Source Code for Module specific_analyses.consistency_tests.parameter_object

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2002-2005,2007-2014 Edward d'Auvergne                         # 
  4  # Copyright (C) 2006 Chris MacRaild                                           # 
  5  # Copyright (C) 2007-2008 Sebastien Morin                                     # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
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 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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 17  # GNU General Public License for more details.                                # 
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 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """The module for the consistency testing parameter list object.""" 
 26   
 27  # relax module imports. 
 28  from lib.physical_constants import N15_CSA 
 29  from specific_analyses.parameter_object import Param_list 
 30   
 31   
 32 -class Consistency_tests_params(Param_list): 
 33      """The consistency testing parameter list singleton.""" 
 34   
 35      # Class variable for storing the class instance (for the singleton design pattern). 
 36      _instance = None 
 37   
 38 -    def __init__(self): 
 39          """Define all the parameters of the analysis.""" 
 40   
 41          # The object is already initialised. 
 42          if self._initialised: return 
 43   
 44          # Execute the base class __init__ method. 
 45          Param_list.__init__(self) 
 46   
 47          # Add the base information for the analysis. 
 48          self._add_csa(default = N15_CSA) 
 49          self._add( 
 50              'orientation', 
 51              scope = 'spin', 
 52              default = 15.7, 
 53              units = 'degrees', 
 54              desc = "Angle between the 15N-1H vector and the principal axis of the 15N chemical shift tensor", 
 55              py_type = float, 
 56              set = 'fixed', 
 57              grace_string = '\\q\\xq\\Q' 
 58          ) 
 59          self._add( 
 60              'tc', 
 61              scope = 'spin', 
 62              default = 13 * 1e-9, 
 63              units = 'ns', 
 64              desc = "The single global correlation time estimate/approximation", 
 65              py_type = float, 
 66              set = 'fixed', 
 67              grace_string = '\\q\\xt\\f{}c\\Q' 
 68          ) 
 69   
 70          # Add the model parameters. 
 71          self._add( 
 72              'j0', 
 73              scope = 'spin', 
 74              desc = 'Spectral density value at 0 MHz (from Farrow et al. (1995) JBNMR, 6: 153-162)', 
 75              py_type = float, 
 76              set = 'params', 
 77              grace_string = '\\qJ(0)\\Q', 
 78              err = True, 
 79              sim = True 
 80          ) 
 81          self._add( 
 82              'f_eta', 
 83              scope = 'spin', 
 84              desc = 'Eta-test (from Fushman et al. (1998) JACS, 120: 10947-10952)', 
 85              py_type = float, 
 86              set = 'params', 
 87              grace_string = '\\qF\\s\\xh\\Q', 
 88              err = True, 
 89              sim = True 
 90          ) 
 91          self._add( 
 92              'f_r2', 
 93              scope = 'spin', 
 94              desc = 'R2-test (from Fushman et al. (1998) JACS, 120: 10947-10952)', 
 95              py_type = float, 
 96              set = 'params', 
 97              grace_string = '\\qF\\sR2\\Q', 
 98              err = True, 
 99              sim = True 
100          ) 
101   
102          # Set up the user function documentation. 
103          self._set_uf_title("Consistency testing parameters") 
104          self._uf_param_table(label="table: consistency testing parameters", caption="Consistency testing parameters.") 
105          self._uf_param_table(label="table: consistency testing parameter value setting", caption="Consistency testing parameters.") 
106          self._uf_param_table(label="table: consistency testing parameter value setting with defaults", caption="Consistency testing parameter value setting.", default=True) 
107   
108          # Value setting documentation. 
109          for doc in self._uf_doc_loop(["table: consistency testing parameter value setting", "table: consistency testing parameter value setting with defaults"]): 
110              doc.add_paragraph("In consistency testing, the CSA value, angle Theta ('orientation') and global correlation time must be set prior to the calculation of consistency functions.") 
111