Source Code for Module specific_analyses.relax_disp.parameter_object

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2014 Edward d'Auvergne                                        # 
  4  # Copyright (C) 2009 Sebastien Morin                                          # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  7  #                                                                             # 
  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           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 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.                                # 
 17  #                                                                             # 
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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 relaxation dispersion parameter list object.""" 
 25   
 26  # relax module imports. 
 27  from specific_analyses.parameter_object import Param_list 
 28   
 29   
 30 -class Relax_disp_params(Param_list): 
 31      """The relaxation dispersion parameter list singleton.""" 
 32   
 33      # Class variable for storing the class instance (for the singleton design pattern). 
 34      _instance = None 
 35   
 36 -    def __init__(self): 
 37          """Define all the parameters of the analysis.""" 
 38   
 39          # The object is already initialised. 
 40          if self._initialised: return 
 41   
 42          # Execute the base class __init__ method. 
 43          Param_list.__init__(self) 
 44   
 45          # Add the base data for the 'R2eff' model. 
 46          self._add_peak_intensity() 
 47   
 48          # Add the base information for the dispersion analysis. 
 49          self._add('relax_times', scope='spin', py_type=dict, grace_string='\\qRelaxation time period (s)\\Q') 
 50          self._add('cpmg_frqs', scope='spin', py_type=dict, grace_string='\\qCPMG pulse train frequency (Hz)\\Q') 
 51          self._add('spin_lock_nu1', scope='spin', py_type=dict, grace_string='\\qSpin-lock field strength (Hz)\\Q') 
 52   
 53          # Add the model variables. 
 54          self._add_model_info() 
 55   
 56          # Add the parameters of the 'R2eff' model. 
 57          self._add('r2eff', scope='spin', default=10.0, desc='The effective transversal relaxation rate', set='params', py_type=dict, grace_string='\\qR\\s2,eff\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 58          self._add('i0', scope='spin', default=10000.0, desc='The initial intensity', py_type=dict, set='params', grace_string='\\qI\\s0\\Q', err=True, sim=True) 
 59   
 60          # Add the parameters of all dispersion models. 
 61          self._add('r2', scope='spin', default=10.0, desc='The transversal relaxation rate', set='params', py_type=dict, grace_string='\\qR\\s2\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 62          self._add('r2a', scope='spin', default=10.0, desc='The transversal relaxation rate for state A in the absence of exchange', set='params', py_type=dict, grace_string='\\qR\\s2,A\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 63          self._add('r2b', scope='spin', default=10.0, desc='The transversal relaxation rate for state B in the absence of exchange', set='params', py_type=dict, grace_string='\\qR\\s2,B\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 64          self._add('pA', scope='spin', default=0.90, desc='The population for state A', set='params', py_type=float, grace_string='\\qp\\sA\\N\\Q', err=True, sim=True) 
 65          self._add('pB', scope='spin', default=0.5, desc='The population for state B', set='params', py_type=float, grace_string='\\qp\\sB\\N\\Q', err=True, sim=True) 
 66          self._add('pC', scope='spin', default=0.5, desc='The population for state C', set='params', py_type=float, grace_string='\\qp\\sC\\N\\Q', err=True, sim=True) 
 67          self._add('phi_ex', scope='spin', default=5.0, desc='The phi_ex = pA.pB.dw**2 value (ppm^2)', set='params', py_type=float, grace_string='\\xF\\B\\sex\\N = \\q p\\sA\\N.p\\sB\\N.\\xDw\\B\\S2\\N\\Q  (ppm\\S2\\N)', err=True, sim=True) 
 68          self._add('phi_ex_B', scope='spin', default=5.0, desc='The fast exchange factor between sites A and B (ppm^2)', set='params', py_type=float, grace_string='\\xF\\B\\sex,B\\N (ppm\\S2\\N)', err=True, sim=True) 
 69          self._add('phi_ex_C', scope='spin', default=5.0, desc='The fast exchange factor between sites A and C (ppm^2)', set='params', py_type=float, grace_string='\\xF\\B\\sex,C\\N (ppm\\S2\\N)', err=True, sim=True) 
 70          self._add('padw2', scope='spin', default=1.0, desc='The pA.dw**2 value (ppm^2)', set='params', py_type=float, grace_string='\\qp\\sA\\N.\\xDw\\B\\S2\\N\\Q  (ppm\\S2\\N)', err=True, sim=True) 
 71          self._add('dw', scope='spin', default=1.0, desc='The chemical shift difference between states A and B (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q (ppm)', err=True, sim=True) 
 72          self._add('dw_AB', scope='spin', default=1.0, desc='The chemical shift difference between states A and B for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAB\\N (ppm)', err=True, sim=True) 
