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')
r11196 - /branches/bieri_gui/gui_bieri/analyses/results_analysis.py