__[0]) 459 except: 460 version.append('') 461 path.append('') 462 463 # optparse. 464 package.append('optparse') 465 status.append(True) 466 try: 467 version.append(dep_check.optparse.__version__) 468 path.append(dep_check.optparse.__file__) 469 except: 470 version.append('') 471 path.append('') 472 473 # readline. 474 package.append('readline') 475 status.append(dep_check.readline_module) 476 version.append('') 477 try: 478 path.append(dep_check.readline.__file__) 479 except: 480 path.append('') 481 482 # profile. 483 package.append('profile') 484 status.append(dep_check.profile_module) 485 version.append('') 486 try: 487 path.append(dep_check.profile.__file__) 488 except: 489 path.append('') 490 491 # BZ2. 492 package.append('bz2') 493 status.append(dep_check.bz2_module) 494 version.append('') 495 try: 496 path.append(dep_check.bz2.__file__) 497 except: 498 path.append('') 499 500 # gzip. 501 package.append('gzip') 502 status.append(dep_check.gzip_module) 503 version.append('') 504 try: 505 path.append(dep_check.gzip.__file__) 506 except: 507 path.append('') 508 509 # IO. 510 package.append('io') 511 status.append(dep_check.io_module) 512 version.append('') 513 try: 514 path.append(dep_check.io.__file__) 515 except: 516 path.append('') 517 518 # XML. 519 package.append('xml') 520 status.append(dep_check.xml_module) 521 if dep_check.xml_module: 522 version.append("%s (%s)" % (dep_check.xml_version, dep_check.xml_type)) 523 path.append(dep_check.xml.__file__) 524 else: 525 version.append('') 526 path.append('') 527 528 # XML minidom. 529 package.append('xml.dom.minidom') 530 version.append('') 531 try: 532 import xml.dom.minidom 533 status.append(True) 534 except: 535 status.append(False) 536 try: 537 path.append(xml.dom.minidom.__file__) 538 except: 539 path.append('') 540 541 # Format the data. 542 fmt_package = "%%-%ss" % (self.format_max_width(package) + 2) 543 fmt_status = "%%-%ss" % (self.format_max_width(status) + 2) 544 fmt_version = "%%-%ss" % (self.format_max_width(version) + 2) 545 fmt_path = "%%-%ss" % (self.format_max_width(path)) 546 547 # Add the text. 548 for i in range(len(package)): 549 text += fmt_package % package[i] 550 text += fmt_status % status[i] 551 text += fmt_version % version[i] 552 text += fmt_path % path[i] 553 text += '\n' 554 555 # Return the info string. 556 return text

557 558

559 - def processor_name(self):

560 """Return a string for the processor name. 561 562 @return: The processor name, in much more detail than platform.processor(). 563 @rtype: str 564 """ 565 566 # Python 2.3 and earlier. 567 if Popen == None: 568 return "" 569 570 # No subprocess module. 571 if not dep_check.subprocess_module: 572 return "" 573 574 # The system. 575 system = platform.system() 576 577 # Linux systems. 578 if system == 'Linux': 579 # The command to run. 580 cmd = "cat /proc/cpuinfo" 581 582 # Execute the command. 583 pipe = Popen(cmd, shell=True, stdout=PIPE, close_fds=False) 584 waitpid(pipe.pid, 0) 585 586 # Get the STDOUT data. 587 data = pipe.stdout.readlines() 588 589 # Loop over the lines, returning the first model name with the leading "model name :" text stripped. 590 for line in data: 591 # Decode Python 3 byte arrays. 592 if hasattr(line, 'decode'): 593 line = line.decode() 594 595 # Find the processor name. 596 if search("model name", line): 597 # Convert the text. 598 name = sub(".*model name.*:", "", line, 1) 599 name = name.strip() 600 601 # Return the name. 602 return name 603 604 # Windows systems. 605 if system == 'Windows' or system == 'Microsoft': 606 return platform.processor() 607 608 # Mac OS X systems. 609 if system == 'Darwin': 610 # Add the 'sysctl' path to the environment (if needed). 611 environ['PATH'] += pathsep + '/usr/sbin' 612 613 # The command to run. 614 cmd = "sysctl -n machdep.cpu.brand_string" 615 616 # Execute the command in a fail safe way, return the result or nothing. 617 try: 618 # Execute. 619 pipe = Popen(cmd, shell=True, stdout=PIPE, close_fds=False) 620 waitpid(pipe.pid, 0) 621 622 # Get the STDOUT data. 623 data = pipe.stdout.readlines() 624 625 # Decode Python 3 byte arrays. 626 string = data[0] 627 if hasattr(string, 'decode'): 628 string = string.decode() 629 630 # Find the processor name. 631 # Return the string. 632 return string.strip() 633 634 # Nothing. 635 except: 636 return "" 637 638 # Unknown. 639 return ""

