Source Code for Module specific_analyses.model_free.model

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation, either version 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """The model-free analysis parameter functions.""" 
 24   
 25  # relax module imports. 
 26  from lib.errors import RelaxError, RelaxNoSequenceError, RelaxNoTensorError 
 27  from pipe_control import diffusion_tensor 
 28  from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop 
 29   
 30   
 31 -def determine_model_type(): 
 32      """Determine the global model type. 
 33   
 34      @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. 
 35      @rtype:     str or None 
 36      """ 
 37   
 38      # Test if sequence data is loaded. 
 39      if not exists_mol_res_spin_data(): 
 40          raise RelaxNoSequenceError 
 41   
 42      # If there is a local tm, fail if not all residues have a local tm parameter. 
 43      local_tm = False 
 44      for spin in spin_loop(): 
 45          # Skip deselected spins. 
 46          if not spin.select: 
 47              continue 
 48   
 49          # No params. 
 50          if not hasattr(spin, 'params') or not spin.params: 
 51              continue 
 52   
 53          # Local tm. 
 54          if not local_tm and 'local_tm' in spin.params: 
 55              local_tm = True 
 56   
 57          # Inconsistencies. 
 58          elif local_tm and not 'local_tm' in spin.params: 
 59              raise RelaxError("All spins must either have a local tm parameter or not.") 
 60   
 61      # Check if any model-free parameters are allowed to vary. 
 62      mf_all_fixed = True 
 63      mf_all_deselected = True 
 64      for spin in spin_loop(): 
 65          # Skip deselected spins. 
 66          if not spin.select: 
 67              continue 
 68   
 69          # At least one spin is selected. 
 70          mf_all_deselected = False 
 71   
 72          # Test the fixed flag. 
 73          if not hasattr(spin, 'fixed'): 
 74              mf_all_fixed = False 
 75              break 
 76          if not spin.fixed: 
 77              mf_all_fixed = False 
 78              break 
 79   
 80      # No spins selected?!? 
 81      if mf_all_deselected: 
 82          # All parameters fixed! 
 83          if not hasattr(cdp, 'diff_tensor') or cdp.diff_tensor.fixed: 
 84              return None 
 85   
 86          return 'diff' 
 87   
 88      # Local tm. 
 89      if local_tm: 
 90          return 'local_tm' 
 91   
 92      # Test if the diffusion tensor data is loaded. 
 93      if not diffusion_tensor.diff_data_exists(): 
 94          # Catch when the local tm value is set but not in the parameter list. 
 95          for spin in spin_loop(): 
 96              if hasattr(spin, 'local_tm') and spin.local_tm != None and not 'local_tm' in spin.params: 
 97                  raise RelaxError("The local tm value is set but not located in the model parameter list.") 
 98   
 99          # Normal error. 
100          raise RelaxNoTensorError('diffusion') 
101   
102      # 'diff' model type. 
103      if mf_all_fixed: 
104          # All parameters fixed! 
105          if cdp.diff_tensor.fixed: 
106              return None 
107   
108          return 'diff' 
109   
110      # 'mf' model type. 
111      if cdp.diff_tensor.fixed: 
112          return 'mf' 
113   
114      # 'all' model type. 
115      else: 
116          return 'all' 
117   
118   
119 -def model_map(model): 
120      """Return the equation name and parameter list corresponding to the given model. 
121   
122      @param model:   The model-free model. 
123      @type model:    str 
124      @return:        The equation type (either 'mf_orig' or 'mf_ext') and the model-free parameter list corresponding to the model. 
125      @rtype:         str, list 
126      """ 
127   
128      # Block 1. 
129      if model == 'm0': 
130          equation = 'mf_orig' 
131          params = [] 
132      elif model == 'm1': 
133          equation = 'mf_orig' 
134          params = ['s2'] 
135      elif model == 'm2': 
136          equation = 'mf_orig' 
137          params = ['s2', 'te'] 
138      elif model == 'm3': 
139          equation = 'mf_orig' 
140          params = ['s2', 'rex'] 
141      elif model == 'm4': 
142          equation = 'mf_orig' 
143          params = ['s2', 'te', 'rex'] 
144      elif model == 'm5': 
145          equation = 'mf_ext' 
146          params = ['s2f', 's2', 'ts'] 
147      elif model == 'm6': 
148          equation = 'mf_ext' 
149          params = ['s2f', 'tf', 's2', 'ts'] 
150      elif model == 'm7': 
151          equation = 'mf_ext' 
152          params = ['s2f', 's2', 'ts', 'rex'] 
153      elif model == 'm8': 
154          equation = 'mf_ext' 
155          params = ['s2f', 'tf', 's2', 'ts', 'rex'] 
156      elif model == 'm9': 
157          equation = 'mf_orig' 
158          params = ['rex'] 
159   
160      # Block 2. 
