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 generic_fns import pipes 
 25  from specific_fns.consistency_tests import Consistency_tests 
 26  from specific_fns.frame_order import Frame_order 
 27  from specific_fns.hybrid import Hybrid 
 28  from specific_fns.jw_mapping import Jw_mapping 
 29  from specific_fns.model_free import Model_free 
 30  from specific_fns.n_state_model import N_state_model 
 31  from specific_fns.noe import Noe 
 32  from specific_fns.relax_fit import Relax_fit 
 33  from relax_errors import RelaxError, RelaxFuncSetupError 
 34   
 35   
 36  # Instantiate all classes. 
 37  consistency_tests_obj = Consistency_tests() 
 38  frame_order_obj = Frame_order() 
 39  hybrid_obj = Hybrid() 
 40  jw_mapping_obj = Jw_mapping() 
 41  model_free_obj = Model_free() 
 42  n_state_model_obj = N_state_model() 
 43  noe_obj = Noe() 
 44  relax_fit_obj = Relax_fit() 
 45   
 46   
 47  # The function for returning the requested specific function. 
 48 -def get_specific_fn(eqi, function_type=None, raise_error=True): 
 49      """The function for returning the requested specific function.""" 
 50   
 51      # Initialise. 
 52      function = None 
 53      if function_type == None: 
 54          function_type = pipes.get_type() 
 55   
 56      # Get the class instance corresponding to function_type. 
 57      inst = get_instance(function_type) 
 58   
 59      # Attempt to retrieve the function. 
 60      try: 
 61          # Back calculation of relaxation data. 
 62          if eqi == 'back_calc_ri': 
 63              function = inst.back_calc_ri 
 64   
 65          # Base data loop generator function. 
 66          if eqi == 'base_data_loop': 
 67              function = inst.base_data_loop 
 68   
 69          # BMRB NMR-STAR v3.1 reading function. 
 70          if eqi == 'bmrb_read': 
 71              function = inst.bmrb_read 
 72   
 73          # BMRB NMR-STAR v3.1 writing function. 
 74          if eqi == 'bmrb_write': 
 75              function = inst.bmrb_write 
 76   
 77          # Calculate function. 
 78          if eqi == 'calculate': 
 79              function = inst.calculate 
 80   
 81          # Create Monte Carlo data function. 
 82          if eqi == 'create_mc_data': 
 83              function = inst.create_mc_data 
 84   
 85          # Data structure initialisation function. 
 86          if eqi == 'data_init': 
 87              function = inst.data_init 
 88   
 89          # List of parameter names returning function. 
 90          if eqi == 'data_names': 
 91              function = inst.data_names 
 92   
 93          # The parameter type function. 
 94          if eqi == 'data_type': 
 95              function = inst.data_type 
 96   
 97          # Default parameter value returning function. 
 98          if eqi == 'default_value': 
 99              function = inst.default_value 
100   
101          # Duplicate data function. 
102          if eqi == 'duplicate_data': 
103              function = inst.duplicate_data 
104   
105          # Eliminate models. 
106          if eqi == 'eliminate': 
107              function = inst.eliminate 
108   
109          # Parameter names function. 
110          if eqi == 'get_param_names': 
111              function = inst.get_param_names 
112   
113          # Parameter values function. 
114          if eqi == 'get_param_values': 
115              function = inst.get_param_values 
116   
117          # Grid search function. 
118          if eqi == 'grid_search': 
119              function = inst.grid_search 
120   
121          # Initial Monte Carlo parameter value search function. 
122          if eqi == 'init_sim_values': 
123              function = inst.sim_init_values 
124   
125          # Spin specific parameter determining function. 
126          if eqi == 'is_spin_param': 
127              function = inst.is_spin_param 
128   
129          # Map bounds function. 
130          if eqi == 'map_bounds': 
131              function = inst.map_bounds 
132   
133          # Minimise function. 
134          if eqi == 'minimise': 
135              function = inst.minimise 
136   
137          # Model loop. 
138          if eqi == 'model_desc': 
139              function = inst.model_desc 
140   
141          # Model loop. 
142          if eqi == 'model_loop': 
143              function = inst.model_loop 
144   
145          # Model statistics. 
146          if eqi == 'model_stats': 
147              function = inst.model_statistics 
148   
149          # Model type. 
150          if eqi == 'model_type': 
151              function = inst.model_type 
152   
153          # Molmol macro creation. 
154          if eqi == 'molmol_macro': 
155              function = inst.molmol_macro 
156   
157          # Number of instances. 
158          if eqi == 'num_instances': 
159              function = inst.num_instances 
160   
161          # Overfit deselect. 
162          if eqi == 'overfit_deselect': 
163              function = inst.overfit_deselect 
164   
165          # Pack Monte Carlo simulation data function. 
166          if eqi == 'pack_sim_data': 
167              function = inst.sim_pack_data 
168   
169          # Pymol macro creation. 
