Source Code for Module test_suite.system_tests.palmer

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008 Sebastien Morin                                          # 
  4  # Copyright (C) 2010-2012 Edward d'Auvergne                                   # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  7  #                                                                             # 
  8  # This program is free software: you can redistribute it and/or modify        # 
  9  # it under the terms of the GNU General Public License as published by        # 
 10  # the Free Software Foundation, either version 3 of the License, or           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 13  # This program is distributed in the hope that it will be useful,             # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 16  # GNU General Public License for more details.                                # 
 17  #                                                                             # 
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 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from math import pi 
 25  from os import sep 
 26  from tempfile import mkdtemp 
 27   
 28  # relax module imports. 
 29  from data import Relax_data_store; ds = Relax_data_store() 
 30  import dep_check 
 31  from generic_fns import pipes 
 32  from generic_fns.mol_res_spin import return_spin 
 33  from relax_errors import RelaxError 
 34  from relax_io import test_binary 
 35  from status import Status; status = Status() 
 36  from test_suite.system_tests.base_classes import SystemTestCase 
 37   
 38   
 39 -class Palmer(SystemTestCase): 
 40      """Class for testing various aspects specific to model-free analysis using the program 'Modelfree4'.""" 
 41   
 42 -    def __init__(self, methodName='runTest'): 
 43          """Skip the tests if the subprocess module is not available (Python 2.3 and earlier). 
 44   
 45          @keyword methodName:    The name of the test. 
 46          @type methodName:       str 
 47          """ 
 48   
 49          # Execute the base class method. 
 50          super(Palmer, self).__init__(methodName) 
 51   
 52          # Missing module. 
 53          if not dep_check.subprocess_module: 
 54              # Store in the status object.  
 55              status.skipped_tests.append([methodName, 'subprocess', self._skip_type]) 
 56   
 57   
 58 -    def setUp(self): 
 59          """Set up for all the functional tests.""" 
 60   
 61          # Create a temporary directory for ModelFree4 outputs. 
 62          ds.tmpdir = mkdtemp() 
 63   
 64   
 65 -    def test_palmer(self): 
 66          """Test a complete model-free analysis using the program 'Modelfree4'.""" 
 67   
 68          # Test for the presence of the Modelfree4 binary (skip the test if not present). 
 69          try: 
 70              test_binary('modelfree4') 
 71          except: 
 72              return 
 73   
 74          # Execute the script. 
 75          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'palmer.py') 
 76   
 77          # Determine if the Gnu gcc or Portland C compiler version is being used. 
 78          spin = return_spin(':0@N', pipe='m2') 
 79          if spin.te == 1.951*1e-12: 
 80              compiler = 'gcc'    # Gnu gcc modelfree4 version. 
 81          else: 
 82              compiler = 'pgf'    # Portland C compiler modelfree4 version. 
 83   
 84          # Checks for model m1, m2, and m3 mfout file reading. 
 85          models = ['m1', 'm2', 'm3'] 
 86          params = [['s2'], ['s2', 'te'], ['s2', 'rex']] 
 87          spin_names = [':-2@N', ':-1@N', ':0@N'] 
 88          if compiler == 'gcc': 
 89              s2 = [[0.869, 0.732, None], [0.869, 0.730, None], [0.715, 0.643, None]] 
 90              te = [[None, None, None], [0.0, 1.951, None], [None, None, None]]    # Gnu gcc modelfree4 version. 
 91              rex = [[None, None, None], [None, None, None], [4.308, 4.278, None]] 
 92          else: 
 93              s2 = [[0.869, 0.732, None], [0.869, 0.730, None], [0.715, 0.643, None]] 
 94              te = [[None, None, None], [0.0, 1.952, None], [None, None, None]]    # Portland C compiler modelfree4 version. 
 95              rex = [[None, None, None], [None, None, None], [4.308, 4.278, None]] 
 96          chi2 = [[36.6223, 20.3954, None], [36.6223, 20.3299, None], [1.9763, 0.6307, None]] 
 97          for model_index in range(3): 
 98              print("Model " + repr(models[model_index])) 
 99              for spin_index in range(3): 
100                  print("Spin " + repr(spin_names[spin_index])) 
101   
102                  # Get the spin. 
103                  spin = return_spin(spin_names[spin_index], pipe=models[model_index]) 
104   
105                  # Conversions. 
