Source Code for Module test_suite.unit_tests._specific_analyses._relax_disp.test_api

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  2  #                                                                             # 
  3  # Copyright (C) 2019 Edward d'Auvergne                                        # 
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  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 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.                                # 
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 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
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 21   
 22   
 23  # Python module imports. 
 24  from copy import deepcopy 
 25   
 26  # relax module imports. 
 27  from data_store import Relax_data_store; ds = Relax_data_store() 
 28  from lib.dispersion.variables import MODEL_LIST_FULL, \ 
 29      MODEL_PARAMS, \ 
 30      MODEL_R2EFF, \ 
 31      MODEL_NOREX, \ 
 32      MODEL_LM63, \ 
 33      MODEL_LM63_3SITE, \ 
 34      MODEL_CR72, \ 
 35      MODEL_CR72_FULL, \ 
 36      MODEL_IT99, \ 
 37      MODEL_TSMFK01, \ 
 38      MODEL_B14, \ 
 39      MODEL_B14_FULL, \ 
 40      MODEL_M61, \ 
 41      MODEL_M61B, \ 
 42      MODEL_DPL94, \ 
 43      MODEL_TP02, \ 
 44      MODEL_TAP03, \ 
 45      MODEL_MP05, \ 
 46      MODEL_NS_CPMG_2SITE_3D, \ 
 47      MODEL_NS_CPMG_2SITE_3D_FULL, \ 
 48      MODEL_NS_CPMG_2SITE_STAR, \ 
 49      MODEL_NS_CPMG_2SITE_STAR_FULL, \ 
 50      MODEL_NS_CPMG_2SITE_EXPANDED, \ 
 51      MODEL_NS_R1RHO_2SITE, \ 
 52      MODEL_NS_R1RHO_3SITE, \ 
 53      MODEL_NS_R1RHO_3SITE_LINEAR, \ 
 54      MODEL_MMQ_CR72, \ 
 55      MODEL_NS_MMQ_2SITE, \ 
 56      MODEL_NS_MMQ_3SITE, \ 
 57      MODEL_NS_MMQ_3SITE_LINEAR, \ 
 58      MODEL_EXP_TYPE_R2EFF, \ 
 59      MODEL_EXP_TYPE_NOREX, \ 
 60      MODEL_EXP_TYPE_LM63, \ 
 61      MODEL_EXP_TYPE_LM63_3SITE, \ 
 62      MODEL_EXP_TYPE_CR72, \ 
 63      MODEL_EXP_TYPE_CR72_FULL, \ 
 64      MODEL_EXP_TYPE_TSMFK01, \ 
 65      MODEL_EXP_TYPE_TSMFK01, \ 
 66      MODEL_EXP_TYPE_B14, \ 
 67      MODEL_EXP_TYPE_B14_FULL, \ 
 68      MODEL_EXP_TYPE_M61, \ 
 69      MODEL_EXP_TYPE_M61B, \ 
 70      MODEL_EXP_TYPE_DPL94, \ 
 71      MODEL_EXP_TYPE_TP02, \ 
 72      MODEL_EXP_TYPE_TAP03, \ 
 73      MODEL_EXP_TYPE_MP05, \ 
 74      MODEL_EXP_TYPE_NS_CPMG_2SITE_3D, \ 
 75      MODEL_EXP_TYPE_NS_CPMG_2SITE_3D_FULL, \ 
 76      MODEL_EXP_TYPE_NS_CPMG_2SITE_STAR, \ 
 77      MODEL_EXP_TYPE_NS_CPMG_2SITE_STAR_FULL, \ 
 78      MODEL_EXP_TYPE_NS_CPMG_2SITE_EXPANDED, \ 
 79      MODEL_EXP_TYPE_NS_R1RHO_2SITE, \ 
 80      MODEL_EXP_TYPE_NS_R1RHO_3SITE, \ 
 81      MODEL_EXP_TYPE_NS_R1RHO_3SITE_LINEAR, \ 
 82      MODEL_EXP_TYPE_MMQ_CR72, \ 
 83      MODEL_EXP_TYPE_NS_MMQ_2SITE, \ 
 84      MODEL_EXP_TYPE_NS_MMQ_3SITE, \ 
 85      MODEL_EXP_TYPE_NS_MMQ_3SITE_LINEAR 
 86  from pipe_control import mol_res_spin 
 87  from specific_analyses.relax_disp.api import Relax_disp 
 88  from specific_analyses.relax_disp.parameters import loop_parameters 
 89  from test_suite.unit_tests.base_classes import UnitTestCase 
 90   
 91   
 92 -class Test_api(UnitTestCase): 
 93      """Unit tests for the functions of the specific_analyses.relax_disp.api module.""" 
