Source Code for Module generic_fns.bruker

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2011-2012 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        # 
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 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           # 
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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module for the reading of Bruker Dynamics Centre (DC) files.""" 
 25   
 26  # Python module imports. 
 27  from re import search, split 
 28  from string import strip 
 29   
 30  # relax module imports. 
 31  from generic_fns import pipes 
 32  from generic_fns import value 
 33  from generic_fns.exp_info import software_select 
 34  from generic_fns.mol_res_spin import exists_mol_res_spin_data, name_spin, spin_loop 
 35  from generic_fns.relax_data import pack_data, peak_intensity_type 
 36  from relax_errors import RelaxError 
 37  from relax_io import open_read_file 
 38   
 39   
 40 -def convert_relax_data(data): 
 41      """Determine the relaxation data from the given DC data. 
 42   
 43      @param data:    The list of Tx, Tx error, and scaling factor for a given residue from the DC file. 
 44      @type data:     list of str 
 45      """ 
 46   
 47      # Convert the value from Tx to Rx. 
 48      rx = 1.0 / float(data[0]) 
 49   
 50      # Remove the scaling. 
 51      rx_err = float(data[1]) / float(data[2]) 
 52   
 53      # Convert the Tx error to an Rx error. 
 54      rx_err = rx**2 * rx_err 
 55   
 56      # Return the value and error. 
 57      return rx, rx_err 
 58   
 59   
 60 -def get_res_num(data): 
 61      """Determine the residue number from the given DC data. 
 62   
 63      @param data:    The list of residue info, split by whitespace, from the DC file. 
 64      @type data:     list of str 
 65      """ 
 66   
 67      # Init. 
 68      res_num = None 
 69   
 70      # Split the data. 
 71      row = split('([0-9]+)', data) 
 72   
 73      # Loop over the new list. 
 74      for j in range(len(row)): 
 75          try: 
 76              res_num = int(row[j]) 
 77          except ValueError: 
 78              pass 
 79   
 80      # Return the value. 
 81      return ":%s" % res_num 
 82   
 83   
 84 -def read(ri_id=None, file=None, dir=None): 
 85      """Read the DC data file and place all the data into the relax data store. 
 86   
 87      @keyword ri_id: The relaxation data ID string. 
 88      @type ri_id:    str 
 89      @keyword file:  The name of the file to open. 
 90      @type file:     str 
 91      @keyword dir:   The directory containing the file (defaults to the current directory if None). 
 92      @type dir:      str or None 
 93      """ 
 94   
 95      # Test if the current pipe exists. 
 96      pipes.test() 
 97   
 98      # Test if sequence data is loaded. 
 99      if not exists_mol_res_spin_data(): 
100          raise RelaxNoSequenceError 
101   
102      # Extract the data from the file. 
103      file_handle = open_read_file(file, dir) 
104      lines = file_handle.readlines() 
105      file_handle.close() 
106   
107      # Init. 
108      values = [] 
109      errors = [] 
110      res_nums = [] 
111      int_type = None 
112   
113      # Loop over the data. 
114      in_ri_data = False 
115      for line in lines: 
116          # Split the line. 
117          row = split("\t", line) 
118   
119          # Strip the rubbish. 
120          for j in range(len(row)): 
121              row[j] = strip(row[j]) 
122   
123          # Empty line. 
124          if len(row) == 0: 
125              continue 
126   
127          # The DC version. 
128          if row[0] == 'generated by:': 
129              version = row[1] 
130   
131          # Check for bad errors. 
132          if row[0] == 'Systematic error estimation of data:': 
133              # Badness. 
134              if row[1] == 'worst case per peak scenario': 
135                  raise RelaxError("The errors estimation method \"worst case per peak scenario\" is not suitable for model-free analysis.  Please go back to the DC and switch to \"average variance calculation\".") 
136   
137          # The data type. 
138          if row[0] == 'Project:': 
139              if search('T1', row[1]): 
140                  ri_type = 'R1' 
141              elif search('T2', row[1]): 
142                  ri_type = 'R2' 
143              elif search('NOE', row[1]): 
144                  ri_type = 'NOE' 
145   
146          # Get the frequency, converting to Hz. 
147          elif row[0] == 'Proton frequency[MHz]:': 
148              frq = float(row[1]) * 1e6 
149   
150          # Inside the relaxation data section. 
151          elif row[0] == 'SECTION:' and row[1] == 'results': 
152              in_ri_data = True 
153   
154          # The relaxation data. 
155          elif in_ri_data: 
156              # Skip the header. 
157              if row[0] == 'Peak name': 
158                  continue 
159   
160              # The residue info. 
161              res_nums.append(get_res_num(row[0])) 
162   
163              # Get the relaxation data. 
164              if ri_type != 'NOE': 
165                  #rx, rx_err = convert_relax_data(row[3:]) 
166                  rx = float(row[-2]) 
167                  rx_err = float(row[-1]) 
168              else: 
169                  rx = float(row[-3]) 
170                  rx_err = float(row[-2]) 
171   
172              # Append the data. 
173              values.append(rx) 
174              errors.append(rx_err) 
175   
176          # The temperature. 
177          elif row[0] == 'Temperature (K):': 
178              # Set the value (not implemented yet). 
179              pass 
180   
181          # The labelling. 
182          elif row[0] == 'Labelling:': 
183              # Set the heteronucleus value. 
184              value.set(row[1], 'heteronuc_type') 
185   
186              # Name the spins. 
187              name = split('([A-Z]+)', row[1])[1] 
188              name_spin(name=name) 
189   
190          # The integration method. 
191          elif row[0] == 'Used integrals:': 
192              # Peak heights. 
193              if row[1] == 'peak intensities': 
194                  int_type = 'height' 
195   
196              # Peak volumes: 
197              if row[1] == 'area integral': 
198                  int_type = 'volume' 
199   
200      # Pack the data. 
201      pack_data(ri_id, ri_type, frq, values, errors, spin_ids=res_nums) 
202   
203      # Set the integration method. 
204      peak_intensity_type(ri_id=ri_id, type=int_type) 
205   
206      # Set the DC as used software. 
207      software_select('Bruker DC', version=version) 
208