106                  if te[model_index][spin_index]: 
107                      te[model_index][spin_index] = te[model_index][spin_index] * 1e-12 
108                  if rex[model_index][spin_index]: 
109                      rex[model_index][spin_index] = rex[model_index][spin_index] / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 
110   
111                  # Checks. 
112                  self.assertEqual(spin.model, models[model_index]) 
113                  self.assertEqual(spin.params, params[model_index]) 
114                  self.assertEqual(spin.s2, s2[model_index][spin_index]) 
115                  self.assertEqual(spin.s2f, None) 
116                  self.assertEqual(spin.s2s, None) 
117                  if te[model_index][spin_index] == None: 
118                      self.assertEqual(spin.te, te[model_index][spin_index]) 
119                  else: 
120                      self.assertAlmostEqual(spin.te, te[model_index][spin_index]) 
121                  self.assertEqual(spin.tf, None) 
122                  self.assertEqual(spin.ts, None) 
123                  self.assertEqual(spin.rex, rex[model_index][spin_index]) 
124                  self.assertEqual(spin.chi2, chi2[model_index][spin_index]) 
125   
126          # Checks for the final mfout file reading. 
127          models = ['m3', 'm3'] 
128          params = [['s2', 'rex'], ['s2', 'rex']] 
129          s2 = [0.844, 0.760] 
130          te = [None, None] 
131          rex = [0.005, 0.404] 
132          chi2 = [1.7966, 0.7389] 
133          for spin_index in range(3): 
134              # Get the spin. 
135              spin = return_spin(spin_names[spin_index], pipe='aic') 
136   
137              # Deselected spin. 
138              if not spin.select: 
139                  continue 
140   
141              # Conversions. 
142              if te[spin_index]: 
143                  te[spin_index] = te[spin_index] * 1e-12 
144              if rex[spin_index]: 
145                  rex[spin_index] = rex[spin_index] / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 
146   
147              # Checks. 
148              self.assertEqual(spin.model, models[spin_index]) 
149              self.assertEqual(spin.params, params[spin_index]) 
150              self.assertEqual(spin.s2, s2[spin_index]) 
151              self.assertEqual(spin.s2f, None) 
152              self.assertEqual(spin.s2s, None) 
153              self.assertEqual(spin.te, te[spin_index]) 
154              self.assertEqual(spin.tf, None) 
155              self.assertEqual(spin.ts, None) 
156              self.assertEqual(spin.rex, rex[spin_index]) 
157              self.assertEqual(spin.chi2, chi2[spin_index]) 
158   
159          # Final global values. 
160          final_pipe = pipes.get_pipe('aic') 
161          self.assertEqual(final_pipe.chi2, 2.5356) 
162          self.assertEqual(final_pipe.diff_tensor.tm, 12.045) 
163   
164   
165 -    def test_palmer_omp(self): 
166          """Test a complete model-free analysis using 'Modelfree4' with the OMP relaxation data, a PDB file, and a spheroid tensor.""" 
167   
168          # Test for the presence of the Modelfree4 binary (skip the test if not present). 
169          try: 
170              test_binary('modelfree4') 
171          except: 
172              return 
173   
174          # Execute the script. 
175          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'palmer_omp.py') 
176   
177          # Catch a the old, buggy modelfree4 versions and complain loudly! 
178          spin = return_spin(':9@N', pipe='m2') 
179          if spin.s2 == 0.855: 
180              raise RelaxError("You are using an old, buggy Modelfree4 version!  You must upgrade to version 4.20 or later.") 
181   
182          # Determine if the Gnu gcc or Portland C compiler version is being used. 
183          if spin.te == 20.043*1e-12: 
184              compiler = 'gcc'    # Gnu gcc modelfree4 version. 
185          else: 
186              compiler = 'pgf'    # Portland C compiler modelfree4 version. 
187   
188          # Model m1, m2, and m3 mfout file data. 
189          models = ['m1', 'm2', 'm3'] 
190          params = [['s2'], ['s2', 'te'], ['s2', 'rex']] 
191          spin_names = [':9@N', ':10@N', ':11@N'] 
192          s2 = [[0.822, 0.799, 0.823], [0.788, 0.777, 0.812], [0.822, 0.799, 0.823]] 
193          if compiler == 'gcc': 
194              te = [[None, None, None], [61.506, 36.084, 20.043], [None, None, None]] 
195          else: 
196              te = [[None, None, None], [61.506, 36.087, 20.039], [None, None, None]] 
197          rex = [[None, None, None], [None, None, None], [0.0, 0.0, 0.0]] 
198          chi2 = [[143.6773, 105.1767, 61.6684], [40.9055, 57.1562, 48.4927], [143.6773, 105.1767, 61.6684]] 
199   
200          # Checks for model m1, m2, and m3 mfout file reading. 
