Source Code for Module test_suite.system_tests.chemical_shift

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
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 10  # (at your option) any later version.                                         # 
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 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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 15  # GNU General Public License for more details.                                # 
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 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """The module for the system tests for chemical shift support in relax.""" 
 24   
 25   
 26  # Python module imports. 
 27  from os import sep 
 28   
 29  # relax module imports. 
 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 Chemical_shift(SystemTestCase): 
 36      """System test class for checking the handling of chemical shifts.""" 
 37   
 38   
 39 -    def setUp(self): 
 40          """Set up for all the system tests.""" 
 41   
 42          # Create the data pipe. 
 43          self.interpreter.pipe.create('cs', 'mf') 
 44   
 45   
 46 -    def test_read_nmrview(self): 
 47          """Test the reading of chemical shifts from an NMRView peak list.""" 
 48   
 49          # Create the sequence data, and name the spins. 
 50          self.interpreter.spin.create(res_num=70, spin_name='N') 
 51          self.interpreter.spin.create(res_num=70, spin_name='HN') 
 52          self.interpreter.spin.create(res_num=72, spin_name='N') 
 53          self.interpreter.spin.create(res_num=72, spin_name='HN') 
 54   
 55          # Read the peak list. 
 56          self.interpreter.chemical_shift.read(file="cNTnC.xpk", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') 
 57   
 58          # Test the data. 
 59          cs = [116.37241, 10.75274, 126.41302, 9.67752] 
 60          i = 0 
 61          for spin in spin_loop(): 
 62              # Check the shift. 
 63              self.assertEqual(spin.chemical_shift, cs[i]) 
 64   
 65              # Increment the index. 
 66              i += 1 
 67   
 68   
 69 -    def test_read_sparky(self): 
 70          """Test the reading of chemical shifts from a Sparky peak list.""" 
 71   
 72          # Create the sequence data, and name the spins. 
 73          for res_num in [3, 4, 5, 6, 40]: 
 74              self.interpreter.spin.create(res_num=res_num, spin_name='N') 
 75              self.interpreter.spin.create(res_num=res_num, spin_name='HN') 
 76          self.interpreter.spin.create(res_num=40, spin_name='NE1') 
 77          self.interpreter.spin.create(res_num=40, spin_name='HE1') 
 78   
 79          # Load the peak list. 
 80          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists' 
 81          self.interpreter.chemical_shift.read(file='ref_ave.list', dir=path) 
 82   
 83          # Test the data. 
 84          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] 
 85          i = 0 
 86          for spin in spin_loop(): 
 87              # No data. 
 88              if i > 12: 
 89                  self.assert_(not hasattr(spin, 'chemical_shift')) 
 90   
 91              # Check the shift. 
 92              self.assertEqual(spin.chemical_shift, cs[i]) 
 93   
 94              # Increment the index. 
 95              i += 1 
 96   
 97   
 98 -    def test_read_xeasy(self): 
 99          """Test the reading of chemical shifts from a XEasy peak list.""" 
100   
101          # Create the sequence data, and name the spins. 
102          for res_num in [21, 96, 104, 110]: 
103              self.interpreter.spin.create(res_num=res_num, spin_name='N') 
104              self.interpreter.spin.create(res_num=res_num, spin_name='HN') 
105          self.interpreter.spin.create(res_num=79, spin_name='NE1') 
106          self.interpreter.spin.create(res_num=79, spin_name='HE1') 
107   
108          # Load the peak list. 
109          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists' 
110          self.interpreter.chemical_shift.read(file='xeasy_r1_20ms.text', dir=path) 
111   
112          # Test the data. 
113          cs = [134.221, 10.014, 118.450, 8.364, 127.582, 9.211, 129.041, 9.882, 132.592, 10.481] 
114          i = 0 
115          for spin in spin_loop(): 
116              # No data. 
117              if i > 10: 
118                  self.assert_(not hasattr(spin, 'chemical_shift')) 
119   
120              # Check the shift. 
121              self.assertEqual(spin.chemical_shift, cs[i]) 
122   
123              # Increment the index. 
124              i += 1 
125