Source Code for Module generic_fns.intensity

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax 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 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax 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 relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  from re import split 
 24   
 25 -class Intensity: 
 26 -    def __init__(self, relax): 
 27          """Class containing functions for handelling peak intensities.""" 
 28   
 29          self.relax = relax 
 30   
 31   
 32 -    def extract_int_data(self, line): 
 33          """Function for returning relevant data from the peak intensity line. 
 34   
 35          The residue number, heteronucleus and proton names, and peak intensity will be returned. 
 36          """ 
 37   
 38          # Sparky formatted line. 
 39          if self.format == 'sparky': 
 40              # The Sparky assignment. 
 41              assignment = split('([A-Z]+)', line[0]) 
 42              assignment = assignment[1:-1] 
 43   
 44              # The residue number. 
 45              try: 
 46                  res_num = int(assignment[1]) 
 47              except: 
 48                  raise RelaxError, "Improperly formatted Sparky file." 
 49   
 50              # Nuclei names. 
 51              x_name = assignment[2] 
 52              h_name = assignment[4] 
 53   
 54              # Intensity. 
 55              intensity = line[self.int_col] 
 56   
 57          # XEasy formatted line. 
 58          elif self.format == 'xeasy': 
 59              # Test for invalid assignment lines which have the column numbers changed and return empty data. 
 60              if line[4] == 'inv.': 
 61                  return None, None, None, 0.0 
 62   
 63              # The residue number. 
 64              try: 
 65                  res_num = int(line[5]) 
 66              except: 
 67                  raise RelaxError, "Improperly formatted XEasy file." 
 68   
 69              # Nuclei names. 
 70              x_name = line[7] 
 71              h_name = line[4] 
 72   
 73              # Intensity. 
 74              intensity = line[self.int_col] 
 75   
 76          # Test the validity of the peak intensity data. 
 77          try: 
 78              intensity = float(intensity) 
 79          except ValueError: 
 80              raise RelaxError, "The peak height value " + `intensity` + " from the line " + `line` + " is invalid." 
 81   
 82          return res_num, x_name, h_name, intensity 
 83   
 84   
 85 -    def read(self, run=None, file=None, dir=None, format=None, heteronuc=None, proton=None, int_col=None, assign_func=None): 
 86          """Function for reading peak intensity data.""" 
 87   
 88          # Arguments. 
 89          self.run = run 
 90          self.format = format 
 91          self.heteronuc = heteronuc 
 92          self.proton = proton 
 93          self.int_col = int_col 
 94          self.assign_func = assign_func 
 95   
 96          # Format argument. 
 97          format_list = ['sparky', 'xeasy'] 
 98          if self.format not in format_list: 
 99              raise RelaxArgNotInListError, ('format', self.format, format_list) 
100          if self.format == 'sparky': 
101              print "Sparky formatted data file.\n" 
102          elif self.format == 'xeasy': 
103              print "XEasy formatted data file.\n" 
104   
105          # Test if the run exists. 
106          if not self.run in self.relax.data.run_names: 
107              raise RelaxNoRunError, self.run 
108   
109          # Test if sequence data is loaded. 
110          if not self.relax.data.res.has_key(self.run): 
111              raise RelaxNoSequenceError, self.run 
112   
113          # Extract the data from the file. 
114          file_data = self.relax.IO.extract_data(file, dir) 
115   
116          # Remove the header. 
117          file_data = file_data[2:] 
118   
119          # Strip the data. 
120          file_data = self.relax.IO.strip(file_data) 
121   
122          # The peak intensity column. 
123          if self.format == 'sparky': 
124              if int_col: 
125                  self.int_col = int_col 
126              else: 
127                  self.int_col = 3 
128          elif self.format == 'xeasy': 
129              self.int_col = 10 
130   
131          # Loop over the peak intensity data. 
132          for i in xrange(len(file_data)): 
133              # Extract the data. 
134              res_num, X_name, H_name, intensity = self.extract_int_data(file_data[i]) 
135   
136              # Skip data. 
137              if X_name != self.heteronuc or H_name != self.proton: 
138                  print "Skipping the data: " + `file_data[i]` 
139                  continue 
140   
141              # Find the index of self.relax.data.res[self.run] which corresponds to res_num. 
142              index = None 
143              for j in xrange(len(self.relax.data.res[self.run])): 
144                  if self.relax.data.res[self.run][j].num == res_num: 
145                      index = j 
146                      break 
147              if index == None: 
148                  print "Skipping the data: " + `file_data[i]` 
149                  continue 
150   
151              # Remap the data structure 'self.relax.data.res[self.run][index]'. 
152              data = self.relax.data.res[self.run][index] 
153   
154              # Skip unselected residues. 
155              if not data.select: 
156                  continue 
157   
158              # Assign the data. 
159              self.assign_func(run=self.run, i=index, intensity=intensity) 
160