Author: bugman
Date: Fri Aug 5 12:29:24 2011
New Revision: 14173
URL: http://svn.gna.org/viewcvs/relax?rev=14173&view=rev
Log:
Deleted the now unused gui.execution.calc_rx module.
Removed:
branches/gui_testing/gui/execution/calc_rx.py
Removed: branches/gui_testing/gui/execution/calc_rx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/gui/execution/calc_rx.py?rev=14172&view=auto
==============================================================================
--- branches/gui_testing/gui/execution/calc_rx.py (original)
+++ branches/gui_testing/gui/execution/calc_rx.py (removed)
@@ -1,260 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2009 Michael Bieri
#
-# Copyright (C) 2010 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# script to calculate rx
-
-# Python module imports.
-from string import replace
-import sys
-import time
-import wx
-
-# relax module imports.
-from generic_fns import monte_carlo, results, minimise, pipes, sequence,
spectrum, selection, value, grace, state
-import generic_fns.structure.main
-from specific_fns.setup import relax_fit_obj
-
-
-def make_rx(target_dir, rx_list, relax_times, structure_pdb, nmr_freq,
r1_r2, freq_no, unres, main, freqno, global_setting, file_setting,
sequencefile, self):
- """Rx calculation."""
-
- # Number of Monte Carlo simulations
- global montecarlo
- montecarlo = int(global_setting[6])
-
- # value for progress bar during monte carlo simulation
- global progress
- progress = 5.0
-
- # redirect relax output and errors to relaxGUI - log panel
- redir = RedirectText(self)
- sys.stdout = redir
- sys.stderr = redir
-
- hetero = global_setting[2]
- prot = global_setting[3]
- resultsdir = str(target_dir)
- gracedir = str(target_dir) + sep + 'grace'
- savefile = str(target_dir) + sep + 'r' + str(r1_r2) + '.' +
str(nmr_freq) + '.out'
-
- wx.CallAfter(self.log_panel.AppendText, ('Starting R' + str(r1_r2) + '
calculation\n------------------------------------------\n\n') )
- time.sleep(0.5)
-
- # Select Peak Lists and Relaxation Times
- peakfiles = rx_list
-
- if r1_r2 == 2:
- if freq_no == 1:
- peakfiles = r2_list
- if freq_no == 2:
- peakfiles = r2_list2
- if freq_no == 3:
- peakfiles = r2_list3
-
- #create unresolved file
- if not unres == '':
- wx.CallAfter(self.log_panel.AppendText, ('Creating unresolved
file\n\n'))
- time.sleep(0.001)
- unres = replace(unres, ",", "\n")
- unres = replace(unres, " ", "")
- filename2 = target_dir + sep + 'unresolved'
- file = open(filename2, 'w')
- file.write(unres)
- file.close()
-
- pipename = 'Rx ' + str(time.asctime(time.localtime()))
-
- # Create the NOE data pipe.
- wx.CallAfter(self.log_panel.AppendText, ("pipes.create("+pipename+",
'relax_fit')\n\n"))
- time.sleep(0.001)
- pipes.create(pipename, 'relax_fit')
-
- # update progress bar
- wx.CallAfter(self.progress_bar.SetValue, (1))
-
- # Load Sequence
- if str(structure_pdb) == '!!! Sequence file selected !!!':
- # Read sequence file
- wx.CallAfter(self.log_panel.AppendText, ("Reading Suquence from "+
sequencefile+'\n\n'))
- time.sleep(0.001)
- sequence.read(sequencefile)
-
- else:
- # Load the backbone amide 15N spins from a PDB file.
- wx.CallAfter(self.log_panel.AppendText, ("Reading sequence from " +
str(structure_pdb) + '\n\n'))
- generic_fns.structure.main.read_pdb(str(structure_pdb))
- generic_fns.structure.main.load_spins(spin_id='@N')
-
- # update progress bar
- wx.CallAfter(self.progress_bar.SetValue, (2))
-
- # Spectrum names.
- names = peakfiles
-
- # Relaxation times (in seconds).
- times = relax_times
-
- # Loop over the spectra.
- print '\n'
- for i in xrange(len(names)):
- # Load the peak intensities.
- wx.CallAfter(self.log_panel.AppendText,
("spectrum.read(file=str("+names[i]+"), spectrum_id=str("+names[i]+"),
int_method='height', heteronuc="+str(hetero)+", proton="+str(prot)+")\n\n"))
- spectrum.read(file=str(names[i]), spectrum_id=str(names[i]),
int_method='height', heteronuc=hetero, proton=prot)
-
- # Set the relaxation times.
- print "\nrelax_fit_obj._relax_time(time=float("+times[i]+"),
spectrum_id="+names[i]+")"
- relax_fit_obj._relax_time(time=float(times[i]), spectrum_id=names[i])
-
- # Specify the duplicated spectra.
- print '\n'
- for i in range(0, (len(names))):
- for j in range(i, (len(names))):
- if times[i] == times[j]:
- if not i == j:
- print "spectrum.replicated(spectrum_ids=[" +
str(names[i]) + ", "+str(names[j])+"])"
- spectrum.replicated(spectrum_ids= [ str(names[i]),
str(names[j])])
-
- # update progress bar
- wx.CallAfter(self.progress_bar.SetValue, (4))
-
- # Peak intensity error analysis.
- print "spectrum.error_analysis()"
- spectrum.error_analysis()
-
- # Deselect unresolved spins.
