Source Code for Module specific_analyses.model_free.parameter_object

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 3  # Copyright (C) 2007-2014 Edward d'Auvergne                                   # 
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21   
22  # Module docstring. 
23  """The module for the Lipari-Szabo model-free parameter list object.""" 
24   
25  # relax module imports. 
26  from lib.physical_constants import N15_CSA 
27  from pipe_control import relax_data 
28  from specific_analyses.parameter_object import Param_list 
29  from specific_analyses.model_free.parameters import conv_factor_rex, units_rex 
30   
31   
32 -class Model_free_params(Param_list): 
33      """The Lipari-Szabo model-free 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 for the models. 
48          self._add('ri_data', scope='spin', desc=relax_data.return_data_desc('ri_data'), py_type=dict, err=False, sim=True) 
49          self._add('ri_data_err', scope='spin', desc=relax_data.return_data_desc('ri_data_err'), py_type=dict, err=False, sim=False) 
50   
51          # Add the model variables. 
52          self._add_model_info(equation_flag=True) 
53   
54          # Add up the global model parameters. 
55          self._add_diffusion_params() 
56   
57          # Add up the spin model parameters. 
58          self._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) 
59          self._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) 
60          self._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) 
61          self._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) 
62          self._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) 
63          self._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) 
64          self._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) 
65          self._add('rex', scope='spin', default=0.0, desc='Chemical exchange relaxation (sigma_ex = Rex / omega**2)', py_type=float, set='params', conv_factor=conv_factor_rex, units=units_rex, grace_string='\\qR\\sex\\Q', err=True, sim=True) 
66          self._add_csa(default=N15_CSA, set='params', err=True, sim=True) 
67   
68          # Add the minimisation data. 
69          self._add_min_data(min_stats_global=True, min_stats_spin=True) 
70   
71          # Set up the user function documentation. 
72          self._set_uf_title("Model-free parameters") 
73          self._uf_param_table(label="table: model-free parameters", caption="Model-free parameters.") 
74          self._uf_param_table(label="table: model-free parameter writing", caption="Model-free parameters.") 
75          self._uf_param_table(label="table: model-free parameters and min stats", caption="Model-free parameters and minimisation statistics.", sets=['params', 'fixed', 'min']) 
76          self._uf_param_table(label="table: all model-free parameters", caption="Model-free parameters.", scope=None) 
77          self._uf_param_table(label="table: model-free parameter value setting", caption="Model-free parameters.") 
78          self._uf_param_table(label="table: model-free parameter value setting with defaults", caption="Model-free parameter value setting.", default=True) 
79   
80          # Parameter setting documentation. 
81          for doc in self._uf_doc_loop(["table: model-free parameter value setting", "table: model-free parameter value setting with defaults"]): 
82              doc.add_paragraph("Setting a parameter value may have no effect depending on which model-free model is chosen.  For example if S2f values and S2s values are set but the data pipe corresponds to the model-free model 'm4' then because these data values are not parameters of the model they will have no effect.") 
83              doc.add_paragraph("Note that the Rex values are scaled quadratically with field strength and should be supplied as a field strength independent value.  Use the following formula to obtain the correct value:") 
84              doc.add_verbatim("    value = rex / (2.0 * pi * frequency) ** 2") 
85              doc.add_paragraph("where:") 
86              doc.add_list_element("rex is the chemical exchange value for the current frequency.") 
87              doc.add_list_element("frequency is the proton frequency corresponding to the data.") 
88   
89          # Parameter writing documentation. 
90          for doc in self._uf_doc_loop(["table: model-free parameter writing"]): 
91              doc.add_paragraph("For model-free theory it is assumed that Rex values are scaled quadratically with field strength.  The values will be very small as they will be written out as a field strength independent value.  Hence use the following formula to convert the value to that expected for a given magnetic field strength:") 
92              doc.add_verbatim("    Rex = value * (2.0 * pi * frequency) ** 2") 
93              doc.add_paragraph("The frequency is that of the proton in Hertz.") 
94