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25 """Module for the automatic model-free protocol frame."""
26
27
28 from math import ceil
29 from os import sep
30 import wx
31 import wx.lib.buttons
32 import wx.lib.mixins.listctrl
33
34
35 from auto_analyses import dauvergne_protocol
36 from data_store import Relax_data_store; ds = Relax_data_store()
37 from graphics import ANALYSIS_IMAGE_PATH, IMAGE_PATH, fetch_icon
38 from gui.about import About_base
39 from gui.analyses.base import Base_analysis
40 from gui.analyses.elements.spin_element import Spin_ctrl
41 from gui.analyses.elements.text_element import Text_ctrl
42 from gui.analyses.execute import Execute
43 from gui.analyses.elements.model_list import Model_list
44 from gui.base_classes import Container
45 from gui.components.relax_data import Relax_data_list
46 from gui.filedialog import RelaxDirDialog
47 from gui.fonts import font
48 from gui.message import error_message, Missing_data
49 from gui.misc import add_border, bitmap_setup
50 from gui.string_conv import gui_to_int, gui_to_str, str_to_gui
51 from gui.uf_objects import Uf_storage; uf_store = Uf_storage()
52 from gui.wizards.wiz_objects import Wiz_window
53 from lib.physical_constants import NH_BOND_LENGTH
54 from lib.errors import RelaxError
55 from lib.text.gui import local_tm, rex, s2, s2f, te, tf, tm, ts
56 from lib.text.string import LIST, PARAGRAPH, SECTION, SUBSECTION, TITLE
57 from pipe_control.interatomic import interatomic_loop
58 from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin, spin_loop
59 from pipe_control.pipes import has_bundle, has_pipe
60 from specific_analyses.api import return_api
61 from status import Status; status = Status()
62
63
148
149
150
152 """The model-free auto-analysis GUI element."""
153
154 - def __init__(self, parent, id=-1, pos=wx.Point(-1, -1), size=wx.Size(-1, -1), style=524288, name='scrolledpanel', gui=None, analysis_name=None, pipe_name=None, pipe_bundle=None, uf_exec=[], data_index=None):
155 """Build the automatic model-free protocol GUI element.
156
157 @param parent: The parent wx element.
158 @type parent: wx object
159 @keyword id: The unique ID number.
160 @type id: int
161 @keyword pos: The position.
162 @type pos: wx.Size object
163 @keyword size: The size.
164 @type size: wx.Size object
165 @keyword style: The style.
166 @type style: int
167 @keyword name: The name for the panel.
168 @type name: unicode
169 @keyword gui: The main GUI class.
170 @type gui: gui.relax_gui.Main instance
171 @keyword analysis_name: The name of the analysis (the name in the tab part of the notebook).
172 @type analysis_name: str
173 @keyword pipe_name: The name of the original data pipe for this analysis.
174 @type pipe_name: str
175 @keyword pipe_bundle: The name of the data pipe bundle associated with this analysis.
176 @type pipe_bundle: str
177 @keyword uf_exec: The list of user function on_execute methods returned from the new analysis wizard.
178 @type uf_exec: list of methods
179 @keyword data_index: The index of the analysis in the relax data store (set to None if no data currently exists).
180 @type data_index: None or int
181 """
182
183
184 self.gui = gui
185
186
187 self.init_flag = True
188
189
190 if data_index == None:
191
192 if not has_pipe(pipe_name):
193 self.gui.interpreter.apply('pipe.create', pipe_name=pipe_name, pipe_type='mf', bundle=pipe_bundle)
194
195
196 if not has_bundle(pipe_bundle):
197 self.gui.interpreter.apply('pipe.bundle', bundle=pipe_bundle, pipe=pipe_name)
198
199
200 data_index = ds.relax_gui.analyses.add('model-free')
201
202
203 ds.relax_gui.analyses[data_index].analysis_name = analysis_name
204 ds.relax_gui.analyses[data_index].pipe_name = pipe_name
205 ds.relax_gui.analyses[data_index].pipe_bundle = pipe_bundle
206
207
208 ds.relax_gui.analyses[data_index].grid_inc = None
209 ds.relax_gui.analyses[data_index].diff_tensor_grid_inc = {'sphere': 11, 'prolate': 11, 'oblate': 11, 'ellipsoid': 6}
210 ds.relax_gui.analyses[data_index].mc_sim_num = None
211 ds.relax_gui.analyses[data_index].save_dir = self.gui.launch_dir
212 ds.relax_gui.analyses[data_index].local_tm_models = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
213 ds.relax_gui.analyses[data_index].mf_models = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
214 ds.relax_gui.analyses[data_index].max_iter = 30
215
216
217 if ds.relax_gui.analyses[data_index].pipe_bundle == None:
218 raise RelaxError("The pipe bundle must be supplied.")
