Source Code for Module lib.spectrum.nmrview

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2004,2006-2013 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 NMRView files.""" 
 25   
 26   
 27  # Python module imports. 
 28  from warnings import warn 
 29   
 30  # relax module imports. 
 31  from lib.errors import RelaxError 
 32  from lib.io import strip 
 33  from lib.warnings import RelaxWarning 
 34   
 35   
 36 -def read_list(peak_list=None, file_data=None, int_col=None): 
 37      """Extract the peak intensity information from the NMRView peak intensity file. 
 38   
 39      @keyword peak_list: The peak list object to place all data into. 
 40      @type peak_list:    lib.spectrum.objects.Peak_list instance 
 41      @keyword file_data: The data extracted from the file converted into a list of lists. 
 42      @type file_data:    list of lists of str 
 43      @keyword int_col:   The column containing the peak intensity data. The default is 16 for intensities. Setting the int_col argument to 15 will use the volumes (or evolumes). For a non-standard formatted file, use a different value. 
 44      @type int_col:      int 
 45      @raises RelaxError: When the expected peak intensity is not a float. 
 46      """ 
 47   
 48      # Assume the NMRView file has six header lines! 
 49      num = 6 
 50      print("Number of header lines: %s" % num) 
 51   
 52      # Remove the header. 
 53      file_data = file_data[num:] 
 54   
 55      # Strip the data. 
 56      file_data = strip(file_data) 
 57   
 58      # The chemical shift columns. 
 59      w2_col = 2 
 60      w1_col = 9 
 61   
 62      # The peak intensity column. 
 63      if int_col == None: 
 64          int_col = 16 
 65      if int_col == 16: 
 66          print('Using peak heights.') 
 67      if int_col == 15: 
 68          print('Using peak volumes (or evolumes).') 
 69   
 70      # Loop over the file data. 
 71      for line in file_data: 
 72          # Unknown assignment. 
 73          if line[1] == '{}': 
 74              warn(RelaxWarning("The assignment '%s' is unknown, skipping this peak." % line[1])) 
 75              continue 
 76   
 77          # The residue number 
 78          res_num = '' 
 79          try: 
 80              res_num = line[1].strip('{') 
 81              res_num = res_num.strip('}') 
 82              res_num = res_num.split('.') 
 83              res_num = int(res_num[0]) 
 84          except ValueError: 
 85              raise RelaxError("Improperly formatted NMRView file, cannot process the assignment '%s'." % line[1]) 
 86   
 87          # Nuclei names. 
 88          name2 = '' 
 89          if line[1]!='{}': 
 90              name2 = line[1].strip('{') 
 91              name2 = name2.strip('}') 
 92              name2 = name2.split('.') 
 93              name2 = name2[1] 
 94          name1 = '' 
 95          if line[8]!='{}': 
 96              name1 = line[8].strip('{') 
 97              name1 = name1.strip('}') 
 98              name1 = name1.split('.') 
 99              name1 = name1[1] 
100   
101          # Chemical shifts. 
102          w1 = None 
103          w2 = None 
104          if w1_col != None: 
105              try: 
106                  w1 = float(line[w1_col]) 
107              except ValueError: 
108                  raise RelaxError("The chemical shift from the line %s is invalid." % line) 
109          if w2_col != None: 
110              try: 
111                  w2 = float(line[w2_col]) 
112              except ValueError: 
113                  raise RelaxError("The chemical shift from the line %s is invalid." % line) 
114   
115          # Intensity. 
116          try: 
117              intensity = float(line[int_col]) 
118          except ValueError: 
119              raise RelaxError("The peak intensity value " + repr(intensity) + " from the line " + repr(line) + " is invalid.") 
120   
121          # Add the assignment to the peak list object. 
122          peak_list.add(res_nums=[res_num, res_num], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity) 
123