Source Code for Module test_suite.system_tests.peak_lists

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2011 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2008 Sebastien Morin                                          # 
  5  #                                                                             # 
  6  # This file is part of the program relax.                                     # 
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 22  ############################################################################### 
 23   
 24  # Python module imports. 
 25  from os import sep 
 26   
 27  # relax module imports. 
 28  from base_classes import SystemTestCase 
 29  from data import Relax_data_store; ds = Relax_data_store() 
 30  from generic_fns.mol_res_spin import spin_loop 
 31  from status import Status; status = Status() 
 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 setUp(self): 
 38          """Set up for all the functional tests.""" 
 39   
 40          # Create a data pipe. 
 41          self.interpreter.pipe.create('mf', 'mf') 
 42   
 43   
 44 -    def test_bug_17276_peak_lists(self): 
 45          """Test catching bug #17276, the duplicated peak list reading failure submitted by Leanne Minall.""" 
 46   
 47          # Execute the script. 
 48          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bug_17276_peak_lists.py') 
 49   
 50   
 51 -    def test_ccpn_analysis(self): 
 52          """Test 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.""" 
 53   
 54          # Execute the script. 
 55          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'peak_lists'+sep+'ccpn_analysis.py') 
 56   
 57          # Spectrum names. 
 58          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'] 
 59   
 60          # Relaxation times (in seconds). 
 61          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] 
 62   
 63          # Check the spectrum IDs and relaxation times. 
 64          for i in range(len(times)): 
 65              self.assertEqual(cdp.spectrum_ids[i], names[i]) 
 66              self.assertEqual(cdp.relax_times[names[i]], times[i]) 
 67   
 68          # The peak heights. 
 69          heights = [ 
 70                  [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], 
 71                  [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] 
 72          ] 
 73   
 74          # Check the heights. 
 75          for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 
 76              print spin 
 77              # The data. 
 78              if res_num == 1501: 
 79                  index = 0 
 80              elif res_num == 1504: 
 81                  index = 1 
 82   
 83              # No data. 
 84              else: 
 85                  # There should be no intensity data. 
 86                  self.assert_(not hasattr(spin, 'intensities')) 
 87   
 88                  # Do not perform the height checks. 
 89                  continue 
 90   
 91              # Check the data. 
 92              self.assert_(hasattr(spin, 'intensities')) 
 93   
 94              # Check the values. 
 95              for i in range(len(times)): 
 96                  self.assertEqual(spin.intensities[names[i]], heights[index][i]) 
 97   
 98   
 99 -    def test_read_peak_list_generic(self): 
100          """Test the reading of a generic peak intensity list.""" 
101   
102          # Create the sequence data, and name the spins. 
103          self.interpreter.residue.create(20, 'GLY') 
104          self.interpreter.residue.create(23, 'ALA') 
105          self.interpreter.residue.create(34, 'CYS') 
106          self.interpreter.residue.create(35, 'MET') 
107          self.interpreter.residue.create(36, 'LYS') 
108          self.interpreter.spin.name(name='N') 
109   
110          # Relaxation delays. 
111          delays = [0.0109016, 
112                    0.0218032, 
113                    0.0436064, 
114                    0.0436064, 
115                    0.0872128, 
116                    0.1744260, 
117                    0.3488510, 
118                    0.6977020, 
119                    1.3954000, 
120                    1.9949900] 
121   
122          # Load the data. 
123          for i in range(10): 
124              # Read the peak intensities. 
125              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) 
126   
127              # Set the relaxation times. 
128              self.interpreter.relax_fit.relax_time(time=delays[i], spectrum_id=repr(i)) 
129   
130          # The actual intensities. 
131          heights = [[1.0000, 0.9714, 0.9602, 0.9626, 0.8839, 0.8327, 0.7088, 0.5098, 0.2410, 0.1116], 
132                     [1.0000, 0.9789, 0.9751, 0.9762, 0.9074, 0.8532, 0.7089, 0.5170, 0.2444, 0.1537], 
133                     [1.0000, 0.9659, 0.9580, 0.9559, 0.9325, 0.8460, 0.7187, 0.5303, 0.2954, 0.1683], 
134                     [1.0000, 0.9657, 0.9389, 0.9366, 0.9331, 0.8683, 0.7169, 0.5357, 0.2769, 0.1625], 
135                     [1.0000, 1.0060, 0.9556, 0.9456, 0.9077, 0.8411, 0.6788, 0.4558, 0.2448, 0.1569] 
136          ] 
137   
138          # Test the data. 
139          for i in range(10): 
140              for j in range(5): 
141                  self.assertEqual(cdp.mol[0].res[j].spin[0].intensities[repr(i)], heights[j][i]) 
142   
143   
144 -    def test_read_peak_list_nmrview(self): 
145          """Test the reading of an NMRView peak list.""" 
146   
147          # Create the sequence data, and name the spins. 
148          self.interpreter.residue.create(70) 
149          self.interpreter.residue.create(72) 
150          self.interpreter.spin.name(name='N') 
151   
152          # Read the peak list. 
153          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') 
154   
155          # Test the data. 
156          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], -0.1694) 
157          self.assertEqual(cdp.mol[0].res[1].spin[0].intensities.values()[0], -0.1142) 
158   
159   
160 -    def test_read_peak_list_sparky(self): 
161          """Test the reading of an Sparky peak list.""" 
162   
163          # Create the sequence data, and name the spins. 