- if not unres == '':
- print '\nDeselect Residues'
- selection.desel_read(file=resultsdir + sep + 'unresolved',
res_num_col= 1)
-
- # update progress bar
- wx.CallAfter(self.progress_bar.SetValue, (5))
-
- # Set the relaxation curve type.
- print "\nrelax_fit_obj._select_model('exp')"
- relax_fit_obj._select_model('exp')
-
- # Grid search.
- print "\nminimise.grid_search(inc=11)"
- minimise.grid_search(inc=11)
-
- # Minimise.
- print "minimise.minimise(min_algor='simplex', min_options=6,
func_tol=1e-25, grad_tol=None, max_iterations=10000000, constraints=False,
scaling=False, verbosity=1)"
- minimise.minimise(min_algor='simplex', min_options=6, func_tol=1e-25,
grad_tol=None, max_iterations=10000000, constraints=False, scaling=False,
verbosity=1)
-
- # Monte Carlo simulations.
- print "\nmonte_carlo.setup(number="+str(montecarlo)+")"
- monte_carlo.setup(number=montecarlo)
-
- print "\nmonte_carlo.create_data('back_calc')"
- monte_carlo.create_data('back_calc')
-
- print "\nmonte_carlo.initial_values()"
- monte_carlo.initial_values()
-
- print "minimise.minimise(min_algor='simplex', min_options=6,
func_tol=1e-25, grad_tol=None, max_iterations=10000000, constraints=False,
scaling=False, verbosity=1)"
- minimise.minimise(min_algor='simplex', min_options=6, func_tol=1e-25,
grad_tol=None, max_iterations=10000000, constraints=False, scaling=False,
verbosity=1)
-
- print "\nmonte_carlo.error_analysis(prune= 0.0)"
- monte_carlo.error_analysis(prune= 0.0)
-
- # Save the relaxation rates.
- print "\nSaving Files:"
- value.write(param='rx', file= savefile, force=True)
-
- # Create Grace plots of the data.
- grace.write(y_data_type='chi2', file='chi2.' + str(nmr_freq) + '.agr',
dir=gracedir, force=True) # Minimised chi-squared value.
- grace.write(y_data_type='i0', file='i0.' + str(nmr_freq) + '.agr',
dir=gracedir, force=True) # Initial peak intensity.
- grace.write(y_data_type='rx', file='r' + str(r1_r2)+'.' + str(nmr_freq)
+ '.agr', dir=gracedir, force=True) # Relaxation rate.
- grace.write(x_data_type='relax_times', y_data_type='int',
file='intensities.' + str(nmr_freq) + '.agr', dir=gracedir, force=True) #
Average peak intensities.
- grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='intensities_norm.' + str(nmr_freq) + '.agr', dir=gracedir, force=True)
# Average peak intensities (normalised).
-
- # Write the results.
- results.write(file='results', directory=resultsdir, force=True)
-
- # Save the program state.
- state.save_state('save', dir=resultsdir, force=True)
-
- print ""
- print ""
- print ""
- print
"________________________________________________________________________________"
- print ""
- print "calculation finished"
- print
"________________________________________________________________________________"
-
- # list files to results
- main.list_rx.Append(target_dir + sep + 'grace' + sep + 'r' +
str(r1_r2)+'.' + str(nmr_freq) + '.agr')
- main.list_rx.Append(target_dir + sep + 'grace' + sep +
'intensities_norm.' + str(nmr_freq) + '.agr')
-
- # add files to model-free tab
- if r1_r2 == 1:
- if freqno == 1:
- main.m_r1_1.SetValue(target_dir + sep + 'r1.' + str(nmr_freq) +
'.out')
- if freqno == 2:
- main.m_r1_2.SetValue(target_dir + sep + 'r1.' + str(nmr_freq) +
'.out')
- if freqno == 3:
- main.m_r1_3.SetValue(target_dir + sep + 'r1.' + str(nmr_freq) +
'.out')
- if r1_r2 == 2:
- if freqno == 1:
- main.m_r2_1.SetValue(target_dir + sep + 'r2.' + str(nmr_freq) +
'.out')
- if freqno == 2:
- main.m_r2_2.SetValue(target_dir + sep + 'r2.' + str(nmr_freq) +
'.out')
- if freqno == 3:
- main.m_r2_3.SetValue(target_dir + sep + 'r2.' + str(nmr_freq) +
'.out')
-
- # update progress bar
- wx.CallAfter(self.progress_bar.SetValue, (100))
-
- # enable close button and disable cancel button
- wx.CallAfter(self.close_button.Enable, True)
- wx.CallAfter(self.cancel_button.Enable, False)
-
- # close thread
- return
-
-
-class RedirectText(object):
- """Class to redirect relax output to relaxGUI - log panel and progress
bar."""
-
- def __init__(self, aWxTextCtrl):
- self.out = aWxTextCtrl
-
-
- def write(self, string):
- global progress
-
- wx.CallAfter(self.out.log_panel.WriteText, string)
- time.sleep(0.001) # allow relaxGUI log panel to get refreshed
-
- # split print out into list
- a = str(string)
- check = []
- check = a.split()
-
- # update progress bar
- if 'Simulation' in string:
- add = round(progress)
- add_int = int(add)
- wx.CallAfter(self.out.progress_bar.SetValue, add_int)
- progress = ( (int(check[1]) * 100) / float(montecarlo + 6)) + 5
- time.sleep(0.001) # allow relaxGUI progressbar to get refreshed
r14173 - /branches/gui_testing/gui/execution/calc_rx.py