Re: r11372 - /branches/bieri_gui/auto_analyses/relax_fit.py -- July 28, 2010 - 11:19

Hi,

Could you please change the "@keyword file_root:" in
auto_analyses/relax_fit.py to the following:

The file root of the output files.  This is used to create the
relaxation rate file by addition of the suffix '.out', the grace
output file by addition of the suffix '.agr', and the saved program
state by addition of the suffix '.save'.

This allows the user to script, as they will know what this code will
spit out and therefore what files their script will need to open.

Cheers,

Edward



On 28 July 2010 06:45,  <michael.bieri@xxxxxxxxxxxxx> wrote:
> Author: michaelbieri
> Date: Wed Jul 28 06:45:29 2010
> New Revision: 11372
>
> URL: http://svn.gna.org/viewcvs/relax?rev=11372&view=rev
> Log:
> Argument 'filename' is replaced to 'file_root', as suggested by Edward 
> d'Auvergne (https://mail.gna.org/public/relax-devel/2010-07/msg00012.html).
>
> 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=11372&r1=11371&r2=11372&view=diff
> ==============================================================================
> --- branches/bieri_gui/auto_analyses/relax_fit.py (original)
> +++ branches/bieri_gui/auto_analyses/relax_fit.py Wed Jul 28 06:45:29 2010
> @@ -34,11 +34,11 @@
>
>
>  class Relax_fit:
> -    def __init__(self, filename='rx', pipe_name='rx', results_directory = 
> None, seq_args=None, file_names=None, relax_times=None, pdb_file=None, 
> unresolved='unresolved', int_method='height', heteronuc='N', proton='H', 
> mc_num=500, inc='11', view_plots=True):
> +    def __init__(self, file_root='rx', pipe_name='rx', 
> results_directory=None, seq_args=None, file_names=None, relax_times=None, 
> pdb_file=None, unresolved='unresolved', int_method='height', heteronuc='N', 
> proton='H', mc_num=500, inc='11', view_plots=True):
>         """Perform relaxation curve fitting.
>
> -        @keyword filename:      Name of the output file.
> -        @type filename:         str
> +        @keyword file_root:     File root of the output filea.
> +        @type file_root:        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.
> @@ -68,7 +68,7 @@
>         """
>
>         # Store the args.
> -        self.filename = filename
> +        self.file_root = file_root
>         self.pipe_name = pipe_name
>         self.results_directory = results_directory
>         if results_directory:
> @@ -152,7 +152,7 @@
>         self.interpreter.monte_carlo.error_analysis()
>
>         # Save the relaxation rates.
> -        self.interpreter.value.write(param='rx', 
> file=self.filename+'.out', dir=self.results_directory, force=True)
> +        self.interpreter.value.write(param='rx', 
> file=self.file_root+'.out', dir=self.results_directory, force=True)
>
>         # Save the results.
>         self.interpreter.results.write(file='results', 
> dir=self.results_directory, force=True)
> @@ -160,7 +160,7 @@
>         # Create Grace plots of the data.
>         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(y_data_type='rx', 
> file=self.file_root+'.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).
>
> @@ -168,12 +168,12 @@
>         if self.view_plots:
>             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=self.file_root+'.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', 
> dir=self.results_directory, force=True)
> +        self.interpreter.state.save(self.file_root+'.save', 
> dir=self.results_directory, force=True)
>
>
>     def check_vars(self):
>
>
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