164          self.interpreter.residue.create(3) 
165          self.interpreter.residue.create(4) 
166          self.interpreter.residue.create(5) 
167          self.interpreter.residue.create(6) 
168          self.interpreter.spin.name(name='N') 
169   
170          # Read the peak list. 
171          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') 
172   
173          # Test the data. 
174          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], 6262) 
175          self.assertEqual(cdp.mol[0].res[1].spin[0].intensities.values()[0], 148614) 
176          self.assertEqual(cdp.mol[0].res[2].spin[0].intensities.values()[0], 166842) 
177          self.assertEqual(cdp.mol[0].res[3].spin[0].intensities.values()[0], 128690) 
178   
179   
180 -    def test_read_peak_list_xeasy(self): 
181          """Test the reading of an XEasy peak list.""" 
182   
183          # Create the sequence data, and name the spins. 
184          self.interpreter.residue.create(15) 
185          self.interpreter.residue.create(21) 
186          self.interpreter.residue.create(22) 
187          self.interpreter.residue.create(29) 
188          self.interpreter.residue.create(52) 
189          self.interpreter.residue.create(69) 
190          self.interpreter.residue.create(70) 
191          self.interpreter.residue.create(73) 
192          self.interpreter.residue.create(79) 
193          self.interpreter.residue.create(84) 
194          self.interpreter.residue.create(87) 
195          self.interpreter.residue.create(95) 
196          self.interpreter.residue.create(96) 
197          self.interpreter.residue.create(100) 
198          self.interpreter.residue.create(104) 
199          self.interpreter.residue.create(107) 
200          self.interpreter.residue.create(110) 
201          self.interpreter.residue.create(112) 
202          self.interpreter.residue.create(120) 
203          self.interpreter.residue.create(141) 
204          self.interpreter.residue.create(165) 
205          self.interpreter.spin.name(name='N') 
206   
207          # Read the peak list. 
208          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') 
209   
210          # Test the data. 
211          self.assertEqual(cdp.mol[0].res[ 0].spin[0].intensities.values()[0], 9.714e+03) 
212          self.assertEqual(cdp.mol[0].res[ 1].spin[0].intensities.values()[0], 7.919e+03) 
213          self.assertEqual(cdp.mol[0].res[ 2].spin[0].intensities.values()[0], 1.356e+04) 
214          self.assertEqual(cdp.mol[0].res[ 3].spin[0].intensities.values()[0], 9.884e+03) 
215          self.assertEqual(cdp.mol[0].res[ 4].spin[0].intensities.values()[0], 2.041e+04) 
216          self.assertEqual(cdp.mol[0].res[ 5].spin[0].intensities.values()[0], 9.305e+03) 
217          self.assertEqual(cdp.mol[0].res[ 6].spin[0].intensities.values()[0], 3.154e+04) 
218          self.assertEqual(cdp.mol[0].res[ 7].spin[0].intensities.values()[0], 9.180e+03) 
219          self.assertEqual(cdp.mol[0].res[ 9].spin[0].intensities.values()[0], 1.104e+04) 
220          self.assertEqual(cdp.mol[0].res[10].spin[0].intensities.values()[0], 7.680e+03) 
221          self.assertEqual(cdp.mol[0].res[11].spin[0].intensities.values()[0], 5.206e+03) 
222          self.assertEqual(cdp.mol[0].res[12].spin[0].intensities.values()[0], 2.863e+04) 
223          self.assertEqual(cdp.mol[0].res[14].spin[0].intensities.values()[0], 9.271e+03) 
224          self.assertEqual(cdp.mol[0].res[15].spin[0].intensities.values()[0], 7.919e+03) 
225          self.assertEqual(cdp.mol[0].res[16].spin[0].intensities.values()[0], 9.962e+03) 
226          self.assertEqual(cdp.mol[0].res[17].spin[0].intensities.values()[0], 1.260e+04) 
227          self.assertEqual(cdp.mol[0].res[18].spin[0].intensities.values()[0], 1.545e+04) 
228          self.assertEqual(cdp.mol[0].res[19].spin[0].intensities.values()[0], 1.963e+04) 
229          self.assertEqual(cdp.mol[0].res[20].spin[0].intensities.values()[0], 1.918e+04) 
230   
231   
232 -    def test_read_peak_list_xeasy_2(self): 
233          """Test the reading of an XEasy peak list (2).""" 
234   
235          # Create the sequence data, and name the spins. 
236          self.interpreter.residue.create(79) 
237          self.interpreter.spin.name(name='NE1') 
238   
239          # Read the peak list. 
240          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') 
241   
242          # Test the data. 
243          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], 1.532e+04) 
244   
245   
246 -    def test_read_peak_list_xeasy_3(self): 
247          """Test the reading of an XEasy peak list (3).""" 
248   
249          # Create the sequence data, and name the spins. 
250          self.interpreter.residue.create(100) 
251          self.interpreter.spin.name(name='C') 
252   
253          # Read the peak list. 
254          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') 
255   
256          # Test the data. 
257          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], 6.877e+03) 
258   
259   
260 -    def test_read_peak_list_xeasy_4(self): 
261          """Test the reading of an XEasy peak list (4).""" 
262   
263          # Create the sequence data, and name the spins. 
264          self.interpreter.residue.create(107) 
265          self.interpreter.spin.name(name='C') 
266   
267          # Read the peak list. 
268          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') 
269   
270          # Test the data. 
271          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], 7.123e+03) 
272