161      elif model == 'm10': 
162          equation = 'mf_orig' 
163          params = ['csa'] 
164      elif model == 'm11': 
165          equation = 'mf_orig' 
166          params = ['csa', 's2'] 
167      elif model == 'm12': 
168          equation = 'mf_orig' 
169          params = ['csa', 's2', 'te'] 
170      elif model == 'm13': 
171          equation = 'mf_orig' 
172          params = ['csa', 's2', 'rex'] 
173      elif model == 'm14': 
174          equation = 'mf_orig' 
175          params = ['csa', 's2', 'te', 'rex'] 
176      elif model == 'm15': 
177          equation = 'mf_ext' 
178          params = ['csa', 's2f', 's2', 'ts'] 
179      elif model == 'm16': 
180          equation = 'mf_ext' 
181          params = ['csa', 's2f', 'tf', 's2', 'ts'] 
182      elif model == 'm17': 
183          equation = 'mf_ext' 
184          params = ['csa', 's2f', 's2', 'ts', 'rex'] 
185      elif model == 'm18': 
186          equation = 'mf_ext' 
187          params = ['csa', 's2f', 'tf', 's2', 'ts', 'rex'] 
188      elif model == 'm19': 
189          equation = 'mf_orig' 
190          params = ['csa', 'rex'] 
191   
192      # Block 3. 
193      elif model == 'm20': 
194          equation = 'mf_orig' 
195          params = ['r'] 
196      elif model == 'm21': 
197          equation = 'mf_orig' 
198          params = ['r', 's2'] 
199      elif model == 'm22': 
200          equation = 'mf_orig' 
201          params = ['r', 's2', 'te'] 
202      elif model == 'm23': 
203          equation = 'mf_orig' 
204          params = ['r', 's2', 'rex'] 
205      elif model == 'm24': 
206          equation = 'mf_orig' 
207          params = ['r', 's2', 'te', 'rex'] 
208      elif model == 'm25': 
209          equation = 'mf_ext' 
210          params = ['r', 's2f', 's2', 'ts'] 
211      elif model == 'm26': 
212          equation = 'mf_ext' 
213          params = ['r', 's2f', 'tf', 's2', 'ts'] 
214      elif model == 'm27': 
215          equation = 'mf_ext' 
216          params = ['r', 's2f', 's2', 'ts', 'rex'] 
217      elif model == 'm28': 
218          equation = 'mf_ext' 
219          params = ['r', 's2f', 'tf', 's2', 'ts', 'rex'] 
220      elif model == 'm29': 
221          equation = 'mf_orig' 
222          params = ['r', 'rex'] 
223   
224      # Block 4. 
225      elif model == 'm30': 
226          equation = 'mf_orig' 
227          params = ['r', 'csa'] 
228      elif model == 'm31': 
229          equation = 'mf_orig' 
230          params = ['r', 'csa', 's2'] 
231      elif model == 'm32': 
232          equation = 'mf_orig' 
233          params = ['r', 'csa', 's2', 'te'] 
234      elif model == 'm33': 
235          equation = 'mf_orig' 
236          params = ['r', 'csa', 's2', 'rex'] 
237      elif model == 'm34': 
238          equation = 'mf_orig' 
239          params = ['r', 'csa', 's2', 'te', 'rex'] 
240      elif model == 'm35': 
241          equation = 'mf_ext' 
242          params = ['r', 'csa', 's2f', 's2', 'ts'] 
243      elif model == 'm36': 
244          equation = 'mf_ext' 
245          params = ['r', 'csa', 's2f', 'tf', 's2', 'ts'] 
246      elif model == 'm37': 
247          equation = 'mf_ext' 
248          params = ['r', 'csa', 's2f', 's2', 'ts', 'rex'] 
249      elif model == 'm38': 
250          equation = 'mf_ext' 
251          params = ['r', 'csa', 's2f', 'tf', 's2', 'ts', 'rex'] 
252      elif model == 'm39': 
253          equation = 'mf_orig' 
254          params = ['r', 'csa', 'rex'] 
255   
256   
257      # Preset models with local correlation time. 
258      ############################################ 
259   
260      # Block 1. 
261      elif model == 'tm0': 
262          equation = 'mf_orig' 
263          params = ['local_tm'] 
264      elif model == 'tm1': 
265          equation = 'mf_orig' 
266          params = ['local_tm', 's2'] 
267      elif model == 'tm2': 
268          equation = 'mf_orig' 
269          params = ['local_tm', 's2', 'te'] 
270      elif model == 'tm3': 
271          equation = 'mf_orig' 
272          params = ['local_tm', 's2', 'rex'] 
273      elif model == 'tm4': 
274          equation = 'mf_orig' 
275          params = ['local_tm', 's2', 'te', 'rex'] 
276      elif model == 'tm5': 
277          equation = 'mf_ext' 
278          params = ['local_tm', 's2f', 's2', 'ts'] 
279      elif model == 'tm6': 
280          equation = 'mf_ext' 
281          params = ['local_tm', 's2f', 'tf', 's2', 'ts'] 
282      elif model == 'tm7': 
283          equation = 'mf_ext' 
284          params = ['local_tm', 's2f', 's2', 'ts', 'rex'] 
285      elif model == 'tm8': 
286          equation = 'mf_ext' 
287          params = ['local_tm', 's2f', 'tf', 's2', 'ts', 'rex'] 
288      elif model == 'tm9': 
289          equation = 'mf_orig' 
290          params = ['local_tm', 'rex'] 
291   
292      # Block 2. 
