Source Code for Module test_suite.system_tests.palmer

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008 Sebastien Morin                                          # 
  4  # Copyright (C) 2008-2009,2012-2014,2017,2020 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_store import Relax_data_store; ds = Relax_data_store() 
 30  import dep_check 
 31  from pipe_control import pipes 
 32  from pipe_control.mol_res_spin import return_spin 
 33  from lib.errors import RelaxError 
 34  from lib.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          # Test for the presence of the Modelfree4 binary (skip the test if not present). 
 58          try: 
 59              test_binary('modelfree4') 
 60          except: 
 61              status.skipped_tests.append([methodName, "Art Palmer's Modelfree4 software", self._skip_type]) 
 62   
 63   
 64 -    def setUp(self): 
 65          """Set up for all the functional tests.""" 
 66   
 67          # Create a temporary directory for ModelFree4 outputs. 
 68          ds.tmpdir = mkdtemp() 
 69   
 70   
 71 -    def test_palmer(self): 
 72          """Test a complete model-free analysis using the program 'Modelfree4'.""" 
 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(spin_id=':0@N', pipe='m2') 
 79          if spin.te == 1.951*1e-12: 
 80              binary = 'linux-i386-gcc'   # Linux Gnu gcc modelfree4 version. 
 81          else: 
 82              binary = 'linux-i386-pgf'   # Linux Portland C compiler modelfree4 version. 
 83          spin = return_spin(spin_id=':-2@N', pipe='m1') 
 84          if spin.chi2 == 36.62: 
 85              binary = 'mac-i386'         # Mac OS X intel binary. 
 86          if not binary: 
 87              raise RelaxError("The Modelfree4 binary cannot be identified, therefore the parameters cannot be meaningfully checked.") 
 88          print("\nDetected the '%s' Modelfree4 binary." % binary) 
 89   
 90          # Checks for model m1, m2, and m3 mfout file reading. 
 91          models = ['m1', 'm2', 'm3'] 
 92          params = [['s2'], ['s2', 'te'], ['s2', 'rex']] 
 93          spin_names = [':-2@N', ':-1@N', ':0@N'] 
 94          s2 = [[0.869, 0.732, None], [0.869, 0.730, None], [0.715, 0.643, None]] 
 95          if binary == 'linux-i386-gcc': 
 96              te = [[None, None, None], [0.0, 1.951, None], [None, None, None]] 
 97          else: 
 98              te = [[None, None, None], [0.0, 1.952, None], [None, None, None]] 
 99          rex = [[None, None, None], [None, None, None], [4.308, 4.278, None]] 
100          chi2 = [[36.6223, 20.3954, None], [36.6223, 20.3299, None], [1.9763, 0.6307, None]] 
101          if binary == 'mac-i386': 
102              chi2 = [[36.62, 20.40, None], [36.62, 20.33, None], [1.976, 0.6307, None]] 
103          for model_index in range(3): 
104              print("Model " + repr(models[model_index])) 
105              for spin_index in range(3): 
106                  print("Spin " + repr(spin_names[spin_index])) 
107   
108                  # Get the spin. 
109                  spin = return_spin(spin_id=spin_names[spin_index], pipe=models[model_index]) 
110   
111                  # Conversions. 
112                  if te[model_index][spin_index]: 
113                      te[model_index][spin_index] = te[model_index][spin_index] * 1e-12 
114                  if rex[model_index][spin_index]: 
115                      rex[model_index][spin_index] = rex[model_index][spin_index] / (2.0 * pi * cdp.spectrometer_frq[cdp.ri_ids[0]])**2 
116   
117                  # Checks. 
118                  self.assertEqual(spin.model, models[model_index]) 
119                  self.assertEqual(spin.params, params[model_index]) 
120                  self.assertEqual(spin.s2, s2[model_index][spin_index]) 
121                  self.assertEqual(spin.s2f, None) 
122                  self.assertEqual(spin.s2s, None) 
123                  if te[model_index][spin_index] == None: 
124                      self.assertEqual(spin.te, te[model_index][spin_index]) 
125                  else: 
126                      self.assertAlmostEqual(spin.te, te[model_index][spin_index]) 
127                  self.assertEqual(spin.tf, None) 
128                  self.assertEqual(spin.ts, None) 
129                  self.assertEqual(spin.rex, rex[model_index][spin_index]) 
130                  self.assertEqual(spin.chi2, chi2[model_index][spin_index]) 
131   
132          # Checks for the final mfout file reading. 
133          models = ['m3', 'm3'] 
134          params = [['s2', 'rex'], ['s2', 'rex']] 
135          s2 = [0.844, 0.760] 
136          te = [None, None] 
137          rex = [0.005, 0.404] 
138          chi2 = [1.7966, 0.7389] 
139          if binary == 'mac-i386': 
140              chi2 = [1.796, 0.7392] 
141          for spin_index in range(3): 
142              # Get the spin. 
143              spin = return_spin(spin_id=spin_names[spin_index], pipe='aic') 
144   
145              # Deselected spin. 
146              if not spin.select: 
147                  continue 
148   
149              # Conversions. 
