Source Code for Module specific_analyses.relax_fit.uf

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2014 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  """The R1 and R2 exponential relaxation curve fitting user functions.""" 
 24   
 25  # relax module imports. 
 26  from lib.errors import RelaxError, RelaxFuncSetupError, RelaxNoSequenceError 
 27  from pipe_control import pipes 
 28  from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop 
 29  from specific_analyses.relax_fit.api import Relax_fit 
 30   
 31  # The API object. 
 32  api_relax_fit = Relax_fit() 
 33   
 34   
 35 -def model_setup(model, params): 
 36      """Update various model specific data structures. 
 37   
 38      @param model:   The exponential curve type. 
 39      @type model:    str 
 40      @param params:  A list consisting of the model parameters. 
 41      @type params:   list of str 
 42      """ 
 43   
 44      # Set the model. 
 45      cdp.curve_type = model 
 46   
 47      # Loop over the sequence. 
 48      for spin in spin_loop(): 
 49          # Skip deselected spins. 
 50          if not spin.select: 
 51              continue 
 52   
 53          # Initialise the data structures (if needed). 
 54          api_relax_fit.data_init(spin) 
 55   
 56          # The model and parameter names. 
 57          spin.model = model 
 58          spin.params = params 
 59   
 60   
 61 -def relax_time(time=0.0, spectrum_id=None): 
 62      """Set the relaxation time period associated with a given spectrum. 
 63   
 64      @keyword time:          The time, in seconds, of the relaxation period. 
 65      @type time:             float 
 66      @keyword spectrum_id:   The spectrum identification string. 
 67      @type spectrum_id:      str 
 68      """ 
 69   
 70      # Test if the spectrum id exists. 
 71      if spectrum_id not in cdp.spectrum_ids: 
 72          raise RelaxError("The peak heights corresponding to spectrum id '%s' have not been loaded." % spectrum_id) 
 73   
 74      # Initialise the global relaxation time data structure if needed. 
 75      if not hasattr(cdp, 'relax_times'): 
 76          cdp.relax_times = {} 
 77   
 78      # Add the time at the correct position. 
 79      cdp.relax_times[spectrum_id] = time 
 80   
 81   
 82 -def select_model(model='exp'): 
 83      """Function for selecting the model of the exponential curve. 
 84   
 85      @keyword model: The exponential curve type.  Can be one of 'exp' or 'inv'. 
 86      @type model:    str 
 87      """ 
 88   
 89      # Test if the current pipe exists. 
 90      pipes.test() 
 91   
 92      # Test if the pipe type is set to 'relax_fit'. 
 93      function_type = cdp.pipe_type 
 94      if function_type != 'relax_fit': 
 95          raise RelaxFuncSetupError(specific_setup.get_string(function_type)) 
 96   
 97      # Test if sequence data is loaded. 
 98      if not exists_mol_res_spin_data(): 
 99          raise RelaxNoSequenceError 
100   
101      # Two parameter exponential fit. 
102      if model == 'exp': 
103          print("Two parameter exponential fit.") 
104          params = ['rx', 'i0'] 
105   
106      # Three parameter inversion recovery fit. 
107      elif model == 'inv': 
108          print("Three parameter inversion recovery fit.") 
109          params = ['rx', 'i0', 'iinf'] 
110   
111      # Invalid model. 
112      else: 
113          raise RelaxError("The model '" + model + "' is invalid.") 
114   
115      # Set up the model. 
116      model_setup(model, params) 
117