219
220
221 self.data = ds.relax_gui.analyses[data_index]
222 self.data_index = data_index
223
224
225 if not hasattr(self.data, 'local_tm_models'):
226 self.data.local_tm_models = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
227 if not hasattr(self.data, 'mf_models'):
228 self.data.mf_models = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
229
230
231 self.mode_win = Protocol_mode_sel_window()
232
233
234 self.observer_register()
235
236
237 super(Auto_model_free, self).__init__(parent, id=id, pos=pos, size=size, style=style, name=name)
238
239
240 - def _about(self, event=None):
241 """The about window.
242
243 @keyword event: The wx event.
244 @type event: wx event
245 """
246
247
248 self.about_dialog = About_window(self)
249
250
251 if status.show_gui:
252 self.about_dialog.Show()
253
254
256 """Activate or deactivate certain elements of the analysis in response to the execution lock."""
257
258
259 enable = False
260 if not status.exec_lock.locked():
261 enable = True
262
263
264 wx.CallAfter(self.field_results_dir.Enable, enable)
265 wx.CallAfter(self.spin_systems.Enable, enable)
266 wx.CallAfter(self.relax_data.Enable, enable)
267 wx.CallAfter(self.button_dipole_pair.Enable, enable)
268 wx.CallAfter(self.button_csa.Enable, enable)
269 wx.CallAfter(self.button_isotope_heteronuc.Enable, enable)
270 wx.CallAfter(self.button_isotope_proton.Enable, enable)
271 wx.CallAfter(self.local_tm_model_field.Enable, enable)
272 wx.CallAfter(self.mf_model_field.Enable, enable)
273 wx.CallAfter(self.grid_inc.Enable, enable)
274 wx.CallAfter(self.mc_sim_num.Enable, enable)
275 wx.CallAfter(self.max_iter.Enable, enable)
276 wx.CallAfter(self.mode.Enable, enable)
277 wx.CallAfter(self.button_exec_relax.Enable, enable)
278
279
281 """Create and add the value.set buttons for the model-free analysis.
282
283 @param box: The box element to pack the GUI element into.
284 @type box: wx.BoxSizer instance
285 """
286
287
288 sizer = wx.BoxSizer(wx.HORIZONTAL)
289
290
291 self.button_dipole_pair = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, " Dipolar relaxation")
292 self.button_dipole_pair.SetBitmapLabel(wx.Bitmap(fetch_icon("relax.dipole_pair", "22x22"), wx.BITMAP_TYPE_ANY))
293 self.button_dipole_pair.SetFont(font.normal)
294 self.button_dipole_pair.SetSize((-1, 25))
295 self.button_dipole_pair.SetToolTipString("Define the magnetic dipole-dipole relaxation mechanism.")
296 self.gui.Bind(wx.EVT_BUTTON, self.setup_dipole_pair, self.button_dipole_pair)
297 sizer.Add(self.button_dipole_pair, 1, wx.ALL|wx.EXPAND, 0)
298
299
300 self.button_csa = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, " CSA relaxation")
301 self.button_csa.SetBitmapLabel(wx.Bitmap(fetch_icon("relax.align_tensor", "22x22"), wx.BITMAP_TYPE_ANY))
302 self.button_csa.SetFont(font.normal)
303 self.button_csa.SetSize((-1, 25))
304 self.button_csa.SetToolTipString("Define the Chemical Shift Anisotropy (CSA) relaxation mechanism via the value.set user function.")
305 self.gui.Bind(wx.EVT_BUTTON, self.value_set_csa, self.button_csa)
306 sizer.Add(self.button_csa, 1, wx.ALL|wx.EXPAND, 0)
307
308
309 self.button_isotope_heteronuc = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, " X isotope")
310 self.button_isotope_heteronuc.SetBitmapLabel(wx.Bitmap(fetch_icon("relax.nuclear_symbol", "22x22"), wx.BITMAP_TYPE_ANY))
311 self.button_isotope_heteronuc.SetFont(font.normal)
312 self.button_isotope_heteronuc.SetSize((-1, 25))
313 self.button_isotope_heteronuc.SetToolTipString("Set the nuclear isotope types of the heteronuclear spins via the spin.isotope user function.")