640 641

642 - def ram_info(self, format=" %-25s%s\n"):

643 """Return a string for printing to STDOUT with info from the Python packages used by relax. 644 645 @keyword format: The formatting string. 646 @type format: str 647 @return: The info string. 648 @rtype: str 649 """ 650 651 # Python 2.3 and earlier. 652 if Popen == None: 653 return '' 654 655 # Init. 656 text = '' 657 658 # The system. 659 system = platform.system() 660 661 # Unix and GNU/Linux systems. 662 if system == 'Linux': 663 pipe = Popen('free -m', shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=False) 664 free_lines = pipe.stdout.readlines() 665 if free_lines: 666 # Extract the info. 667 for line in free_lines: 668 # Split up the line. 669 row = line.split() 670 671 # The RAM size. 672 if row[0] == 'Mem:': 673 text += format % ("Total RAM size: ", row[1], "Mb") 674 675 # The swap size. 676 if row[0] == 'Swap:': 677 text += format % ("Total swap size: ", row[1], "Mb") 678 679 # Windows systems (supported by ctypes.windll). 680 if system == 'Windows' or system == 'Microsoft': 681 # Initialise the memory info class. 682 mem = MemoryStatusEx() 683 684 # The RAM size. 685 text += format % ("Total RAM size: ", mem.ullTotalPhys / 1024.**2, "Mb") 686 687 # The swap size. 688 text += format % ("Total swap size: ", mem.ullTotalVirtual / 1024.**2, "Mb") 689 690 # Mac OS X systems. 691 if system == 'Darwin': 692 # Add the 'sysctl' path to the environment (if needed). 693 environ['PATH'] += pathsep + '/usr/sbin' 694 695 # The commands to run. 696 cmd = "sysctl -n hw.physmem" 697 cmd2 = "sysctl -n hw.memsize" 698 699 # Execute the command in a fail safe way, return the result or nothing. 700 try: 701 # Execute. 702 pipe = Popen(cmd, shell=True, stdout=PIPE, close_fds=False) 703 waitpid(pipe.pid, 0) 704 705 # Get the STDOUT data. 706 data = pipe.stdout.readlines() 707 708 # Execute. 709 pipe = Popen(cmd2, shell=True, stdout=PIPE, close_fds=False) 710 waitpid(pipe.pid, 0) 711 712 # Get the STDOUT data. 713 data2 = pipe.stdout.readlines() 714 715 # Convert the values. 716 ram = int(data[0].strip()) 717 total = int(data2[0].strip()) 718 swap = total - ram 719 720 # The RAM size. 721 text += format % ("Total RAM size: ", ram / 1024.**2, "Mb") 722 723 # The swap size. 724 text += format % ("Total swap size: ", swap / 1024.**2, "Mb") 725 726 # Nothing. 727 except: 728 pass 729 730 # Unknown. 731 if not text: 732 text += format % ("Total RAM size: ", "?", "Mb") 733 text += format % ("Total swap size: ", "?", "Mb") 734 735 # Return the info string. 736 return text

737 738

739 - def relax_module_info(self):

740 """Return a string with info about the relax modules. 741 742 @return: The info string. 743 @rtype: str 744 """ 745 746 # Init. 747 text = '' 748 name = [] 749 status = [] 750 file_type = [] 751 path = [] 752 753 # Intro. 754 text = text + ("\nrelax C modules:\n\n") 755 756 # Header. 757 name.append("Module") 758 status.append("Compiled") 759 file_type.append("File type") 760 path.append("Path") 761 762 # relaxation curve-fitting. 763 name.append('target_functions.relax_fit') 764 status.append(dep_check.C_module_exp_fn) 765 if hasattr(dep_check, 'relax_fit'): 766 file_type.append(self.file_type(dep_check.relax_fit.__file__)) 767 path.append(dep_check.relax_fit.__file__) 768 else: 769 file_type.append('') 770 path.append('') 771 772 # Format the data. 773 fmt_name = "%%-%ss" % (self.format_max_width(name) + 2) 774 fmt_status = "%%-%ss" % (self.format_max_width(status) + 2) 775 fmt_file_type = "%%-%ss" % (self.format_max_width(file_type) + 2) 776 fmt_path = "%%-%ss" % (self.format_max_width(path) + 2) 777 778 # Add the text. 779 for i in range(len(name)): 780 text += fmt_name % name[i] 781 text += fmt_status % status[i] 782 text += fmt_file_type % file_type[i] 783 text += fmt_path % path[i] 784 text += '\n' 785 786 # Return the info string. 787 return text

788 789

790 - def sys_info(self):

