Source Code for Module pipe_control.bruker

 1  ############################################################################### 
 2  #                                                                             # 
 3  # Copyright (C) 2011-2013,2019 Edward d'Auvergne                              # 
 4  #                                                                             # 
 5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 7  # This program is free software: you can redistribute it and/or modify        # 
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15  # GNU General Public License for more details.                                # 
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20  ############################################################################### 
21   
22  # Module docstring. 
23  """Module for the reading of Bruker Dynamics Centre (DC) files.""" 
24   
25  # relax module imports. 
26  from lib.errors import RelaxNoSequenceError 
27  from lib.physical_constants import element_from_isotope 
28  from lib.software.bruker_dc import create_object 
29  from pipe_control.exp_info import software_select 
30  from pipe_control.mol_res_spin import exists_mol_res_spin_data, name_spin 
31  from pipe_control.pipes import check_pipe 
32  from pipe_control.relax_data import pack_data, peak_intensity_type 
33   
34   
35 -def read(ri_id=None, file=None, dir=None): 
36      """Read the DC data file and place all the data into the relax data store. 
37   
38      @keyword ri_id: The relaxation data ID string. 
39      @type ri_id:    str 
40      @keyword file:  The name of the file to open. 
41      @type file:     str 
42      @keyword dir:   The directory containing the file (defaults to the current directory if None). 
43      @type dir:      str or None 
44      """ 
45   
46      # Test if the current pipe exists. 
47      check_pipe() 
48   
49      # Test if sequence data is loaded. 
50      if not exists_mol_res_spin_data(): 
51          raise RelaxNoSequenceError 
52   
53      # Extract the data from the file. 
54      dc_object = create_object(file=file, dir=dir) 
55   
56      # Name the spins if needed. 
57      name_spin(name=dc_object.sample_information.spin_name, force=False, warn_flag=False) 
58   
59      # Pack the data. 
60      values = [] 
61      errors = [] 
62      spin_ids = [] 
63      for res_id in dc_object.results.sequence: 
64          spin_ids.append('%s@%s' % (res_id, dc_object.sample_information.atom_name)) 
65          values.append(dc_object.results.Rx[res_id]) 
66          errors.append(dc_object.results.Rx_err[res_id]) 
67      pack_data(ri_id, dc_object.ri_type, dc_object.parameters.frq, values, errors, spin_ids=spin_ids) 
68   
69      # Set the integration method. 
70      peak_intensity_type(ri_id=ri_id, type=dc_object.details.int_type) 
71   
72      # Set the DC as used software. 
73      software_select('Bruker DC', version=dc_object.version) 
74