Source Code for Module specific_analyses.model_free.model

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2002-2014 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2006 Chris MacRaild                                           # 
  5  # Copyright (C) 2008-2009 Sebastien Morin                                     # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  8  #                                                                             # 
  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """The model-free analysis parameter functions.""" 
 26   
 27  # relax module imports. 
 28  from lib.errors import RelaxError, RelaxNoSequenceError, RelaxNoTensorError 
 29  from pipe_control import diffusion_tensor 
 30  from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop 
 31   
 32   
 33 -def determine_model_type(): 
 34      """Determine the global model type. 
 35   
 36      @return:    The name of the model type, which will be one of 'all', 'diff', 'mf', or 'local_tm'.  If all parameters are fixed (and no spins selected), None is returned. 
 37      @rtype:     str or None 
 38      """ 
 39   
 40      # Test if sequence data is loaded. 
 41      if not exists_mol_res_spin_data(): 
 42          raise RelaxNoSequenceError 
 43   
 44      # If there is a local tm, fail if not all residues have a local tm parameter. 
 45      local_tm = False 
 46      for spin in spin_loop(): 
 47          # Skip deselected spins. 
 48          if not spin.select: 
 49              continue 
 50   
 51          # No params. 
 52          if not hasattr(spin, 'params') or not spin.params: 
 53              continue 
 54   
 55          # Local tm. 
 56          if not local_tm and 'local_tm' in spin.params: 
 57              local_tm = True 
 58   
 59          # Inconsistencies. 
 60          elif local_tm and not 'local_tm' in spin.params: 
 61              raise RelaxError("All spins must either have a local tm parameter or not.") 
 62   
 63      # Check if any model-free parameters are allowed to vary. 
 64      mf_all_fixed = True 
 65      mf_all_deselected = True 
 66      for spin in spin_loop(): 
 67          # Skip deselected spins. 
 68          if not spin.select: 
 69              continue 
 70   
 71          # At least one spin is selected. 
 72          mf_all_deselected = False 
 73   
 74          # Test the fixed flag. 
 75          if not hasattr(spin, 'fixed'): 
 76              mf_all_fixed = False 
 77              break 
 78          if not spin.fixed: 
 79              mf_all_fixed = False 
 80              break 
 81   
 82      # No spins selected?!? 
 83      if mf_all_deselected: 
 84          # All parameters fixed! 
 85          if not hasattr(cdp, 'diff_tensor') or cdp.diff_tensor.fixed: 
 86              return None 
 87   
 88          return 'diff' 
 89   
 90      # Local tm. 
 91      if local_tm: 
 92          return 'local_tm' 
 93   
 94      # Test if the diffusion tensor data is loaded. 
 95      if not diffusion_tensor.diff_data_exists(): 
 96          # Catch when the local tm value is set but not in the parameter list. 
 97          for spin in spin_loop(): 
 98              if hasattr(spin, 'local_tm') and spin.local_tm != None and not 'local_tm' in spin.params: 
 99                  raise RelaxError("The local tm value is set but not located in the model parameter list.") 
100   
101          # Normal error. 
102          raise RelaxNoTensorError('diffusion') 
103   
104      # 'diff' model type. 
105      if mf_all_fixed: 
106          # All parameters fixed! 
107          if cdp.diff_tensor.fixed: 
108              return None 
109   
110          return 'diff' 
111   
112      # 'mf' model type. 
113      if cdp.diff_tensor.fixed: 
114          return 'mf' 
115   
116      # 'all' model type. 
117      else: 
118          return 'all' 
119   
120   
121 -def model_map(model): 
122      """Return the equation name and parameter list corresponding to the given model. 
123   
124      @param model:   The model-free model. 
125      @type model:    str 
126      @return:        The equation type (either 'mf_orig' or 'mf_ext') and the model-free parameter list corresponding to the model. 
