Source Code for Package bmrblib

  1  ############################################################################# 
  2  #                                                                           # 
  3  # The BMRB library.                                                         # 
  4  #                                                                           # 
  5  # Copyright (C) 2008-2013 Edward d'Auvergne                                 # 
  6  #                                                                           # 
  7  # This program is free software: you can redistribute it and/or modify      # 
  8  # it under the terms of the GNU General Public License as published by      # 
  9  # the Free Software Foundation, either version 3 of the License, or         # 
 10  # (at your option) any later version.                                       # 
 11  #                                                                           # 
 12  # This program is distributed in the hope that it will be useful,           # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of            # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             # 
 15  # GNU General Public License for more details.                              # 
 16  #                                                                           # 
 17  # You should have received a copy of the GNU General Public License         # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.     # 
 19  #                                                                           # 
 20  ############################################################################# 
 21   
 22  # Module docstring. 
 23  """Package for interfacing with the U{BioMagResBank<http://www.bmrb.wisc.edu/>}. 
 24   
 25  The Biological Magnetic Resonance Data Bank, or BioMagResBank and BMRB for short, is a repository for data from NMR spectroscopy on proteins, peptides, nucleic acids, and other biomolecules.  This U{bmrblib library<https://sourceforge.net/projects/bmrblib/>} handles the U{NMR-STAR formatted files<http://www.bmrb.wisc.edu/dictionary/>}, the base format of all BMRB data.  It can both read and write NMR-STAR files. 
 26  """ 
 27   
 28  # The version number. 
 29  __version__ = '1.0.2' 
 30   
 31  # The list of all modules and packages. 
 32  __all__ = ['base_classes', 
 33             'misc', 
 34             'nmr_star_dict', 
 35             'nmr_star_dict_v2_1', 
 36             'nmr_star_dict_v3_1'] 
 37   
 38  # Python module imports. 
 39  from os import F_OK, access 
 40  from re import search 
 41  import sys 
 42   
 43  # Bmrblib module imports. 
 44  from bmrblib.nmr_star_dict_v2_1 import NMR_STAR_v2_1 
 45  from bmrblib.nmr_star_dict_v3_1 import NMR_STAR_v3_1 
 46  from bmrblib.version import Star_version 
 47   
 48   
 49 -def create_nmr_star(title, file_path, version=None): 
 50      """Initialise the NMR-STAR object. 
 51   
 52      @param title:       The title of the NMR-STAR data. 
 53      @type title:        str 
 54      @param file_path:   The full file path. 
 55      @type file_path:    str 
 56      @keyword version:   The NMR-STAR version to use. 
 57      @type version:      str 
 58      @return:            The NMR-STAR python object. 
 59      @rtype:             class instance 
 60      """ 
 61   
 62      # Determine the version. 
 63      if not version and access(file_path, F_OK): 
 64          version = determine_version(file_path) 
 65   
 66      # The default version. 
 67      if not version: 
 68          version = '3.1' 
 69   
 70      # Store the version in the singleton. 
 71      star_version = Star_version() 
 72      star_version.set_version(version) 
 73   
 74      # Print out. 
 75      sys.stdout.write("NMR-STAR version %s\n" % star_version.version) 
 76   
 77      # Initialise the NMR-STAR data object. 
 78      if star_version.major == 3: 
 79          star = NMR_STAR_v3_1('relax_model_free_results', file_path) 
 80      elif star_version.major == 2: 
 81          star = NMR_STAR_v2_1('relax_model_free_results', file_path) 
 82      else: 
 83          raise NameError("The NMR-STAR version %s is unknown." % star_version.version) 
 84   
 85      # Return the object. 
 86      return star 
 87   
 88   
 89 -def determine_version(file_path): 
 90      """Determine the version of the given NMR-STAR file. 
 91   
 92      @param file_path:   The full file path. 
 93      @type file_path:    str 
 94      @return:            The NMR-STAR version number. 
 95      @rtype:             str 
 96      """ 
 97   
 98      # Read the file. 
 99      file = open(file_path) 
100      lines = file.readlines() 
101      file.close() 
102   
103      # Loop over the lines of the file. 
104      for line in lines: 
105          # Find the version line. 
106          if search('\.NMR_STAR_version', line) or search('_NMR_STAR_version', line): 
107              # Split the line. 
108              row = line.split() 
109   
110              # Return the version number. 
111              return row[1] 
112