791 """Return a string for printing to STDOUT with info about the current relax instance. 792 793 @return: The info string. 794 @rtype: str 795 """ 796 797 # Init. 798 text = '' 799 800 # Formatting string. 801 format = " %-25s%s\n" 802 format2 = " %-25s%s %s\n" 803 804 # Hardware info. 805 text = text + ("\nHardware information:\n") 806 if hasattr(platform, 'machine'): 807 text = text + (format % ("Machine: ", platform.machine())) 808 if hasattr(platform, 'processor'): 809 text = text + (format % ("Processor: ", platform.processor())) 810 text = text + (format % ("Processor name: ", self.processor_name())) 811 text = text + (format % ("Endianness: ", sys.byteorder)) 812 text = text + self.ram_info(format=format2) 813 814 # OS info. 815 text = text + ("\nOperating system information:\n") 816 if hasattr(platform, 'system'): 817 text = text + (format % ("System: ", platform.system())) 818 if hasattr(platform, 'release'): 819 text = text + (format % ("Release: ", platform.release())) 820 if hasattr(platform, 'version'): 821 text = text + (format % ("Version: ", platform.version())) 822 if hasattr(platform, 'win32_ver') and platform.win32_ver()[0]: 823 text = text + (format % ("Win32 version: ", (platform.win32_ver()[0] + " " + platform.win32_ver()[1] + " " + platform.win32_ver()[2] + " " + platform.win32_ver()[3]))) 824 if linux_distribution()[0]: 825 text = text + (format % ("GNU/Linux version: ", (linux_distribution()[0] + " " + linux_distribution()[1] + " " + linux_distribution()[2]))) 826 if hasattr(platform, 'mac_ver') and platform.mac_ver()[0]: 827 text = text + (format % ("Mac version: ", (platform.mac_ver()[0] + " (" + platform.mac_ver()[1][0] + ", " + platform.mac_ver()[1][1] + ", " + platform.mac_ver()[1][2] + ") " + platform.mac_ver()[2]))) 828 if hasattr(platform, 'dist'): 829 text = text + (format % ("Distribution: ", (platform.dist()[0] + " " + platform.dist()[1] + " " + platform.dist()[2]))) 830 if hasattr(platform, 'platform'): 831 text = text + (format % ("Full platform string: ", (platform.platform()))) 832 if hasattr(ctypes, 'windll'): 833 text = text + (format % ("Windows architecture: ", (self.win_arch()))) 834 835 # Python info. 836 text = text + ("\nPython information:\n") 837 if hasattr(platform, 'architecture'): 838 text = text + (format % ("Architecture: ", (platform.architecture()[0] + " " + platform.architecture()[1]))) 839 if hasattr(platform, 'python_version'): 840 text = text + (format % ("Python version: ", platform.python_version())) 841 if hasattr(platform, 'python_branch'): 842 text = text + (format % ("Python branch: ", platform.python_branch())) 843 if hasattr(platform, 'python_build'): 844 text = text + ((format[:-1]+', %s\n') % ("Python build: ", platform.python_build()[0], platform.python_build()[1])) 845 if hasattr(platform, 'python_compiler'): 846 text = text + (format % ("Python compiler: ", platform.python_compiler())) 847 if hasattr(platform, 'libc_ver'): 848 text = text + (format % ("Libc version: ", (platform.libc_ver()[0] + " " + platform.libc_ver()[1]))) 849 if hasattr(platform, 'python_implementation'): 850 text = text + (format % ("Python implementation: ", platform.python_implementation())) 851 if hasattr(platform, 'python_revision'): 852 text = text + (format % ("Python revision: ", platform.python_revision())) 853 if sys.executable: 854 text = text + (format % ("Python executable: ", sys.executable)) 855 if hasattr(sys, 'flags'): 856 text = text + (format % ("Python flags: ", sys.flags)) 857 if hasattr(sys, 'float_info'): 858 text = text + (format % ("Python float info: ", sys.float_info)) 859 text = text + (format % ("Python module path: ", sys.path)) 860 861 # Python packages. 862 text = text + self.package_info() 863 864 # relax info: 865 text = text + "\nrelax information:\n" 866 text = text + (format % ("Version: ", version_full())) 867 if hasattr(self, "multi_processor_string"): 868 text += format % ("Processor fabric: ", self.multi_processor_string) 869 870 # relax modules. 871 text = text + self.relax_module_info() 872 873 # End with an empty newline. 874 text = text + ("\n") 875 876 # Return the text. 877 return text

878 879

880 - def win_arch(self):

881 """Determine the MS Windows architecture. 882 883 @return: The architecture string. 884 @rtype: str 885 """ 886 887 # 64-bit versions. 888 if 'PROCESSOR_ARCHITEW6432' in environ: 889 arch = environ['PROCESSOR_ARCHITEW6432'] 890 891 # Default 32-bit. 892 else: 893 arch = environ['PROCESSOR_ARCHITECTURE'] 894 895 # Return the architecture. 896 return arch

897 898 899

900 -class MemoryStatusEx(Structure):

