Author: michaelbieri Date: Tue Jul 27 03:54:02 2010 New Revision: 11349 URL: http://svn.gna.org/viewcvs/relax?rev=11349&view=rev Log: Directory for saving files can be specified. Default is None. Grace files will be saved in subdirectory 'grace'. Modified: branches/bieri_gui/auto_analyses/relax_fit.py Modified: branches/bieri_gui/auto_analyses/relax_fit.py URL: http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/relax_fit.py?rev=11349&r1=11348&r2=11349&view=diff ============================================================================== --- branches/bieri_gui/auto_analyses/relax_fit.py (original) +++ branches/bieri_gui/auto_analyses/relax_fit.py Tue Jul 27 03:54:02 2010 @@ -29,13 +29,15 @@ class Relax_fit: - def __init__(self, filename='rx', pipe_name='rx', seq_args=None, file_names=None, relax_times=None, pdb_file=None, view_plots=True, int_method='height', mc_num=500): + def __init__(self, filename='rx', pipe_name='rx', results_directory = None, seq_args=None, file_names=None, relax_times=None, pdb_file=None, view_plots=True, int_method='height', mc_num=500): """Perform relaxation curve fitting. @keyword filename: Name of the output file. @type filename: str @keyword pipe_name: The name of the data pipe to create. @type pipe_name: str + @keyword directory: The directory, where results files are saved. + @type directory: str @keyword seq_args: The sequence data (file name, dir, mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, sep). These are the arguments to the sequence.read() user function, for more information please see the documentation for that function. @type seq_args: list of lists of [str, None or str, None or int, None or int, None or int, None or int, None or int, None or int, None or int, None or str] @keyword file_names: A list of all the peak list file names. @@ -55,6 +57,11 @@ # Store the args. self.filename = filename self.pipe_name = pipe_name + self.results_directory = results_directory + if results_directory: + self.grace_dir = results_directory+sep+'grace' + else: + self.grace_dir = None self.seq_args = seq_args self.file_names = file_names self.relax_times = relax_times @@ -127,28 +134,28 @@ self.interpreter.monte_carlo.error_analysis() # Save the relaxation rates. - self.interpreter.value.write(param='rx', file=self.filename+'.out', force=True) + self.interpreter.value.write(param='rx', file=self.filename+'.out', dir=self.results_directory, force=True) # Save the results. - self.interpreter.results.write(file='results', force=True) + self.interpreter.results.write(file='results', dir=self.results_directory, force=True) # Create Grace plots of the data. - self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr', force=True) # Minimised chi-squared value. - self.interpreter.grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial peak intensity. - self.interpreter.grace.write(y_data_type='rx', file=self.filename+'.agr', force=True) # Relaxation rate. - self.interpreter.grace.write(x_data_type='relax_times', y_data_type='int', file='intensities.agr', force=True) # Average peak intensities. - self.interpreter.grace.write(x_data_type='relax_times', y_data_type='int', norm=True, file='intensities_norm.agr', force=True) # Average peak intensities (normalised). + self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr', dir=self.grace_dir, force=True) # Minimised chi-squared value. + self.interpreter.grace.write(y_data_type='i0', file='i0.agr', dir=self.grace_dir, force=True) # Initial peak intensity. + self.interpreter.grace.write(y_data_type='rx', file=self.filename+'.agr', dir=self.grace_dir, force=True) # Relaxation rate. + self.interpreter.grace.write(x_data_type='relax_times', y_data_type='int', file='intensities.agr', dir=self.grace_dir, force=True) # Average peak intensities. + self.interpreter.grace.write(x_data_type='relax_times', y_data_type='int', norm=True, file='intensities_norm.agr', dir=self.grace_dir, force=True) # Average peak intensities (normalised). # Display the Grace plots if selected. if self.view_plots: - self.interpreter.grace.view(file='chi2.agr') - self.interpreter.grace.view(file='i0.agr') - self.interpreter.grace.view(file=self.filename+'.agr') - self.interpreter.grace.view(file='intensities.agr') - self.interpreter.grace.view(file='intensities_norm.agr') + self.interpreter.grace.view(file='chi2.agr', dir=self.grace_dir) + self.interpreter.grace.view(file='i0.agr', dir=self.grace_dir) + self.interpreter.grace.view(file=self.filename+'.agr', dir=self.grace_dir) + self.interpreter.grace.view(file='intensities.agr', dir=self.grace_dir) + self.interpreter.grace.view(file='intensities_norm.agr', dir=self.grace_dir) # Save the program state. - self.interpreter.state.save(self.filename+'.save', force=True) + self.interpreter.state.save(self.filename+'.save', dir=self.results_directory, force=True) def check_vars(self):