Author: bugman
Date: Wed May 30 17:45:23 2012
New Revision: 16535
URL: http://svn.gna.org/viewcvs/relax?rev=16535&view=rev
Log:
Deleted a ton of now unused and useless code from
gui.analyses.results_analysis.
Modified:
branches/uf_redesign/gui/analyses/results_analysis.py
Modified: branches/uf_redesign/gui/analyses/results_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/gui/analyses/results_analysis.py?rev=16535&r1=16534&r2=16535&view=diff
==============================================================================
--- branches/uf_redesign/gui/analyses/results_analysis.py (original)
+++ branches/uf_redesign/gui/analyses/results_analysis.py Wed May 30 17:45:23
2012
@@ -22,19 +22,11 @@
###############################################################################
# Python module imports.
-from os import sep, system
-import time
-import wx
-import wx.grid
+from os import sep
# relax module imports.
-from prompt.interpreter import Interpreter
from generic_fns.mol_res_spin import spin_loop
from status import Status; status = Status()
-
-# relax GUI module imports.
-from gui.fonts import font
-from gui.paths import IMAGE_PATH
def color_code_noe(target_dir, pdb_file):
@@ -82,344 +74,3 @@
# Close the macro.
file.close()
-
-
-def model_free_results(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()))
- interpreter.pipe.create(pipename, 'mf')
- interpreter.results.read(directory+sep+'results')
-
- #create a table file and variables for results table
-
- residue = []
- model = []
- s2 = []
- rex = []
- te = []
-
- #create file
- file = open(str(directory) + sep + 'Model-free_Results.csv', 'w')
- file.write('Data Extraction by relaxGUI, (C) 2009 Michael Bieri')
- file.write("\n")
- file.write("\n")
- file.write("Residue;Model;S2;Rex [1/s];Te;Relaxation Parameters\n")
- file.write("\n")
-
- #loop over residues
- for spin, spin_id in spin_loop(return_id=True):
- # The spin ID string.
- spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')]
- spin_res = spin_id[spin_id.index('&')+2:spin_id.index('@')]
- file.write((spin_res) + " " + (spin_no))
- residue.append(spin_res)
- # The spin is not selected.
- if not spin.select:
- file.write("\n")
- continue
-
- # The model-free model.
- if hasattr(spin, 'model'):
- # Tm0-9 models
- if 'tm' in spin.model:
- spin.model = spin.model[2:3]
- # m0-9
- else:
- spin.model = spin.model[1:2]
- file.write(";" + spin.model)
- model.append(spin.model)
-
- # S2.
- if hasattr(spin, 's2'):
- s2_value = str(spin.s2)
- s2_err = str(spin.s2_err)
- if spin.s2 == None:
- file.write(";")
- 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_value = str(spin.rex)
- rex_err = str(spin.rex_err)
- if spin.rex == None:
- file.write(";")
- 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_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.append('')
- else:
- te_ps = spin.te * 1e-12
- te_value = str(te_ps)
- te_err = str(spin.te_err)
- 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'):
- file.write(";" + str(spin.params[0:len(spin.params)]))
- else:
- file.write(";\n")
- continue
-
- # Start a new line.
- file.write("\n")
-
- file.close()
-
-
##################################################################################################
-
- #Create Single Data Files
-
- 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
-
- 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
- try:
- # Display the diffusion tensor.
- interpreter.diffusion_tensor.display()
-
- # Create the tensor PDB file.
- tensor_file = 'tensor.pdb'
- 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')
- file.write('load ' + pdbfile + '\n')
- file.write('color red, ss h\n')
- file.write('color yellow, ss s\n')
- file.write('color green, ss l+''\n')
- file.write('set cartoon_discrete_colors, 1\n')
- file.write('hide all\n')
- file.write('show cartoon\n')
- file.write('load ' + str(directory) + sep + 'tensor.pdb' + '\n')
- file.close()
-
- # No diffusion tensor (local tm model was selected)
- except:
- print("\nModel without diffusion tensor was selected (local TM)!\nNo
diffusion tensor was created!\n\n")
-
-
##################################################################################################
-
- # Create S2 Macro for PyMol
-
- #create file
-
- file = open(str(directory) +sep + 's2.pml', 'w')
- if pdbfile:
- file.write("load " + pdbfile + '\n')
- file.write("bg_color white\n")
- file.write("color gray90\n")
- file.write("hide all\n")
- file.write("show ribbon\n")
-
- for spin, spin_id in spin_loop(return_id=True):
- #select residue
- spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')]
-
- #ribbon color
- if hasattr(spin, 's2'):
- if spin.s2 == None:
- file.write("")
- else:
- width = ((1-spin.s2) * 2)
- green = 1 - ((spin.s2)**3)
- green = green * green * green #* green * green
- green = 1 - green
