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  # Copyright (C) 2013 Troels E. Linnet                                         # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  8  #                                                                             # 
  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Python module imports. 
 25  from os import sep 
 26   
 27  # relax module imports. 
 28  from data_store import Relax_data_store; ds = Relax_data_store() 
 29  import dep_check 
 30  from pipe_control.mol_res_spin import spin_loop 
 31  from status import Status; status = Status() 
 32  from test_suite.system_tests.base_classes import SystemTestCase 
 33   
 34   
 35 -class Peak_lists(SystemTestCase): 
 36      """TestCase class for the functional tests for the support of different peak intensity files.""" 
 37   
 38 -    def __init__(self, methodName='runTest'): 
 39          """Skip the tests if the C modules are non-functional. 
 40   
 41          @keyword methodName:    The name of the test. 
 42          @type methodName:       str 
 43          """ 
 44   
 45          # Execute the base class method. 
 46          super(Peak_lists, self).__init__(methodName) 
 47   
 48          # Missing module. 
 49          if not dep_check.C_module_exp_fn and methodName in ['test_bug_17276_peak_lists', 'test_bug_20873_peak_lists', 'test_ccpn_analysis']: 
 50              # Store in the status object. 
 51              status.skipped_tests.append([methodName, 'Relax curve-fitting C module', self._skip_type]) 
 52   
 53   
 54 -    def setUp(self): 
 55          """Set up for all the functional tests.""" 
 56   
 57          # Create a data pipe. 
 58          self.interpreter.pipe.create('mf', 'mf') 
 59   
 60   
 61 -    def test_bug_17276_peak_lists(self): 
 62          """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.""" 
 63   
 64          # Execute the script. 
 65          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bug_17276_peak_lists.py') 
 66   
 67   
 68 -    def test_bug_20873_peak_lists(self): 
 69          """Test catching U{bug #20873<https://web.archive.org/web/https://gna.org/bugs/?20873>}, the custom peak intensity reading with a list of spectrum_ids submitted by Troels E. Linnet.""" 
 70   
 71          # The path to the files. 
 72          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists' 
 73   
 74          # First create a data pipe. 
 75          self.interpreter.pipe.create(pipe_name='origin rx', pipe_type='relax_fit', bundle='rx') 
 76   
 77          # Load the spin systems. 
 78          self.interpreter.sequence.read(file='test.seq', dir=path, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None) 
 79   
 80          # Load the intensities. 
 81          self.interpreter.spectrum.read_intensities(file='test.seq', dir=path, spectrum_id=['2', '0'], dim=1, int_method='height', int_col=[6, 7], spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None) 
 82   
 83          # The peak intensities. 
 84          data_2 = [337765.90000000002, 1697771.0, 867389.80000000005, 2339480.0, 2574062.0, 1609356.0, 2179341.0, 1563795.0, 1535896.0, 3578841.0] 
 85          data_0 = [636244.59999999998, 3015788.0, 1726064.0, 4039142.0, 4313824.0, 2927111.0, 4067343.0, 2921316.0, 3005234.0, 6352595.0] 
 86   
 87          # Data checks. 
 88          for i in range(len(cdp.mol[0].res)): 
 89              # Alias the spin. 
 90              spin = cdp.mol[0].res[i].spin[0] 
 91   
 92              # The intensities. 
 93              self.assertEqual(spin.intensities['0'], data_0[i]) 
 94              self.assertEqual(spin.intensities['2'], data_2[i]) 
 95   
 96   
 97 -    def test_ccpn_analysis(self): 
 98          """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.""" 
 99   
100          # Execute the script. 
101          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'peak_lists'+sep+'ccpn_analysis.py') 
102   
103          # Spectrum names. 
104          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'] 
105   
106          # Relaxation times (in seconds). 
107          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] 
108   
109          # Check the spectrum IDs and relaxation times. 
110          for i in range(len(times)): 
111              self.assertEqual(cdp.spectrum_ids[i], names[i]) 
112              self.assertEqual(cdp.relax_times[names[i]], times[i]) 
113   
114          # The peak heights. 
115          heights = [ 
116                  [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], 
117                  [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] 
118          ] 
119   
120          # Check the heights. 
121          for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 
122              # The data. 
123              if res_num == 1501: 
124                  index = 0 
125              elif res_num == 1504: 
126                  index = 1 
127   
128              # No data. 
129              else: 
130                  # There should be no intensity data. 
