Source Code for Module test_suite.system_tests.peak_lists

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2013 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2008 Sebastien Morin                                          # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 16  # GNU General Public License for more details.                                # 
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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 os import sep 
 25   
 26  # relax module imports. 
 27  from data import Relax_data_store; ds = Relax_data_store() 
 28  import dep_check 
 29  from generic_fns.mol_res_spin import spin_loop 
 30  from status import Status; status = Status() 
 31  from test_suite.system_tests.base_classes import SystemTestCase 
 32   
 33   
 34 -class Peak_lists(SystemTestCase): 
 35      """TestCase class for the functional tests for the support of different peak intensity files.""" 
 36   
 37 -    def __init__(self, methodName='runTest'): 
 38          """Skip the tests if the C modules are non-functional. 
 39   
 40          @keyword methodName:    The name of the test. 
 41          @type methodName:       str 
 42          """ 
 43   
 44          # Execute the base class method. 
 45          super(Peak_lists, self).__init__(methodName) 
 46   
 47          # Missing module. 
 48          if not dep_check.C_module_exp_fn and methodName in ['test_bug_17276_peak_lists', 'test_ccpn_analysis']: 
 49              # Store in the status object.  
 50              status.skipped_tests.append([methodName, 'Relax curve-fitting C module', self._skip_type]) 
 51   
 52   
 53 -    def setUp(self): 
 54          """Set up for all the functional tests.""" 
 55   
 56          # Create a data pipe. 
 57          self.interpreter.pipe.create('mf', 'mf') 
 58   
 59   
 60 -    def test_bug_17276_peak_lists(self): 
 61          """Test catching U{bug #17276<https://web.archive.org/web/https://gna.org/bugs/?17276>}, the duplicated peak list reading failure submitted by Leanne Minall.""" 
 62   
 63          # Execute the script. 
 64          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bug_17276_peak_lists.py') 
 65   
 66   
 67 -    def test_ccpn_analysis(self): 
 68          """Test U{bug #17341<https://web.archive.org/web/https://gna.org/bugs/index.php?17341>}, the CCPN Analysis 2.1 peak list reading submitted by Madeleine Strickland.""" 
 69   
 70          # Execute the script. 
 71          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'peak_lists'+sep+'ccpn_analysis.py') 
 72   
 73          # Spectrum names. 
 74          names = ['T1A_0010', 'T1A_0020', 'T1A_0030', 'T1A_0050', 'T1A_0070', 'T1A_0100', 'T1A_0150', 'T1A_0200', 'T1A_0300', 'T1A_0400', 'T1A_0600', 'T1A_0800', 'T1A_1000', 'T1A_1200'] 
 75   
 76          # Relaxation times (in seconds). 
 77          times = [0.01, 0.02, 0.03, 0.05, 0.07, 0.1, 0.15, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 1.2] 
 78   
 79          # Check the spectrum IDs and relaxation times. 
 80          for i in range(len(times)): 
 81              self.assertEqual(cdp.spectrum_ids[i], names[i]) 
 82              self.assertEqual(cdp.relax_times[names[i]], times[i]) 
 83   
 84          # The peak heights. 
 85          heights = [ 
 86                  [1.41e06, 1.33e06, 1.31e06, 1.31e06, 1.28e06, 1.20e06, 1.18e06, 1.07e06, 9.70e05, 8.47e05, 7.00e05, 5.25e05, 4.23e05, 3.10e05], 
 87                  [1.79e06, 1.76e06, 1.71e06, 1.70e06, 1.66e06, 1.56e06, 1.51e06, 1.41e06, 1.24e06, 1.11e06, 8.43e05, 6.79e05, 5.04e05, 4.18e05] 
 88          ] 
 89   
 90          # Check the heights. 
 91          for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 
 92              # The data. 
 93              if res_num == 1501: 
 94                  index = 0 
 95              elif res_num == 1504: 
 96                  index = 1 
 97   
 98              # No data. 
 99              else: 
100                  # There should be no intensity data. 
101                  self.assert_(not hasattr(spin, 'intensities')) 
102   
103                  # Do not perform the height checks. 
104                  continue 
105   
106              # Check the data. 
107              self.assert_(hasattr(spin, 'intensities')) 
108   
109              # Check the values. 
110              for i in range(len(times)): 
111                  self.assertEqual(spin.intensities[names[i]], heights[index][i]) 
112   
113   
114 -    def test_read_peak_list_generic(self): 
115          """Test the reading of a generic peak intensity list.""" 