 73          self._add('dw_AC', scope='spin', default=1.0, desc='The chemical shift difference between states A and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAC\\N (ppm)', err=True, sim=True) 
 74          self._add('dw_BC', scope='spin', default=1.0, desc='The chemical shift difference between states B and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SBC\\N (ppm)', err=True, sim=True) 
 75          self._add('dwH', scope='spin', default=1.0, desc='The proton chemical shift difference between states A and B (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q (ppm)', err=True, sim=True) 
 76          self._add('dwH_AB', scope='spin', default=1.0, desc='The proton chemical shift difference between states A and B for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAB\\N (ppm)', err=True, sim=True) 
 77          self._add('dwH_AC', scope='spin', default=1.0, desc='The proton chemical shift difference between states A and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAC\\N (ppm)', err=True, sim=True) 
 78          self._add('dwH_BC', scope='spin', default=1.0, desc='The proton chemical shift difference between states B and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SBC\\N (ppm)', err=True, sim=True) 
 79          self._add('kex', scope='spin', default=1000.0, desc='The exchange rate', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 80          self._add('kex_AB', scope='spin', default=1000.0, desc='The exchange rate between sites A and B for 3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SAB\\N (rad.s\\S-1\\N)', err=True, sim=True) 
 81          self._add('kex_AC', scope='spin', default=1000.0, desc='The exchange rate between sites A and C for 3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SAC\\N (rad.s\\S-1\\N)', err=True, sim=True) 
 82          self._add('kex_BC', scope='spin', default=1000.0, desc='The exchange rate between sites B and C for 3-site exchange with kex_BC = k_BC + k_CB (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SBC\\N (rad.s\\S-1\\N)', err=True, sim=True) 
 83          self._add('kB', scope='spin', default=1000.0, desc='Approximate chemical exchange rate constant between sites A and B (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sB\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 84          self._add('kC', scope='spin', default=1000.0, desc='Approximate chemical exchange rate constant between sites A and C (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sC\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 85          self._add('tex', scope='spin', default=1.0/1000.0, desc='The time of exchange (tex = 1/kex)', set='params', py_type=float, grace_string='\\q\\xt\\B\\sex\\N\\Q (s.rad\\S-1\\N)', err=True, sim=True) 
 86          self._add('theta', scope='spin', desc='Rotating frame tilt angle : ( theta = arctan(w_1 / Omega) ) (rad)', grace_string='Rotating frame tilt angle (rad)', py_type=dict, set='all', err=False, sim=False) 
 87          self._add('w_eff', scope='spin', desc='Effective field in rotating frame : ( w_eff = sqrt(Omega^2 + w_1^2) ) (rad.s^-1)', grace_string='Effective field in rotating frame (rad.s\\S-1\\N)', py_type=dict, set='all', err=False, sim=False) 
 88          self._add('k_AB', scope='spin', default=1000.0, desc='The exchange rate from state A to state B', set='params', py_type=float, grace_string='\\qk\\sAB\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 89          self._add('k_BA', scope='spin', default=1000.0, desc='The exchange rate from state B to state A', set='params', py_type=float, grace_string='\\qk\\sBA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) 
 90   
 91          # Add the minimisation data. 
 92          self._add_min_data(min_stats_global=False, min_stats_spin=True) 
 93   
 94          # Set up the user function documentation. 
 95          self._set_uf_title("Relaxation dispersion parameters") 
 96          self._uf_param_table(label="table: dispersion parameters", caption="Relaxation dispersion parameters.", type=True) 
 97          self._uf_param_table(label="table: dispersion parameters and min stats", caption="Relaxation dispersion parameters and minimisation statistics.", sets=['params', 'fixed', 'min']) 
 98          self._uf_param_table(label="table: dispersion parameter value setting", caption="Relaxation dispersion parameters.", type=True) 
 99          self._uf_param_table(label="table: dispersion parameter value setting with defaults", caption="Relaxation dispersion parameter value setting.", default=True, type=True) 
100   
101          # Value setting documentation. 
102          for doc in self._uf_doc_loop(["table: dispersion parameter value setting", "table: dispersion parameter value setting with defaults"]): 
103              doc.add_paragraph("Any of the relaxation dispersion parameters which are of the 'float' type can be set.  Note that setting values for parameters which are not part of the model will have no effect.") 
104