131                  self.assert_(not hasattr(spin, 'intensities')) 
132   
133                  # Do not perform the height checks. 
134                  continue 
135   
136              # Check the data. 
137              self.assert_(hasattr(spin, 'intensities')) 
138   
139              # Check the values. 
140              for i in range(len(times)): 
141                  self.assertEqual(spin.intensities[names[i]], heights[index][i]) 
142   
143   
144 -    def test_read_peak_list_generic(self): 
145          """Test the reading of a generic peak intensity list.""" 
146   
147          # Create the sequence data, and name the spins. 
148          self.interpreter.residue.create(20, 'GLY') 
149          self.interpreter.residue.create(23, 'ALA') 
150          self.interpreter.residue.create(34, 'CYS') 
151          self.interpreter.residue.create(35, 'MET') 
152          self.interpreter.residue.create(36, 'LYS') 
153          self.interpreter.spin.name(name='N') 
154   
155          # Relaxation delays. 
156          delays = [0.0109016, 
157                    0.0218032, 
158                    0.0436064, 
159                    0.0436064, 
160                    0.0872128, 
161                    0.1744260, 
162                    0.3488510, 
163                    0.6977020, 
164                    1.3954000, 
165                    1.9949900] 
166   
167          # Load the data. 
168          for i in range(10): 
169              # Read the peak intensities. 
170              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) 
171   
172              # Set the relaxation times. 
173              self.interpreter.relax_fit.relax_time(time=delays[i], spectrum_id=repr(i)) 
174   
175          # The actual intensities. 
176          heights = [[1.0000, 0.9714, 0.9602, 0.9626, 0.8839, 0.8327, 0.7088, 0.5098, 0.2410, 0.1116], 
177                     [1.0000, 0.9789, 0.9751, 0.9762, 0.9074, 0.8532, 0.7089, 0.5170, 0.2444, 0.1537], 
178                     [1.0000, 0.9659, 0.9580, 0.9559, 0.9325, 0.8460, 0.7187, 0.5303, 0.2954, 0.1683], 
179                     [1.0000, 0.9657, 0.9389, 0.9366, 0.9331, 0.8683, 0.7169, 0.5357, 0.2769, 0.1625], 
180                     [1.0000, 1.0060, 0.9556, 0.9456, 0.9077, 0.8411, 0.6788, 0.4558, 0.2448, 0.1569] 
181          ] 
182   
183          # Test the data. 
184          for i in range(10): 
185              for j in range(5): 
186                  self.assertEqual(cdp.mol[0].res[j].spin[0].intensities[repr(i)], heights[j][i]) 
187   
188   
189 -    def test_read_peak_list_nmrview(self): 
190          """Test the reading of an NMRView peak list.""" 
191   
192          # Create the sequence data, and name the spins. 
193          self.interpreter.residue.create(70) 
194          self.interpreter.residue.create(72) 
195          self.interpreter.spin.name(name='N') 
196   
197          # Read the peak list. 
198          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') 
199   
200          # Test the data. 
201          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], -0.1694) 
202          self.assertEqual(list(cdp.mol[0].res[1].spin[0].intensities.values())[0], -0.1142) 
203   
204   
205 -    def test_read_peak_list_NMRPipe_seriesTab(self): 
206          """Test the reading of an NMRPipe seriesTab peak list.""" 
207   
208          # Create the sequence data, and name the spins. 
209          self.interpreter.residue.create(res_num = 62) 
210          self.interpreter.spin.name(name='NE1', spin_id=':62') 
211          self.interpreter.residue.create(res_num = 10) 
212          self.interpreter.spin.name(name='N', spin_id=':10') 
213          self.interpreter.residue.create(res_num = 6) 
214          self.interpreter.spin.name(name='N', spin_id=':6') 
215   
216          # Read the peak list. 
217          self.interpreter.spectrum.read_intensities(file="seriesTab.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='point sum') 
218   
219          # Test the data. 
220          self.assertEqual(cdp.mol[0].res[0].spin[0].intensities['test'], +1.851056e+06) 
221          self.assertEqual(cdp.mol[0].res[1].spin[0].intensities['test'], +3.224387e+05) 
222          self.assertEqual(cdp.mol[0].res[2].spin[0].intensities['test'], +1.479366e+06) 
223   
224   
225 -    def test_read_peak_list_NMRPipe_seriesTab_multi(self): 
226          """Test the reading of an NMRPipe seriesTab peak list.""" 
227   
228          # Create the sequence data, and name the spins. 