116   
117          # Create the sequence data, and name the spins. 
118          self.interpreter.residue.create(20, 'GLY') 
119          self.interpreter.residue.create(23, 'ALA') 
120          self.interpreter.residue.create(34, 'CYS') 
121          self.interpreter.residue.create(35, 'MET') 
122          self.interpreter.residue.create(36, 'LYS') 
123          self.interpreter.spin.name(name='N') 
124   
125          # Relaxation delays. 
126          delays = [0.0109016, 
127                    0.0218032, 
128                    0.0436064, 
129                    0.0436064, 
130                    0.0872128, 
131                    0.1744260, 
132                    0.3488510, 
133                    0.6977020, 
134                    1.3954000, 
135                    1.9949900] 
136   
137          # Load the data. 
138          for i in range(10): 
139              # Read the peak intensities. 
140              self.interpreter.spectrum.read_intensities(file="generic_intensity.txt", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id=repr(i), int_method='height', int_col=i+3, res_num_col=1, res_name_col=2) 
141   
142              # Set the relaxation times. 
143              self.interpreter.relax_fit.relax_time(time=delays[i], spectrum_id=repr(i)) 
144   
145          # The actual intensities. 
146          heights = [[1.0000, 0.9714, 0.9602, 0.9626, 0.8839, 0.8327, 0.7088, 0.5098, 0.2410, 0.1116], 
147                     [1.0000, 0.9789, 0.9751, 0.9762, 0.9074, 0.8532, 0.7089, 0.5170, 0.2444, 0.1537], 
148                     [1.0000, 0.9659, 0.9580, 0.9559, 0.9325, 0.8460, 0.7187, 0.5303, 0.2954, 0.1683], 
149                     [1.0000, 0.9657, 0.9389, 0.9366, 0.9331, 0.8683, 0.7169, 0.5357, 0.2769, 0.1625], 
150                     [1.0000, 1.0060, 0.9556, 0.9456, 0.9077, 0.8411, 0.6788, 0.4558, 0.2448, 0.1569] 
151          ] 
152   
153          # Test the data. 
154          for i in range(10): 
155              for j in range(5): 
156                  self.assertEqual(cdp.mol[0].res[j].spin[0].intensities[repr(i)], heights[j][i]) 
157   
158   
159 -    def test_read_peak_list_nmrview(self): 
160          """Test the reading of an NMRView peak list.""" 
161   
162          # Create the sequence data, and name the spins. 
163          self.interpreter.residue.create(70) 
164          self.interpreter.residue.create(72) 
165          self.interpreter.spin.name(name='N') 
166   
167          # Read the peak list. 
168          self.interpreter.spectrum.read_intensities(file="cNTnC.xpk", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 
169   
170          # Test the data. 
171          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], -0.1694) 
172          self.assertEqual(list(cdp.mol[0].res[1].spin[0].intensities.values())[0], -0.1142) 
173   
174   
175 -    def test_read_peak_list_sparky(self): 
176          """Test the reading of an Sparky peak list.""" 
177   
178          # Create the sequence data, and name the spins. 
179          self.interpreter.residue.create(3) 
180          self.interpreter.residue.create(4) 
181          self.interpreter.residue.create(5) 
182          self.interpreter.residue.create(6) 
183          self.interpreter.spin.name(name='N') 
184   
185          # Read the peak list. 
186          self.interpreter.spectrum.read_intensities(file="ref_ave.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 
187   
188          # Test the data. 
189          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 6262) 
190          self.assertEqual(list(cdp.mol[0].res[1].spin[0].intensities.values())[0], 148614) 
191          self.assertEqual(list(cdp.mol[0].res[2].spin[0].intensities.values())[0], 166842) 
192          self.assertEqual(list(cdp.mol[0].res[3].spin[0].intensities.values())[0], 128690) 
193   
194   
195 -    def test_read_peak_list_xeasy(self): 
196          """Test the reading of an XEasy peak list.""" 
197   
198          # Create the sequence data, and name the spins. 
199          self.interpreter.residue.create(15) 
200          self.interpreter.residue.create(21) 
201          self.interpreter.residue.create(22) 
202          self.interpreter.residue.create(29) 
203          self.interpreter.residue.create(52) 
204          self.interpreter.residue.create(69) 
205          self.interpreter.residue.create(70) 
206          self.interpreter.residue.create(73) 
207          self.interpreter.residue.create(79) 
208          self.interpreter.residue.create(84) 
209          self.interpreter.residue.create(87) 
210          self.interpreter.residue.create(95) 
211          self.interpreter.residue.create(96) 
212          self.interpreter.residue.create(100) 
213          self.interpreter.residue.create(104) 
214          self.interpreter.residue.create(107) 
215          self.interpreter.residue.create(110) 
216          self.interpreter.residue.create(112) 
217          self.interpreter.residue.create(120) 
218          self.interpreter.residue.create(141) 
219          self.interpreter.residue.create(165) 
220          self.interpreter.spin.name(name='N') 
221   
222          # Read the peak list. 
