Source Code for Module specific_fns.setup

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004, 2006-2011 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               # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation; either version 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax 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 relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # relax module imports. 
 24  from specific_fns.consistency_tests import Consistency_tests 
 25  from specific_fns.frame_order import Frame_order 
 26  from specific_fns.hybrid import Hybrid 
 27  from specific_fns.jw_mapping import Jw_mapping 
 28  from specific_fns.model_free import Model_free 
 29  from specific_fns.n_state_model import N_state_model 
 30  from specific_fns.noe import Noe 
 31  from specific_fns.relax_fit import Relax_fit 
 32  from relax_errors import RelaxError, RelaxFuncSetupError 
 33   
 34   
 35  # Instantiate all classes. 
 36  consistency_tests_obj = Consistency_tests() 
 37  frame_order_obj = Frame_order() 
 38  hybrid_obj = Hybrid() 
 39  jw_mapping_obj = Jw_mapping() 
 40  model_free_obj = Model_free() 
 41  n_state_model_obj = N_state_model() 
 42  noe_obj = Noe() 
 43  relax_fit_obj = Relax_fit() 
 44   
 45   
 46  # The function for returning the requested specific function. 
 47 -def get_specific_fn(eqi, function_type, raise_error=True): 
 48      """The function for returning the requested specific function.""" 
 49   
 50      # Initialise. 
 51      function = None 
 52   
 53      # Get the class instance corresponding to function_type. 
 54      inst = get_instance(function_type) 
 55   
 56      # Attempt to retrieve the function. 
 57      try: 
 58          # Back calculation of relaxation data. 
 59          if eqi == 'back_calc_ri': 
 60              function = inst.back_calc_ri 
 61   
 62          # Base data loop generator function. 
 63          if eqi == 'base_data_loop': 
 64              function = inst.base_data_loop 
 65   
 66          # BMRB NMR-STAR v3.1 reading function. 
 67          if eqi == 'bmrb_read': 
 68              function = inst.bmrb_read 
 69   
 70          # BMRB NMR-STAR v3.1 writing function. 
 71          if eqi == 'bmrb_write': 
 72              function = inst.bmrb_write 
 73   
 74          # Calculate function. 
 75          if eqi == 'calculate': 
 76              function = inst.calculate 
 77   
 78          # Create Monte Carlo data function. 
 79          if eqi == 'create_mc_data': 
 80              function = inst.create_mc_data 
 81   
 82          # Data structure initialisation function. 
 83          if eqi == 'data_init': 
 84              function = inst.data_init 
 85   
 86          # List of parameter names returning function. 
 87          if eqi == 'data_names': 
 88              function = inst.data_names 
 89   
 90          # The parameter type function. 
 91          if eqi == 'data_type': 
 92              function = inst.data_type 
 93   
 94          # Default parameter value returning function. 
 95          if eqi == 'default_value': 
 96              function = inst.default_value 
 97   
 98          # Duplicate data function. 
 99          if eqi == 'duplicate_data': 
100              function = inst.duplicate_data 
101   
102          # Eliminate models. 
103          if eqi == 'eliminate': 
104              function = inst.eliminate 
105   
106          # Parameter names function. 
107          if eqi == 'get_param_names': 
108              function = inst.get_param_names 
109   
110          # Parameter values function. 
111          if eqi == 'get_param_values': 
112              function = inst.get_param_values 
113   
114          # Grid search function. 
115          if eqi == 'grid_search': 
116              function = inst.grid_search 
117   
118          # Initial Monte Carlo parameter value search function. 
119          if eqi == 'init_sim_values': 
120              function = inst.sim_init_values 
121   
122          # Spin specific parameter determining function. 
123          if eqi == 'is_spin_param': 
124              function = inst.is_spin_param 
125   
126          # Map bounds function. 
127          if eqi == 'map_bounds': 
128              function = inst.map_bounds 
129   
130          # Minimise function. 
131          if eqi == 'minimise': 
132              function = inst.minimise 
133   
134          # Model loop. 
135          if eqi == 'model_desc': 
136              function = inst.model_desc 
137   
138          # Model loop. 
139          if eqi == 'model_loop': 
140              function = inst.model_loop 
141   
142          # Model statistics. 
143          if eqi == 'model_stats': 
144              function = inst.model_statistics 
145   
146          # Model type. 
147          if eqi == 'model_type': 
148              function = inst.model_type 
149   
150          # Molmol macro creation. 
151          if eqi == 'molmol_macro': 
152              function = inst.molmol_macro 
153   
154          # Number of instances. 
155          if eqi == 'num_instances': 
156              function = inst.num_instances 
157   
158          # Overfit deselect. 
159          if eqi == 'overfit_deselect': 
160              function = inst.overfit_deselect 
161   
162          # Pack Monte Carlo simulation data function. 
163          if eqi == 'pack_sim_data': 
164              function = inst.sim_pack_data 
165   
166          # Pymol macro creation. 
