Source Code for Module test_suite.gui_tests.model_free

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006-2012 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax is free software; you can redistribute it and/or modify               # 
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 11  #                                                                             # 
 12  # relax is distributed in the hope that it will be useful,                    # 
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 15  # GNU General Public License for more details.                                # 
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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
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 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  import numpy 
 25  from os import F_OK, access, sep 
 26  import wx 
 27   
 28  # relax module imports. 
 29  from data import Relax_data_store; ds = Relax_data_store() 
 30  from generic_fns.mol_res_spin import spin_loop 
 31  from generic_fns.pipes import cdp_name 
 32  from status import Status; status = Status() 
 33  from test_suite.gui_tests.base_classes import GuiTestCase 
 34   
 35  # relax GUI imports. 
 36  from gui.analyses import auto_model_free 
 37  from gui.interpreter import Interpreter; interpreter = Interpreter() 
 38  from gui.string_conv import float_to_gui, str_to_gui 
 39  from gui.uf_objects import Uf_storage; uf_store = Uf_storage() 
 40  from gui.wizard import Wiz_window 
 41   
 42   
 43 -class Mf(GuiTestCase): 
 44      """Class for testing various aspects specific to the model-free auto-analysis.""" 
 45   
 46 -    def test_mf_auto_analysis(self): 
 47          """Test the model-free auto-analysis.""" 
 48   
 49          # Simulate the new analysis wizard. 
 50          self.app.gui.analysis.menu_new(None) 
 51          page = self.app.gui.analysis.new_wizard.wizard.get_page(0) 
 52          page.select_mf(None) 
 53          page.analysis_name.SetValue(str_to_gui("Model-free test")) 
 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("Model-free test") 
 66   
 67          # Change the results directory. 
 68          analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir)) 
 69   
 70          # The data path. 
 71          data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'model_free' + sep + 'sphere' + sep 
 72   
 73          # Open and close the about window (mimicking user behaviour). 
 74          analysis._about() 
 75          analysis.about_dialog.Close() 
 76   
 77          # Launch the spin viewer window. 
 78          self.app.gui.show_tree() 
 79   
 80          # Run through the spin loading wizard. 
 81          self.app.gui.spin_viewer.load_spins_wizard() 
 82          self.app.gui.spin_viewer.wizard._go_next() 
 83          page = self.app.gui.spin_viewer.wizard.get_page(1) 
 84          page.SetValue('file', data_path+'noe.500.out') 
 85          self.app.gui.spin_viewer.wizard._go_next() 
 86          self.app.gui.spin_viewer.wizard._go_next() 
 87   
 88          # Close the spin viewer window. 
 89          self.app.gui.spin_viewer.handler_close() 
 90   
 91          # Flush the interpreter in preparation for the synchronous user functions of the peak list wizard. 
 92          interpreter.flush() 
 93   
 94          # Load the relaxation data. 
 95          data = [ 
 96              ['noe.500.out', 'noe_500', 'NOE', 500e6], 
 97              ['r1.500.out',  'r1_500',  'R1',  500e6], 
 98              ['r2.500.out',  'r2_500',  'R2',  500e6], 
 99              ['noe.900.out', 'noe_900', 'NOE', 900e6], 
100              ['r1.900.out',  'r1_900',  'R1',  900e6], 
101              ['r2.900.out',  'r2_900',  'R2',  900e6] 
102          ] 
103          for i in range(len(data)): 
104              self._execute_uf(uf_name='relax_data.read', file=data_path+data[i][0], ri_id=data[i][1], ri_type=data[i][2], frq=data[i][3], mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) 
105   
106          # Set the values, using the methods behind the buttons to set up the user functions with default values, and then manually executing the user function. 
107          analysis.value_set_csa() 
108          uf_store['value.set'].wizard._ok() 
109          interpreter.flush()    # Required because of the asynchronous uf call. 
110          analysis.value_set_r() 
111          uf_store['value.set'].wizard._ok() 
112          interpreter.flush()    # Required because of the asynchronous uf call. 
113          analysis.value_set_heteronuc_type() 
114          uf_store['value.set'].wizard._ok() 
115          interpreter.flush()    # Required because of the asynchronous uf call. 
116          analysis.value_set_proton_type() 
117          uf_store['value.set'].wizard._ok() 
118          interpreter.flush()    # Required because of the asynchronous uf call. 
119   
120          # The unit vector loading wizard. 
121          analysis.load_unit_vectors() 
122   
123          # The PDB file. 
124          page = analysis.vect_wizard.get_page(0) 
125          page.uf_args['file'].SetValue(str_to_gui(status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'model_free' + sep + 'sphere' + sep + 'sphere.pdb')) 
126          analysis.vect_wizard._go_next() 
127          interpreter.flush()    # Required because of the asynchronous uf call. 
128   
129          # The unit vectors. 
130          analysis.vect_wizard._go_next() 
131          interpreter.flush()    # Required because of the asynchronous uf call. 
132   
133          # Select only the tm0 and tm1 local tm models. 
134          analysis.local_tm_model_field.select = [True, True, False, False, False, False, False, False, False, False] 
135          analysis.local_tm_model_field.modify() 
136   
137          # Select only the m1 and m2 model-free models. 
138          analysis.mf_model_field.select = [False, True, True, False, False, False, False, False, False, False] 
139          analysis.mf_model_field.modify() 
140   
141          # Change the grid increments. 