229          self.interpreter.residue.create(res_num = 2) 
230          self.interpreter.spin.name(name='N', spin_id=':2') 
231          self.interpreter.residue.create(res_num = 3) 
232          self.interpreter.spin.name(name='N', spin_id=':3') 
233          self.interpreter.residue.create(res_num = 4) 
234          self.interpreter.spin.name(name='N', spin_id=':4') 
235          self.interpreter.residue.create(res_num = 5) 
236          self.interpreter.spin.name(name='N', spin_id=':5') 
237          self.interpreter.residue.create(res_num = 6) 
238          self.interpreter.spin.name(name='N', spin_id=':6') 
239   
240          # Read the peak list. 
241          self.interpreter.spectrum.read_intensities(file="seriesTab_multi.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='auto', int_method='point sum') 
242   
243          # Test the data. 
244          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A0'], 1179448.0) 
245          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A0'], 4407306.0) 
246          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A0'], 3480382.0) 
247          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A0'], 4306408.0) 
248          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A0'], 3454030.0) 
249          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A1'], 1411799.256) 
250          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A1'], 5263645.5558) 
251          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A1'], 4159404.5282) 
252          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A1'], 5147018.8416) 
253          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A1'], 4132401.492) 
254          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A2'], 1411209.532) 
255          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A2'], 5262764.0946) 
256          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A2'], 4159404.5282) 
257          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A2'], 5147018.8416) 
258          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A2'], 4133092.298) 
259          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A3'], 1408496.8016) 
260          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A3'], 5264527.017) 
261          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A3'], 4162536.872) 
262          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A3'], 5146588.2008) 
263          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A3'], 4134128.507) 
264          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A4'], 1411327.4768) 
265          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A4'], 5258797.5192) 
266          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A4'], 4163232.9484) 
267          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A4'], 5162952.5512) 
268          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A4'], 4119966.984) 
269          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A5'], 1414040.2072) 
270          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A5'], 5275104.5514) 
271          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A5'], 4150703.5732) 
272          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A5'], 5151755.8904) 
273          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A5'], 4128947.462) 
274          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A6'], 1406727.6296) 
275          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A6'], 5265849.2088) 
276          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A6'], 4158360.4136) 
277          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A6'], 5149172.0456) 
278          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A6'], 4130674.477) 
279          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A7'], 1415691.4344) 
280          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A7'], 5267171.4006) 
281          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A7'], 4144438.8856) 
282          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A7'], 5137114.1032) 
283          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A7'], 4127911.253) 
284          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A8'], 1401184.224) 
285          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A8'], 5264527.017) 
286          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A8'], 4149659.4586) 
287          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A8'], 5144004.356) 
288          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A8'], 4133783.104) 
289          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].intensities['Z_A9'], 1415573.4896) 
290          self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].intensities['Z_A9'], 5261882.6334) 
291          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].intensities['Z_A9'], 4138870.2744) 
292          self.assertAlmostEqual(cdp.mol[0].res[3].spin[0].intensities['Z_A9'], 5123764.2384) 
293          self.assertAlmostEqual(cdp.mol[0].res[4].spin[0].intensities['Z_A9'], 4128602.059) 
294   
295   
296 -    def test_read_peak_list_sparky(self): 
297          """Test the reading of an Sparky peak list.""" 
298   
299          # Create the sequence data, and name the spins. 
300          self.interpreter.residue.create(3) 
301          self.interpreter.residue.create(4) 
302          self.interpreter.residue.create(5) 
303          self.interpreter.residue.create(6) 
304          self.interpreter.spin.name(name='N') 
305   
306          # Read the peak list. 
307          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') 
308   
309          # Test the data. 
310          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 6262) 
311          self.assertEqual(list(cdp.mol[0].res[1].spin[0].intensities.values())[0], 148614) 
312          self.assertEqual(list(cdp.mol[0].res[2].spin[0].intensities.values())[0], 166842) 
313          self.assertEqual(list(cdp.mol[0].res[3].spin[0].intensities.values())[0], 128690) 
314   
315   
316 -    def test_read_peak_list_xeasy(self): 
317          """Test the reading of an XEasy peak list.""" 
318   
319          # Create the sequence data, and name the spins. 