 94   
 95 -    def setUp(self): 
 96          """Setup some structures for the unit tests.""" 
 97   
 98          # Create a dispersion data pipe. 
 99          ds.add(pipe_name='testing', pipe_type='relax_disp') 
100   
101          # The experiment types for all models. 
102          self.exp_type = { 
103              MODEL_R2EFF: MODEL_EXP_TYPE_R2EFF, 
104              MODEL_NOREX: MODEL_EXP_TYPE_NOREX, 
105              MODEL_LM63: MODEL_EXP_TYPE_LM63, 
106              MODEL_LM63_3SITE: MODEL_EXP_TYPE_LM63_3SITE, 
107              MODEL_CR72: MODEL_EXP_TYPE_CR72, 
108              MODEL_CR72_FULL: MODEL_EXP_TYPE_CR72_FULL, 
109              MODEL_IT99: MODEL_EXP_TYPE_TSMFK01, 
110              MODEL_TSMFK01: MODEL_EXP_TYPE_TSMFK01, 
111              MODEL_B14: MODEL_EXP_TYPE_B14, 
112              MODEL_B14_FULL: MODEL_EXP_TYPE_B14_FULL, 
113              MODEL_M61: MODEL_EXP_TYPE_M61, 
114              MODEL_M61B: MODEL_EXP_TYPE_M61B, 
115              MODEL_DPL94: MODEL_EXP_TYPE_DPL94, 
116              MODEL_TP02: MODEL_EXP_TYPE_TP02, 
117              MODEL_TAP03: MODEL_EXP_TYPE_TAP03, 
118              MODEL_MP05: MODEL_EXP_TYPE_MP05, 
119              MODEL_NS_CPMG_2SITE_3D: MODEL_EXP_TYPE_NS_CPMG_2SITE_3D, 
120              MODEL_NS_CPMG_2SITE_3D_FULL: MODEL_EXP_TYPE_NS_CPMG_2SITE_3D_FULL, 
121              MODEL_NS_CPMG_2SITE_STAR: MODEL_EXP_TYPE_NS_CPMG_2SITE_STAR, 
122              MODEL_NS_CPMG_2SITE_STAR_FULL: MODEL_EXP_TYPE_NS_CPMG_2SITE_STAR_FULL, 
123              MODEL_NS_CPMG_2SITE_EXPANDED: MODEL_EXP_TYPE_NS_CPMG_2SITE_EXPANDED, 
124              MODEL_NS_R1RHO_2SITE: MODEL_EXP_TYPE_NS_R1RHO_2SITE, 
125              MODEL_NS_R1RHO_3SITE: MODEL_EXP_TYPE_NS_R1RHO_3SITE, 
126              MODEL_NS_R1RHO_3SITE_LINEAR: MODEL_EXP_TYPE_NS_R1RHO_3SITE_LINEAR, 
127              MODEL_MMQ_CR72: MODEL_EXP_TYPE_MMQ_CR72, 
128              MODEL_NS_MMQ_2SITE: MODEL_EXP_TYPE_NS_MMQ_2SITE, 
129              MODEL_NS_MMQ_3SITE: MODEL_EXP_TYPE_NS_MMQ_3SITE, 
130              MODEL_NS_MMQ_3SITE_LINEAR: MODEL_EXP_TYPE_NS_MMQ_3SITE_LINEAR 
131          } 
132   
133   
134 -    def test_sim_init_values(self): 
135          """Test the specific_analyses.relax_disp.api.sim_init_values() function for a cluster of 2 spins.""" 
136   
137          # Test parameter values. 
138          fixed_values = { 
139              'r1': 2.2, 
140              'r2eff': 10.0, 
141              'r2': 15.0, 
142              'r2a': 12.0, 
143              'r2b': 18.0, 
144              'pA': 0.80, 
145              'pB': 0.15, 
146              'k_AB': 0.001, 
147              'k_BA': 0.003, 
148              'kex': 0.01, 
149              'kex_AB': 0.015, 
150              'kex_BC': 0.017, 
151              'kex_AC': 0.016, 
152              'kB': 0.005, 
153              'kC': 0.004, 
154              'tex': 50.0, 
155              'dw': 1.0, 
156              'dw_AB': 1.02, 
157              'dw_BC': 1.03, 
158              'dwH': 0.1, 
159              'dwH_AB': 0.12, 
160              'dwH_BC': 0.13, 
161              'phi_ex': 0.5, 
162              'phi_ex_B': 0.4, 
163              'phi_ex_C': 0.3, 
164          } 
165   
166          # Loop over all models. 
167          print("Checking the parameter conversion and setting for a cluster of 2 spins.") 