314 self.gui.Bind(wx.EVT_BUTTON, self.spin_isotope_heteronuc, self.button_isotope_heteronuc)
315 sizer.Add(self.button_isotope_heteronuc, 1, wx.ALL|wx.EXPAND, 0)
316
317
318 self.button_isotope_proton = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, " H isotope")
319 self.button_isotope_proton.SetBitmapLabel(wx.Bitmap(fetch_icon("relax.nuclear_symbol", "22x22"), wx.BITMAP_TYPE_ANY))
320 self.button_isotope_proton.SetFont(font.normal)
321 self.button_isotope_proton.SetSize((-1, 25))
322 self.button_isotope_proton.SetToolTipString("Set the nuclear isotope types of the proton spins via the spin.isotope user function.")
323 self.gui.Bind(wx.EVT_BUTTON, self.spin_isotope_proton, self.button_isotope_proton)
324 sizer.Add(self.button_isotope_proton, 1, wx.ALL|wx.EXPAND, 0)
325
326
327 box.Add(sizer, 0, wx.ALL|wx.EXPAND, 0)
328
329
331 """Assemble the data required for the auto-analysis.
332
333 See the docstring for auto_analyses.dauvernge_protocol for details. All data is taken from the relax data store, so data upload from the GUI to there must have been previously performed.
334
335 @return: A container with all the data required for the auto-analysis.
336 @rtype: class instance, list of str
337 """
338
339
340 data = Container()
341 missing = []
342
343
344 data.pipe_name = self.data.pipe_name
345 data.pipe_bundle = self.data.pipe_bundle
346
347
348 data.local_tm_models = self.local_tm_model_field.GetValue()
349 data.mf_models = self.mf_model_field.GetValue()
350
351
352 data.conv_loop = True
353
354
355 data.inc = gui_to_int(self.grid_inc.GetValue())
356 if hasattr(self.data, 'diff_tensor_grid_inc'):
357 data.diff_tensor_grid_inc = self.data.diff_tensor_grid_inc
358 else:
359 data.diff_tensor_grid_inc = {'sphere': 11, 'prolate': 11, 'oblate': 11, 'ellipsoid': 6}
360
361
362 data.mc_sim_num = gui_to_int(self.mc_sim_num.GetValue())
363
364
365 data.max_iter = self.data.max_iter
366
367
368 data.save_dir = self.data.save_dir
369
370
371 if not exists_mol_res_spin_data():
372 missing.append("Sequence data")
373
374
375 if not hasattr(cdp, 'ri_ids') or len(cdp.ri_ids) == 0:
376 missing.append("Relaxation data")
377
378
379 if hasattr(cdp, 'ri_ids') and len(cdp.ri_ids) <= 3:
380 missing.append("Insufficient relaxation data, 4 or more data sets are essential for the execution of the dauvergne_protocol auto-analysis. Check that you have entered data for a least two spectrometer fields.")
381
382
383 if not hasattr(cdp, 'interatomic') or len(cdp.interatomic) == 0:
384 missing.append("Interatomic data (for the dipole-dipole interaction)")
385
386
387 mode = gui_to_str(self.mode.GetValue())
388
389
390 if mode == 'Fully automated':
391
392 data.global_models = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']
393
394
395 else:
396 data.global_models = [mode]
397
398
399 vector_check = False
400 if 'prolate' in data.global_models or 'oblate' in data.global_models or 'ellipsoid' in data.global_models:
401 vector_check = True
402
403
404 for spin, spin_id in spin_loop(return_id=True):
405
406 if not spin.select:
407 continue
408
409
410 msg = "Spin '%s' - %s (try the %s user function)." % (spin_id, "%s", "%s")
411
412
413 if not hasattr(spin, 'isotope') or spin.isotope == None:
414 missing.append(msg % ("nuclear isotope data", "spin.isotope"))
415
416
417 if (hasattr(spin, 'isotope') and spin.isotope in ['15N', '13C']) and (not hasattr(spin, 'csa') or spin.csa == None):
418 missing.append(msg % ("CSA data", "value.set"))
419
420
421 for interatom in interatomic_loop():
422
423 spin1 = return_spin(interatom.spin_id1)
424 spin2 = return_spin(interatom.spin_id2)
425
426
427 if not spin1.select:
428 continue
429 if not spin2.select:
430 continue
431
432
433 msg = "Spin pair '%s' and '%s' - %s (try the %s user function)." % (interatom.spin_id1, interatom.spin_id2, "%s", "%s")
434
435
436 if not hasattr(interatom, 'r') or interatom.r == None:
437 missing.append(msg % ("bond length data", "value.set"))
438
439
440 if vector_check and (not hasattr(interatom, 'vector') or interatom.vector == None):
441 missing.append(msg % ("unit vectors", "interatom.unit_vectors"))
442
443
444 return data, missing
445
446
448 """Construct the left hand box to pack into the main model-free box.