901 """Special object for obtaining hardware info in MS Windows.""" 902 903 if hasattr(ctypes, 'windll'): 904 _fields_ = [ 905 ('dwLength', ctypes.wintypes.DWORD), 906 ('dwMemoryLoad', ctypes.wintypes.DWORD), 907 ('ullTotalPhys', ctypes.c_ulonglong), 908 ('ullAvailPhys', ctypes.c_ulonglong), 909 ('ullTotalPageFile', ctypes.c_ulonglong), 910 ('ullAvailPageFile', ctypes.c_ulonglong), 911 ('ullTotalVirtual', ctypes.c_ulonglong), 912 ('ullAvailVirtual', ctypes.c_ulonglong), 913 ('ullExtendedVirtual', ctypes.c_ulonglong), 914 ] 915

916 - def __init__(self):

917 """Set up the information and handle non MS Windows systems.""" 918 919 # Get the required info (for MS Windows only). 920 if hasattr(ctypes, 'windll'): 921 self.dwLength = ctypes.sizeof(self) 922 ctypes.windll.kernel32.GlobalMemoryStatusEx(ctypes.byref(self))

923 924 925

926 -class Ref:

927 """Reference base class.""" 928 929 # Initialise all class variables to None. 930 type = None 931 author = None 932 author2 = None 933 title = None 934 status = None 935 journal = None 936 journal_full = None 937 volume = None 938 number = None 939 doi = None 940 pubmed_id = None 941 url = None 942 pages = None 943 year = None 944 945

946 - def __getattr__(self, name):

947 """Generate some variables on the fly. 948 949 This is only called for objects not found in the class. 950 951 @param name: The name of the object. 952 @type name: str 953 @raises AttributeError: If the object cannot be created. 954 @returns: The generated object. 955 @rtype: anything 956 """ 957 958 # Page numbers. 959 if name in ['page_first', 'page_last']: 960 # No page info. 961 if not self.pages: 962 return None 963 964 # First split the page range. 965 vals = self.pages.split('-') 966 967 # Single page. 968 if len(vals) == 1: 969 return vals[0] 970 971 # First page. 972 if name == 'page_first': 973 return vals[0] 974 975 # Last page. 976 if name == 'page_last': 977 return vals[1] 978 979 raise AttributeError(name)

980 981

982 - def cite_short(self, author=True, title=True, journal=True, volume=True, number=True, pages=True, year=True, doi=True, url=True, status=True):

983 """Compile a short citation. 984 985 The returned text will have the form of: 986 987 - d'Auvergne, E.J. and Gooley, P.R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119. 988 989 990 @keyword author: The author flag. 991 @type author: bool 992 @keyword title: The title flag. 993 @type title: bool 994 @keyword journal: The journal flag. 995 @type journal: bool 996 @keyword volume: The volume flag. 997 @type volume: bool 998 @keyword number: The number flag. 999 @type number: bool 1000 @keyword pages: The pages flag. 1001 @type pages: bool 1002 @keyword year: The year flag. 1003 @type year: bool 1004 @keyword doi: The doi flag. 1005 @type doi: bool 1006 @keyword url: The url flag. 1007 @type url: bool 1008 @keyword status: The status flag. This will only be shown if not 'published'. 1009 @type status: bool 1010 @return: The full citation. 1011 @rtype: str 1012 """ 1013 1014 # Build the citation. 1015 cite = '' 1016 if author and self.author and hasattr(self, 'author'): 1017 cite = cite + self.author 1018 if year and self.year and hasattr(self, 'year'): 1019 cite = cite + ' (' + repr(self.year) + ').' 1020 if title and self.title and hasattr(self, 'title'): 1021 cite = cite + ' ' + self.title 1022 if journal and self.journal and hasattr(self, 'journal'): 1023 cite = cite + ' ' + self.journal + ',' 1024 if volume and self.volume and hasattr(self, 'volume'): 1025 cite = cite + ' ' + self.volume 1026 if number and self.number and hasattr(self, 'number'): 1027 cite = cite + '(' + self.number + '),' 1028 if pages and self.pages and hasattr(self, 'pages'): 1029 cite = cite + ' ' + self.pages 1030 if doi and self.doi and hasattr(self, 'doi'): 1031 cite = cite + ' (http://dx.doi.org/'+self.doi + ')' 1032 if url and self.url and hasattr(self, 'url'): 1033 cite = cite + ' (' + self.url + ')' 1034 if status and hasattr(self, 'status') and self.status != 'published': 1035 cite = cite + ' (' + self.status + ')' 1036 1037 # End. 1038 if cite[-1] != '.': 1039 cite = cite + '.' 1040 1041 # Return the citation. 1042 return cite

1043 1044

1045 - def cite_html(self, author=True, title=True, journal=True, volume=True, number=True, pages=True, year=True, doi=True, url=True, status=True):

