Source Code for Module specific_analyses.relax_fit.uf

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2014 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2006 Chris MacRaild                                           # 
  5  # Copyright (C) 2008 Sebastien Morin                                          # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  8  #                                                                             # 
  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """The R1 and R2 exponential relaxation curve fitting user functions.""" 
 26   
 27  # relax module imports. 
 28  from lib.errors import RelaxError, RelaxFuncSetupError, RelaxNoSequenceError 
 29  from pipe_control.pipes import check_pipe 
 30  from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop 
 31  from specific_analyses.relax_fit.api import Relax_fit 
 32   
 33  # The API object. 
 34  api_relax_fit = Relax_fit() 
 35   
 36   
 37 -def model_setup(model, params): 
 38      """Update various model specific data structures. 
 39   
 40      @param model:   The exponential curve type. 
 41      @type model:    str 
 42      @param params:  A list consisting of the model parameters. 
 43      @type params:   list of str 
 44      """ 
 45   
 46      # Set the model. 
 47      cdp.curve_type = model 
 48   
 49      # Loop over the sequence. 
 50      for spin, spin_id in spin_loop(return_id=True): 
 51          # Skip deselected spins. 
 52          if not spin.select: 
 53              continue 
 54   
 55          # Initialise the data structures (if needed). 
 56          api_relax_fit.data_init(spin_id) 
 57   
 58          # The model and parameter names. 
 59          spin.model = model 
 60          spin.params = params 
 61   
 62   
 63 -def relax_time(time=0.0, spectrum_id=None): 
 64      """Set the relaxation time period associated with a given spectrum. 
 65   
 66      @keyword time:          The time, in seconds, of the relaxation period. 
 67      @type time:             float 
 68      @keyword spectrum_id:   The spectrum identification string. 
 69      @type spectrum_id:      str 
 70      """ 
 71   
 72      # Test if the spectrum id exists. 
 73      if spectrum_id not in cdp.spectrum_ids: 
 74          raise RelaxError("The peak heights corresponding to spectrum id '%s' have not been loaded." % spectrum_id) 
 75   
 76      # Initialise the global relaxation time data structure if needed. 
 77      if not hasattr(cdp, 'relax_times'): 
 78          cdp.relax_times = {} 
 79   
 80      # Add the time at the correct position. 
 81      cdp.relax_times[spectrum_id] = time 
 82   
 83   
 84 -def select_model(model='exp'): 
 85      """Function for selecting the model of the exponential curve. 
 86   
 87      @keyword model: The exponential curve type.  Can be one of 'exp', 'inv', or 'sat'. 
 88      @type model:    str 
 89      """ 
 90   
 91      # Test if the current pipe exists. 
 92      check_pipe() 
 93   
 94      # Test if the pipe type is set to 'relax_fit'. 
 95      function_type = cdp.pipe_type 
 96      if function_type != 'relax_fit': 
 97          raise RelaxFuncSetupError(specific_setup.get_string(function_type)) 
 98   
 99      # Test if sequence data is loaded. 
100      if not exists_mol_res_spin_data(): 
101          raise RelaxNoSequenceError 
102   
103      # Two parameter exponential fit. 
104      if model == 'exp': 
105          print("Two parameter exponential fit.") 
106          params = ['rx', 'i0'] 
107   
108      # Three parameter inversion recovery fit. 
109      elif model == 'inv': 
110          print("The inversion recovery experiment.") 
111          params = ['rx', 'i0', 'iinf'] 
112   
113      # The saturation recovery. 
114      elif model == 'sat': 
115          print("The saturation recovery experiment.") 
116          params = ['rx', 'iinf'] 
117   
118      # Invalid model. 
119      else: 
120          raise RelaxError("The model '" + model + "' is invalid.") 
121   
122      # Set up the model. 
123      model_setup(model, params) 
124