Source Code for Module specific_analyses.n_state_model.parameter_object

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2007-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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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              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 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  """The module for the N-state model parameter list object.""" 
 24   
 25  # Python module imports. 
 26  from math import pi 
 27   
 28  # relax module imports. 
 29  from specific_analyses.parameter_object import Param_list 
 30   
 31   
 32 -class N_state_params(Param_list): 
 33      """The N-state model 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 data. 
 48          self._add_align_data() 
 49          self._add_align_tensor() 
 50   
 51          # Add up the model parameters. 
 52          self._add( 
 53              'probs', 
 54              scope = 'global', 
 55              default = 0.0, 
 56              desc = 'The probabilities of each state', 
 57              py_type = list, 
 58              set = 'params', 
 59              scaling = 0.1, 
 60              grid_lower = 0.0, 
 61              grid_upper = 1.0, 
 62              err = True, 
 63              sim = True 
 64          ) 
 65          self._add( 
 66              'alpha', 
 67              scope = 'global', 
 68              units = 'rad', 
 69              default = 0.0, 
 70              desc = 'The alpha Euler angles (for the rotation of each state)', 
 71              py_type = list, 
 72              set = 'params', 
 73              grid_lower = 0.0, 
 74              grid_upper = 2*pi, 
 75              err = True, 
 76              sim = True 
 77          ) 
 78          self._add( 
 79              'beta', 
 80              scope = 'global', 
 81              units = 'rad', 
 82              default = 0.0, 
 83              desc = 'The beta Euler angles (for the rotation of each state)', 
 84              py_type = list, 
 85              set = 'params', 
 86              grid_lower = 0.0, 
 87              grid_upper = 2*pi, 
 88              err = True, 
 89              sim = True 
 90          ) 
 91          self._add( 
 92              'gamma', 
 93              scope = 'global', 
 94              units = 'rad', 
 95              default = 0.0, 
 96              desc = 'The gamma Euler angles (for the rotation of each state)', 
 97              py_type = list, 
 98              set = 'params', 
 99              grid_lower = 0.0, 
100              grid_upper = 2*pi, 
101              err = True, 
102              sim = True 
103          ) 
104          self._add( 
105              'paramagnetic_centre', 
106              scope = 'global', 
107              units = 'Angstrom', 
108              desc = 'The paramagnetic centre', 
109              py_type = list, 
110              set = 'params', 
111              scaling = 1e2, 
112              grid_lower = -100.0, 
113              grid_upper = 100, 
114              err = True, 
115              sim = True 
116          ) 
117   
118          # Add the minimisation data. 
119          self._add_min_data(min_stats_global=False, min_stats_spin=True) 
120   
121          # Set up the user function documentation. 
122          self._set_uf_title("N-state model parameters") 
123          self._uf_param_table(label="table: N-state parameters", caption="N-state model parameters.", scope='global', type=True) 
124          self._uf_param_table(label="table: N-state parameter value setting", caption="N-state model parameters.", scope='global', type=True) 
125          self._uf_param_table(label="table: N-state parameter value setting with defaults", caption="N-state model parameter value setting.", scope='global', default=True, type=True) 
126   
127          # Value setting documentation. 
128          for doc in self._uf_doc_loop(["table: N-state parameter value setting", "table: N-state parameter value setting with defaults"]): 
129              doc.add_paragraph("Setting parameters for the N-state model is a little different from the other type of analyses as each state has a set of parameters with the same names as the other states.  To set the parameters for a specific state c (ranging from 0 for the first to N-1 for the last, the number c should be given as the index argument.  So the Euler angle gamma of the third state is specified using the parameter name 'gamma' and index of 2.") 
130