Source Code for Module auto_analyses.noe

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2011 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2010 Michael Bieri                                            # 
  5  #                                                                             # 
  6  # This file is part of the program relax.                                     # 
  7  #                                                                             # 
  8  # relax 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 2 of the License, or           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 13  # relax is distributed in the hope that it will be useful,                    # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 16  # GNU General Public License for more details.                                # 
 17  #                                                                             # 
 18  # You should have received a copy of the GNU General Public License           # 
 19  # along with relax; if not, write to the Free Software                        # 
 20  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """The automatic relaxation curve fitting protocol.""" 
 26   
 27  # Python module imports. 
 28  from os import sep 
 29   
 30  # relax module imports. 
 31  from generic_fns.pipes import cdp_name, has_pipe, switch 
 32  import generic_fns.structure.main 
 33  from prompt.interpreter import Interpreter 
 34  from status import Status; status = Status() 
 35   
 36   
 37   
 38 -class NOE_calc: 
 39 -    def __init__(self, pipe_name=None, pipe_bundle=None, file_root='noe', results_dir=None, save_state=True): 
 40          """Perform relaxation curve fitting. 
 41   
 42          To use this auto-analysis, a data pipe with all the required data needs to be set up.  This data pipe should contain the following: 
 43   
 44              - All the spins loaded. 
 45              - Unresolved spins deselected. 
 46              - The NOE peak intensities from the saturated and reference spectra. 
 47              - Either the baseplane noise RMDS values should be set or replicated spectra loaded. 
 48   
 49          @keyword pipe_name:     The name of the data pipe containing all of the data for the analysis. 
 50          @type pipe_name:        str 
 51          @keyword pipe_bundle:   The data pipe bundle to associate all spawned data pipes with. 
 52          @type pipe_bundle:      str 
 53          @keyword file_root:     File root of the output filea. 
 54          @type file_root:        str 
 55          @keyword results_dir:   The directory where results files are saved. 
 56          @type results_dir:      str 
 57          @keyword save_state:    A flag which if True will cause a relax save state to be created at the end of the analysis. 
 58          @type save_state:       bool 
 59          """ 
 60   
 61          # Execution lock. 
 62          status.exec_lock.acquire(pipe_bundle, mode='auto-analysis') 
 63   
 64          # Set up the analysis status object. 
 65          status.init_auto_analysis(pipe_bundle, type='noe') 
 66          status.current_analysis = pipe_bundle 
 67   
 68          # Store the args. 
 69          self.save_state = save_state 
 70          self.pipe_name = pipe_name 
 71          self.pipe_bundle = pipe_bundle 
 72          self.file_root = file_root 
 73          self.results_dir = results_dir 
 74          if self.results_dir: 
 75              self.grace_dir = results_dir + sep + 'grace' 
 76          else: 
 77              self.grace_dir = 'grace' 
 78   
 79          # Data checks. 
 80          self.check_vars() 
 81   
 82          # Set the data pipe to the current data pipe. 
 83          if self.pipe_name != cdp_name(): 
 84              switch(self.pipe_name) 
 85   
 86          # Load the interpreter. 
 87          self.interpreter = Interpreter(show_script=False, quit=False, raise_relax_error=True) 
 88          self.interpreter.populate_self() 
 89          self.interpreter.on(verbose=False) 
 90   
 91          # Execute. 
 92          self.run() 
 93   
 94          # Finish and unlock execution. 
 95          status.auto_analysis[self.pipe_bundle].fin = True 
 96          status.current_analysis = None 
 97          status.exec_lock.release() 
 98   
 99   
100 -    def run(self): 
101          """Set up and run the NOE analysis.""" 
102   
103          # Peak intensity error analysis. 
104          self.interpreter.spectrum.error_analysis() 
105   
106          # Calculate the NOEs. 
107          self.interpreter.calc() 
108   
109          # Save the NOEs. 
110          self.interpreter.value.write(param='noe', file=self.file_root+'.out', dir=self.results_dir, force=True) 
111   
112          # Save the results. 
113          self.interpreter.results.write(file='results', dir=self.results_dir, force=True) 
114   
115          # Create Grace plots of the data. 
116          self.interpreter.grace.write(y_data_type='ref', file='ref.agr', dir=self.grace_dir, force=True) 
117          self.interpreter.grace.write(y_data_type='sat', file='sat.agr', dir=self.grace_dir, force=True) 
118          self.interpreter.grace.write(y_data_type='noe', file='noe.agr', dir=self.grace_dir, force=True) 
119   
120          # Save the program state. 
121          if self.save_state: 
122              self.interpreter.state.save(state=self.file_root+'.save', dir=self.results_dir, force=True) 
123   
124   
125 -    def check_vars(self): 
126          """Check that the user has set the variables correctly.""" 
127   
128          # The pipe name. 
129          if not has_pipe(self.pipe_name): 
130              raise RelaxNoPipeError(self.pipe_name) 
131