223          self.interpreter.spectrum.read_intensities(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') 
224   
225          # Test the data. 
226          self.assertEqual(list(cdp.mol[0].res[ 0].spin[0].intensities.values())[0], 9.714e+03) 
227          self.assertEqual(list(cdp.mol[0].res[ 1].spin[0].intensities.values())[0], 7.919e+03) 
228          self.assertEqual(list(cdp.mol[0].res[ 2].spin[0].intensities.values())[0], 1.356e+04) 
229          self.assertEqual(list(cdp.mol[0].res[ 3].spin[0].intensities.values())[0], 9.884e+03) 
230          self.assertEqual(list(cdp.mol[0].res[ 4].spin[0].intensities.values())[0], 2.041e+04) 
231          self.assertEqual(list(cdp.mol[0].res[ 5].spin[0].intensities.values())[0], 9.305e+03) 
232          self.assertEqual(list(cdp.mol[0].res[ 6].spin[0].intensities.values())[0], 3.154e+04) 
233          self.assertEqual(list(cdp.mol[0].res[ 7].spin[0].intensities.values())[0], 9.180e+03) 
234          self.assertEqual(list(cdp.mol[0].res[ 9].spin[0].intensities.values())[0], 1.104e+04) 
235          self.assertEqual(list(cdp.mol[0].res[10].spin[0].intensities.values())[0], 7.680e+03) 
236          self.assertEqual(list(cdp.mol[0].res[11].spin[0].intensities.values())[0], 5.206e+03) 
237          self.assertEqual(list(cdp.mol[0].res[12].spin[0].intensities.values())[0], 2.863e+04) 
238          self.assertEqual(list(cdp.mol[0].res[14].spin[0].intensities.values())[0], 9.271e+03) 
239          self.assertEqual(list(cdp.mol[0].res[15].spin[0].intensities.values())[0], 7.919e+03) 
240          self.assertEqual(list(cdp.mol[0].res[16].spin[0].intensities.values())[0], 9.962e+03) 
241          self.assertEqual(list(cdp.mol[0].res[17].spin[0].intensities.values())[0], 1.260e+04) 
242          self.assertEqual(list(cdp.mol[0].res[18].spin[0].intensities.values())[0], 1.545e+04) 
243          self.assertEqual(list(cdp.mol[0].res[19].spin[0].intensities.values())[0], 1.963e+04) 
244          self.assertEqual(list(cdp.mol[0].res[20].spin[0].intensities.values())[0], 1.918e+04) 
245   
246   
247 -    def test_read_peak_list_xeasy_2(self): 
248          """Test the reading of an XEasy peak list (2).""" 
249   
250          # Create the sequence data, and name the spins. 
251          self.interpreter.residue.create(79) 
252          self.interpreter.spin.name(name='NE1') 
253   
254          # Read the peak list. 
255          self.interpreter.spectrum.read_intensities(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', heteronuc='NE1', proton='HE1', int_method='height') 
256   
257          # Test the data. 
258          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 1.532e+04) 
259   
260   
261 -    def test_read_peak_list_xeasy_3(self): 
262          """Test the reading of an XEasy peak list (3).""" 
263   
264          # Create the sequence data, and name the spins. 
265          self.interpreter.residue.create(100) 
266          self.interpreter.spin.name(name='C') 
267   
268          # Read the peak list. 
269          self.interpreter.spectrum.read_intensities(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', heteronuc='C', int_method='height') 
270   
271          # Test the data. 
272          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 6.877e+03) 
273   
274   
275 -    def test_read_peak_list_xeasy_4(self): 
276          """Test the reading of an XEasy peak list (4).""" 
277   
278          # Create the sequence data, and name the spins. 
279          self.interpreter.residue.create(107) 
280          self.interpreter.spin.name(name='C') 
281   
282          # Read the peak list. 
283          self.interpreter.spectrum.read_intensities(file="xeasy_r1_20ms.text", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', heteronuc='C', proton='HE1', int_method='height') 
284   
285          # Test the data. 
286          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 7.123e+03) 
287