Source Code for Module auto_analyses.noe

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2014 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2010 Michael Bieri                                            # 
  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              # 
 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 this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """The automatic relaxation curve fitting protocol.""" 
 25   
 26  # Python module imports. 
 27  from os import sep 
 28   
 29  # relax module imports. 
 30  from pipe_control.pipes import cdp_name, has_pipe, switch 
 31  from prompt.interpreter import Interpreter 
 32  from status import Status; status = Status() 
 33   
 34   
 35   
 36 -class NOE_calc: 
 37 -    def __init__(self, pipe_name=None, pipe_bundle=None, file_root='noe', results_dir=None, save_state=True): 
 38          """Perform relaxation curve fitting. 
 39   
 40          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: 
 41   
 42              - All the spins loaded. 
 43              - Unresolved spins deselected. 
 44              - The NOE peak intensities from the saturated and reference spectra. 
 45              - Either the baseplane noise RMDS values should be set or replicated spectra loaded. 
 46   
 47          @keyword pipe_name:     The name of the data pipe containing all of the data for the analysis. 
 48          @type pipe_name:        str 
 49          @keyword pipe_bundle:   The data pipe bundle to associate all spawned data pipes with. 
 50          @type pipe_bundle:      str 
 51          @keyword file_root:     File root of the output filea. 
 52          @type file_root:        str 
 53          @keyword results_dir:   The directory where results files are saved. 
 54          @type results_dir:      str 
 55          @keyword save_state:    A flag which if True will cause a relax save state to be created at the end of the analysis. 
 56          @type save_state:       bool 
 57          """ 
 58   
 59          # Execution lock. 
 60          status.exec_lock.acquire(pipe_bundle, mode='auto-analysis') 
 61   
 62          # Set up the analysis status object. 
 63          status.init_auto_analysis(pipe_bundle, type='noe') 
 64          status.current_analysis = pipe_bundle 
 65   
 66          # Store the args. 
 67          self.save_state = save_state 
 68          self.pipe_name = pipe_name 
 69          self.pipe_bundle = pipe_bundle 
 70          self.file_root = file_root 
 71          self.results_dir = results_dir 
 72          if self.results_dir: 
 73              self.grace_dir = results_dir + sep + 'grace' 
 74          else: 
 75              self.grace_dir = 'grace' 
 76   
 77          # Data checks. 
 78          self.check_vars() 
 79   
 80          # Set the data pipe to the current data pipe. 
 81          if self.pipe_name != cdp_name(): 
 82              switch(self.pipe_name) 
 83   
 84          # Load the interpreter. 
 85          self.interpreter = Interpreter(show_script=False, raise_relax_error=True) 
 86          self.interpreter.populate_self() 
 87          self.interpreter.on(verbose=False) 
 88   
 89          # Execute. 
 90          self.run() 
 91   
 92          # Finish and unlock execution. 
 93          status.auto_analysis[self.pipe_bundle].fin = True 
 94          status.current_analysis = None 
 95          status.exec_lock.release() 
 96   
 97   
 98 -    def run(self): 
 99          """Set up and run the NOE analysis.""" 
100   
101          # Peak intensity error analysis. 
102          self.interpreter.spectrum.error_analysis() 
103   
104          # Calculate the NOEs. 
105          self.interpreter.calc() 
106   
107          # Save the NOEs. 
108          self.interpreter.value.write(param='noe', file=self.file_root+'.out', dir=self.results_dir, force=True) 
109   
110          # Save the results. 
111          self.interpreter.results.write(file='results', dir=self.results_dir, force=True) 
112   
113          # Create Grace plots of the data. 
114          self.interpreter.grace.write(y_data_type='peak_intensity', file='intensities.agr', dir=self.grace_dir, force=True) 
115          self.interpreter.grace.write(y_data_type='noe', file='noe.agr', dir=self.grace_dir, force=True) 
116   
117          # Save the program state. 
118          if self.save_state: 
119              self.interpreter.state.save(state=self.file_root+'.save', dir=self.results_dir, force=True) 
120   
121   
122 -    def check_vars(self): 
123          """Check that the user has set the variables correctly.""" 
124   
125          # The pipe name. 
126          if not has_pipe(self.pipe_name): 
127              raise RelaxNoPipeError(self.pipe_name) 
128