150              if te[spin_index]: 
151                  te[spin_index] = te[spin_index] * 1e-12 
152              if rex[spin_index]: 
153                  rex[spin_index] = rex[spin_index] / (2.0 * pi * cdp.spectrometer_frq[cdp.ri_ids[0]])**2 
154   
155              # Checks. 
156              self.assertEqual(spin.model, models[spin_index]) 
157              self.assertEqual(spin.params, params[spin_index]) 
158              self.assertAlmostEqual(spin.s2, s2[spin_index]) 
159              self.assertEqual(spin.s2f, None) 
160              self.assertEqual(spin.s2s, None) 
161              if te[spin_index]: 
162                  self.assertAlmostEqual(spin.te, te[spin_index]) 
163              else: 
164                  self.assertEqual(spin.te, None) 
165              self.assertEqual(spin.tf, None) 
166              self.assertEqual(spin.ts, None) 
167              self.assertAlmostEqual(spin.rex, rex[spin_index]) 
168              self.assertEqual(spin.chi2, chi2[spin_index]) 
169   
170          # Final global values. 
171          final_pipe = pipes.get_pipe('aic') 
172          if binary == 'mac-i386': 
173              self.assertAlmostEqual(final_pipe.chi2, 2.5355) 
174              self.assertAlmostEqual(final_pipe.diff_tensor.tm, 12.051) 
175          else: 
176              self.assertAlmostEqual(final_pipe.chi2, 2.5356) 
177              self.assertAlmostEqual(final_pipe.diff_tensor.tm, 12.045) 
178   
179   
180 -    def test_palmer_omp(self): 
181          """Test a complete model-free analysis using 'Modelfree4' with the OMP relaxation data, a PDB file, and a spheroid tensor.""" 
182   
183          # Execute the script. 
184          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'palmer_omp.py') 
185   
186          # Catch a the old, buggy modelfree4 versions and complain loudly! 
187          spin = return_spin(spin_id=':9@N', pipe='m2') 
188          if spin.s2 == 0.855: 
189              raise RelaxError("You are using an old, buggy Modelfree4 version!  You must upgrade to version 4.20 or later.") 
190   
191          # Determine the Modelfree4 binary type used. 
192          spin = return_spin(spin_id=':9@N', pipe='aic') 
193          binary = None 
194          if spin.te * 1e12 == 52.195: 
195              binary = 'linux-i386-gcc'   # Linux Gnu gcc modelfree4 version. 
196          elif spin.te * 1e12 == 52.197: 
197              binary = 'linux-i386-pgf'   # Linux Portland C compiler modelfree4 version. 
198          elif spin.te * 1e12 == 52.194: 
199              binary = 'linux-x86_64-gcc'   # 64-bit Linux Gnu gcc modelfree4 version. 
200          elif spin.te * 1e12 == 52.199: 
201              binary = 'linux-x86_64-gcc_2024'   # 64-bit Linux Gnu gcc modelfree4 version (with newer linked libraries from around 2024). 
202          spin = return_spin(spin_id=':9@N', pipe='m1') 
203          if binary == None and spin.chi2 == 143.7: 
204              binary = 'mac-i386'         # Mac OS X intel binary. 
205          if not binary: 
206              raise RelaxError("The Modelfree4 binary cannot be identified, therefore the parameters cannot be meaningfully checked.") 
207          print("\nDetected the '%s' Modelfree4 binary." % binary) 
208   
209          # Model m1, m2, and m3 mfout file data. 
210          models = ['m1', 'm2', 'm3'] 
211          params = [['s2'], ['s2', 'te'], ['s2', 'rex']] 
212          spin_names = [':9@N', ':10@N', ':11@N'] 
213          s2 = [[0.822, 0.799, 0.823], [0.788, 0.777, 0.812], [0.822, 0.799, 0.823]] 
214          te = [[None, None, None], [61.506, 36.087, 20.039], [None, None, None]] 
215          if binary in ['mac-i386', 'linux-x86_64-gcc', 'linux-x86_64-gcc_2024']: 
216              te = [[None, None, None], [61.504, 36.087, 20.039], [None, None, None]] 
217          rex = [[None, None, None], [None, None, None], [0.0, 0.0, 0.0]] 
218          chi2 = [[143.6773, 105.1767, 61.6684], [40.9055, 57.1562, 48.4927], [143.6773, 105.1767, 61.6684]] 
219          if binary in ['mac-i386', 'linux-x86_64-gcc', 'linux-x86_64-gcc_2024']: 
220              chi2 = [[143.7, 105.2, 61.67], [40.91, 57.16, 48.49], [143.7, 105.2, 61.67]] 
221   
222          # Checks for model m1, m2, and m3 mfout file reading. 
223          for model_index in range(3): 
224              print("Model " + repr(models[model_index])) 
225              for spin_index in range(3): 
226                  print("Spin " + repr(spin_names[spin_index])) 
227   
228                  # Get the spin. 
229                  spin = return_spin(spin_id=spin_names[spin_index], pipe=models[model_index]) 
230   
231                  # Conversions. 
