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