293      elif model == 'tm10': 
294          equation = 'mf_orig' 
295          params = ['local_tm', 'csa'] 
296      elif model == 'tm11': 
297          equation = 'mf_orig' 
298          params = ['local_tm', 'csa', 's2'] 
299      elif model == 'tm12': 
300          equation = 'mf_orig' 
301          params = ['local_tm', 'csa', 's2', 'te'] 
302      elif model == 'tm13': 
303          equation = 'mf_orig' 
304          params = ['local_tm', 'csa', 's2', 'rex'] 
305      elif model == 'tm14': 
306          equation = 'mf_orig' 
307          params = ['local_tm', 'csa', 's2', 'te', 'rex'] 
308      elif model == 'tm15': 
309          equation = 'mf_ext' 
310          params = ['local_tm', 'csa', 's2f', 's2', 'ts'] 
311      elif model == 'tm16': 
312          equation = 'mf_ext' 
313          params = ['local_tm', 'csa', 's2f', 'tf', 's2', 'ts'] 
314      elif model == 'tm17': 
315          equation = 'mf_ext' 
316          params = ['local_tm', 'csa', 's2f', 's2', 'ts', 'rex'] 
317      elif model == 'tm18': 
318          equation = 'mf_ext' 
319          params = ['local_tm', 'csa', 's2f', 'tf', 's2', 'ts', 'rex'] 
320      elif model == 'tm19': 
321          equation = 'mf_orig' 
322          params = ['local_tm', 'csa', 'rex'] 
323   
324      # Block 3. 
325      elif model == 'tm20': 
326          equation = 'mf_orig' 
327          params = ['local_tm', 'r'] 
328      elif model == 'tm21': 
329          equation = 'mf_orig' 
330          params = ['local_tm', 'r', 's2'] 
331      elif model == 'tm22': 
332          equation = 'mf_orig' 
333          params = ['local_tm', 'r', 's2', 'te'] 
334      elif model == 'tm23': 
335          equation = 'mf_orig' 
336          params = ['local_tm', 'r', 's2', 'rex'] 
337      elif model == 'tm24': 
338          equation = 'mf_orig' 
339          params = ['local_tm', 'r', 's2', 'te', 'rex'] 
340      elif model == 'tm25': 
341          equation = 'mf_ext' 
342          params = ['local_tm', 'r', 's2f', 's2', 'ts'] 
343      elif model == 'tm26': 
344          equation = 'mf_ext' 
345          params = ['local_tm', 'r', 's2f', 'tf', 's2', 'ts'] 
346      elif model == 'tm27': 
347          equation = 'mf_ext' 
348          params = ['local_tm', 'r', 's2f', 's2', 'ts', 'rex'] 
349      elif model == 'tm28': 
350          equation = 'mf_ext' 
351          params = ['local_tm', 'r', 's2f', 'tf', 's2', 'ts', 'rex'] 
352      elif model == 'tm29': 
353          equation = 'mf_orig' 
354          params = ['local_tm', 'r', 'rex'] 
355   
356      # Block 4. 
357      elif model == 'tm30': 
358          equation = 'mf_orig' 
359          params = ['local_tm', 'r', 'csa'] 
360      elif model == 'tm31': 
361          equation = 'mf_orig' 
362          params = ['local_tm', 'r', 'csa', 's2'] 
363      elif model == 'tm32': 
364          equation = 'mf_orig' 
365          params = ['local_tm', 'r', 'csa', 's2', 'te'] 
366      elif model == 'tm33': 
367          equation = 'mf_orig' 
368          params = ['local_tm', 'r', 'csa', 's2', 'rex'] 
369      elif model == 'tm34': 
370          equation = 'mf_orig' 
371          params = ['local_tm', 'r', 'csa', 's2', 'te', 'rex'] 
372      elif model == 'tm35': 
373          equation = 'mf_ext' 
374          params = ['local_tm', 'r', 'csa', 's2f', 's2', 'ts'] 
375      elif model == 'tm36': 
376          equation = 'mf_ext' 
377          params = ['local_tm', 'r', 'csa', 's2f', 'tf', 's2', 'ts'] 
378      elif model == 'tm37': 
379          equation = 'mf_ext' 
380          params = ['local_tm', 'r', 'csa', 's2f', 's2', 'ts', 'rex'] 
381      elif model == 'tm38': 
382          equation = 'mf_ext' 
383          params = ['local_tm', 'r', 'csa', 's2f', 'tf', 's2', 'ts', 'rex'] 
384      elif model == 'tm39': 
385          equation = 'mf_orig' 
386          params = ['local_tm', 'r', 'csa', 'rex'] 
387   
388      # Invalid model. 
389      else: 
390          raise RelaxError("The model '%s' is invalid." % model) 
391   
392      # Return the values. 
393      return equation, params 
394