232                  if rex[model_index][spin_index]: 
233                      rex[model_index][spin_index] = rex[model_index][spin_index] / (2.0 * pi * cdp.spectrometer_frq[cdp.ri_ids[0]])**2 
234   
235                  # Checks. 
236                  self.assertEqual(spin.model, models[model_index]) 
237                  self.assertEqual(spin.params, params[model_index]) 
238                  self.assertAlmostEqual(spin.s2, s2[model_index][spin_index]) 
239                  self.assertEqual(spin.s2f, None) 
240                  self.assertEqual(spin.s2s, None) 
241                  if te[model_index][spin_index]: 
242                      self.assertAlmostEqual(spin.te * 1e12, te[model_index][spin_index]) 
243                  self.assertEqual(spin.tf, None) 
244                  self.assertEqual(spin.ts, None) 
245                  self.assertEqual(spin.rex, rex[model_index][spin_index]) 
246                  self.assertEqual(spin.chi2, chi2[model_index][spin_index]) 
247   
248          # Final mfout file data. 
249          models = ['m2', 'm2', 'm2'] 
250          params = [['s2', 'te'], ['s2', 'te'], ['s2', 'te']] 
251          s2 = [0.755, 0.761, 0.787] 
252          if binary == 'linux-i386-gcc': 
253              te = [52.195, 29.356, 12.678] 
254          elif binary == 'linux-i386-pgf': 
255              te = [52.197, 29.361, 12.677] 
256          elif binary == 'mac-i386': 
257              te = [52.197, 29.357, 12.676] 
258          elif binary == 'linux-x86_64-gcc': 
259              te = [52.194, 29.351, 12.673] 
260          elif binary == 'linux-x86_64-gcc_2024': 
261              te = [52.199, 29.357, 12.677] 
262          chi2 = [7.254, 8.0437, 0.5327] 
263          if binary in ['mac-i386', 'linux-x86_64-gcc', 'linux-x86_64-gcc_2024']: 
264              chi2 = [7.254, 8.044, 0.5327] 
265   
266          # Checks for the final mfout file reading. 
267          for spin_index in range(3): 
268              # Get the spin. 
269              spin = return_spin(spin_id=spin_names[spin_index], pipe='aic') 
270   
271              # Checks. 
272              self.assertEqual(spin.model, models[spin_index]) 
273              self.assertEqual(spin.params, params[spin_index]) 
274              self.assertAlmostEqual(spin.s2, s2[spin_index]) 
275              self.assertEqual(spin.s2f, None) 
276              self.assertEqual(spin.s2s, None) 
277              if te[spin_index]: 
278                  self.assertAlmostEqual(spin.te * 1e12, te[spin_index]) 
279              self.assertEqual(spin.tf, None) 
280              self.assertEqual(spin.ts, None) 
281              self.assertEqual(spin.rex, None) 
282              self.assertAlmostEqual(spin.chi2, chi2[spin_index]) 
283   
284          # Final global values. 
285          final_pipe = pipes.get_pipe('aic') 
286          if binary == 'linux-i386-gcc': 
287              self.assertEqual(final_pipe.chi2, 15.8304) 
288              self.assertAlmostEqual(final_pipe.diff_tensor.tm, 8.443) 
289              self.assertAlmostEqual(final_pipe.diff_tensor.Dratio, 1.053) 
290              self.assertAlmostEqual(final_pipe.diff_tensor.theta * 360 / 2.0 / pi, 68.592) 
291              self.assertAlmostEqual(final_pipe.diff_tensor.phi * 360 / 2.0 / pi, 73.756) 
292          elif binary == 'linux-i386-pgf': 
293              self.assertEqual(final_pipe.chi2, 15.8304) 
294              self.assertAlmostEqual(final_pipe.diff_tensor.tm, 8.443) 
295              self.assertAlmostEqual(final_pipe.diff_tensor.Dratio, 1.053) 
296              self.assertAlmostEqual(final_pipe.diff_tensor.theta * 360 / 2.0 / pi, 68.864) 
297              self.assertAlmostEqual(final_pipe.diff_tensor.phi * 360 / 2.0 / pi, 73.913) 
298          elif binary == 'mac-i386': 
299              self.assertEqual(final_pipe.chi2, 15.8304) 
300              self.assertAlmostEqual(final_pipe.diff_tensor.tm, 8.459) 
301              self.assertAlmostEqual(final_pipe.diff_tensor.Dratio, 1.049) 
302              self.assertAlmostEqual(final_pipe.diff_tensor.theta * 360 / 2.0 / pi, 64.611) 
303              self.assertAlmostEqual(final_pipe.diff_tensor.phi * 360 / 2.0 / pi, 79.281) 
304          elif binary == 'linux-x86_64-gcc': 
305              self.assertEqual(final_pipe.chi2, 15.8308) 
306              self.assertAlmostEqual(final_pipe.diff_tensor.tm, 8.394) 
307              self.assertAlmostEqual(final_pipe.diff_tensor.Dratio, 1.073) 
308              self.assertAlmostEqual(final_pipe.diff_tensor.theta * 360 / 2.0 / pi, 77.152) 
309              self.assertAlmostEqual(final_pipe.diff_tensor.phi * 360 / 2.0 / pi, 63.848) 
310