Source Code for Package specific_fns.model_free

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2007-2012 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax 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 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax 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           # 
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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """The model-free specific code.""" 
 25   
 26   
 27  # The available modules. 
 28  __all__ = [ 'bmrb', 
 29              'macro_base', 
 30              'main', 
 31              'mf_minimise', 
 32              'molmol', 
 33              'multi_processor_commands', 
 34              'pymol', 
 35              'results' 
 36  ] 
 37   
 38  # relax module imports. 
 39  from bmrb import Bmrb 
 40  from generic_fns import diffusion_tensor 
 41  from main import Model_free_main 
 42  from mf_minimise import Mf_minimise 
 43  from molmol import Molmol 
 44  from physical_constants import N15_CSA, NH_BOND_LENGTH 
 45  from pymol import Pymol 
 46  from results import Results 
 47  from specific_fns.api_base import API_base 
 48  from specific_fns.api_common import API_common 
 49   
 50   
 51 -class Model_free(Model_free_main, Mf_minimise, Results, Bmrb, API_base, API_common): 
 52      """Parent class containing all the model-free specific functions.""" 
 53   
 54 -    def __init__(self): 
 55          """Initialise the class by placing API_common methods into the API.""" 
 56   
 57          # Place methods into the API. 
 58          self.base_data_loop = self._base_data_loop_spin 
 59          self.return_error = self._return_error_relax_data 
 60          self.return_conversion_factor = self._return_conversion_factor_spin 
 61          self.return_grace_string = self._return_grace_string_spin 
 62          self.return_units = self._return_units_spin 
 63          self.return_value = self._return_value_general 
 64          self.sim_pack_data = self._sim_pack_relax_data 
 65          self.test_grid_ops = self._test_grid_ops_general 
 66   
 67          # Initialise the macro classes. 
 68          self._molmol_macros = Molmol() 
 69          self._pymol_macros = Pymol() 
 70   
 71          # Alias the macro creation methods. 
 72          self.pymol_macro = self._pymol_macros.create_macro 
 73          self.molmol_macro = self._molmol_macros.create_macro 
 74   
 75          # Set up the spin parameters. 
 76          self.SPIN_PARAMS.add('tm', default=diffusion_tensor.default_value('tm'), conv_factor=1e-9, grace_string='\\xt\\f{}\\sm', units='ns') 
 77          self.SPIN_PARAMS.add('Diso', default=diffusion_tensor.default_value('Diso')) 
 78          self.SPIN_PARAMS.add('Dx', default=diffusion_tensor.default_value('Dx')) 
 79          self.SPIN_PARAMS.add('Dy', default=diffusion_tensor.default_value('Dy')) 
 80          self.SPIN_PARAMS.add('Dz', default=diffusion_tensor.default_value('Dz')) 
 81          self.SPIN_PARAMS.add('Dpar', default=diffusion_tensor.default_value('Dpar')) 
 82          self.SPIN_PARAMS.add('Dper', default=diffusion_tensor.default_value('Dper')) 
 83          self.SPIN_PARAMS.add('Da', default=diffusion_tensor.default_value('Da')) 
 84          self.SPIN_PARAMS.add('Dratio', default=diffusion_tensor.default_value('Dratio')) 
 85          self.SPIN_PARAMS.add('alpha', default=diffusion_tensor.default_value('alpha')) 
 86          self.SPIN_PARAMS.add('beta', default=diffusion_tensor.default_value('beta')) 
 87          self.SPIN_PARAMS.add('gamma', default=diffusion_tensor.default_value('gamma')) 
 88          self.SPIN_PARAMS.add('theta', default=diffusion_tensor.default_value('theta')) 
 89          self.SPIN_PARAMS.add('phi', default=diffusion_tensor.default_value('phi')) 
 90          self.SPIN_PARAMS.add('local_tm', default=10.0 * 1e-9, desc='The spin specific global correlation time (seconds)', grace_string='\\xt\\f{}\\sm', units='ns') 
 91          self.SPIN_PARAMS.add('s2', default=0.8, desc='S2, the model-free generalised order parameter (S2 = S2f.S2s)', grace_string='\\qS\\v{0.4}\\z{0.71}2\\Q') 
 92          self.SPIN_PARAMS.add('s2f', default=0.8, desc='S2f, the faster motion model-free generalised order parameter', grace_string='\\qS\\sf\\N\\h{-0.2}\\v{0.4}\\z{0.71}2\\Q') 
 93          self.SPIN_PARAMS.add('s2s', default=0.8, desc='S2s, the slower motion model-free generalised order parameter', grace_string='\\qS\\ss\\N\\h{-0.2}\\v{0.4}\\z{0.71}2\\Q') 
 94          self.SPIN_PARAMS.add('te', default=100.0 * 1e-12, desc='Single motion effective internal correlation time (seconds)', conv_factor=1e-12, grace_string='\\xt\\f{}\\se', units='ps') 
 95          self.SPIN_PARAMS.add('tf', default=10.0 * 1e-12, desc='Faster motion effective internal correlation time (seconds)', conv_factor=1e-12, grace_string='\\xt\\f{}\\sf', units='ps') 
 96          self.SPIN_PARAMS.add('ts', default=1000.0 * 1e-12, desc='Slower motion effective internal correlation time (seconds)', conv_factor=1e-12, grace_string='\\xt\\f{}\\ss', units='ps') 
 97          self.SPIN_PARAMS.add('rex', default=0.0, desc='Chemical exchange relaxation (sigma_ex = Rex / omega**2)', conv_factor=self._conv_factor_rex, units=self._units_rex, grace_string='\\qR\\sex\\Q') 
 98          self.SPIN_PARAMS.add('r', default=NH_BOND_LENGTH, units='Angstrom', desc='Bond length (meters)', conv_factor=1e-10, grace_string='Bond length') 
 99          self.SPIN_PARAMS.add('csa', default=N15_CSA, units='ppm', desc='Chemical shift anisotropy (unitless)', conv_factor=1e-6, grace_string='\\qCSA\\Q') 
100          self.SPIN_PARAMS.add('heteronuc_type', default='15N', desc='The heteronucleus spin type') 
101          self.SPIN_PARAMS.add('proton_type', default='1H', desc='The proton spin type') 
102          self.SPIN_PARAMS.add('model', desc='The model') 
103          self.SPIN_PARAMS.add('equation', desc='The model equation') 
104          self.SPIN_PARAMS.add('params', desc='The model parameters') 
105          self.SPIN_PARAMS.add('xh_vect', desc='XH bond vector') 
106