449
450 @return: The left hand box element containing the bitmap and about button to pack into the main model-free box.
451 @rtype: wx.BoxSizer instance
452 """
453
454
455 left_box = wx.BoxSizer(wx.VERTICAL)
456
457
458 bitmaps = [ANALYSIS_IMAGE_PATH+"model_free"+sep+"model_free_200x200.png",
459 IMAGE_PATH+'modelfree.png']
460
461
462 for i in range(len(bitmaps)):
463
464 bitmap = wx.StaticBitmap(self, -1, bitmap_setup(bitmaps[i]))
465
466
467 left_box.Add(bitmap, 0, wx.ALL, 0)
468
469
470 left_box.AddStretchSpacer()
471
472
473 button_sizer = wx.BoxSizer(wx.HORIZONTAL)
474
475
476 button = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, "About")
477 button.SetBitmapLabel(wx.Bitmap(fetch_icon('oxygen.actions.help-about', "22x22"), wx.BITMAP_TYPE_ANY))
478 button.SetFont(font.normal)
479 button.SetToolTipString("Information about this automatic analysis")
480
481
482 self.Bind(wx.EVT_BUTTON, self._about, button)
483
484
485 cursor = wx.StockCursor(wx.CURSOR_QUESTION_ARROW)
486 button.SetCursor(cursor)
487
488
489 button_sizer.Add(button, 0, 0, 0)
490 left_box.Add(button_sizer, 0, wx.ALL, 0)
491
492
493 return left_box
494
495
497 """Construct the right hand box to pack into the main model-free box.
498
499 @return: The right hand box element containing all model-free GUI elements (excluding the bitmap) to pack into the main model-free box.
500 @rtype: wx.BoxSizer instance
501 """
502
503
504 box = wx.BoxSizer(wx.VERTICAL)
505
506
507 self.add_title(box, "Model-free analysis")
508
509
510 Text_ctrl(box, self, text="The data pipe bundle:", default=self.data.pipe_bundle, tooltip="This is the data pipe bundle associated with this analysis.", editable=False, width_text=self.width_text, width_button=self.width_button, spacer=self.spacer_horizontal)
511
512
513 self.field_results_dir = Text_ctrl(box, self, text="Results directory:", icon=fetch_icon('oxygen.actions.document-open-folder', "16x16"), default=self.data.save_dir, tooltip="The directory in which all automatically created files will be saved.", tooltip_button="Select the results directory.", fn=self.results_directory, button=True, width_text=self.width_text, width_button=self.width_button, spacer=self.spacer_horizontal)
514
515
516 self.add_spin_systems(box, self)
517
518
519 box.AddSpacer(10)
520 self.relax_data = Relax_data_list(gui=self.gui, parent=self, box=box, id=str(self.data_index))
521 box.AddSpacer(10)
522
523
524 self.add_values(box)
525 box.AddSpacer(10)
526
527
528 self.local_tm_model_field = Local_tm_list(self, box)
529 self.local_tm_model_field.set_value(self.data.local_tm_models)
530
531
532 self.mf_model_field = Mf_list(self, box)
533 self.mf_model_field.set_value(self.data.mf_models)
534
535
536 self.grid_inc = Spin_ctrl(box, self, text="Grid search increments:", default=11, min=1, max=100, tooltip="This is the number of increments per dimension of the grid search performed prior to numerical optimisation.", width_text=self.width_text, width_button=self.width_button, spacer=self.spacer_horizontal)
537 self.mc_sim_num = Spin_ctrl(box, self, text="Monte Carlo simulation number:", default=500, min=1, max=100000, tooltip="This is the number of Monte Carlo simulations performed for error propagation and analysis.", width_text=self.width_text, width_button=self.width_button, spacer=self.spacer_horizontal)
538
539
540 self.max_iter = Spin_ctrl(box, self, text="Maximum iterations:", default=self.data.max_iter, tooltip="The maximum number of iterations for the protocol. This is the limit for the global looping over the optimisation of the model-free models, model elimination, model selection and then optimisation of the diffusion tensor.", min=25, max=100, width_text=self.width_text, width_button=self.width_button, spacer=self.spacer_horizontal)
541
542
543 self.mode = Text_ctrl(box, self, text="Protocol mode:", default='Fully automated', tooltip="Select if the dauvergne_protocol analysis will be fully automated or whether the individual global models will be optimised separately.", tooltip_button="Open the protocol mode selection window.", icon=fetch_icon('oxygen.actions.system-run', "16x16"), fn=self.mode_dialog, editable=False, button=True, width_text=self.width_text, width_button=self.width_button, spacer=self.spacer_horizontal)
544
545
546 box.AddSpacer(30)
547 box.AddStretchSpacer()
548
549
550 self.button_exec_relax = self.add_execute_analysis(box, self.execute)
551
552
553 return box
554
555
557 """Unregister the spin count from the user functions."""
