Author: bugman
Date: Mon Aug 1 10:20:34 2011
New Revision: 14023
URL: http://svn.gna.org/viewcvs/relax?rev=14023&view=rev
Log:
Removed a no longer used NOE calculation module.
Removed:
branches/gui_testing/gui/execution/calc_noe.py
Removed: branches/gui_testing/gui/execution/calc_noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/gui/execution/calc_noe.py?rev=14022&view=auto
==============================================================================
--- branches/gui_testing/gui/execution/calc_noe.py (original)
+++ branches/gui_testing/gui/execution/calc_noe.py (removed)
@@ -1,188 +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
#
-#
#
-###############################################################################
-
-# Python module imports.
-from os import sep
-from string import replace
-import sys
-import time
-import wx
-
-# relax module imports.
-from generic_fns import grace, minimise, pipes, results, selection,
spectrum, state, value
-import generic_fns.structure.main
-from specific_fns.setup import noe_obj
-
-
-def make_noe(target_dir, noe_ref, noe_sat, rmsd_ref, rmsd_sat, nmr_freq,
struct_pdb, unres, execute, main, freqno, global_setting, file_setting,
sequencefile, self):
- """NOE 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'
- save_file = str(target_dir) + sep + 'noe.' + str(nmr_freq) + '.out'
- noe_ref_1 = noe_ref
- noe_sat_1 = noe_sat
- unres = str(unres)
-
- wx.CallAfter(self.log_panel.AppendText, ('Starting NOE
calculation\n------------------------------------------\n\n') )
- time.sleep(0.5)
-
- #create unresolved file
- if not unres == '':
- print "\nCreate unresolved file"
- unres = replace(unres, ",", "\n")
- unres = replace(unres, " ", "")
- filename3 = target_dir + sep + 'unresolved'
- unresolved = open(filename3, 'w')
- unresolved.write(unres)
- unresolved.close()
-
- pipename = 'NOE ' + str(time.asctime(time.localtime()))
-
- # Create the NOE data pipe.
- print "pipe.create("+pipename+")"
- pipes.create(pipename, 'noe')
-
- # Load Sequence
- if str(struct_pdb) == '!!! Sequence file selected !!!':
-
- # Read sequence file
- print "\nLoad sequence from "+ sequencefile
- sequence.read(sequencefile, res_name_col = 1)
-
- else:
- # Load the backbone amide 15N spins from a PDB file.
- print "\nLoad sequence from "+ str(struct_pdb)
- generic_fns.structure.main.read_pdb(str(struct_pdb))
- generic_fns.structure.main.load_spins(spin_id='@N')
-
- # Load the reference spectrum and saturated spectrum peak intensities.
- print "\nspectrum.read(file="+str(noe_ref)+", spectrum_id='ref_spec',
heteronuc="+hetero+", proton="+prot+", int_method='height')"
- spectrum.read(file=str(noe_ref), spectrum_id='ref_spec',
heteronuc=hetero, proton=prot, int_method='height')
- print "\nspectrum.read(file="+str(noe_sat)+", spectrum_id='sat_spec',
heteronuc="+hetero+", proton="+prot+", int_method='height')"
- spectrum.read(file=str(noe_sat), spectrum_id='sat_spec',
heteronuc=hetero, proton=prot, int_method='height')
-
- # Set the spectrum types.
- noe_obj._spectrum_type('ref', 'ref_spec')
- noe_obj._spectrum_type('sat', 'sat_spec')
-
- # Set the errors.
- spectrum.baseplane_rmsd(error=int(rmsd_ref), spectrum_id='ref_spec')
- spectrum.baseplane_rmsd(error=int(rmsd_sat), spectrum_id='sat_spec')
-
- # Peak intensity error analysis.
- print "\nspectrum.error_analysis()"
- spectrum.error_analysis()
-
- # Deselect unresolved residues.
- if not unres == '':
- print "\nDeselect residues"
- selection.desel_read(file=resultsdir + sep + 'unresolved',
res_num_col= 1)
-
- # Calculate the NOEs.
- print "\nminimise.calc()"
- minimise.calc()
-
- # Save the NOEs.
- print "\nSave Files:\n"
- value.write(param='noe', file=save_file, force=True)
-
- # Create grace files.
- grace.write(y_data_type='ref_spec', file='ref.' + str(nmr_freq) +
'.agr', dir=gracedir, force=True)
- grace.write(y_data_type='sat_spec', file='sat.' + str(nmr_freq) +
'.agr', dir=gracedir, force=True)
- grace.write(y_data_type='noe', file='noe.' + str(nmr_freq) + '.agr',
dir=gracedir, force=True)
-
- # 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
"________________________________________________________________________________"
-
- if freqno == 1:
- main.m_noe_1.SetValue(target_dir + sep + 'noe.' + str(nmr_freq) +
'.out')
- if freqno == 2:
- main.m_noe_2.SetValue(target_dir + sep + 'noe.' + str(nmr_freq) +
'.out')
- if freqno == 3:
- main.m_noe_3.SetValue(target_dir + sep + 'noe.' + str(nmr_freq) +
'.out')
- main.list_noe.Append(target_dir + sep + 'grace' + sep + 'noe.' +
str(nmr_freq) + '.agr')
-
- # 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
r14023 - /branches/gui_testing/gui/execution/calc_noe.py