- file.write("set_color resicolor" + spin_no + ", [1," +
str(green) + ",0]\n")
- file.write("color resicolor" + spin_no + ", resi " + spin_no
+ "\n")
- file.write("set_bond stick_radius, " + str(width) + ", resi
" + spin_no + "\n")
-
- file.write("hide all\n")
- file.write("show sticks, name C+N+CA\n")
- file.write("set stick_quality, 10\n")
- file.write("ray\n")
- file.close()
-
-
##################################################################################################
-
- # Create Rex Macro for PyMol
-
- #create file
-
- file = open(str(directory) + sep + 'rex.pml', 'w')
- if pdbfile:
- file.write("load " + pdbfile + '\n')
- file.write("bg_color white\n")
- file.write("color gray90\n")
- file.write("hide all\n")
- file.write("show ribbon\n")
-
- max_rex = 0
-
- #find max Rex
- for spin, spin_id in spin_loop(return_id=True):
- if hasattr(spin, 'rex'):
- if not spin.rex == None:
- if spin.rex > max_rex:
- max_rex = spin.rex
-
-
- for spin, spin_id in spin_loop(return_id=True):
- #select residue
- spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')]
-
- #ribbon color
- if hasattr(spin, 'rex'):
- if spin.rex == None:
- file.write("")
- else:
- rel_rex = spin.rex / max_rex
- width = ((rel_rex) * 2)
- green = ((rel_rex))
- green = green * green * green #* green * green
- green = 1 - green
- file.write("set_color resicolor" + spin_no + ", [1," +
str(green) + ",0]\n")
- file.write("color resicolor" + spin_no + ", resi " + spin_no
+ "\n")
- file.write("set_bond stick_radius, " + str(width) + ", resi
" + spin_no + "\n")
-
- file.write("hide all\n")
- file.write("show sticks, name C+N+CA\n")
- file.write("set stick_quality, 10\n")
- file.write("ray\n")
- file.close()
-
-
##################################################################################################
-
-
print('\n\n__________________________________________________________\n\nSuccessfully
generated model-free results files\nsee results
tab\n__________________________________________________________')
-
- returnstring = [residue, model, s2, rex, te]
- return returnstring # return data for results table dialog
-
-
-def see_results(openfile, import_results):
- """Open results."""
-
- if '.agr' in openfile:
- system('xmgrace ' + openfile + ' &')
-
- if '.csv' in openfile:
- system('gedit ' + openfile + ' &')
-
- if '.pml' in openfile:
- system('pymol ' + openfile + ' &')
-
- if 'Table_of_Results' in openfile:
- summary = Final_results(import_results, None, -1, "")
- if status.show_gui:
- summary.Show()
-
-
-
-class Final_results(wx.Frame): # Dialog that displays relax results
in window
- def __init__(self, results, *args, **kwds):
- # begin final_results.__init__
-
- # Load results.
- self.results = results
-
- # Create Frame.
- kwds["style"] = wx.DEFAULT_FRAME_STYLE
- wx.Frame.__init__(self, *args, **kwds)
- self.label_1 = wx.StaticText(self, -1, "Results of relax Analysis")
- self.grid_1 = wx.grid.Grid(self, -1, size=(1, 1))
- self.close_button = wx.Button(self, -1, "Close")
- self.close_button.SetFont(font.normal)
-
- self.__set_properties()
- self.__do_layout()
- self._fill_values()
-
- self.Bind(wx.EVT_BUTTON, self.close_table, self.close_button)
-
-
- def __do_layout(self):
- # begin final_results.__do_layout
- sizer_2 = wx.BoxSizer(wx.VERTICAL)
- sizer_2.Add(self.label_1, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 10)
- sizer_2.Add(self.grid_1, 1, wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL, 0)
- sizer_2.Add(self.close_button, 0, wx.ALIGN_CENTER_HORIZONTAL, 0)
- self.SetSizer(sizer_2)
- self.Layout()
-
-
- def __set_properties(self):
- # begin final_results.__set_properties
- self.SetTitle("relaxGUI")
- _icon = wx.EmptyIcon()
- _icon.CopyFromBitmap(wx.Bitmap(IMAGE_PATH+'relax_start.gif',
wx.BITMAP_TYPE_ANY))
- self.SetIcon(_icon)
- self.SetSize((700, 600))
- self.label_1.SetFont(wx.Font(12, wx.DEFAULT, wx.NORMAL, wx.BOLD, 0,
""))
- self.grid_1.CreateGrid(len(self.results[0]), 5)
- self.grid_1.SetColLabelValue(0, "Residue")
- self.grid_1.SetColSize(0, 80)
- self.grid_1.SetColLabelValue(1, "Model")
- self.grid_1.SetColSize(1, 70)
- self.grid_1.SetColLabelValue(2, "S2")
- self.grid_1.SetColSize(2, 150)
- self.grid_1.SetColLabelValue(3, "Rex [1/s]")
- self.grid_1.SetColSize(3, 150)
- self.grid_1.SetColLabelValue(4, "te")
- self.grid_1.SetColSize(4, 150)
-
-
- def _fill_values(self): # fill entries in table
- for i in range(0, len(self.results[0])):
- self.grid_1.SetCellValue(i, 0, self.results[0][i])
- self.grid_1.SetCellValue(i, 1, self.results[1][i])
- self.grid_1.SetCellValue(i, 2, self.results[2][i])
- self.grid_1.SetCellValue(i, 3, self.results[3][i])
- self.grid_1.SetCellValue(i, 4, self.results[4][i])
-
-
- def close_table(self, event): # close
- self.Destroy()
- event.Skip()
r16535 - /branches/uf_redesign/gui/analyses/results_analysis.py