Source Code for Package specific_fns.model_free

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2007-2013 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  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           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 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.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Analysis specific code for the Lipari-Szabo model-free analysis.""" 
 24   
 25   
 26  # The available modules. 
 27  __all__ = [ 'bmrb', 
 28              'macro_base', 
 29              'main', 
 30              'mf_minimise', 
 31              'molmol', 
 32              'multi_processor_commands', 
 33              'pymol', 
 34              'results' 
 35  ] 
 36   
 37  # relax module imports. 
 38  from generic_fns import diffusion_tensor, relax_data 
 39  from physical_constants import N15_CSA, NH_BOND_LENGTH 
 40  from specific_fns.api_base import API_base 
 41  from specific_fns.api_common import API_common 
 42  from specific_fns.model_free.bmrb import Bmrb 
 43  from specific_fns.model_free.main import Model_free_main 
 44  from specific_fns.model_free.mf_minimise import Mf_minimise 
 45  from specific_fns.model_free.molmol import Molmol 
 46  from specific_fns.model_free.pymol import Pymol 
 47  from specific_fns.model_free.results import Results 
 48   
 49   
 50 -class Model_free(Model_free_main, Mf_minimise, Results, Bmrb, API_base, API_common): 
 51      """Parent class containing all the model-free specific functions.""" 
 52   
 53 -    def __init__(self): 
 54          """Initialise the class by placing API_common methods into the API.""" 
 55   
 56          # Execute the base class __init__ method. 
 57          super(Model_free, self).__init__() 
 58   
 59          # Place methods into the API. 
 60          self.base_data_loop = self._base_data_loop_spin 
 61          self.return_error = self._return_error_relax_data 
 62          self.return_value = self._return_value_general 
 63          self.sim_pack_data = self._sim_pack_relax_data 
 64          self.test_grid_ops = self._test_grid_ops_general 
 65   
 66          # Initialise the macro classes. 
 67          self._molmol_macros = Molmol() 
 68          self._pymol_macros = Pymol() 
 69   
 70          # Alias the macro creation methods. 
 71          self.pymol_macro = self._pymol_macros.create_macro 
 72          self.molmol_macro = self._molmol_macros.create_macro 
 73   
 74          # Set up the global parameters. 
 75          self.PARAMS.add('tm', scope='global', default=diffusion_tensor.default_value('tm'), conv_factor=1e-9, grace_string='\\xt\\f{}\\sm', units='ns', py_type=float, set='params', err=True, sim=True) 
 76          self.PARAMS.add('Diso', scope='global', default=diffusion_tensor.default_value('Diso'), py_type=float, set='params', err=True, sim=True) 
 77          self.PARAMS.add('Dx', scope='global', default=diffusion_tensor.default_value('Dx'), py_type=float, set='params', err=True, sim=True) 
 78          self.PARAMS.add('Dy', scope='global', default=diffusion_tensor.default_value('Dy'), py_type=float, set='params', err=True, sim=True) 
 79          self.PARAMS.add('Dz', scope='global', default=diffusion_tensor.default_value('Dz'), py_type=float, set='params', err=True, sim=True) 
 80          self.PARAMS.add('Dpar', scope='global', default=diffusion_tensor.default_value('Dpar'), py_type=float, set='params', err=True, sim=True) 
 81          self.PARAMS.add('Dper', scope='global', default=diffusion_tensor.default_value('Dper'), py_type=float, set='params', err=True, sim=True) 
 82          self.PARAMS.add('Da', scope='global', default=diffusion_tensor.default_value('Da'), py_type=float, set='params', err=True, sim=True) 
 83          self.PARAMS.add('Dratio', scope='global', default=diffusion_tensor.default_value('Dratio'), py_type=float, set='params', err=True, sim=True) 
 84          self.PARAMS.add('Dr', scope='global', default=diffusion_tensor.default_value('Dr'), py_type=float, set='params', err=True, sim=True) 
 85          self.PARAMS.add('alpha', scope='global', default=diffusion_tensor.default_value('alpha'), py_type=float, set='params', err=True, sim=True) 
 86          self.PARAMS.add('beta', scope='global', default=diffusion_tensor.default_value('beta'), py_type=float, set='params', err=True, sim=True) 
 87          self.PARAMS.add('gamma', scope='global', default=diffusion_tensor.default_value('gamma'), py_type=float, set='params', err=True, sim=True) 
 88          self.PARAMS.add('theta', scope='global', default=diffusion_tensor.default_value('theta'), py_type=float, set='params', err=True, sim=True) 
 89          self.PARAMS.add('phi', scope='global', default=diffusion_tensor.default_value('phi'), py_type=float, set='params', err=True, sim=True) 
 90   
 91          # Set up the spin parameters. 