558
559
560 self.observer_register(remove=True)
561
562
563 self.relax_data.delete()
564
565
566 if hasattr(self, 'dipole_wizard'):
567 self.dipole_wizard.Destroy()
568 del self.dipole_wizard
569
570
571 self.mode_win.Destroy()
572 del self.mode_win
573
574
575 self.local_tm_model_field.model_win.Destroy()
576 del self.local_tm_model_field
577 self.mf_model_field.model_win.Destroy()
578 del self.mf_model_field
579
580
581 if hasattr(self, 'missing_data'):
582 self.missing_data.Destroy()
583 del self.missing_data
584
585
626
627
629 """The calculation mode selection.
630
631 @keyword event: The wx event.
632 @type event: wx event
633 """
634
635
636 if status.show_gui:
637 self.mode_win.ShowModal()
638
639
640 self.mode.SetValue(str_to_gui(self.mode_win.select))
641
642
663
664
666 """The results directory selection.
667
668 @keyword event: The wx event.
669 @type event: wx event
670 """
671
672
673 dialog = RelaxDirDialog(parent=self, message='Select the results directory', defaultPath=self.field_results_dir.GetValue())
674
675
676 if status.show_gui and dialog.ShowModal() != wx.ID_OK:
677
678 return
679
680
681 path = gui_to_str(dialog.get_path())
682 if not path:
683 return
684
685
686 self.data.save_dir = path
687
688
689 self.field_results_dir.SetValue(str_to_gui(path))
690
691
693 """Create the wizard for the dipole-dipole interaction.
694
695 @keyword event: The wx event.
696 @type event: wx event
697 """
698
699
700 wx.BeginBusyCursor()
701
702
703 if hasattr(self, 'dipole_wizard'):
704 self.dipole_wizard.Destroy()
705
706
707 self.dipole_wizard = Wiz_window(parent=self.gui, size_x=1000, size_y=750, title="Dipole-dipole interaction setup")
708
709
710 if not hasattr(cdp, 'structure'):
711
712 page = uf_store['structure.read_pdb'].create_page(self.dipole_wizard, sync=True)
713 self.dipole_wizard.add_page(page, skip_button=True)
714
715
716 page = uf_store['structure.get_pos'].create_page(self.dipole_wizard, sync=True)
717 self.dipole_wizard.add_page(page, skip_button=True)
718
719
720 page = uf_store['interatom.define'].create_page(self.dipole_wizard, sync=True)
721 page.SetValue('spin_id1', '@N')
722 page.SetValue('spin_id2', '@H')
723 self.dipole_wizard.add_page(page)
724
725
726 page = uf_store['interatom.set_dist'].create_page(self.dipole_wizard, sync=True)
727 page.SetValue('spin_id1', '@N*')
728 page.SetValue('spin_id2', '@H*')
729 page.SetValue('ave_dist', NH_BOND_LENGTH)
730 self.dipole_wizard.add_page(page)
731
732
733 page = uf_store['interatom.unit_vectors'].create_page(self.dipole_wizard, sync=True)
734 self.dipole_wizard.add_page(page)
735
736
737 if wx.IsBusy():
738 wx.EndBusyCursor()
739
740
741 self.dipole_wizard.run()
742
743
745 """Set the nuclear isotope types of the heteronuclear spins via the spin.isotope user function.
746
747 @keyword event: The wx event.
748 @type event: wx event
749 """
750
751
752 uf_store['spin.isotope'](isotope='15N', spin_id='@N*')
753
754
756 """Set the nuclear isotope types of the proton spins via the spin.isotope user function.
757
758 @keyword event: The wx event.
759 @type event: wx event
760 """
761
762
763 uf_store['spin.isotope'](isotope='1H', spin_id='@H*')
764
765
767 """Synchronise the analysis frame and the relax data store, both ways.
768
769 This method allows the frame information to be uploaded into the relax data store, or for the information in the relax data store to be downloaded by the frame.
770
771 @keyword upload: A flag which if True will cause the frame to send data to the relax data store. If False, data will be downloaded from the relax data store to update the frame.
