Source Code for Module lib.spectrum.nmrview

  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 NMRView 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 NMRView peak intensity 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. 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. 
 45      @type int_col:      int 
 46      @raises RelaxError: When the expected peak intensity is not a float. 
 47      """ 
 48   
 49      # Assume the NMRView file has six header lines! 
 50      num = 6 
 51      print("Number of header lines: %s" % num) 
 52   
 53      # Remove the header. 
 54      file_data = file_data[num:] 
 55   
 56      # Strip the data. 
 57      file_data = strip(file_data) 
 58   
 59      # The chemical shift columns. 
 60      w2_col = 2 
 61      w1_col = 9 
 62   
 63      # The peak intensity column. 
 64      if int_col == None: 
 65          int_col = 16 
 66      if int_col == 16: 
 67          print('Using peak heights.') 
 68      if int_col == 15: 
 69          print('Using peak volumes (or evolumes).') 
 70   
 71      # Loop over the file data. 
 72      for line in file_data: 
 73          # Unknown assignment. 
 74          if line[1] == '{}': 
 75              warn(RelaxWarning("The assignment '%s' is unknown, skipping this peak." % line[1])) 
 76              continue 
 77   
 78          # The residue number 
 79          res_num = '' 
 80          try: 
 81              res_num = line[1].strip('{') 
 82              res_num = res_num.strip('}') 
 83              res_num = res_num.split('.') 
 84              res_num = int(res_num[0]) 
 85          except ValueError: 
 86              raise RelaxError("Improperly formatted NMRView file, cannot process the assignment '%s'." % line[1]) 
 87   
 88          # Nuclei names. 
 89          name2 = '' 
 90          if line[1]!='{}': 
 91              name2 = line[1].strip('{') 
 92              name2 = name2.strip('}') 
 93              name2 = name2.split('.') 
 94              name2 = name2[1] 
 95          name1 = '' 
 96          if line[8]!='{}': 
 97              name1 = line[8].strip('{') 
 98              name1 = name1.strip('}') 
 99              name1 = name1.split('.') 
100              name1 = name1[1] 
101   
102          # Chemical shifts. 
103          w1 = None 
104          w2 = None 
105          if w1_col != None: 
106              try: 
107                  w1 = float(line[w1_col]) 
108              except ValueError: 
109                  raise RelaxError("The chemical shift from the line %s is invalid." % line) 
110          if w2_col != None: 
111              try: 
112                  w2 = float(line[w2_col]) 
113              except ValueError: 
114                  raise RelaxError("The 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 " + repr(intensity) + " from the line " + repr(line) + " is invalid.") 
121   
122          # Add the assignment to the peak list object. 
123          peak_list.add(res_nums=[res_num, res_num], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity) 
124