Re: r11196 - /branches/bieri_gui/gui_bieri/analyses/results_analysis.py -- May 19, 2010 - 11:37

Hi Michael,

It is better to have this in 2 commits.  That way if you decide in the
future that the use of the interpreter object is not ideal and there
is a better way to do this, you can revert this commit without losing
the bug fix.

Cheers,

Edward


On 19 May 2010 07:16,  <michael.bieri@xxxxxxxxxxxxx> wrote:
> Author: michaelbieri
> Date: Wed May 19 07:16:47 2010
> New Revision: 11196
>
> URL: http://svn.gna.org/viewcvs/relax?rev=11196&view=rev
> Log:
> relax interpreter is used for generating model-free final run results.
>
> In addition, spelling mistake of appen to append was corrected.
>
> Modified:
>    branches/bieri_gui/gui_bieri/analyses/results_analysis.py
>
> Modified: branches/bieri_gui/gui_bieri/analyses/results_analysis.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/analyses/results_analysis.py?rev=11196&r1=11195&r2=11196&view=diff
> ==============================================================================
> --- branches/bieri_gui/gui_bieri/analyses/results_analysis.py (original)
> +++ branches/bieri_gui/gui_bieri/analyses/results_analysis.py Wed May 19 
> 07:16:47 2010
> @@ -28,6 +28,7 @@
>  import wx.grid
>
>  # relax module imports.
> +from prompt.interpreter import Interpreter
>  from generic_fns.mol_res_spin import spin_loop
>
>  # relax GUI module imports.
> @@ -76,12 +77,17 @@
>  def model_free_results(self, directory, pdbfile):
>     """Create the model-free results."""
>
> +    # Load the interpreter.
> +    interpreter = Interpreter(show_script=False, quit=False, 
> raise_relax_error=True)
> +    interpreter.populate_self()
> +    interpreter.on(verbose=False)
> +
>     directory = directory + sep + 'final'
>
>     #Read results
>     pipename = 'Data_extraction ' + str(time.asctime(time.localtime()))
> -    pipe.create(pipename, 'mf')
> -    results.read()
> +    interpreter.pipe.create(pipename, 'mf')
> +    interpreter.results.read(directory+sep+'results')
>
>     #create a table file and variables for results table
>
> @@ -96,7 +102,7 @@
>     file.write('Data Extraction by relaxGUI, (C) 2009 Michael Bieri')
>     file.write("\n")
>     file.write("\n")
> -    
> "self.file.write(""Residue;Model;S2;Rex_[1/s];Te;Relaxation_Parameters\n"")"
> +    file.write("Residue;Model;S2;Rex [1/s];Te;Relaxation Parameters\n")
>     file.write("\n")
>
>     #loop over residues
> @@ -119,41 +125,41 @@
>
>         # S2.
>         if hasattr(spin, 's2'):
> -            s2 = str(spin.s2)
> +            s2_value = str(spin.s2)
>             s2_err = str(spin.s2_err)
>             if spin.s2 == None:
>                 file.write(";")
> -                s2.appen('')
> -            else:
> -                file.write(";" + s2[0:5]+ " +/- " + s2_err[0:4])
> -                s2.appen(s2[0:5]+ " +/- " + s2_err[0:4])
> +                s2.append('')
> +            else:
> +                file.write(";" + s2_value[0:5]+ " +/- " + s2_err[0:4])
> +                s2.append(s2_value[0:5]+ " +/- " + s2_err[0:4])
>
>         # Rex.
>         if hasattr(spin, 'rex'):
> -            rex = str(spin.rex)
> +            rex_value = str(spin.rex)
>             rex_err = str(spin.rex_err)
>             if spin.rex == None:
>                 file.write(";")
> -                rex.appen('')
> -            else:
> -                rex_eff = spin.rex * (int(spin.frq_labels[1]) * 1000000 * 
> 2 * 3.14159)**2
> -                rex = str(rex_eff)
> -                rex_err_eff = spin.rex_err * (int(spin.frq_labels[1]) * 
> 1000000 * 2 * 3.14159)**2
> +                rex.append('')
> +            else:
> +                rex_eff = float(spin.rex) * (int(spin.frq_labels[1]) * 
> 1000000 * 2 * 3.14159)**2
> +                rex_value = str(rex_eff)
> +                rex_err_eff = float(spin.rex_err) * 
> (int(spin.frq_labels[1]) * 1000000 * 2 * 3.14159)**2
>                 rex_err = str(rex_err_eff)
> -                file.write(";" + rex[0:5]+ " +/- " + rex_err[0:4])
> -                rex.appen(rex[0:5]+ " +/- " + rex_err[0:4])
> +                file.write(";" + rex_value[0:5]+ " +/- " + rex_err[0:4])
> +                rex.append(rex_value[0:5]+ " +/- " + rex_err[0:4])
>
>         # Te
>         if hasattr(spin, 'te'):
>             if spin.te == None:
>                 file.write(";")
> -                te.appen('')
> +                te.append('')
>             else:
>                 te_ps = spin.te * 1e-12
> -                te = str(te_ps)
> +                te_value = str(te_ps)
>                 te_err = str(spin.te_err)
> -                file.write(";" + te[0:5]+ " +/- " + te_err[0:4])
> -                te.appen(te[0:5]+ " +/- " + te_err[0:4])
> +                file.write(";" + te_value[0:5]+ " +/- " + te_err[0:4])
> +                te.append(te_value[0:5]+ " +/- " + te_err[0:4])
>
>         # Parameters.
>         if hasattr(spin, 'params'):
> @@ -170,44 +176,44 @@
>     
> ##################################################################################################
>
>     #Create Single Data Files
> -
