Source Code for Module test_suite.system_tests.peak_lists

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2012 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.script_exec(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.script_exec(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              # The data. 
 77              if res_num == 1501: 
 78                  index = 0 
 79              elif res_num == 1504: 
 80                  index = 1 
 81   
 82              # No data. 
 83              else: 
 84                  # There should be no intensity data. 
 85                  self.assert_(not hasattr(spin, 'intensities')) 
 86   
 87                  # Do not perform the height checks. 
 88                  continue 
 89   
 90              # Check the data. 
 91              self.assert_(hasattr(spin, 'intensities')) 
 92   
 93              # Check the values. 
 94              for i in range(len(times)): 
 95                  self.assertEqual(spin.intensities[names[i]], heights[index][i]) 
 96   
 97   
 98 -    def test_read_peak_list_generic(self): 
 99          """Test the reading of a generic peak intensity list.""" 
100   
101          # Create the sequence data, and name the spins. 
102          self.interpreter.residue.create(20, 'GLY') 
103          self.interpreter.residue.create(23, 'ALA') 
104          self.interpreter.residue.create(34, 'CYS') 
105          self.interpreter.residue.create(35, 'MET') 
106          self.interpreter.residue.create(36, 'LYS') 
107          self.interpreter.spin.name(name='N') 
108   
109          # Relaxation delays. 
110          delays = [0.0109016, 
111                    0.0218032, 
112                    0.0436064, 
113                    0.0436064, 
114                    0.0872128, 
115                    0.1744260, 
116                    0.3488510, 
117                    0.6977020, 
118                    1.3954000, 
119                    1.9949900] 
120   
121          # Load the data. 
122          for i in range(10): 
123              # Read the peak intensities. 
124              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) 
125   
126              # Set the relaxation times. 
127              self.interpreter.relax_fit.relax_time(time=delays[i], spectrum_id=repr(i)) 
128   
129          # The actual intensities. 
130          heights = [[1.0000, 0.9714, 0.9602, 0.9626, 0.8839, 0.8327, 0.7088, 0.5098, 0.2410, 0.1116], 
131                     [1.0000, 0.9789, 0.9751, 0.9762, 0.9074, 0.8532, 0.7089, 0.5170, 0.2444, 0.1537], 
132                     [1.0000, 0.9659, 0.9580, 0.9559, 0.9325, 0.8460, 0.7187, 0.5303, 0.2954, 0.1683], 
133                     [1.0000, 0.9657, 0.9389, 0.9366, 0.9331, 0.8683, 0.7169, 0.5357, 0.2769, 0.1625], 
134                     [1.0000, 1.0060, 0.9556, 0.9456, 0.9077, 0.8411, 0.6788, 0.4558, 0.2448, 0.1569] 
135          ] 
136   
137          # Test the data. 
138          for i in range(10): 
139              for j in range(5): 
140                  self.assertEqual(cdp.mol[0].res[j].spin[0].intensities[repr(i)], heights[j][i]) 
141   
142   
143 -    def test_read_peak_list_nmrview(self): 
144          """Test the reading of an NMRView peak list.""" 
145   
146          # Create the sequence data, and name the spins. 
147          self.interpreter.residue.create(70) 
148          self.interpreter.residue.create(72) 
149          self.interpreter.spin.name(name='N') 
150   
151          # Read the peak list. 
152          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') 
153   
154          # Test the data. 
155          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], -0.1694) 
156          self.assertEqual(cdp.mol[0].res[1].spin[0].intensities.values()[0], -0.1142) 
157   
158   
159 -    def test_read_peak_list_sparky(self): 
160          """Test the reading of an Sparky peak list.""" 
161   
162          # Create the sequence data, and name the spins. 
163          self.interpreter.residue.create(3) 
164          self.interpreter.residue.create(4) 
165          self.interpreter.residue.create(5) 
166          self.interpreter.residue.create(6) 
167          self.interpreter.spin.name(name='N') 
168   
169          # Read the peak list. 
170          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') 
171   
172          # Test the data. 
173          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], 6262) 
174          self.assertEqual(cdp.mol[0].res[1].spin[0].intensities.values()[0], 148614) 
175          self.assertEqual(cdp.mol[0].res[2].spin[0].intensities.values()[0], 166842) 
176          self.assertEqual(cdp.mol[0].res[3].spin[0].intensities.values()[0], 128690) 
177   
178   
179 -    def test_read_peak_list_xeasy(self): 
180          """Test the reading of an XEasy peak list.""" 
181   
182          # Create the sequence data, and name the spins. 
