Source Code for Module pipe_control.chemical_shift

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
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  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           # 
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 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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 15  # GNU General Public License for more details.                                # 
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 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Module containing functions for the handling of chemical shifts.""" 
 24   
 25   
 26  # Python module imports. 
 27  import sys 
 28  from warnings import warn 
 29   
 30  # relax module imports. 
 31  from lib.errors import RelaxError, RelaxNoSequenceError 
 32  from lib.io import write_data 
 33  from lib.spectrum.peak_list import read_peak_list 
 34  from lib.warnings import RelaxNoSpinWarning 
 35  from pipe_control import pipes 
 36  from pipe_control.mol_res_spin import exists_mol_res_spin_data, generate_spin_id_unique, return_spin 
 37   
 38   
 39 -def read(file=None, dir=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, verbose=True): 
 40      """Read the peak intensity data. 
 41   
 42      @keyword file:          The name of the file containing the peak intensities. 
 43      @type file:             str 
 44      @keyword dir:           The directory where the file is located. 
 45      @type dir:              str 
 46      @keyword spin_id_col:   The column containing the spin ID strings (used by the generic intensity file format).  If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none. 
 47      @type spin_id_col:      int or None 
 48      @keyword mol_name_col:  The column containing the molecule name information (used by the generic intensity file format).  If supplied, spin_id_col must be None. 
 49      @type mol_name_col:     int or None 
 50      @keyword res_name_col:  The column containing the residue name information (used by the generic intensity file format).  If supplied, spin_id_col must be None. 
 51      @type res_name_col:     int or None 
 52      @keyword res_num_col:   The column containing the residue number information (used by the generic intensity file format).  If supplied, spin_id_col must be None. 
 53      @type res_num_col:      int or None 
 54      @keyword spin_name_col: The column containing the spin name information (used by the generic intensity file format).  If supplied, spin_id_col must be None. 
 55      @type spin_name_col:    int or None 
 56      @keyword spin_num_col:  The column containing the spin number information (used by the generic intensity file format).  If supplied, spin_id_col must be None. 
 57      @type spin_num_col:     int or None 
 58      @keyword sep:           The column separator which, if None, defaults to whitespace. 
 59      @type sep:              str or None 
 60      @keyword spin_id:       The spin ID string used to restrict data loading to a subset of all spins.  If 'auto' is provided for a NMRPipe seriesTab formatted file, the ID's are auto generated in form of Z_Ai. 
 61      @type spin_id:          None or str 
 62      @keyword verbose:       A flag which if True will cause all chemical shift data loaded to be printed out. 
 63      @type verbose:          bool 
 64      """ 
 65   
 66      # Test if the current data pipe exists. 
 67      pipes.test() 
 68   
 69      # Test if sequence data is loaded. 
 70      if not exists_mol_res_spin_data(): 
 71          raise RelaxNoSequenceError 
 72   
 73      # Check the file name. 
 74      if file == None: 
 75          raise RelaxError("The file name must be supplied.") 
 76   
 77      # Read the peak list data. 
 78      peak_list = read_peak_list(file=file, dir=dir, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id) 
 79   
 80      # Loop over the assignments. 
 81      data = [] 
 82      data_flag = False 
 83      for assign in peak_list: 
 84          # Loop over the dimensions of the peak list. 
 85          for i in range(peak_list.dimensionality): 
 86              # Generate the spin_id. 
 87              spin_id = generate_spin_id_unique(res_num=assign.res_nums[i], spin_name=assign.spin_names[i]) 
 88   
 89              # Get the spin container. 
 90              spin = return_spin(spin_id) 
 91              if not spin: 
 92                  warn(RelaxNoSpinWarning(spin_id)) 
 93                  continue 
 94   
 95              # Skip deselected spins. 
 96              if not spin.select: 
 97                  continue 
 98   
 99              # Store the shift. 
100              spin.chemical_shift = assign.shifts[i] 
101   
102              # Switch the flag. 
103              data_flag = True 
104   
105              # Append the data for printing out. 
106              data.append([spin_id, repr(spin.chemical_shift)]) 
107   
108      # No data. 
109      if not data_flag: 
110          raise RelaxError("No chemical shifts could be loaded from the peak list") 
111   
112      # Print out. 
113      if verbose: 
114          print("\nThe following chemical shifts have been loaded into the relax data store:\n") 
115          write_data(out=sys.stdout, headings=["Spin_ID", "Chemical shift"], data=data) 
116