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List: relax-devel
Subject: Re: r11196 - /branches/bieri_gui/gui_bieri/analyses/results_analysis.py
From: "Edward d'Auvergne" <edward () domain ! hid>
Date: 2010-05-19 9:37:11
Message-ID: AANLkTimfWhVOHfu_h5VVkvHBxiNmdr7WgPqSlWoQKaCm () domain ! hid
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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@domain.hid> 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')
>
>
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>
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