Source Code for Module lib.spectrum.xeasy

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2013 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2008 Sebastien Morin                                          # 
  5  # Copyright (C) 2013 Troels E. Linnet                                         # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  8  #                                                                             # 
  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """Module containing functions for handling XEasy files.""" 
 26   
 27   
 28  # Python module imports. 
 29  from warnings import warn 
 30   
 31  # relax module imports. 
 32  from lib.errors import RelaxError 
 33  from lib.io import strip 
 34  from lib.warnings import RelaxWarning 
 35   
 36   
 37 -def read_list(peak_list=None, file_data=None, int_col=None): 
 38      """Extract the peak intensity information from the XEasy file. 
 39   
 40      @keyword peak_list: The peak list object to place all data into. 
 41      @type peak_list:    lib.spectrum.objects.Peak_list instance 
 42      @keyword file_data: The data extracted from the file converted into a list of lists. 
 43      @type file_data:    list of lists of str 
 44      @keyword int_col:   The column containing the peak intensity data (for a non-standard formatted file). 
 45      @type int_col:      int 
 46      @raises RelaxError: When the expected peak intensity is not a float. 
 47      """ 
 48   
 49      # The hardcoded column positions (note that w1 and w2 are swapped!). 
 50      w1_col = 3 
 51      w2_col = 2 
 52      ass_w1_col = 7 
 53      ass_w2_col = 4 
 54      res_name1_col = 9 
 55      res_name2_col = 5 
 56      if int_col == None: 
 57          int_col = 10 
 58   
 59      # Determine the number of header lines. 
 60      num = 0 
 61      for line in file_data: 
 62          # Try to see if the intensity can be extracted. 
 63          try: 
 64              intensity = float(line[int_col]) 
 65          except ValueError: 
 66              num = num + 1 
 67          except IndexError: 
 68              num = num + 1 
 69          else: 
 70              break 
 71      print("Number of header lines found: " + repr(num)) 
 72   
 73      # Remove the header. 
 74      file_data = file_data[num:] 
 75   
 76      # Strip the data. 
 77      file_data = strip(file_data) 
 78   
 79      # Loop over the file data. 
 80      for line in file_data: 
 81          # Test for invalid assignment lines which have the column numbers changed and return empty data. 
 82          if line[ass_w1_col] == 'inv.' or line[ass_w2_col] == 'inv.': 
 83              continue 
 84   
 85          # The residue number for dimension 1. 
 86          try: 
 87              res_num1 = int(line[8]) 
 88          except: 
 89              raise RelaxError("Improperly formatted XEasy file, cannot process the residue number for dimension 1 in assignment: %s." % line) 
 90   
 91          # The residue number for dimension 2. 
 92          try: 
 93              res_num2 = int(line[5]) 
 94          except: 
 95              warn(RelaxWarning("Improperly formatted XEasy file, cannot process the residue number for dimension 2 in assignment: %s. Setting residue number to None." % line)) 
 96              res_num2 = None 
 97   
 98          # Nuclei names. 
 99          name1 = line[ass_w1_col] 
100          name2 = line[ass_w2_col] 
101   
102          # Residue names. 
103          res_name1 = line[res_name1_col] 
104          res_name2 = line[res_name2_col] 
105   
106          # Chemical shifts. 
107          try: 
108              w1 = float(line[w1_col]) 
109          except ValueError: 
110              raise RelaxError("The w1 chemical shift from the line %s is invalid." % line) 
111          try: 
112              w2 = float(line[w2_col]) 
113          except ValueError: 
114              raise RelaxError("The w2 chemical shift from the line %s is invalid." % line) 
115   
116          # Intensity. 
117          try: 
118              intensity = float(line[int_col]) 
119          except ValueError: 
120              raise RelaxError("The peak intensity value from the line %s is invalid." % line) 
121   
122          # Add the assignment to the peak list object. 
123          peak_list.add(res_nums=[res_num1, res_num2], res_names=[res_name1, res_name2], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity) 
124