167          if eqi == 'pymol_macro': 
168              function = inst.pymol_macro 
169   
170          # Read results file function (Columnar format). 
171          if eqi == 'read_columnar_results': 
172              function = inst.read_columnar_results 
173   
174          # Read results file function (XML format). 
175          #if eqi == 'read_xml_results': 
176          #    function = inst.read_xml_results 
177   
178          # Data returning function. 
179          if eqi == 'return_data': 
180              function = inst.return_data 
181   
182          # Parameter description returning function. 
183          if eqi == 'return_data_desc': 
184              function = inst.return_data_desc 
185   
186          # Data or parameter name returning function. 
187          if eqi == 'return_data_name': 
188              function = inst.return_data_name 
189   
190          # Data error returning function. 
191          if eqi == 'return_error': 
192              function = inst.return_error 
193   
194          # Factor of conversion between different parameter units returning function. 
195          if eqi == 'return_conversion_factor': 
196              function = inst.return_conversion_factor 
197   
198          # Grace string returning function. 
199          if eqi == 'return_grace_string': 
200              function = inst.return_grace_string 
201   
202          # Selected simulation array returning function. 
203          if eqi == 'return_selected_sim': 
204              function = inst.sim_return_selected 
205   
206          # Simulation chi-squared array returning function. 
207          if eqi == 'return_sim_chi2': 
208              function = inst.sim_return_chi2 
209   
210          # Simulation parameter array returning function. 
211          if eqi == 'return_sim_param': 
212              function = inst.sim_return_param 
213   
214          # String of the external parameter units returning function. 
215          if eqi == 'return_units': 
216              function = inst.return_units 
217   
218          # Value and error returning function. 
219          if eqi == 'return_value': 
220              function = inst.return_value 
221   
222          # Set error function. 
223          if eqi == 'set_error': 
224              function = inst.set_error 
225   
226          # Set parameter values function. 
227          if eqi == 'set_param_values': 
228              function = inst.set_param_values 
229   
230          # Set the selected simulations array. 
231          if eqi == 'set_selected_sim': 
232              function = inst.set_selected_sim 
233   
234          # Set update function. 
235          if eqi == 'set_update': 
236              function = inst.set_update 
237   
238          # Skip function. 
239          if eqi == 'skip_function': 
240              function = inst.skip_function 
241   
242          # Deselection function. 
243          if eqi == 'deselect': 
244              function = inst.deselect 
245   
246      # Catch if the function is missing. 
247      except AttributeError: 
248          function = None 
249   
250      # Raise an error if the function doesn't exist. 
251      if raise_error and function == None: 
252          # Raise the error. 
253          raise RelaxFuncSetupError(get_string(function_type)) 
254   
255      # Return the function. 
256      return function 
257   
258   
259 -def get_instance(function_type): 
260      """Function for returning the class instance corresponding to the function type.""" 
261   
262      # Consistency testing. 
263      if function_type == 'ct': 
264          return consistency_tests_obj 
265   
266      # The Frame Order theories. 
267      if function_type == 'frame order': 
268          return frame_order_obj 
269   
270      # NOE calculation. 
271      if function_type == 'noe': 
272          return noe_obj 
273   
274      # The N-state model. 
275      if function_type == 'N-state': 
276          return n_state_model_obj 
277   
278      # Relaxation curve fitting. 
279      if function_type == 'relax_fit': 
280          return relax_fit_obj 
281   
282      # Reduced spectral density mapping. 
283      if function_type == 'jw': 
284          return jw_mapping_obj 
285   
286      # Model-free analysis. 
287      if function_type == 'mf': 
288          return model_free_obj 
289   
290      # Hybrid models. 
291      if function_type == 'hybrid': 
292          return hybrid_obj 
293   
294      # Unknown analysis. 
295      raise RelaxError("The function_type " + repr(function_type) + " is unknown.") 
296   
297   
298 -def get_string(function_type): 
299      """Function for returning a string corresponding to the function type.""" 
300   
301      # Consistency testing. 
302      if function_type == 'ct': 
303          return "consistency testing" 
304   
305      # The Frame Order theories. 
306      if function_type == 'frame order': 
307          return "Frame Order theories" 
308   
309      # NOE calculation. 
310      if function_type == 'noe': 
311          return "NOE calculations" 
312   
313      # The N-state model. 
314      if function_type == 'N-state': 
315          return "the N-state model" 
316   
317      # Relaxation curve fitting. 
318      if function_type == 'relax_fit': 
319          return "relaxation curve fitting" 
320   
321      # Reduced spectral density mapping. 
322      if function_type == 'jw': 
323          return "reduced spectral density mapping" 
324   
325      # Model-free analysis. 
326      if function_type == 'mf': 
327          return "Model-free analysis" 
328   
329      # Hybrid models. 
330      if function_type == 'hybrid': 
331          return "hybrid models" 
332   
333      # Unknown analysis. 
334      raise RelaxError("The function_type " + repr(function_type) + " is unknown.") 
335