170          if eqi == 'pymol_macro': 
171              function = inst.pymol_macro 
172   
173          # Read results file function (Columnar format). 
174          if eqi == 'read_columnar_results': 
175              function = inst.read_columnar_results 
176   
177          # Read results file function (XML format). 
178          #if eqi == 'read_xml_results': 
179          #    function = inst.read_xml_results 
180   
181          # Data returning function. 
182          if eqi == 'return_data': 
183              function = inst.return_data 
184   
185          # Parameter description returning function. 
186          if eqi == 'return_data_desc': 
187              function = inst.return_data_desc 
188   
189          # Data or parameter name returning function. 
190          if eqi == 'return_data_name': 
191              function = inst.return_data_name 
192   
193          # Data error returning function. 
194          if eqi == 'return_error': 
195              function = inst.return_error 
196   
197          # Factor of conversion between different parameter units returning function. 
198          if eqi == 'return_conversion_factor': 
199              function = inst.return_conversion_factor 
200   
201          # Grace string returning function. 
202          if eqi == 'return_grace_string': 
203              function = inst.return_grace_string 
204   
205          # Selected simulation array returning function. 
206          if eqi == 'return_selected_sim': 
207              function = inst.sim_return_selected 
208   
209          # Simulation chi-squared array returning function. 
210          if eqi == 'return_sim_chi2': 
211              function = inst.sim_return_chi2 
212   
213          # Simulation parameter array returning function. 
214          if eqi == 'return_sim_param': 
215              function = inst.sim_return_param 
216   
217          # String of the external parameter units returning function. 
218          if eqi == 'return_units': 
219              function = inst.return_units 
220   
221          # Value and error returning function. 
222          if eqi == 'return_value': 
223              function = inst.return_value 
224   
225          # Set error function. 
226          if eqi == 'set_error': 
227              function = inst.set_error 
228   
229          # Set parameter values function. 
230          if eqi == 'set_param_values': 
231              function = inst.set_param_values 
232   
233          # Set the selected simulations array. 
234          if eqi == 'set_selected_sim': 
235              function = inst.set_selected_sim 
236   
237          # Set update function. 
238          if eqi == 'set_update': 
239              function = inst.set_update 
240   
241          # Skip function. 
242          if eqi == 'skip_function': 
243              function = inst.skip_function 
244   
245          # Deselection function. 
246          if eqi == 'deselect': 
247              function = inst.deselect 
248   
249      # Catch if the function is missing. 
250      except AttributeError: 
251          function = None 
252   
253      # Raise an error if the function doesn't exist. 
254      if raise_error and function == None: 
255          # Raise the error. 
256          raise RelaxFuncSetupError(get_string(function_type)) 
257   
258      # Return the function. 
259      return function 
260   
261   
262 -def get_instance(function_type): 
263      """Function for returning the class instance corresponding to the function type.""" 
264   
265      # Consistency testing. 
266      if function_type == 'ct': 
267          return consistency_tests_obj 
268   
269      # The Frame Order theories. 
270      if function_type == 'frame order': 
271          return frame_order_obj 
272   
273      # NOE calculation. 
274      if function_type == 'noe': 
275          return noe_obj 
276   
277      # The N-state model. 
278      if function_type == 'N-state': 
279          return n_state_model_obj 
280   
281      # Relaxation curve fitting. 
282      if function_type == 'relax_fit': 
283          return relax_fit_obj 
284   
285      # Reduced spectral density mapping. 
286      if function_type == 'jw': 
287          return jw_mapping_obj 
288   
289      # Model-free analysis. 
290      if function_type == 'mf': 
291          return model_free_obj 
292   
293      # Hybrid models. 
294      if function_type == 'hybrid': 
295          return hybrid_obj 
296   
297      # Unknown analysis. 
298      raise RelaxError("The function_type " + repr(function_type) + " is unknown.") 
299   
300   
301 -def get_string(function_type): 
302      """Function for returning a string corresponding to the function type.""" 
303   
304      # Consistency testing. 
305      if function_type == 'ct': 
306          return "consistency testing" 
307   
308      # The Frame Order theories. 
309      if function_type == 'frame order': 
310          return "Frame Order theories" 
311   
312      # NOE calculation. 
313      if function_type == 'noe': 
314          return "NOE calculations" 
315   
316      # The N-state model. 
317      if function_type == 'N-state': 
318          return "the N-state model" 
319   
320      # Relaxation curve fitting. 
321      if function_type == 'relax_fit': 
322          return "relaxation curve fitting" 
323   
324      # Reduced spectral density mapping. 
325      if function_type == 'jw': 
326          return "reduced spectral density mapping" 
327   
328      # Model-free analysis. 
329      if function_type == 'mf': 
330          return "Model-free analysis" 
331   
332      # Hybrid models. 
333      if function_type == 'hybrid': 
334          return "hybrid models" 
335   
336      # Unknown analysis. 
337      raise RelaxError("The function_type " + repr(function_type) + " is unknown.") 
338