Source Code for Module lib.spectrum.nmrpipe

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013 Troels E. Linnet                                         # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  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  """Module containing functions for handling NMRPipe SeriesTab files.""" 
 24   
 25   
 26  # Python module imports. 
 27  import re 
 28   
 29  # relax module imports. 
 30  from lib.errors import RelaxError 
 31  from lib.io import open_write_file, strip 
 32   
 33   
 34 -def read_seriestab(peak_list=None, file_data=None, int_col=None): 
 35      """Extract the intensity information from the NMRPipe SeriesTab peak intensity file. 
 36   
 37      @keyword peak_list: The peak list object to place all data into. 
 38      @type peak_list:    lib.spectrum.objects.Peak_list instance 
 39      @keyword file_data: The data extracted from the file converted into a list of lists. 
 40      @type file_data:    list of lists of str 
 41      @keyword int_col:  The column which to multiply the peak intensity data (used by the SeriesTab intensity file format). 
 42      @type int_col:     int 
 43      @raises RelaxError: When the expected peak intensity is not a float. 
 44      """ 
 45   
 46      # Set start variables. 
 47      modeline = False 
 48      mode = False 
 49      varsline = False 
 50      header = False 
 51   
 52      # Loop over lines, to extract variables and find header size. 
 53      line_nr = 0 
 54      for line in file_data: 
 55          if len(line) > 0: 
 56              if line[0] == 'REMARK' and line[1] == 'Mode:': 
 57                  modeline = line[2:] 
 58                  mode = modeline[0] 
 59              elif line[0] == 'VARS': 
 60                  varsline = line[1:] 
 61              elif line[0] == '1': 
 62                  header = line_nr 
 63                  break 
 64          line_nr += 1 
 65   
 66      # Raise RelaxError, if the MODE is not found. 
 67      if not (modeline and mode): 
 68          raise RelaxError("MODE not detected. Expecting line 2:\nREMARK Mode: Summation") 
 69   
 70      # Raise RelaxError, if the VARS line is not found. 
 71      if not (varsline): 
 72          raise RelaxError("VARS not detected. Expecting line 8:\nVARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0") 
 73   
 74      # Raise RelaxError, if the header size is not found. 
 75      if not header: 
 76          raise RelaxError("'1' not detected in start of line. Cannot determine header size.") 
 77   
 78      # Find index of assignment ASS. 
 79      ass_i = varsline.index('ASS') 
 80   
 81      # Make a regular search for Z_A entries. 
 82      Z_A = re.compile("Z_A*") 
 83      spectra = list(filter(Z_A.search, varsline)) 
 84   
 85      # Find index of Z_A entries. 
 86      spectra_i = [] 
 87      for y in spectra: 
 88          spectra_i.append(varsline.index(y)) 
 89   
 90      # Remove the header. 
 91      file_data = file_data[header:] 
 92   
 93      # Loop over the file data. 
 94      for line in file_data: 
 95          # Skip non-assigned peaks. 
 96          if line[ass_i] == '?-?': 
 97              continue 
 98   
 99          # First split by the 2D separator. 
100          assign1, assign2 = re.split('-', line[ass_i]) 
101   
102          # The assignment of the first dimension. 
103          row1 = re.split('([a-zA-Z]+)', assign1) 
104          name1 = row1[-2] + row1[-1] 
105   
106          # The assignment of the second dimension. 
107          row2 = re.split('([a-zA-Z]+)', assign2) 
108          name2 = row2[-2] + row2[-1] 
109   
110          # Get the residue number. 
111          try: 
112              res_num = int(row1[-3]) 
113          except: 
114              raise RelaxError("Improperly formatted NMRPipe SeriesTab file., cannot process the assignment '%s'." % line[0]) 
115   
116          # Get the intensities. 
117          try: 
118              # Loop over the spectra. 
119              intensities = [] 
120              for i in range(len(spectra)): 
121                  # The intensity is given by column multiplication. 
122                  intensities.append(float(line[spectra_i[i]])*float(line[5])) 
123   
124          # Bad data. 
125          except ValueError: 
126              raise RelaxError("The peak intensity value %s from the line %s is invalid." % (intensity, line)) 
127   
128          # Add the assignment to the peak list object. 
129          peak_list.add(res_nums=[res_num, res_num], spin_names=[name1, name2], intensity=intensities, intensity_name=spectra) 
130