Source Code for Module test_suite.gui_tests.noe

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006-2013 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from os import F_OK, access, sep 
 24  import wx 
 25   
 26  # relax module imports. 
 27  from data import Relax_data_store; ds = Relax_data_store() 
 28  from generic_fns.mol_res_spin import spin_loop 
 29  from generic_fns.pipes import cdp_name 
 30  from status import Status; status = Status() 
 31  from test_suite.gui_tests.base_classes import GuiTestCase 
 32   
 33  # relax GUI imports. 
 34  from gui.interpreter import Interpreter; interpreter = Interpreter() 
 35  from gui.string_conv import int_to_gui, str_to_gui 
 36  from gui.wizard import Wiz_window 
 37   
 38   
 39 -class Noe(GuiTestCase): 
 40      """Class for testing various aspects specific to the NOE analysis.""" 
 41   
 42 -    def test_noe_analysis(self): 
 43          """Test the NOE analysis.""" 
 44   
 45          # Initialise all the special windows (to sometimes catch rare race conditions). 
 46          self.app.gui.show_prompt(None) 
 47          self.app.gui.show_tree(None) 
 48          self.app.gui.show_pipe_editor(None) 
 49   
 50          # Simulate the new analysis wizard. 
 51          self.app.gui.analysis.menu_new(None) 
 52          page = self.app.gui.analysis.new_wizard.wizard.get_page(0) 
 53          page.select_noe(None) 
 54          self.app.gui.analysis.new_wizard.wizard._go_next(None) 
 55          page = self.app.gui.analysis.new_wizard.wizard.get_page(1) 
 56          self.app.gui.analysis.new_wizard.wizard._go_next(None) 
 57   
 58          # Get the data. 
 59          analysis_type, analysis_name, pipe_name, pipe_bundle = self.app.gui.analysis.new_wizard.get_data() 
 60   
 61          # Set up the analysis. 
 62          self.app.gui.analysis.new_analysis(analysis_type=analysis_type, analysis_name=analysis_name, pipe_name=pipe_name, pipe_bundle=pipe_bundle) 
 63   
 64          # Alias the analysis. 
 65          analysis = self.app.gui.analysis.get_page_from_name("Steady-state NOE") 
 66   
 67          # The frequency label. 
 68          analysis.field_nmr_frq.SetValue(str_to_gui('500')) 
 69   
 70          # Change the results directory. 
 71          analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir)) 
 72   
 73          # Load the sequence. 
 74          file = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'Ap4Aase.seq' 
 75          self._execute_uf(uf_name='sequence.read', file=file, mol_name_col=None, res_name_col=2, res_num_col=1, spin_name_col=None, spin_num_col=None) 
 76   
 77          # Unresolved spins. 
 78          self._execute_uf(uf_name='deselect.spin', spin_id=":3") 
 79   
 80          # Name the spins. 
 81          self._execute_uf(uf_name='spin.name', name="N") 
 82   
 83          # Create a Trp indole N spin. 
 84          self._execute_uf(uf_name='spin.create', res_num=40, spin_name="NE1") 
 85   
 86          # Flush the interpreter in preparation for the synchronous user functions of the peak list wizard. 
 87          interpreter.flush() 
 88   
 89          # The intensity data. 
 90          ids = ['ref', 'sat'] 
 91          files = [ 
 92              status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'peak_lists' + sep + 'ref_ave.list', 
 93              status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'peak_lists' + sep + 'sat_ave.list' 
 94          ] 
 95          errors = [3600, 3000] 
 96          errors_5 = [122000, 8500] 
 97          types = ['ref', 'sat'] 
 98   
 99          # Loop over the 2 spectra. 
100          for i in range(2): 
101              # Set up the peak intensity wizard. 
102              analysis.peak_wizard(None) 
103   
104              # The spectrum. 
105              page = analysis.wizard.get_page(analysis.page_indices['read']) 
106              page.uf_args['file'].SetValue(str_to_gui(files[i])) 
107              page.uf_args['spectrum_id'].SetValue(str_to_gui(ids[i])) 
108              page.uf_args['proton'].SetValue(str_to_gui('HN')) 
109   
110              # Apply to load the backbone NH, then set up for the Trp indoles. 
111              analysis.wizard._apply(None) 
112              interpreter.flush() 
113              page.uf_args['heteronuc'].SetValue(str_to_gui('NE1')) 
114              page.uf_args['proton'].SetValue(str_to_gui('HE1')) 
115   
116              # Move down 2 pages. 
117              analysis.wizard._go_next(None) 
118              analysis.wizard._go_next(None) 
119   
120              # Set the errors. 
121              page = analysis.wizard.get_page(analysis.page_indices['rmsd']) 
122              page.uf_args['error'].SetValue(int_to_gui(errors[i])) 
123   
124              # Apply, then set the individual spin errors. 
125              analysis.wizard._apply(None) 
126              interpreter.flush() 
127              page.uf_args['error'].SetValue(int_to_gui(errors_5[i])) 
128              page.uf_args['spin_id'].SetValue(str_to_gui(':5')) 
129   
130              # Go to the next page. 
131              analysis.wizard._go_next(None) 
132   
133              # Set the type. 
134              page = analysis.wizard.get_page(analysis.page_indices['spectrum_type']) 
135              page.uf_args['spectrum_type'].SetValue(types[i]) 
136   
137              # Go to the next page (i.e. finish). 
138              analysis.wizard._go_next(None) 
139   
140          # Execute relax. 
141          analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId())) 
142   
143          # Wait for execution to complete. 
144          analysis.thread.join() 
145   
146          # Flush all wx events. 
147          wx.Yield() 
148   
149          # Exceptions in the thread. 
150          self.check_exceptions() 
151   
152          # Check the relax controller. 
153          # FIXME: skipping the checks for certain wxPython bugs. 
154          if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2 (classic)': 
155              self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100) 
156   
157          # The real data. 
158          res_nums = [4, 5, 6, 40, 40, 55] 
159          sat = [5050.0, 51643.0, 53663.0, -65111.0, -181131.0, -105322.0] 
160          ref = [148614.0, 166842.0, 128690.0, 99566.0, 270047.0, 130959.0] 
161          noe = [0.033980647852826784, 0.30953237194471417, 0.4169943274535706, -0.6539481349054899, -0.6707387973204665, -0.8042364404126482] 
162          noe_err = [0.02020329903276632, 0.2320024671657343, 0.026067523940084526, 0.038300618865378507, 0.014260663438353431, 0.03183614777183591] 
163   
164          # Check the data pipe. 
165          self.assertEqual(cdp_name(), ds.relax_gui.analyses[0].pipe_name) 
166   
167          # Check the data. 
168          i = 0 
169          for spin_cont, mol_name, res_num, res_name in spin_loop(full_info=True): 
170              # Skip deselected spins. 
171              if not spin_cont.select: 
172                  continue 
173   
174              # Spin info. 
175              self.assertEqual(res_nums[i], res_num) 
176   
177              # Check the intensity data. 
178              self.assertEqual(sat[i], spin_cont.intensities['sat']) 
179              self.assertEqual(ref[i], spin_cont.intensities['ref']) 
180   
181              # Check the NOE data. 
182              self.assertEqual(noe[i], spin_cont.noe) 
183              self.assertAlmostEqual(noe_err[i], spin_cont.noe_err) 
184   
185              # Increment the spin index. 
186              i += 1 
187   
188          # Check the created files. 
189          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'noe.agr', F_OK)) 
190