Source Code for Module test_suite.system_tests.chemical_shift

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013 Edward d'Auvergne                                        # 
  4  # Copyright (C) 2013 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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  8  # This program is free software: you can redistribute it and/or modify        # 
  9  # it under the terms of the GNU General Public License as published by        # 
 10  # the Free Software Foundation, either version 3 of the License, or           # 
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 13  # This program is distributed in the hope that it will be useful,             # 
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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  # Module docstring. 
 24  """The module for the system tests for chemical shift support in relax.""" 
 25   
 26   
 27  # Python module imports. 
 28  from os import sep 
 29   
 30  # relax module imports. 
 31  from pipe_control.mol_res_spin import spin_loop 
 32  from status import Status; status = Status() 
 33  from test_suite.system_tests.base_classes import SystemTestCase 
 34   
 35   
 36 -class Chemical_shift(SystemTestCase): 
 37      """System test class for checking the handling of chemical shifts.""" 
 38   
 39   
 40 -    def setUp(self): 
 41          """Set up for all the system tests.""" 
 42   
 43          # Create the data pipe. 
 44          self.interpreter.pipe.create('cs', 'mf') 
 45   
 46   
 47 -    def test_read_nmrpipe_seriestab(self): 
 48          """Test the reading of chemical shifts from an NMRPipe seriesTab peak list.""" 
 49   
 50          # Read the spins from peak list. 
 51          self.interpreter.spectrum.read_spins(file="seriesTab.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') 
 52   
 53          # Read the chemical shift from the list. 
 54          self.interpreter.chemical_shift.read(file="seriesTab.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') 
 55   
 56          # Test the data. 
 57          cs = [128.374, 127.066, 124.523] 
 58          i = 0 
 59          for spin in spin_loop(): 
 60              # Check the shift. 
 61              self.assertEqual(spin.chemical_shift, cs[i]) 
 62   
 63              # Increment the index. 
 64              i += 1 
 65   
 66   
 67 -    def test_read_nmrpipe_seriestab_multi(self): 
 68          """Test the reading of chemical shifts from an NMRPipe seriesTab peak list with multi columns.""" 
 69   
 70          # Read the spins from peak list. 
 71          self.interpreter.spectrum.read_spins(file="seriesTab_multi.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') 
 72   
 73          # Read the chemical shift from the list. 
 74          self.interpreter.chemical_shift.read(file="seriesTab_multi.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') 
 75   
 76          # Test the data. 
 77          cs = [115.994, 125.899, 123.001, 120.839, 128.998] 
 78          i = 0 
 79          for spin in spin_loop(): 
 80              # Check the shift. 
 81              self.assertEqual(spin.chemical_shift, cs[i]) 
 82   
 83              # Increment the index. 
 84              i += 1 
 85   
 86   
 87 -    def test_read_nmrview(self): 
 88          """Test the reading of chemical shifts from an NMRView peak list.""" 
 89   
 90          # Create the sequence data, and name the spins. 
 91          self.interpreter.spin.create(res_num=70, spin_name='N') 
 92          self.interpreter.spin.create(res_num=70, spin_name='HN') 
 93          self.interpreter.spin.create(res_num=72, spin_name='N') 
 94          self.interpreter.spin.create(res_num=72, spin_name='HN') 
 95   
 96          # Read the peak list. 
 97          self.interpreter.chemical_shift.read(file="cNTnC.xpk", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') 
 98   
 99          # Test the data. 
100          cs = [116.37241, 10.75274, 126.41302, 9.67752] 
101          i = 0 
102          for spin in spin_loop(): 
103              # Check the shift. 
104              self.assertEqual(spin.chemical_shift, cs[i]) 
105   
106              # Increment the index. 
107              i += 1 
108   
109   
110 -    def test_read_sparky(self): 
111          """Test the reading of chemical shifts from a Sparky peak list.""" 
112   
113          # Create the sequence data, and name the spins. 
114          for res_num in [3, 4, 5, 6, 40]: 
115              self.interpreter.spin.create(res_num=res_num, spin_name='N') 
116              self.interpreter.spin.create(res_num=res_num, spin_name='HN') 
117          self.interpreter.spin.create(res_num=40, spin_name='NE1') 
118          self.interpreter.spin.create(res_num=40, spin_name='HE1') 
119   
120          # Load the peak list. 
121          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists' 
122          self.interpreter.chemical_shift.read(file='ref_ave.list', dir=path) 
123   
124          # Test the data. 
125          cs = [122.454, 8.397, 111.978, 8.720, 115.069, 8.177, 120.910, 8.813, 123.335, 8.005, 130.204, 10.294] 
126          i = 0 
127          for spin in spin_loop(): 
128              # No data. 
129              if i > 12: 
130                  self.assertTrue(not hasattr(spin, 'chemical_shift')) 
131   
132              # Check the shift. 
133              self.assertEqual(spin.chemical_shift, cs[i]) 
134   
135              # Increment the index. 
136              i += 1 
137   
138   
139 -    def test_read_xeasy(self): 
140          """Test the reading of chemical shifts from a XEasy peak list.""" 
141   
142          # Create the sequence data, and name the spins. 
143          for res_num in [21, 96, 104, 110]: 
144              self.interpreter.spin.create(res_num=res_num, spin_name='N') 
145              self.interpreter.spin.create(res_num=res_num, spin_name='HN') 
146          self.interpreter.spin.create(res_num=79, spin_name='NE1') 
147          self.interpreter.spin.create(res_num=79, spin_name='HE1') 
148   
149          # Load the peak list. 
150          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists' 
151          self.interpreter.chemical_shift.read(file='xeasy_r1_20ms.text', dir=path) 
152   
153          # Test the data. 
154          cs = [134.221, 10.014, 118.450, 8.364, 127.582, 9.211, 129.041, 9.882, 132.592, 10.481] 
155          i = 0 
156          for spin in spin_loop(): 
157              # No data. 
158              if i > 10: 
159                  self.assertTrue(not hasattr(spin, 'chemical_shift')) 
160   
161              # Check the shift. 
162              self.assertEqual(spin.chemical_shift, cs[i]) 
163   
164              # Increment the index. 
165              i += 1 
166