Source Code for Module specific_analyses.setup

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2013 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  """Module for handling the setup of the specific analyses.""" 
 24   
 25  # relax module imports. 
 26  from lib.errors import RelaxError, RelaxFuncSetupError 
 27  from pipe_control import pipes 
 28  from specific_analyses.consistency_tests import Consistency_tests 
 29  from specific_analyses.frame_order import Frame_order 
 30  from specific_analyses.hybrid import Hybrid 
 31  from specific_analyses.jw_mapping import Jw_mapping 
 32  from specific_analyses.model_free import Model_free 
 33  from specific_analyses.n_state_model import N_state_model 
 34  from specific_analyses.noe import Noe 
 35  from specific_analyses.relax_disp.api import Relax_disp 
 36  from specific_analyses.relax_fit import Relax_fit 
 37   
 38   
 39  # Instantiate all classes. 
 40  consistency_tests_obj = Consistency_tests() 
 41  frame_order_obj = Frame_order() 
 42  hybrid_obj = Hybrid() 
 43  jw_mapping_obj = Jw_mapping() 
 44  model_free_obj = Model_free() 
 45  n_state_model_obj = N_state_model() 
 46  noe_obj = Noe() 
 47  relax_disp_obj = Relax_disp() 
 48  relax_fit_obj = Relax_fit() 
 49   
 50   
 51  # The function for returning the requested specific function. 
 52 -def get_specific_fn(eqi, function_type=None, raise_error=True): 
 53      """The function for returning the requested specific function.""" 
 54   
 55      # Initialise. 
 56      function = None 
 57      if function_type == None: 
 58          function_type = pipes.get_type() 
 59   
 60      # Get the class instance corresponding to function_type. 
 61      inst = get_instance(function_type) 
 62   
 63      # Attempt to retrieve the function. 
 64      try: 
 65          # Back calculation of relaxation data. 
 66          if eqi == 'back_calc_ri': 
 67              function = inst.back_calc_ri 
 68   
 69          # Base data loop generator function. 
 70          if eqi == 'base_data_loop': 
 71              function = inst.base_data_loop 
 72   
 73          # BMRB NMR-STAR v3.1 reading function. 
 74          if eqi == 'bmrb_read': 
 75              function = inst.bmrb_read 
 76   
 77          # BMRB NMR-STAR v3.1 writing function. 
 78          if eqi == 'bmrb_write': 
 79              function = inst.bmrb_write 
 80   
 81          # Calculate function. 
 82          if eqi == 'calculate': 
 83              function = inst.calculate 
 84   
 85          # Optimisation constraint algorithm override. 
 86          if eqi == 'constraint_algorithm': 
 87              function = inst.constraint_algorithm 
 88   
 89          # Create Monte Carlo data function. 
 90          if eqi == 'create_mc_data': 
 91              function = inst.create_mc_data 
 92   
 93          # Data structure initialisation function. 
 94          if eqi == 'data_init': 
 95              function = inst.data_init 
 96   
 97          # List of parameter names returning function. 
 98          if eqi == 'data_names': 
 99              function = inst.data_names 
100   
101          # The parameter type function. 
102          if eqi == 'data_type': 
103              function = inst.data_type 
104   
105          # Default parameter value returning function. 
106          if eqi == 'default_value': 
107              function = inst.default_value 
108   
109          # Duplicate data function. 
110          if eqi == 'duplicate_data': 
111              function = inst.duplicate_data 
112   
113          # Eliminate models. 
114          if eqi == 'eliminate': 
115              function = inst.eliminate 
116   
117          # Parameter names function. 
118          if eqi == 'get_param_names': 
119              function = inst.get_param_names 
120   
121          # Parameter values function. 
122          if eqi == 'get_param_values': 
123              function = inst.get_param_values 
124   
125          # Grid search function. 
126          if eqi == 'grid_search': 
127              function = inst.grid_search 
128   
129          # Initial Monte Carlo parameter value search function. 
130          if eqi == 'init_sim_values': 
131              function = inst.sim_init_values 
132   
133          # Spin specific parameter determining function. 
134          if eqi == 'is_spin_param': 
135              function = inst.is_spin_param 
136   
137          # Map bounds function. 
138          if eqi == 'map_bounds': 
139              function = inst.map_bounds 
140   
141          # Minimise function. 
142          if eqi == 'minimise': 
143              function = inst.minimise 
144   
145          # Model loop. 
146          if eqi == 'model_desc': 
147              function = inst.model_desc 
148   
149          # Model loop. 
150          if eqi == 'model_loop': 
151              function = inst.model_loop 
152   
153          # Model statistics. 
154          if eqi == 'model_stats': 
155              function = inst.model_statistics 
156   
157          # Model type. 
158          if eqi == 'model_type': 
159              function = inst.model_type 
160   
161          # Molmol macro creation. 
162          if eqi == 'molmol_macro': 
163              function = inst.molmol_macro 
164   
165          # Number of instances. 
166          if eqi == 'num_instances': 
167              function = inst.num_instances 
168   
169          # Overfit deselect. 
170          if eqi == 'overfit_deselect': 
171              function = inst.overfit_deselect 
172   
173          # Pack Monte Carlo simulation data function. 
174          if eqi == 'pack_sim_data': 
175              function = inst.sim_pack_data 
176   
177          # Pymol macro creation. 