168          for model in MODEL_LIST_FULL: 
169              # Printout. 
170              print("    Model '%s'." % model) 
171   
172              # Set up the data store. 
173              ds.add(pipe_name=model, pipe_type='relax_disp') 
174              if model == MODEL_R2EFF: 
175                  cdp.model_type = 'R2eff' 
176              else: 
177                  cdp.model_type = 'disp' 
178              cdp.exp_type_list = [self.exp_type[model]] 
179              cdp.spectrometer_frq_list = [1e6] 
180              cdp.sim_number = 2 
181   
182              # Set up the spin systems. 
183              cdp.mol.add_item(mol_name="sim test") 
184              cdp.mol[0].res[0].num = 1 
185              cdp.mol[0].res.add_item(res_num=2) 
186              mol_res_spin.metadata_update() 
187              spins = [cdp.mol[0].res[0].spin[0], cdp.mol[0].res[1].spin[0]] 
188              for spin in spins: 
189                  spin.model = model 
190                  if model == MODEL_R2EFF: 
191                      spin.params = ['r2eff'] 
192                  else: 
193                      spin.params = deepcopy(MODEL_PARAMS[model]) 
194                  spin.chi2 = 1000.0 
195                  spin.iter = 20 
196                  spin.f_count = 300 
197                  spin.g_count = 200 
198                  spin.h_count = 100 
199                  spin.warning = None 
200                  spin.isotope = '15N' 
201   
202              # Set the ordinary parameter values, as these are copied into the simulation structures. 
203              for name, param_index, spin_index, R20_key in loop_parameters(spins): 
204                  # R1/R2 parameters. 
205                  if name in ['r1', 'r2', 'r2a', 'r2b']: 
206                      key = "%s - %.8f MHz" % (cdp.exp_type_list[0], cdp.spectrometer_frq_list[0]/1e6) 
207                      print("        Setting spin %i parameter %s['%s'] to %s." % (spin_index, name, key, fixed_values[name])) 
208                      setattr(spins[spin_index], name, {key: fixed_values[name]}) 
209   
210                  # Global parameters. 
211                  elif spin_index == None: 
212                      print("        Setting global parameter %s to %s." % (name, fixed_values[name])) 
213                      setattr(spins[0], name, fixed_values[name]) 
214                      setattr(spins[1], name, fixed_values[name]) 
215   
216                  # Spin parameters. 
217                  else: 
218                      print("        Setting spin %i parameter %s to %s." % (spin_index, name, fixed_values[name])) 
219                      setattr(spins[spin_index], name, fixed_values[name]) 
220   
221              # MC simulation setup. 
222              api = Relax_disp() 
223              api.sim_init_values() 
224   
225              # Checks. 
226              for i in range(cdp.sim_number): 
227                  print("        Simulation %i." % i) 
228   
229                  # Check the probabilities. 
230                  if 'pB' in MODEL_PARAMS[model]: 
231                      print("        Checking parameter pC.") 
232                      self.assertAlmostEqual(spins[0].pC_sim[i], 0.05) 
233                      self.assertAlmostEqual(spins[1].pC_sim[i], 0.05) 
234                  elif 'pA' in MODEL_PARAMS[model]: 
235                      print("        Checking parameter pB.") 
236                      self.assertAlmostEqual(spins[0].pB_sim[i], 0.20) 
237                      self.assertAlmostEqual(spins[1].pB_sim[i], 0.20) 
238   
239                  # Check the kex-tex pair. 
240                  if 'kex' in MODEL_PARAMS[model]: 
241                      print("        Checking parameter tex.") 
242                      self.assertAlmostEqual(spins[0].tex_sim[i], 100.0) 
243                      self.assertAlmostEqual(spins[1].tex_sim[i], 100.0) 
244                  elif 'tex' in MODEL_PARAMS[model]: 
245                      print("        Checking parameter kex.") 
246                      self.assertAlmostEqual(spins[0].kex_sim[i], 0.02) 
247                      self.assertAlmostEqual(spins[1].kex_sim[i], 0.02) 
248   
249                  # Check the rates. 
250                  if 'kex' in MODEL_PARAMS[model] and 'pA' in MODEL_PARAMS[model]: 
251                      print("        Checking parameter k_AB.") 
252                      self.assertAlmostEqual(spins[0].k_AB_sim[i], 0.002) 
253                      self.assertAlmostEqual(spins[1].k_AB_sim[i], 0.002) 
254                      print("        Checking parameter k_BA.") 
255                      self.assertAlmostEqual(spins[0].k_BA_sim[i], 0.008) 
256                      self.assertAlmostEqual(spins[1].k_BA_sim[i], 0.008) 
257