183          self.interpreter.residue.create(15) 
184          self.interpreter.residue.create(21) 
185          self.interpreter.residue.create(22) 
186          self.interpreter.residue.create(29) 
187          self.interpreter.residue.create(52) 
188          self.interpreter.residue.create(69) 
189          self.interpreter.residue.create(70) 
190          self.interpreter.residue.create(73) 
191          self.interpreter.residue.create(79) 
192          self.interpreter.residue.create(84) 
193          self.interpreter.residue.create(87) 
194          self.interpreter.residue.create(95) 
195          self.interpreter.residue.create(96) 
196          self.interpreter.residue.create(100) 
197          self.interpreter.residue.create(104) 
198          self.interpreter.residue.create(107) 
199          self.interpreter.residue.create(110) 
200          self.interpreter.residue.create(112) 
201          self.interpreter.residue.create(120) 
202          self.interpreter.residue.create(141) 
203          self.interpreter.residue.create(165) 
204          self.interpreter.spin.name(name='N') 
205   
206          # Read the peak list. 
207          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') 
208   
209          # Test the data. 
210          self.assertEqual(cdp.mol[0].res[ 0].spin[0].intensities.values()[0], 9.714e+03) 
211          self.assertEqual(cdp.mol[0].res[ 1].spin[0].intensities.values()[0], 7.919e+03) 
212          self.assertEqual(cdp.mol[0].res[ 2].spin[0].intensities.values()[0], 1.356e+04) 
213          self.assertEqual(cdp.mol[0].res[ 3].spin[0].intensities.values()[0], 9.884e+03) 
214          self.assertEqual(cdp.mol[0].res[ 4].spin[0].intensities.values()[0], 2.041e+04) 
215          self.assertEqual(cdp.mol[0].res[ 5].spin[0].intensities.values()[0], 9.305e+03) 
216          self.assertEqual(cdp.mol[0].res[ 6].spin[0].intensities.values()[0], 3.154e+04) 
217          self.assertEqual(cdp.mol[0].res[ 7].spin[0].intensities.values()[0], 9.180e+03) 
218          self.assertEqual(cdp.mol[0].res[ 9].spin[0].intensities.values()[0], 1.104e+04) 
219          self.assertEqual(cdp.mol[0].res[10].spin[0].intensities.values()[0], 7.680e+03) 
220          self.assertEqual(cdp.mol[0].res[11].spin[0].intensities.values()[0], 5.206e+03) 
221          self.assertEqual(cdp.mol[0].res[12].spin[0].intensities.values()[0], 2.863e+04) 
222          self.assertEqual(cdp.mol[0].res[14].spin[0].intensities.values()[0], 9.271e+03) 
223          self.assertEqual(cdp.mol[0].res[15].spin[0].intensities.values()[0], 7.919e+03) 
224          self.assertEqual(cdp.mol[0].res[16].spin[0].intensities.values()[0], 9.962e+03) 
225          self.assertEqual(cdp.mol[0].res[17].spin[0].intensities.values()[0], 1.260e+04) 
226          self.assertEqual(cdp.mol[0].res[18].spin[0].intensities.values()[0], 1.545e+04) 
227          self.assertEqual(cdp.mol[0].res[19].spin[0].intensities.values()[0], 1.963e+04) 
228          self.assertEqual(cdp.mol[0].res[20].spin[0].intensities.values()[0], 1.918e+04) 
229   
230   
231 -    def test_read_peak_list_xeasy_2(self): 
232          """Test the reading of an XEasy peak list (2).""" 
233   
234          # Create the sequence data, and name the spins. 
235          self.interpreter.residue.create(79) 
236          self.interpreter.spin.name(name='NE1') 
237   
238          # Read the peak list. 
239          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') 
240   
241          # Test the data. 
242          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], 1.532e+04) 
243   
244   
245 -    def test_read_peak_list_xeasy_3(self): 
246          """Test the reading of an XEasy peak list (3).""" 
247   
248          # Create the sequence data, and name the spins. 
249          self.interpreter.residue.create(100) 
250          self.interpreter.spin.name(name='C') 
251   
252          # Read the peak list. 
253          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') 
254   
255          # Test the data. 
256          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], 6.877e+03) 
257   
258   
259 -    def test_read_peak_list_xeasy_4(self): 
260          """Test the reading of an XEasy peak list (4).""" 
261   
262          # Create the sequence data, and name the spins. 
263          self.interpreter.residue.create(107) 
264          self.interpreter.spin.name(name='C') 
265   
266          # Read the peak list. 
267          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') 
268   
269          # Test the data. 
270          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities.values()[0], 7.123e+03) 
271