1046 """Compile a citation for HTML display. 1047 1048 @keyword author: The author flag. 1049 @type author: bool 1050 @keyword title: The title flag. 1051 @type title: bool 1052 @keyword journal: The journal flag. 1053 @type journal: bool 1054 @keyword volume: The volume flag. 1055 @type volume: bool 1056 @keyword number: The number flag. 1057 @type number: bool 1058 @keyword pages: The pages flag. 1059 @type pages: bool 1060 @keyword year: The year flag. 1061 @type year: bool 1062 @keyword doi: The doi flag. 1063 @type doi: bool 1064 @keyword url: The url flag. 1065 @type url: bool 1066 @keyword status: The status flag. This will only be shown if not 'published'. 1067 @type status: bool 1068 @return: The full citation. 1069 @rtype: str 1070 """ 1071 1072 # Build the citation. 1073 cite = '' 1074 if author and hasattr(self, 'author') and self.author: 1075 cite = cite + self.author 1076 if year and hasattr(self, 'year') and self.year: 1077 cite = cite + ' (' + repr(self.year) + ').' 1078 if title and hasattr(self, 'title') and self.title: 1079 cite = cite + ' ' + self.title 1080 if journal and hasattr(self, 'journal') and self.journal: 1081 cite = cite + ' ' + self.journal + ',' 1082 if volume and hasattr(self, 'volume') and self.volume: 1083 cite = cite + ' ' + self.volume + '' 1084 if number and hasattr(self, 'number') and self.number: 1085 cite = cite + '(' + self.number + '),' 1086 if pages and hasattr(self, 'pages') and self.pages: 1087 cite = cite + ' ' + self.pages 1088 if doi and hasattr(self, 'doi') and self.doi: 1089 cite = cite + ' (<a href="http://dx.doi.org/%s">abstract</a>)' % self.doi 1090 if url and hasattr(self, 'url') and self.url: 1091 cite = cite + ' (<a href="%s">url</a>)' % self.url 1092 if status and hasattr(self, 'status') and self.status != 'published': 1093 cite = cite + ' (%s)' % self.status 1094 1095 # End. 1096 if cite[-1] != '.': 1097 cite = cite + '.' 1098 1099 # Return the citation. 1100 return cite

1101 1102 1103

1104 -class Bieri11(Ref):

1105 """Bibliography container.""" 1106 1107 type = "journal" 1108 author = "Bieri, M., d'Auvergne, E. J. and Gooley, P. R." 1109 author2 = [["Michael", "Bieri", "M.", ""], ["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]] 1110 title = "relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and micro-s motion of proteins" 1111 journal = "J. Biomol. NMR" 1112 journal_full = "Journal of Biomolecular NMR" 1113 abstract = "Investigation of protein dynamics on the ps-ns and mus-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax." 1114 authoraddress = "Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia." 1115 doi = "10.1007/s10858-011-9509-1" 1116 pubmed_id = 21618018 1117 status = "published" 1118 year = 2011

1119 1120 1121

1122 -class Clore90(Ref):

1123 """Bibliography container.""" 1124 1125 type = "journal" 1126 author = "Clore, G. M. and Szabo, A. and Bax, A. and Kay, L. E. and Driscoll, P. C. and Gronenborn, A. M." 1127 title = "Deviations from the simple 2-parameter model-free approach to the interpretation of N-15 nuclear magnetic-relaxation of proteins" 1128 journal = "J. Am. Chem. Soc." 1129 journal_full = "Journal of the American Chemical Society" 1130 volume = "112" 1131 number = "12" 1132 pages = "4989-4991" 1133 address = "1155 16th St, NW, Washington, DC 20036" 1134 sourceid = "ISI:A1990DH27700070" 1135 status = "published" 1136 year = 1990

1137 1138 1139

1140 -class dAuvergne06(Ref):

1141 """Bibliography container.""" 1142 1143 type = "thesis" 1144 author = "d'Auvergne, E. J." 1145 author2 = [["Edward", "d'Auvergne", "E.", "J."]] 1146 title = "Protein dynamics: a study of the model-free analysis of NMR relaxation data." 1147 school = "Biochemistry and Molecular Biology, University of Melbourne." 1148 url = "http://eprints.infodiv.unimelb.edu.au/archive/00002799/" 1149 status = "published" 1150 year = 2006

1151 1152 1153

1154 -class dAuvergneGooley03(Ref):