127      @rtype:         str, list 
128      """ 
129   
130      # Block 1. 
131      if model == 'm0': 
132          equation = 'mf_orig' 
133          params = [] 
134      elif model == 'm1': 
135          equation = 'mf_orig' 
136          params = ['s2'] 
137      elif model == 'm2': 
138          equation = 'mf_orig' 
139          params = ['s2', 'te'] 
140      elif model == 'm3': 
141          equation = 'mf_orig' 
142          params = ['s2', 'rex'] 
143      elif model == 'm4': 
144          equation = 'mf_orig' 
145          params = ['s2', 'te', 'rex'] 
146      elif model == 'm5': 
147          equation = 'mf_ext' 
148          params = ['s2f', 's2', 'ts'] 
149      elif model == 'm6': 
150          equation = 'mf_ext' 
151          params = ['s2f', 'tf', 's2', 'ts'] 
152      elif model == 'm7': 
153          equation = 'mf_ext' 
154          params = ['s2f', 's2', 'ts', 'rex'] 
155      elif model == 'm8': 
156          equation = 'mf_ext' 
157          params = ['s2f', 'tf', 's2', 'ts', 'rex'] 
158      elif model == 'm9': 
159          equation = 'mf_orig' 
160          params = ['rex'] 
161   
162      # Block 2. 
163      elif model == 'm10': 
164          equation = 'mf_orig' 
165          params = ['csa'] 
166      elif model == 'm11': 
167          equation = 'mf_orig' 
168          params = ['csa', 's2'] 
169      elif model == 'm12': 
170          equation = 'mf_orig' 
171          params = ['csa', 's2', 'te'] 
172      elif model == 'm13': 
173          equation = 'mf_orig' 
174          params = ['csa', 's2', 'rex'] 
175      elif model == 'm14': 
176          equation = 'mf_orig' 
177          params = ['csa', 's2', 'te', 'rex'] 
178      elif model == 'm15': 
179          equation = 'mf_ext' 
180          params = ['csa', 's2f', 's2', 'ts'] 
181      elif model == 'm16': 
182          equation = 'mf_ext' 
183          params = ['csa', 's2f', 'tf', 's2', 'ts'] 
184      elif model == 'm17': 
185          equation = 'mf_ext' 
186          params = ['csa', 's2f', 's2', 'ts', 'rex'] 
187      elif model == 'm18': 
188          equation = 'mf_ext' 
189          params = ['csa', 's2f', 'tf', 's2', 'ts', 'rex'] 
190      elif model == 'm19': 
191          equation = 'mf_orig' 
192          params = ['csa', 'rex'] 
193   
194      # Block 3. 
195      elif model == 'm20': 
196          equation = 'mf_orig' 
197          params = ['r'] 
198      elif model == 'm21': 
199          equation = 'mf_orig' 
200          params = ['r', 's2'] 
201      elif model == 'm22': 
202          equation = 'mf_orig' 
203          params = ['r', 's2', 'te'] 
204      elif model == 'm23': 
205          equation = 'mf_orig' 
206          params = ['r', 's2', 'rex'] 
207      elif model == 'm24': 
208          equation = 'mf_orig' 
209          params = ['r', 's2', 'te', 'rex'] 
210      elif model == 'm25': 
211          equation = 'mf_ext' 
212          params = ['r', 's2f', 's2', 'ts'] 
213      elif model == 'm26': 
214          equation = 'mf_ext' 
215          params = ['r', 's2f', 'tf', 's2', 'ts'] 
216      elif model == 'm27': 
217          equation = 'mf_ext' 
218          params = ['r', 's2f', 's2', 'ts', 'rex'] 
219      elif model == 'm28': 
220          equation = 'mf_ext' 
221          params = ['r', 's2f', 'tf', 's2', 'ts', 'rex'] 
222      elif model == 'm29': 
223          equation = 'mf_orig' 
224          params = ['r', 'rex'] 
225   
226      # Block 4. 