772 @type upload: bool
773 """
774
775
776 if upload:
777 self.data.local_tm_models = self.local_tm_model_field.GetValue()
778 else:
779 self.local_tm_model_field.set_value(self.data.local_tm_models)
780
781
782 if upload:
783 self.data.mf_models = self.mf_model_field.GetValue()
784 else:
785 self.mf_model_field.set_value(self.data.mf_models)
786
787
788 if upload:
789 self.data.grid_inc = gui_to_int(self.grid_inc.GetValue())
790 elif hasattr(self.data, 'grid_inc'):
791 self.grid_inc.SetValue(int(self.data.grid_inc))
792
793
794 if upload:
795 self.data.mc_sim_num = gui_to_int(self.mc_sim_num.GetValue())
796 elif hasattr(self.data, 'mc_sim_num'):
797 self.mc_sim_num.SetValue(int(self.data.mc_sim_num))
798
799
800 if upload:
801 self.data.save_dir = str(self.field_results_dir.GetValue())
802 else:
803 self.field_results_dir.SetValue(str_to_gui(self.data.save_dir))
804
805
806 if upload:
807 self.data.max_iter = gui_to_int(self.max_iter.GetValue())
808 else:
809 self.max_iter.SetValue(int(self.data.max_iter))
810
811
813 """Set the CSA via the value.set uf.
814
815 @keyword event: The wx event.
816 @type event: wx event
817 """
818
819
820 api = return_api()
821 val = api.default_value('csa')
822
823
824 uf_store['value.set'](val=val, param='csa', spin_id='@N*')
825
826
827
829 """The model-free analysis execution object."""
830
832 """Execute the calculation."""
833
834
835 dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, diff_model=self.data.global_models, mf_models=self.data.mf_models, local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, conv_loop=self.data.conv_loop)
836
837
838
840 """The local model-free model list GUI element."""
841
842
843 desc = "Local %s models:" % tm
844 model_desc = [
845 "Model m0 with a local molecular correlation time (%s)." % tm,
846 "Model m1 with a local molecular correlation time (%s)." % tm,
847 "Model m2 with a local molecular correlation time (%s)." % tm,
848 "Model m3 with a local molecular correlation time (%s)." % tm,
849 "Model m4 with a local molecular correlation time (%s)." % tm,
850 "Model m5 with a local molecular correlation time (%s)." % tm,
851 "Model m6 with a local molecular correlation time (%s)." % tm,
852 "Model m7 with a local molecular correlation time (%s)." % tm,
853 "Model m8 with a local molecular correlation time (%s)." % tm,
854 "Model m9 with a local molecular correlation time (%s)." % tm
855 ]
856 models = [
857 "tm0",
858 "tm1",
859 "tm2",
860 "tm3",
861 "tm4",
862 "tm5",
863 "tm6",
864 "tm7",
865 "tm8",
866 "tm9"
867 ]
868 params = [
869 "{%s}" % local_tm,
870 "{%s, %s}" % (local_tm, s2),
871 "{%s, %s, %s}" % (local_tm, s2, te),
872 "{%s, %s, %s}" % (local_tm, s2, rex),
873 "{%s, %s, %s, %s}" % (local_tm, s2, te, rex),
874 "{%s, %s, %s, %s}" % (local_tm, s2, s2f, ts),
875 "{%s, %s, %s, %s, %s}" % (local_tm, s2, tf, s2f, ts),
876 "{%s, %s, %s, %s, %s}" % (local_tm, s2, s2f, ts, rex),
877 "{%s, %s, %s, %s, %s, %s}" % (local_tm, s2, tf, s2f, ts, rex),
878 "{%s, %s}" % (local_tm, rex)
879 ]
880 warning = "The model-free models used in dauvergne_protocol auto-analysis should almost never be changed! The consequences will be unpredictable. Please proceed only if you are sure of what you are doing. Would you like to modify the model-free model list?"
881 red_flag = True
882 size = wx.Size(680, 350)
883 tooltip = "The list model-free models with the %s parameter to optimise as the first step of the protocol (see the about window for details). This really should not be changed." % local_tm
884 tooltip_button = "Open the model list selector window."
885
886
887
889 """The model-free model list GUI element."""
