Source Code for Module specific_analyses.consistency_tests.parameter_object

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2014 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2007-2009 Sebastien Morin                                     # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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  8  # This program is free software: you can redistribute it and/or modify        # 
  9  # it under the terms of the GNU General Public License as published by        # 
 10  # the Free Software Foundation, either version 3 of the License, or           # 
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 13  # This program is distributed in the hope that it will be useful,             # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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 16  # GNU General Public License for more details.                                # 
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 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """The module for the consistency testing parameter list object.""" 
 25   
 26  # relax module imports. 
 27  from lib.physical_constants import N15_CSA 
 28  from specific_analyses.parameter_object import Param_list 
 29   
 30   
 31 -class Consistency_tests_params(Param_list): 
 32      """The consistency testing parameter list singleton.""" 
 33   
 34      # Class variable for storing the class instance (for the singleton design pattern). 
 35      _instance = None 
 36   
 37 -    def __init__(self): 
 38          """Define all the parameters of the analysis.""" 
 39   
 40          # The object is already initialised. 
 41          if self._initialised: return 
 42   
 43          # Execute the base class __init__ method. 
 44          Param_list.__init__(self) 
 45   
 46          # Add the base information for the analysis. 
 47          self._add_csa(default = N15_CSA) 
 48          self._add( 
 49              'orientation', 
 50              scope = 'spin', 
 51              default = 15.7, 
 52              units = 'degrees', 
 53              desc = "Angle between the 15N-1H vector and the principal axis of the 15N chemical shift tensor", 
 54              py_type = float, 
 55              set = 'fixed', 
 56              grace_string = '\\q\\xq\\Q' 
 57          ) 
 58          self._add( 
 59              'tc', 
 60              scope = 'spin', 
 61              default = 13 * 1e-9, 
 62              units = 'ns', 
 63              desc = "The single global correlation time estimate/approximation", 
 64              py_type = float, 
 65              set = 'fixed', 
 66              grace_string = '\\q\\xt\\f{}c\\Q' 
 67          ) 
 68   
 69          # Add the model parameters. 
 70          self._add( 
 71              'j0', 
 72              scope = 'spin', 
 73              desc = 'Spectral density value at 0 MHz (from Farrow et al. (1995) JBNMR, 6: 153-162)', 
 74              py_type = float, 
 75              set = 'params', 
 76              grace_string = '\\qJ(0)\\Q', 
 77              err = True, 
 78              sim = True 
 79          ) 
 80          self._add( 
 81              'f_eta', 
 82              scope = 'spin', 
 83              desc = 'Eta-test (from Fushman et al. (1998) JACS, 120: 10947-10952)', 
 84              py_type = float, 
 85              set = 'params', 
 86              grace_string = '\\qF\\s\\xh\\Q', 
 87              err = True, 
 88              sim = True 
 89          ) 
 90          self._add( 
 91              'f_r2', 
 92              scope = 'spin', 
 93              desc = 'R2-test (from Fushman et al. (1998) JACS, 120: 10947-10952)', 
 94              py_type = float, 
 95              set = 'params', 
 96              grace_string = '\\qF\\sR2\\Q', 
 97              err = True, 
 98              sim = True 
 99          ) 
100   
101          # Set up the user function documentation. 
102          self._set_uf_title("Consistency testing parameters") 
103          self._uf_param_table(label="table: consistency testing parameters", caption="Consistency testing parameters.") 
104          self._uf_param_table(label="table: consistency testing parameter value setting", caption="Consistency testing parameters.") 
105          self._uf_param_table(label="table: consistency testing parameter value setting with defaults", caption="Consistency testing parameter value setting.", default=True) 
106   
107          # Value setting documentation. 
108          for doc in self._uf_doc_loop(["table: consistency testing parameter value setting", "table: consistency testing parameter value setting with defaults"]): 
109              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.") 
110