178          if eqi == 'pymol_macro': 
179              function = inst.pymol_macro 
180   
181          # Read results file function (Columnar format). 
182          if eqi == 'read_columnar_results': 
183              function = inst.read_columnar_results 
184   
185          # Read results file function (XML format). 
186          #if eqi == 'read_xml_results': 
187          #    function = inst.read_xml_results 
188   
189          # Data returning function. 
190          if eqi == 'return_data': 
191              function = inst.return_data 
192   
193          # Parameter description returning function. 
194          if eqi == 'return_data_desc': 
195              function = inst.return_data_desc 
196   
197          # Data or parameter name returning function. 
198          if eqi == 'return_data_name': 
199              function = inst.return_data_name 
200   
201          # Data error returning function. 
202          if eqi == 'return_error': 
203              function = inst.return_error 
204   
205          # Factor of conversion between different parameter units returning function. 
206          if eqi == 'return_conversion_factor': 
207              function = inst.return_conversion_factor 
208   
209          # Grace string returning function. 
210          if eqi == 'return_grace_string': 
211              function = inst.return_grace_string 
212   
213          # Selected simulation array returning function. 
214          if eqi == 'return_selected_sim': 
215              function = inst.sim_return_selected 
216   
217          # Simulation chi-squared array returning function. 
218          if eqi == 'return_sim_chi2': 
219              function = inst.sim_return_chi2 
220   
221          # Simulation parameter array returning function. 
222          if eqi == 'return_sim_param': 
223              function = inst.sim_return_param 
224   
225          # String of the external parameter units returning function. 
226          if eqi == 'return_units': 
227              function = inst.return_units 
228   
229          # Value and error returning function. 
230          if eqi == 'return_value': 
231              function = inst.return_value 
232   
233          # Set error function. 
234          if eqi == 'set_error': 
235              function = inst.set_error 
236   
237          # Set parameter values function. 
238          if eqi == 'set_param_values': 
239              function = inst.set_param_values 
240   
241          # Set the selected simulations array. 
242          if eqi == 'set_selected_sim': 
243              function = inst.set_selected_sim 
244   
245          # Set update function. 
246          if eqi == 'set_update': 
247              function = inst.set_update 
248   
249          # Skip function. 
250          if eqi == 'skip_function': 
251              function = inst.skip_function 
252   
253          # Deselection function. 
254          if eqi == 'deselect': 
255              function = inst.deselect 
256   
257      # Catch if the function is missing. 
258      except AttributeError: 
259          function = None 
260   
261      # Raise an error if the function doesn't exist. 
262      if raise_error and function == None: 
263          # Raise the error. 
264          raise RelaxFuncSetupError(get_string(function_type)) 
265   
266      # Return the function. 
267      return function 
268   
269   
270 -def get_instance(function_type): 
271      """Function for returning the class instance corresponding to the function type.""" 
272   
273      # Consistency testing. 
274      if function_type == 'ct': 
275          return consistency_tests_obj 
276   
277      # The Frame Order theories. 
278      if function_type == 'frame order': 
279          return frame_order_obj 
280   
281      # NOE calculation. 
282      if function_type == 'noe': 
283          return noe_obj 
284   
285      # The N-state model. 
286      if function_type == 'N-state': 
287          return n_state_model_obj 
288   
289      # Relaxation dispersion curve fitting. 
290      if function_type == 'relax_disp': 
291          return relax_disp_obj 
292   
293      # Relaxation curve fitting. 
294      if function_type == 'relax_fit': 
295          return relax_fit_obj 
296   
297      # Reduced spectral density mapping. 
298      if function_type == 'jw': 
299          return jw_mapping_obj 
300   
301      # Model-free analysis. 
302      if function_type == 'mf': 
303          return model_free_obj 
304   
305      # Hybrid models. 
306      if function_type == 'hybrid': 
307          return hybrid_obj 
308   
309      # Unknown analysis. 
310      raise RelaxError("The function_type " + repr(function_type) + " is unknown.") 
311   
312   
313 -def get_string(function_type): 
314      """Function for returning a string corresponding to the function type.""" 
315   
316      # Consistency testing. 
317      if function_type == 'ct': 
318          return "consistency testing" 
319   
320      # The Frame Order theories. 
321      if function_type == 'frame order': 
322          return "Frame Order theories" 
323   
324      # NOE calculation. 
325      if function_type == 'noe': 
326          return "NOE calculations" 
327   
328      # The N-state model. 
329      if function_type == 'N-state': 
330          return "the N-state model" 
331   
332      # Relaxation dispersion curve fitting. 
333      if function_type == 'relax_disp': 
334          return "relaxation dispersion curve fitting" 
335   
336      # Relaxation curve fitting. 
337      if function_type == 'relax_fit': 
338          return "relaxation curve fitting" 
339   
340      # Reduced spectral density mapping. 
341      if function_type == 'jw': 
342          return "reduced spectral density mapping" 
343   
344      # Model-free analysis. 
345      if function_type == 'mf': 
346          return "Model-free analysis" 
347   
348      # Hybrid models. 
349      if function_type == 'hybrid': 
350          return "hybrid models" 
351   
352      # Unknown analysis. 
353      raise RelaxError("The function_type " + repr(function_type) + " is unknown.") 
354