1155 """Bibliography container.""" 1156 1157 type = "journal" 1158 author = "d'Auvergne, E. J. and Gooley, P. R." 1159 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]] 1160 title = "The use of model selection in the model-free analysis of protein dynamics." 1161 journal = "J. Biomol. NMR" 1162 journal_full = "Journal of Biomolecular NMR" 1163 volume = "25" 1164 number = "1" 1165 pages = "25-39" 1166 abstract = "Model-free analysis of NMR relaxation data, which is widely used for the study of protein dynamics, consists of the separation of the global rotational diffusion from internal motions relative to the diffusion frame and the description of these internal motions by amplitude and timescale. Five model-free models exist, each of which describes a different type of motion. Model-free analysis requires the selection of the model which best describes the dynamics of the NH bond. It will be demonstrated that the model selection technique currently used has two significant flaws, under-fitting, and not selecting a model when one ought to be selected. Under-fitting breaks the principle of parsimony causing bias in the final model-free results, visible as an overestimation of S2 and an underestimation of taue and Rex. As a consequence the protein falsely appears to be more rigid than it actually is. Model selection has been extensively developed in other fields. The techniques known as Akaike's Information Criteria (AIC), small sample size corrected AIC (AICc), Bayesian Information Criteria (BIC), bootstrap methods, and cross-validation will be compared to the currently used technique. To analyse the variety of techniques, synthetic noisy data covering all model-free motions was created. The data consists of two types of three-dimensional grid, the Rex grids covering single motions with chemical exchange [S2,taue,Rex], and the Double Motion grids covering two internal motions [S f 2,S s 2,tau s ]. The conclusion of the comparison is that for accurate model-free results, AIC model selection is essential. As the method neither under, nor over-fits, AIC is the best tool for applying Occam's razor and has the additional benefits of simplifying and speeding up model-free analysis." 1167 authoraddress = "Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia." 1168 keywords = "Amines ; Diffusion ; *Models, Molecular ; Motion ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Proteins/*chemistry ; Research Support, Non-U.S. Gov't ; Rotation" 1169 doi = "10.1023/A:1021902006114" 1170 pubmed_id = 12566997 1171 status = "published" 1172 year = 2003

1173 1174 1175

1176 -class dAuvergneGooley06(Ref):

1177 """Bibliography container.""" 1178 1179 type = "journal" 1180 author = "d'Auvergne, E. J. and Gooley, P. R." 1181 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]] 1182 title = "Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data." 1183 journal = "J. Biomol. NMR" 1184 journal_full = "Journal of Biomolecular NMR" 1185 volume = "35" 1186 number = "2" 1187 pages = "117-135" 1188 abstract = "Model-free analysis is a technique commonly used within the field of NMR spectroscopy to extract atomic resolution, interpretable dynamic information on multiple timescales from the R (1), R (2), and steady state NOE. Model-free approaches employ two disparate areas of data analysis, the discipline of mathematical optimisation, specifically the minimisation of a chi(2) function, and the statistical field of model selection. By searching through a large number of model-free minimisations, which were setup using synthetic relaxation data whereby the true underlying dynamics is known, certain model-free models have been identified to, at times, fail. This has been characterised as either the internal correlation times, tau( e ), tau( f ), or tau( s ), or the global correlation time parameter, local tau( m ), heading towards infinity, the result being that the final parameter values are far from the true values. In a number of cases the minimised chi(2) value of the failed model is significantly lower than that of all other models and, hence, will be the model which is chosen by model selection techniques. If these models are not removed prior to model selection the final model-free results could be far from the truth. By implementing a series of empirical rules involving inequalities these models can be specifically isolated and removed. Model-free analysis should therefore consist of three distinct steps: model-free minimisation, model-free model elimination, and finally model-free model selection. Failure has also been identified to affect the individual Monte Carlo simulations used within error analysis. Each simulation involves an independent randomised relaxation data set and model-free minimisation, thus simulations suffer from exactly the same types of failure as model-free models. Therefore, to prevent these outliers from causing a significant overestimation of the errors the failed Monte Carlo simulations need to be culled prior to calculating the parameter standard deviations." 1189 authoraddress = "Department of Biochemistry and Molecular Biology, Bio21 Institute of Biotechnology and Molecular Science, University of Melbourne, Parkville, Victoria, 3010, Australia" 1190 doi = "10.1007/s10858-006-9007-z" 1191 pubmed_id = 16791734 1192 status = "published" 1193 year = 2006

1194 1195 1196

1197 -class dAuvergneGooley07(Ref):

1198 """Bibliography container.""" 1199 1200 type = "journal" 1201 author = "d'Auvergne, E. J. and Gooley, P. R." 1202 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]] 1203 title = "Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm." 1204 journal = "Mol. Biosys." 1205 journal_full = "Molecular BioSystems" 1206 volume = "3" 1207 number = "7" 1208 pages = "483-494" 1209 abstract = "Model-free analysis of NMR relaxation data, which describes the motion of individual atoms, is a problem intricately linked to the Brownian rotational diffusion of the macromolecule. The diffusion tensor parameters strongly influence the optimisation of the various model-free models and the subsequent model selection between them. Finding the optimal model of the dynamics of the system among the numerous diffusion and model-free models is hence quite complex. Using set theory, the entirety of this global problem has been encapsulated by the universal set Ll, and its resolution mathematically formulated as the universal solution Ll. Ever since the original Lipari and Szabo papers the model-free dynamics of a molecule has most often been solved by initially estimating the diffusion tensor. The model-free models which depend on the diffusion parameter values are then optimised and the best model is chosen to represent the dynamics of the residue. Finally, the global model of all diffusion and model-free parameters is optimised. These steps are repeated until convergence. For simplicity this approach to Ll will be labelled the diffusion seeded model-free paradigm. Although this technique suffers from a number of problems many have been solved. All aspects of the diffusion seeded paradigm and its consequences, together with a few alternatives to the paradigm, will be reviewed through the use of set notation." 1210 authoraddress = "Department of Biochemistry and Molecular Biology, Bio21 Institute of Biotechnology and Molecular Science, University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia." 1211 keywords = "Magnetic Resonance Spectroscopy/*methods ; *Models, Theoretical ; Proteins/chemistry ; Thermodynamics" 1212 doi = "10.1039/b702202f" 1213 pubmed_id = 17579774 1214 status = "published" 1215 year = 2007