227      elif model == 'm30': 
228          equation = 'mf_orig' 
229          params = ['r', 'csa'] 
230      elif model == 'm31': 
231          equation = 'mf_orig' 
232          params = ['r', 'csa', 's2'] 
233      elif model == 'm32': 
234          equation = 'mf_orig' 
235          params = ['r', 'csa', 's2', 'te'] 
236      elif model == 'm33': 
237          equation = 'mf_orig' 
238          params = ['r', 'csa', 's2', 'rex'] 
239      elif model == 'm34': 
240          equation = 'mf_orig' 
241          params = ['r', 'csa', 's2', 'te', 'rex'] 
242      elif model == 'm35': 
243          equation = 'mf_ext' 
244          params = ['r', 'csa', 's2f', 's2', 'ts'] 
245      elif model == 'm36': 
246          equation = 'mf_ext' 
247          params = ['r', 'csa', 's2f', 'tf', 's2', 'ts'] 
248      elif model == 'm37': 
249          equation = 'mf_ext' 
250          params = ['r', 'csa', 's2f', 's2', 'ts', 'rex'] 
251      elif model == 'm38': 
252          equation = 'mf_ext' 
253          params = ['r', 'csa', 's2f', 'tf', 's2', 'ts', 'rex'] 
254      elif model == 'm39': 
255          equation = 'mf_orig' 
256          params = ['r', 'csa', 'rex'] 
257   
258   
259      # Preset models with local correlation time. 
260      ############################################ 
261   
262      # Block 1. 
263      elif model == 'tm0': 
264          equation = 'mf_orig' 
265          params = ['local_tm'] 
266      elif model == 'tm1': 
267          equation = 'mf_orig' 
268          params = ['local_tm', 's2'] 
269      elif model == 'tm2': 
270          equation = 'mf_orig' 
271          params = ['local_tm', 's2', 'te'] 
272      elif model == 'tm3': 
273          equation = 'mf_orig' 
274          params = ['local_tm', 's2', 'rex'] 
275      elif model == 'tm4': 
276          equation = 'mf_orig' 
277          params = ['local_tm', 's2', 'te', 'rex'] 
278      elif model == 'tm5': 
279          equation = 'mf_ext' 
280          params = ['local_tm', 's2f', 's2', 'ts'] 
281      elif model == 'tm6': 
282          equation = 'mf_ext' 
283          params = ['local_tm', 's2f', 'tf', 's2', 'ts'] 
284      elif model == 'tm7': 
285          equation = 'mf_ext' 
286          params = ['local_tm', 's2f', 's2', 'ts', 'rex'] 
287      elif model == 'tm8': 
288          equation = 'mf_ext' 
289          params = ['local_tm', 's2f', 'tf', 's2', 'ts', 'rex'] 
290      elif model == 'tm9': 
291          equation = 'mf_orig' 
292          params = ['local_tm', 'rex'] 
293   
294      # Block 2. 
295      elif model == 'tm10': 
296          equation = 'mf_orig' 
297          params = ['local_tm', 'csa'] 
298      elif model == 'tm11': 
299          equation = 'mf_orig' 
300          params = ['local_tm', 'csa', 's2'] 
301      elif model == 'tm12': 
302          equation = 'mf_orig' 
303          params = ['local_tm', 'csa', 's2', 'te'] 
304      elif model == 'tm13': 
305          equation = 'mf_orig' 
306          params = ['local_tm', 'csa', 's2', 'rex'] 
307      elif model == 'tm14': 
308          equation = 'mf_orig' 
309          params = ['local_tm', 'csa', 's2', 'te', 'rex'] 
310      elif model == 'tm15': 
311          equation = 'mf_ext' 
312          params = ['local_tm', 'csa', 's2f', 's2', 'ts'] 
313      elif model == 'tm16': 
314          equation = 'mf_ext' 
315          params = ['local_tm', 'csa', 's2f', 'tf', 's2', 'ts'] 
316      elif model == 'tm17': 
317          equation = 'mf_ext' 
318          params = ['local_tm', 'csa', 's2f', 's2', 'ts', 'rex'] 
319      elif model == 'tm18': 
320          equation = 'mf_ext' 
321          params = ['local_tm', 'csa', 's2f', 'tf', 's2', 'ts', 'rex'] 
322      elif model == 'tm19': 
323          equation = 'mf_orig' 
324          params = ['local_tm', 'csa', 'rex'] 
325   
326      # Block 3. 