320          self.interpreter.residue.create(15) 
321          self.interpreter.residue.create(21) 
322          self.interpreter.residue.create(22) 
323          self.interpreter.residue.create(29) 
324          self.interpreter.residue.create(52) 
325          self.interpreter.residue.create(69) 
326          self.interpreter.residue.create(70) 
327          self.interpreter.residue.create(73) 
328          self.interpreter.residue.create(79) 
329          self.interpreter.residue.create(84) 
330          self.interpreter.residue.create(87) 
331          self.interpreter.residue.create(95) 
332          self.interpreter.residue.create(96) 
333          self.interpreter.residue.create(100) 
334          self.interpreter.residue.create(104) 
335          self.interpreter.residue.create(107) 
336          self.interpreter.residue.create(110) 
337          self.interpreter.residue.create(112) 
338          self.interpreter.residue.create(120) 
339          self.interpreter.residue.create(141) 
340          self.interpreter.residue.create(165) 
341          self.interpreter.spin.name(name='N') 
342   
343          # Read the peak list. 
344          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') 
345   
346          # Test the data. 
347          self.assertEqual(list(cdp.mol[0].res[ 0].spin[0].intensities.values())[0], 9.714e+03) 
348          self.assertEqual(list(cdp.mol[0].res[ 1].spin[0].intensities.values())[0], 7.919e+03) 
349          self.assertEqual(list(cdp.mol[0].res[ 2].spin[0].intensities.values())[0], 1.356e+04) 
350          self.assertEqual(list(cdp.mol[0].res[ 3].spin[0].intensities.values())[0], 9.884e+03) 
351          self.assertEqual(list(cdp.mol[0].res[ 4].spin[0].intensities.values())[0], 2.041e+04) 
352          self.assertEqual(list(cdp.mol[0].res[ 5].spin[0].intensities.values())[0], 9.305e+03) 
353          self.assertEqual(list(cdp.mol[0].res[ 6].spin[0].intensities.values())[0], 3.154e+04) 
354          self.assertEqual(list(cdp.mol[0].res[ 7].spin[0].intensities.values())[0], 9.180e+03) 
355          self.assertEqual(list(cdp.mol[0].res[ 9].spin[0].intensities.values())[0], 1.104e+04) 
356          self.assertEqual(list(cdp.mol[0].res[10].spin[0].intensities.values())[0], 7.680e+03) 
357          self.assertEqual(list(cdp.mol[0].res[11].spin[0].intensities.values())[0], 5.206e+03) 
358          self.assertEqual(list(cdp.mol[0].res[12].spin[0].intensities.values())[0], 2.863e+04) 
359          self.assertEqual(list(cdp.mol[0].res[14].spin[0].intensities.values())[0], 9.271e+03) 
360          self.assertEqual(list(cdp.mol[0].res[15].spin[0].intensities.values())[0], 7.919e+03) 
361          self.assertEqual(list(cdp.mol[0].res[16].spin[0].intensities.values())[0], 9.962e+03) 
362          self.assertEqual(list(cdp.mol[0].res[17].spin[0].intensities.values())[0], 1.260e+04) 
363          self.assertEqual(list(cdp.mol[0].res[18].spin[0].intensities.values())[0], 1.545e+04) 
364          self.assertEqual(list(cdp.mol[0].res[19].spin[0].intensities.values())[0], 1.963e+04) 
365          self.assertEqual(list(cdp.mol[0].res[20].spin[0].intensities.values())[0], 1.918e+04) 
366   
367   
368 -    def test_read_peak_list_xeasy_2(self): 
369          """Test the reading of an XEasy peak list (2).""" 
370   
371          # Create the sequence data, and name the spins. 
372          self.interpreter.residue.create(79) 
373          self.interpreter.spin.name(name='NE1') 
374   
375          # Read the peak list. 
376          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') 
377   
378          # Test the data. 
379          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 1.532e+04) 
380   
381   
382 -    def test_read_peak_list_xeasy_3(self): 
383          """Test the reading of an XEasy peak list (3).""" 
384   
385          # Create the sequence data, and name the spins. 
386          self.interpreter.residue.create(100) 
387          self.interpreter.spin.name(name='C') 
388   
389          # Read the peak list. 
390          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') 
391   
392          # Test the data. 
393          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 6.877e+03) 
394   
395   
396 -    def test_read_peak_list_xeasy_4(self): 
397          """Test the reading of an XEasy peak list (4).""" 
398   
399          # Create the sequence data, and name the spins. 
400          self.interpreter.residue.create(107) 
401          self.interpreter.spin.name(name='C') 
402   
403          # Read the peak list. 
404          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') 
405   
406          # Test the data. 
407          self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 7.123e+03) 
408