1216 1217 1218

1219 -class dAuvergneGooley08a(Ref):

1220 """Bibliography container.""" 1221 1222 type = "journal" 1223 author = "d'Auvergne, E. J. and Gooley, P. R." 1224 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]] 1225 title = "Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces." 1226 journal = "J. Biomol. NMR" 1227 journal_full = "Journal of Biomolecular NMR" 1228 volume = "40" 1229 number = "2" 1230 pages = "107-119" 1231 abstract = "The key to obtaining the model-free description of the dynamics of a macromolecule is the optimisation of the model-free and Brownian rotational diffusion parameters using the collected R (1), R (2) and steady-state NOE relaxation data. The problem of optimising the chi-squared value is often assumed to be trivial, however, the long chain of dependencies required for its calculation complicates the model-free chi-squared space. Convolutions are induced by the Lorentzian form of the spectral density functions, the linear recombinations of certain spectral density values to obtain the relaxation rates, the calculation of the NOE using the ratio of two of these rates, and finally the quadratic form of the chi-squared equation itself. Two major topological features of the model-free space complicate optimisation. The first is a long, shallow valley which commences at infinite correlation times and gradually approaches the minimum. The most severe convolution occurs for motions on two timescales in which the minimum is often located at the end of a long, deep, curved tunnel or multidimensional valley through the space. A large number of optimisation algorithms will be investigated and their performance compared to determine which techniques are suitable for use in model-free analysis. Local optimisation algorithms will be shown to be sufficient for minimisation not only within the model-free space but also for the minimisation of the Brownian rotational diffusion tensor. In addition the performance of the programs Modelfree and Dasha are investigated. A number of model-free optimisation failures were identified: the inability to slide along the limits, the singular matrix failure of the Levenberg-Marquardt minimisation algorithm, the low precision of both programs, and a bug in Modelfree. Significantly, the singular matrix failure of the Levenberg-Marquardt algorithm occurs when internal correlation times are undefined and is greatly amplified in model-free analysis by both the grid search and constraint algorithms. The program relax ( http://www.nmr-relax.com ) is also presented as a new software package designed for the analysis of macromolecular dynamics through the use of NMR relaxation data and which alleviates all of the problems inherent within model-free analysis." 1232 authoraddress = "Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077, Goettingen, Germany" 1233 keywords = "*Algorithms ; Cytochromes c2/chemistry ; Diffusion ; *Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Rhodobacter capsulatus/chemistry ; *Rotation" 1234 doi = "10.1007/s10858-007-9214-2" 1235 pubmed_id = 18085410 1236 status = "published" 1237 year = 2008

1238 1239 1240

1241 -class dAuvergneGooley08b(Ref):

1242 """Bibliography container.""" 1243 1244 type = "journal" 1245 author = "d'Auvergne, E. J. and Gooley, P. R." 1246 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]] 1247 title = "Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor." 1248 journal = "J. Biomol. NMR" 1249 journal_full = "Journal of Biomolecular NMR" 1250 volume = "40" 1251 number = "2" 1252 pages = "121-133" 1253 abstract = "Finding the dynamics of an entire macromolecule is a complex problem as the model-free parameter values are intricately linked to the Brownian rotational diffusion of the molecule, mathematically through the autocorrelation function of the motion and statistically through model selection. The solution to this problem was formulated using set theory as an element of the universal set [formula: see text]-the union of all model-free spaces (d'Auvergne EJ and Gooley PR (2007) Mol. BioSyst. 3(7), 483-494). The current procedure commonly used to find the universal solution is to initially estimate the diffusion tensor parameters, to optimise the model-free parameters of numerous models, and then to choose the best model via model selection. The global model is then optimised and the procedure repeated until convergence. In this paper a new methodology is presented which takes a different approach to this diffusion seeded model-free paradigm. Rather than starting with the diffusion tensor this iterative protocol begins by optimising the model-free parameters in the absence of any global model parameters, selecting between all the model-free models, and finally optimising the diffusion tensor. The new model-free optimisation protocol will be validated using synthetic data from Schurr JM et al. (1994) J. Magn. Reson. B 105(3), 211-224 and the relaxation data of the bacteriorhodopsin (1-36)BR fragment from Orekhov VY (1999) J. Biomol. NMR 14(4), 345-356. To demonstrate the importance of this new procedure the NMR relaxation data of the Olfactory Marker Protein (OMP) of Gitti R et al. (2005) Biochem. 44(28), 9673-9679 is reanalysed. The result is that the dynamics for certain secondary structural elements is very different from those originally reported." 1254 authoraddress = "Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, D-37077, Germany" 1255 keywords = "Algorithms ; Amides/chemistry ; Bacteriorhodopsins/chemistry ; Crystallography, X-Ray ; Diffusion ; *Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Olfactory Marker Protein/chemistry ; Peptide Fragments/chemistry ; Protein Structure, Secondary ; *Rotation" 1256 language = "eng" 1257 doi = "10.1007/s10858-007-9213-3" 1258 pubmed_id = 18085411 1259 status = "published" 1260 year = 2008