142          analysis.grid_inc.SetValue(3) 
143          analysis.data.diff_tensor_grid_inc = {'sphere': 5, 'prolate': 5, 'oblate': 5, 'ellipsoid': 3} 
144   
145          # Set the number of Monte Carlo simulations. 
146          analysis.mc_sim_num.SetValue(2) 
147   
148          # Set the maximum number of iterations (changing the allowed values). 
149          analysis.max_iter.control.SetRange(0, 100) 
150          analysis.max_iter.SetValue(1) 
151   
152          # Set the protocol mode to automatic. 
153          analysis.mode_win.select_full_analysis() 
154          analysis.mode_dialog() 
155   
156          # Check that the data has been correctly updated prior to execution. 
157          analysis.sync_ds(upload=True) 
158          self.assertEqual(analysis.data.save_dir, ds.tmpdir) 
159          self.assertEqual(analysis.data.local_tm_models, ['tm0', 'tm1']) 
160          self.assertEqual(analysis.data.mf_models, ['m1', 'm2']) 
161          self.assertEqual(analysis.data.grid_inc, 3) 
162          self.assertEqual(analysis.data.mc_sim_num, 2) 
163          self.assertEqual(analysis.data.max_iter, 1) 
164          self.assertEqual(analysis.data.diff_tensor_grid_inc['sphere'], 5) 
165          self.assertEqual(analysis.data.diff_tensor_grid_inc['prolate'], 5) 
166          self.assertEqual(analysis.data.diff_tensor_grid_inc['oblate'], 5) 
167          self.assertEqual(analysis.data.diff_tensor_grid_inc['ellipsoid'], 3) 
168   
169          # Modify some of the class variables to speed up optimisation. 
170          auto_model_free.dauvergne_protocol.dAuvergne_protocol.opt_func_tol = 1e-5 
171          auto_model_free.dauvergne_protocol.dAuvergne_protocol.opt_max_iterations = 1000 
172   
173          # Execute relax. 
174          analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId())) 
175   
176          # Wait for execution to complete. 
177          analysis.thread.join() 
178   
179          # Flush all wx events. 
180          wx.Yield() 
181   
182          # Exceptions in the thread. 
183          self.check_exceptions() 
184   
185          # Check the relax controller. 
186          if status.relax_mode != 'gui': 
187              self.assertEqual(self.app.gui.controller.mc_gauge_mf.GetValue(), 100) 
188              self.assertEqual(self.app.gui.controller.progress_gauge_mf.GetValue(), 100) 
189              self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100) 
190   
191          # Check the diffusion tensor. 
192          self.assertEqual(cdp.diff_tensor.type, 'sphere') 
193          self.assertAlmostEqual(cdp.diff_tensor.tm, 1e-8) 
194          self.assertEqual(cdp.diff_tensor.fixed, True) 
195   
196          # The global minimisation info. 
197          self.assertAlmostEqual(cdp.chi2, 4e-19) 
198   
199          # The spin ID info. 
200          mol_names = ["sphere_mol1"] * 9 
201          res_names = ["GLY"] * 9 
202          res_nums = range(1, 10) 
203          spin_names = ["N"] * 9 
204          spin_nums = numpy.array(range(9)) * 2 + 1 
205   
206          # Check the spin data. 
207          i = 0 
208          for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 
209              # The ID info. 
210              self.assertEqual(mol_name, mol_names[i]) 
211              self.assertEqual(res_name, res_names[i]) 
212              self.assertEqual(res_num,  res_nums[i]) 
213              self.assertEqual(spin.name, spin_names[i]) 
214              self.assertEqual(spin.num,  spin_nums[i]) 
215   
216              # The data. 
217              self.assertEqual(spin.select, True) 
218              self.assertEqual(spin.fixed, False) 
219              self.assertEqual(spin.proton_type, '1H') 
220              self.assertEqual(spin.heteronuc_type, '15N') 
221              self.assertEqual(spin.attached_proton, None) 
222              self.assertAlmostEqual(spin.r, 1.02 * 1e-10) 
223              self.assertAlmostEqual(spin.csa, -172e-6) 
224   
225              # The model-free data. 
226              self.assertEqual(spin.model, 'm2') 
227              self.assertEqual(spin.equation, 'mf_orig') 
228              self.assertEqual(len(spin.params), 2) 
229              self.assertEqual(spin.params[0], 's2') 
230              self.assertEqual(spin.params[1], 'te') 
231              self.assertAlmostEqual(spin.s2, 0.8) 
232              self.assertEqual(spin.s2f, None) 
233              self.assertEqual(spin.s2s, None) 
234              self.assertEqual(spin.local_tm, None) 
235              self.assertAlmostEqual(spin.te, 20e-12) 
236              self.assertEqual(spin.tf, None) 
237              self.assertEqual(spin.ts, None) 
238              self.assertEqual(spin.rex, None) 
239   
240              # The spin minimisation info. 
241              self.assertEqual(spin.chi2, None) 
242              self.assertEqual(spin.iter, None) 
243              self.assertEqual(spin.f_count, None) 
244              self.assertEqual(spin.g_count, None) 
245              self.assertEqual(spin.h_count, None) 
246              self.assertEqual(spin.warning, None) 
247   
248              # Increment the index. 
249              i += 1 
250