890
891
892 desc = "Model-free models:"
893 model_desc = [
894 "No statistically significant internal motions.",
895 "The original model with a statistically insignificant %s." % te,
896 "The original Lipari and Szabo model.",
897 "The original model with chemical exchange relaxation but a statistically insignificant %s." % te,
898 "The original model with chemical exchange relaxation.",
899 "The extended model with a statistically insignificant %s." % tf,
900 "The Clore et al., 1991 extended model-free model.",
901 "The extended model with chemical exchange relaxation but a statistically insignificant %s." % tf,
902 "The extended model with chemical exchange relaxation.",
903 "No statistically significant internal motions but chemical exchange relaxation present."
904 ]
905 models = [
906 "m0",
907 "m1",
908 "m2",
909 "m3",
910 "m4",
911 "m5",
912 "m6",
913 "m7",
914 "m8",
915 "m9"
916 ]
917 params = [
918 "{}",
919 "{%s}" % s2,
920 "{%s, %s}" % (s2, te),
921 "{%s, %s}" % (s2, rex),
922 "{%s, %s, %s}" % (s2, te, rex),
923 "{%s, %s, %s}" % (s2, s2f, ts),
924 "{%s, %s, %s, %s}" % (s2, tf, s2f, ts),
925 "{%s, %s, %s, %s}" % (s2, s2f, ts, rex),
926 "{%s, %s, %s, %s, %s}" % (s2, tf, s2f, ts, rex),
927 "{%s}" % rex
928 ]
929 warning = "The model-free models used in dauvergne_protocol auto-analysis should almost never be changed! The consequences will be unpredictable. Please proceed only if you are sure of what you are doing. Would you like to modify the model-free model list?"
930 red_flag = True
931 size = wx.Size(850, 350)
932 tooltip = "The list model-free models to optimise as the iterative part of the protocol (see the about window for details). This really should not be changed."
933 tooltip_button = "Open the model list selector window."
934
935
936
938 """The protocol mode selector window object."""
939
941 """Set up the window."""
942
943
944 wx.Dialog.__init__(self, None, id=-1, title="Protocol mode selection")
945
946
947 size_x = 600
948 size_y = 600
949 border = 10
950 self.select = 'Fully automated'
951
952
953 self.SetSize((size_x, size_y))
954 self.Centre()
955 self.SetFont(font.normal)
956
957
958 main_sizer = wx.BoxSizer(wx.VERTICAL)
959
960
961 self.SetSizer(main_sizer)
962
963
964 sizer = add_border(main_sizer, border=border, packing=wx.HORIZONTAL)
965
966
967 self.build_auto(sizer)
968
969
970 sizer.Add(wx.StaticLine(self, -1, style=wx.LI_VERTICAL), 0, wx.EXPAND|wx.ALL, border)
971
972
973 self.build_manual(sizer)
974
975
977 """Build the fully automated part of the window.
978
979 @param sizer: The sizer to pack the elements into.
980 @type sizer: wx.BoxSizer instance
981 """
982
983
984 sub_sizer = wx.BoxSizer(wx.VERTICAL)
985
986
987 title = wx.StaticText(self, -1, "Fully automated")
988 title.SetFont(font.subtitle)
989 sub_sizer.Add(title, 0, wx.ALIGN_CENTRE_HORIZONTAL, 0)
990
991
992 sub_sizer.AddStretchSpacer()
993
994
995 button = wx.BitmapButton(self, -1, wx.Bitmap(fetch_icon('oxygen.actions.go-bottom', "48x48"), wx.BITMAP_TYPE_ANY))
996 button.SetMinSize((80, 80))
997 button.SetToolTipString("Perform a fully automated analysis, looping over global models I to V and terminating with the final run. Please click on the 'About' button for more information.")
998 sub_sizer.Add(button, 3, wx.EXPAND, 0)
999 self.Bind(wx.EVT_BUTTON, self.select_full_analysis, button)
1000
1001
1002 sub_sizer.AddStretchSpacer()
1003
1004
1005 sizer.Add(sub_sizer, 1, wx.ALL|wx.EXPAND, 0)
1006
1007
1009 """Build the manual part of the window.
1010
1011 @param sizer: The sizer to pack the elements into.
1012 @type sizer: wx.BoxSizer instance
1013 """
1014
1015
1016 sub_sizer = wx.BoxSizer(wx.VERTICAL)
1017
1018
1019 title = wx.StaticText(self, -1, "Manual modes")
1020 title.SetFont(font.subtitle)
1021 sub_sizer.Add(title, 0, wx.ALIGN_CENTRE_HORIZONTAL, 0)
1022
1023
1024 sub_sizer.AddSpacer(10)
1025
1026
1027 button = wx.Button(self, -1, "Local %s" % tm)
1028 button.SetToolTipString("Optimise global model I, the %s models. Please click on the 'About' button for more information." % local_tm)
1029 button.SetFont(font.normal)
1030 sub_sizer.Add(button, 1, wx.EXPAND, 0)
1031 self.Bind(wx.EVT_BUTTON, self.select_local_tm, button)
1032
1033
1034 button = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, str_to_gui(" Sphere"))
1035 button.SetBitmapLabel(wx.Bitmap(IMAGE_PATH+'sphere.png', wx.BITMAP_TYPE_ANY))
1036 button.SetFont(font.normal)
1037 button.SetToolTipString("Optimise global model II, the spherical diffusion model. Please click on the 'About' button for more information.")