> -    value.write(param='rex', file='rex.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='s2', file='s2.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='s2f', file='s2f.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='s2s', file='s2s.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='te', file='te.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='tf', file='tf.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='ts', file='ts.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='rex', file='rex.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='r', file='r.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='rex', file='rex.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='csa', file='csa.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='rex', file='rex.txt', dir=str(directory) + sep + 
> 'final_results', force=True)
> -    value.write(param='local_tm', file='local_tm.txt', dir=str(directory) 
> + sep + 'final_results', force=True)
> +    print 'here'
> +    interpreter.value.write(param='rex', file='rex.txt', 
> dir=str(directory) + sep + 'final_results', force=True)
> +    interpreter.value.write(param='s2', file='s2.txt', dir=str(directory) 
> + sep + 'final_results', force=True)
> +    interpreter.value.write(param='s2f', file='s2f.txt', 
> dir=str(directory) + sep + 'final_results', force=True)
> +    interpreter.value.write(param='s2s', file='s2s.txt', 
> dir=str(directory) + sep + 'final_results', force=True)
> +    interpreter.value.write(param='te', file='te.txt', dir=str(directory) 
> + sep + 'final_results', force=True)
> +    interpreter.value.write(param='tf', file='tf.txt', dir=str(directory) 
> + sep + 'final_results', force=True)
> +    interpreter.value.write(param='ts', file='ts.txt', dir=str(directory) 
> + sep + 'final_results', force=True)
> +    interpreter.value.write(param='rex', file='rex.txt', 
> dir=str(directory) + sep + 'final_results', force=True)
> +    interpreter.value.write(param='r', file='r.txt', dir=str(directory) + 
> sep + 'final_results', force=True)
> +    interpreter.value.write(param='rex', file='rex.txt', 
> dir=str(directory) + sep + 'final_results', force=True)
> +    interpreter.value.write(param='csa', file='csa.txt', 
> dir=str(directory) + sep + 'final_results', force=True)
> +    interpreter.value.write(param='rex', file='rex.txt', 
> dir=str(directory) + sep + 'final_results', force=True)
> +    interpreter.value.write(param='local_tm', file='local_tm.txt', 
> dir=str(directory) + sep + 'final_results', force=True)
>
>     
> ##################################################################################################
>
>     #Create Grace Plots
>
> -    grace.write(x_data_type='spin', y_data_type='s2', file='s2.agr', 
> dir=str(directory) + sep + 'grace', force=True)
> -    grace.write(x_data_type='spin', y_data_type='te', file='te.agr', 
> dir=str(directory) + sep + 'grace', force=True)
> -    grace.write(x_data_type='spin', y_data_type='s2f', file='s2f.agr', 
> dir=str(directory) + sep + 'grace', force=True)
> -    grace.write(x_data_type='spin', y_data_type='s2s', file='s2s.agr', 
> dir=str(directory) + sep + 'grace', force=True)
> -    grace.write(x_data_type='spin', y_data_type='ts', file='ts.agr', 
> dir=str(directory) + sep + 'grace', force=True)
> -    grace.write(x_data_type='spin', y_data_type='tf', file='tf.agr', 
> dir=str(directory) + sep + 'grace', force=True)
> -    grace.write(x_data_type='spin', y_data_type='csa', file='csa.agr', 
> dir=str(directory) + sep + 'grace', force=True)
> -    grace.write(x_data_type='te', y_data_type='s2', file='s2-te.agr', 
> dir=str(directory) + sep + 'grace', force=True)
> +    interpreter.grace.write(x_data_type='spin', y_data_type='s2', 
> file='s2.agr', dir=str(directory) + sep + 'grace', force=True)
> +    interpreter.grace.write(x_data_type='spin', y_data_type='te', 
> file='te.agr', dir=str(directory) + sep + 'grace', force=True)
> +    interpreter.grace.write(x_data_type='spin', y_data_type='s2f', 
> file='s2f.agr', dir=str(directory) + sep + 'grace', force=True)
> +    interpreter.grace.write(x_data_type='spin', y_data_type='s2s', 
> file='s2s.agr', dir=str(directory) + sep + 'grace', force=True)
> +    interpreter.grace.write(x_data_type='spin', y_data_type='ts', 
> file='ts.agr', dir=str(directory) + sep + 'grace', force=True)
> +    interpreter.grace.write(x_data_type='spin', y_data_type='tf', 
> file='tf.agr', dir=str(directory) + sep + 'grace', force=True)
> +    interpreter.grace.write(x_data_type='spin', y_data_type='csa', 
> file='csa.agr', dir=str(directory) + sep + 'grace', force=True)
> +    interpreter.grace.write(x_data_type='te', y_data_type='s2', 
> file='s2-te.agr', dir=str(directory) + sep + 'grace', force=True)
>
>     
> ##################################################################################################
>
>     #Create Diffusion Tensor
>
>     # Display the diffusion tensor.
> -    diffusion_tensor.display()
> +    interpreter.diffusion_tensor.display()
>
>     # Create the tensor PDB file.
>     tensor_file = 'tensor.pdb'
> -    structure.create_diff_tensor_pdb(file=tensor_file, dir=str(directory) 
> + sep, force=True)
> +    interpreter.structure.create_diff_tensor_pdb(file=tensor_file, 
> dir=str(directory) + sep, force=True)
>
>     # create diffusion tensor macro
>     file = open(str(directory) + sep + 'diffusion_tensor.pml', 'w')
>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
> This is the relax-commits mailing list
> relax-commits@xxxxxxx
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-commits