1261 1262 1263

1264 -class Delaglio95(Ref):

1265 """Bibliography container.""" 1266 1267 type = "journal" 1268 author = "Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, A." 1269 author2 = [["Frank", "Delaglio", "F.", None], ["Stephan", "Grzesiek", "S.", None], ["Geerten", "Vuister", "G.", "W."], ["Guang", "Zhu", "G.", None], ["John", "Pfeifer", "J.", None], ["Ad", "Bax", "A.", None]] 1270 title = "NMRPipe: a multidimensional spectral processing system based on UNIX pipes." 1271 journal = "J. Biomol. NMR" 1272 journal_full = "Journal of Biomolecular NMR" 1273 volume = "6" 1274 number = "3" 1275 pages = "277-293" 1276 abstract = "The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks." 1277 authoraddress = "Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA." 1278 keywords = "Magnetic Resonance Spectroscopy/*instrumentation ; *Software" 1279 language = "eng" 1280 doi = "10.1007/BF00197809" 1281 pubmed_id = 8520220 1282 status = "published" 1283 year = 1995

1284 1285 1286

1287 -class GoddardKneller(Ref):

1288 """Bibliography container.""" 1289 1290 author = "Goddard, T.D. and Kneller, D.G." 1291 author2 = [["Tom", "Goddard", "T.", "D."], ["Donald", "Kneller", "D.", "G."]] 1292 journal = "University of California, San Francisco." 1293 title = "Sparky 3." 1294 status = "unpublished" 1295 type = "internet"

1296 1297 1298

1299 -class LipariSzabo82a(Ref):

1300 """Bibliography container.""" 1301 1302 type = "journal" 1303 author = "Lipari, G. and Szabo, A." 1304 title = "Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules I. Theory and range of validity" 1305 journal = "J. Am. Chem. Soc." 1306 journal_full = "Journal of the American Chemical Society" 1307 volume = "104" 1308 number = "17" 1309 pages = "4546-4559" 1310 authoraddress = "NIADDKD,Chem Phys Lab,Bethesda,MD 20205." 1311 sourceid = "ISI:A1982PC82900009" 1312 status = "published" 1313 year = 1982

1314 1315 1316

1317 -class LipariSzabo82b(Ref):

1318 """Bibliography container.""" 1319 1320 type = "journal" 1321 author = "Lipari, G. and Szabo, A." 1322 title = "Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules II. Analysis of experimental results" 1323 journal = "J. Am. Chem. Soc." 1324 journal_full = "Journal of the American Chemical Society" 1325 volume = "104" 1326 number = "17" 1327 pages = "4559-4570" 1328 abstract = "For pt.I see ibid., vol.104, p.4546 (1982). In the preceding paper it has been shown that the unique dynamic information on fast internal motions in an NMR relaxation experiment on macromolecules in solution is specified by a generalized order parameter, S , and an effective correlation time, tau /sub e/. The authors now deal with the extraction and interpretation of this information. The procedure used to obtain S /sup 2/ and tau /sub e/ from experimental data by using a least-squares method and, in certain favorable circumstances, by using an analytical formula is described. A variety of experiments are then analyzed to yield information on the time scale and spatial restriction of internal motions of isoleucines in myoglobin, methionines in dihydrofolate reductase and myoglobin, a number of aliphatic residues in basic pancreatic trypsin inhibitor, and ethyl isocyanide bound to myoglobin, hemoglobin, and aliphatic side chains in three random-coil polymers. The numerical values of S /sup 2/ and tau /sub e / can be readily interpreted within the framework of a variety of models." 1329 authoraddress = "NIADDKD,Chem Phys Lab,Bethesda,MD 20205." 1330 sourceid = "ISI:A1982PC82900010" 1331 status = "published" 1332 year = 1982

1333

Source Code for Module info