1038 sub_sizer.Add(button, 1, wx.EXPAND, 0)
1039 self.Bind(wx.EVT_BUTTON, self.select_sphere, button)
1040
1041
1042 button = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, str_to_gui(" Prolate spheroid"))
1043 button.SetBitmapLabel(wx.Bitmap(IMAGE_PATH+'prolate.png', wx.BITMAP_TYPE_ANY))
1044 button.SetFont(font.normal)
1045 button.SetToolTipString("Optimise global model III, the prolate spheroid diffusion model. Please click on the 'About' button for more information.")
1046 sub_sizer.Add(button, 1, wx.EXPAND, 0)
1047 self.Bind(wx.EVT_BUTTON, self.select_prolate, button)
1048
1049
1050 button = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, str_to_gui(" Oblate spheroid"))
1051 button.SetBitmapLabel(wx.Bitmap(IMAGE_PATH+'oblate.png', wx.BITMAP_TYPE_ANY))
1052 button.SetFont(font.normal)
1053 button.SetToolTipString("Optimise global model IV, the oblate spheroid diffusion model. Please click on the 'About' button for more information.")
1054 sub_sizer.Add(button, 1, wx.EXPAND, 0)
1055 self.Bind(wx.EVT_BUTTON, self.select_oblate, button)
1056
1057
1058 button = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, str_to_gui(" Ellipsoid"))
1059 button.SetBitmapLabel(wx.Bitmap(IMAGE_PATH+'ellipsoid.png', wx.BITMAP_TYPE_ANY))
1060 button.SetFont(font.normal)
1061 button.SetToolTipString("Optimise global model V, the ellipsoid diffusion model. Please click on the 'About' button for more information.")
1062 sub_sizer.Add(button, 1, wx.EXPAND, 0)
1063 self.Bind(wx.EVT_BUTTON, self.select_ellipsoid, button)
1064
1065
1066 button = wx.Button(self, -1, str_to_gui("Final"))
1067 button.SetToolTipString("The final run of the protocol. Please click on the 'About' button for more information.")
1068 button.SetFont(font.normal)
1069 sub_sizer.Add(button, 1, wx.EXPAND, 0)
1070 self.Bind(wx.EVT_BUTTON, self.select_final, button)
1071
1072
1073 sizer.Add(sub_sizer, 1, wx.ALL|wx.EXPAND, 0)
1074
1075
1077 """The ellipsoid global model has been selected.
1078
1079 @keyword event: The wx event.
1080 @type event: wx event
1081 """
1082
1083
1084 self.select = 'ellipsoid'
1085
1086
1087 self.Close()
1088
1089
1091 """The final stage of the protocol has been selected.
1092
1093 @keyword event: The wx event.
1094 @type event: wx event
1095 """
1096
1097
1098 self.select = 'final'
1099
1100
1101 self.Close()
1102
1103
1105 """The full analysis has been selected.
1106
1107 @keyword event: The wx event.
1108 @type event: wx event
1109 """
1110
1111
1112 self.select = 'Fully automated'
1113
1114
1115 self.Close()
1116
1117
1119 """The local_tm global model has been selected.
1120
1121 @keyword event: The wx event.
1122 @type event: wx event
1123 """
1124
1125
1126 self.select = 'local_tm'
1127
1128
1129 self.Close()
1130
1131
1133 """The prolate global model has been selected.
1134
1135 @keyword event: The wx event.
1136 @type event: wx event
1137 """
1138
1139
1140 self.select = 'prolate'
1141
1142
1143 self.Close()
1144
1145
1147 """The oblate global model has been selected.
1148
1149 @keyword event: The wx event.
1150 @type event: wx event
1151 """
1152
1153
1154 self.select = 'oblate'
1155
1156
1157 self.Close()
1158
1159
1161 """The sphere global model has been selected.
1162
1163 @keyword event: The wx event.
1164 @type event: wx event
1165 """
1166
1167
1168 self.select = 'sphere'
1169
1170
1171 self.Close()
1172