Source Code for Module lib.spectrum.xeasy

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2013 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 functions for handling XEasy files.""" 
 25   
 26   
 27  # relax module imports. 
 28  from lib.errors import RelaxError 
 29  from lib.io import strip 
 30   
 31   
 32 -def read_list(peak_list=None, file_data=None, int_col=None): 
 33      """Extract the peak intensity information from the XEasy file. 
 34   
 35      @keyword peak_list: The peak list object to place all data into. 
 36      @type peak_list:    lib.spectrum.objects.Peak_list instance 
 37      @keyword file_data: The data extracted from the file converted into a list of lists. 
 38      @type file_data:    list of lists of str 
 39      @keyword int_col:   The column containing the peak intensity data (for a non-standard formatted file). 
 40      @type int_col:      int 
 41      @raises RelaxError: When the expected peak intensity is not a float. 
 42      """ 
 43   
 44      # The hardcoded column positions (note that w1 and w2 are swapped!). 
 45      w1_col = 3 
 46      w2_col = 2 
 47      ass_w1_col = 7 
 48      ass_w2_col = 4 
 49      if int_col == None: 
 50          int_col = 10 
 51   
 52      # Determine the number of header lines. 
 53      num = 0 
 54      for line in file_data: 
 55          # Try to see if the intensity can be extracted. 
 56          try: 
 57              intensity = float(line[int_col]) 
 58          except ValueError: 
 59              num = num + 1 
 60          except IndexError: 
 61              num = num + 1 
 62          else: 
 63              break 
 64      print("Number of header lines found: " + repr(num)) 
 65   
 66      # Remove the header. 
 67      file_data = file_data[num:] 
 68   
 69      # Strip the data. 
 70      file_data = strip(file_data) 
 71   
 72      # Loop over the file data. 
 73      for line in file_data: 
 74          # Test for invalid assignment lines which have the column numbers changed and return empty data. 
 75          if line[ass_w1_col] == 'inv.' or line[ass_w2_col] == 'inv.': 
 76              continue 
 77   
 78          # The residue number. 
 79          try: 
 80              res_num = int(line[5]) 
 81          except: 
 82              raise RelaxError("Improperly formatted XEasy file, cannot read the line %s." % line) 
 83   
 84          # Nuclei names. 
 85          name1 = line[ass_w1_col] 
 86          name2 = line[ass_w2_col] 
 87   
 88          # Chemical shifts. 
 89          try: 
 90              w1 = float(line[w1_col]) 
 91          except ValueError: 
 92              raise RelaxError("The w1 chemical shift from the line %s is invalid." % line) 
 93          try: 
 94              w2 = float(line[w2_col]) 
 95          except ValueError: 
 96              raise RelaxError("The w2 chemical shift from the line %s is invalid." % line) 
 97   
 98          # Intensity. 
 99          try: 
100              intensity = float(line[int_col]) 
101          except ValueError: 
102              raise RelaxError("The peak intensity value from the line %s is invalid." % line) 
103   
104          # Add the assignment to the peak list object. 
105          peak_list.add(res_nums=[res_num, res_num], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity) 
106