327      elif model == 'tm20': 
328          equation = 'mf_orig' 
329          params = ['local_tm', 'r'] 
330      elif model == 'tm21': 
331          equation = 'mf_orig' 
332          params = ['local_tm', 'r', 's2'] 
333      elif model == 'tm22': 
334          equation = 'mf_orig' 
335          params = ['local_tm', 'r', 's2', 'te'] 
336      elif model == 'tm23': 
337          equation = 'mf_orig' 
338          params = ['local_tm', 'r', 's2', 'rex'] 
339      elif model == 'tm24': 
340          equation = 'mf_orig' 
341          params = ['local_tm', 'r', 's2', 'te', 'rex'] 
342      elif model == 'tm25': 
343          equation = 'mf_ext' 
344          params = ['local_tm', 'r', 's2f', 's2', 'ts'] 
345      elif model == 'tm26': 
346          equation = 'mf_ext' 
347          params = ['local_tm', 'r', 's2f', 'tf', 's2', 'ts'] 
348      elif model == 'tm27': 
349          equation = 'mf_ext' 
350          params = ['local_tm', 'r', 's2f', 's2', 'ts', 'rex'] 
351      elif model == 'tm28': 
352          equation = 'mf_ext' 
353          params = ['local_tm', 'r', 's2f', 'tf', 's2', 'ts', 'rex'] 
354      elif model == 'tm29': 
355          equation = 'mf_orig' 
356          params = ['local_tm', 'r', 'rex'] 
357   
358      # Block 4. 
359      elif model == 'tm30': 
360          equation = 'mf_orig' 
361          params = ['local_tm', 'r', 'csa'] 
362      elif model == 'tm31': 
363          equation = 'mf_orig' 
364          params = ['local_tm', 'r', 'csa', 's2'] 
365      elif model == 'tm32': 
366          equation = 'mf_orig' 
367          params = ['local_tm', 'r', 'csa', 's2', 'te'] 
368      elif model == 'tm33': 
369          equation = 'mf_orig' 
370          params = ['local_tm', 'r', 'csa', 's2', 'rex'] 
371      elif model == 'tm34': 
372          equation = 'mf_orig' 
373          params = ['local_tm', 'r', 'csa', 's2', 'te', 'rex'] 
374      elif model == 'tm35': 
375          equation = 'mf_ext' 
376          params = ['local_tm', 'r', 'csa', 's2f', 's2', 'ts'] 
377      elif model == 'tm36': 
378          equation = 'mf_ext' 
379          params = ['local_tm', 'r', 'csa', 's2f', 'tf', 's2', 'ts'] 
380      elif model == 'tm37': 
381          equation = 'mf_ext' 
382          params = ['local_tm', 'r', 'csa', 's2f', 's2', 'ts', 'rex'] 
383      elif model == 'tm38': 
384          equation = 'mf_ext' 
385          params = ['local_tm', 'r', 'csa', 's2f', 'tf', 's2', 'ts', 'rex'] 
386      elif model == 'tm39': 
387          equation = 'mf_orig' 
388          params = ['local_tm', 'r', 'csa', 'rex'] 
389   
390      # Invalid model. 
391      else: 
392          raise RelaxError("The model '%s' is invalid." % model) 
393   
394      # Return the values. 
395      return equation, params 
396