201          for model_index in range(3): 
202              print("Model " + repr(models[model_index])) 
203              for spin_index in range(3): 
204                  print("Spin " + repr(spin_names[spin_index])) 
205   
206                  # Get the spin. 
207                  spin = return_spin(spin_names[spin_index], pipe=models[model_index]) 
208   
209                  # Conversions. 
210                  if te[model_index][spin_index]: 
211                      te[model_index][spin_index] = te[model_index][spin_index] * 1e-12 
212                  if rex[model_index][spin_index]: 
213                      rex[model_index][spin_index] = rex[model_index][spin_index] / (2.0 * pi * cdp.frq[cdp.ri_ids[0]])**2 
214   
215                  # Checks. 
216                  self.assertEqual(spin.model, models[model_index]) 
217                  self.assertEqual(spin.params, params[model_index]) 
218                  self.assertEqual(spin.s2, s2[model_index][spin_index]) 
219                  self.assertEqual(spin.s2f, None) 
220                  self.assertEqual(spin.s2s, None) 
221                  self.assertEqual(spin.te, te[model_index][spin_index]) 
222                  self.assertEqual(spin.tf, None) 
223                  self.assertEqual(spin.ts, None) 
224                  self.assertEqual(spin.rex, rex[model_index][spin_index]) 
225                  self.assertEqual(spin.chi2, chi2[model_index][spin_index]) 
226   
227          # Final mfout file data. 
228          models = ['m2', 'm2', 'm2'] 
229          params = [['s2', 'te'], ['s2', 'te'], ['s2', 'te']] 
230          if compiler == 'gcc': 
231              s2 = [0.782, 0.760, 0.785] 
232              te = [60.009, 29.134, 12.590] 
233              chi2 = [24.0495, 8.1168, 0.5332] 
234          else: 
235              s2 = [0.755, 0.761, 0.787] 
236              te = [52.197, 29.361, 12.677] 
237              chi2 = [7.254, 8.0437, 0.5327] 
238   
239          # Checks for the final mfout file reading. 
240          for spin_index in range(3): 
241              # Get the spin. 
242              spin = return_spin(spin_names[spin_index], pipe='aic') 
243   
244              # Conversions. 
245              if te[spin_index]: 
246                  te[spin_index] = te[spin_index] * 1e-12 
247   
248              # Checks. 
249              self.assertEqual(spin.model, models[spin_index]) 
250              self.assertEqual(spin.params, params[spin_index]) 
251              self.assertEqual(spin.s2, s2[spin_index]) 
252              self.assertEqual(spin.s2f, None) 
253              self.assertEqual(spin.s2s, None) 
254              self.assertAlmostEqual(spin.te, te[spin_index]) 
255              self.assertEqual(spin.tf, None) 
256              self.assertEqual(spin.ts, None) 
257              self.assertEqual(spin.rex, None) 
258              self.assertEqual(spin.chi2, chi2[spin_index]) 
259   
260          # Final global values. 
261          final_pipe = pipes.get_pipe('aic') 
262          if compiler == 'gcc': 
263              self.assertEqual(final_pipe.chi2, 32.6995) 
264              self.assertEqual(final_pipe.diff_tensor.tm, 8.964) 
265              self.assertEqual(final_pipe.diff_tensor.Dratio, 1.324) 
266              self.assertEqual(final_pipe.diff_tensor.theta, (-52.070 / 360.0) * 2.0 * pi + pi) 
267              self.assertEqual(final_pipe.diff_tensor.phi, (2.377 / 360.0) * 2.0 * pi) 
268          else: 
269              self.assertEqual(final_pipe.chi2, 15.8304) 
270              self.assertEqual(final_pipe.diff_tensor.tm, 8.443) 
271              self.assertEqual(final_pipe.diff_tensor.Dratio, 1.053) 
272              self.assertEqual(final_pipe.diff_tensor.theta, (68.864 / 360.0) * 2.0 * pi) 
273              self.assertEqual(final_pipe.diff_tensor.phi, (73.913 / 360.0) * 2.0 * pi) 
274