 92          self.PARAMS.add('model', scope='spin', desc='The model', py_type=str) 
 93          self.PARAMS.add('equation', scope='spin', desc='The model equation', py_type=str) 
 94          self.PARAMS.add('params', scope='spin', desc='The model parameters', py_type=list) 
 95          self.PARAMS.add('s2', scope='spin', default=0.8, desc='S2, the model-free generalised order parameter (S2 = S2f.S2s)', py_type=float, set='params', grace_string='\\qS\\v{0.4}\\z{0.71}2\\Q', err=True, sim=True) 
 96          self.PARAMS.add('s2f', scope='spin', default=0.8, desc='S2f, the faster motion model-free generalised order parameter', py_type=float, set='params', grace_string='\\qS\\sf\\N\\h{-0.2}\\v{0.4}\\z{0.71}2\\Q', err=True, sim=True) 
 97          self.PARAMS.add('s2s', scope='spin', default=0.8, desc='S2s, the slower motion model-free generalised order parameter', py_type=float, set='params', grace_string='\\qS\\ss\\N\\h{-0.2}\\v{0.4}\\z{0.71}2\\Q', err=True, sim=True) 
 98          self.PARAMS.add('local_tm', scope='spin', default=10.0 * 1e-9, desc='The spin specific global correlation time (seconds)', py_type=float, set='params', grace_string='\\xt\\f{}\\sm', units='ns', err=True, sim=True) 
 99          self.PARAMS.add('te', scope='spin', default=100.0 * 1e-12, desc='Single motion effective internal correlation time (seconds)', py_type=float, set='params', conv_factor=1e-12, grace_string='\\xt\\f{}\\se', units='ps', err=True, sim=True) 
100          self.PARAMS.add('tf', scope='spin', default=10.0 * 1e-12, desc='Faster motion effective internal correlation time (seconds)', py_type=float, set='params', conv_factor=1e-12, grace_string='\\xt\\f{}\\sf', units='ps', err=True, sim=True) 
101          self.PARAMS.add('ts', scope='spin', default=1000.0 * 1e-12, desc='Slower motion effective internal correlation time (seconds)', py_type=float, set='params', conv_factor=1e-12, grace_string='\\xt\\f{}\\ss', units='ps', err=True, sim=True) 
102          self.PARAMS.add('rex', scope='spin', default=0.0, desc='Chemical exchange relaxation (sigma_ex = Rex / omega**2)', py_type=float, set='params', conv_factor=self._conv_factor_rex, units=self._units_rex, grace_string='\\qR\\sex\\Q', err=True, sim=True) 
103          self.PARAMS.add('csa', scope='spin', default=N15_CSA, units='ppm', desc='Chemical shift anisotropy (unitless)', py_type=float, set='params', conv_factor=1e-6, grace_string='\\qCSA\\Q', err=True, sim=True) 
104   
105          # Add the minimisation data. 
106          self.PARAMS.add_min_data(min_stats_global=True, min_stats_spin=True) 
107   
108          # Add the relaxation data parameters. 
109          self.PARAMS.add('ri_data', scope='spin', desc=relax_data.return_data_desc('ri_data'), py_type=dict, err=False, sim=True) 
110          self.PARAMS.add('ri_data_err', scope='spin', desc=relax_data.return_data_desc('ri_data_err'), py_type=dict, err=False, sim=False) 
111