Source Code for Module test_suite.system_tests.unit_vectors

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2011 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
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  7  # relax is free software; you can redistribute it and/or modify               # 
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 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax is distributed in the hope that it will be useful,                    # 
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 15  # GNU General Public License for more details.                                # 
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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from os import sep 
 25   
 26  # relax module imports. 
 27  from base_classes import SystemTestCase 
 28  from data import Relax_data_store; ds = Relax_data_store() 
 29  import dep_check 
 30  from status import Status; status = Status() 
 31   
 32   
 33 -class Unit_vectors(SystemTestCase): 
 34      """Class for testing the calculation of unit vectors.""" 
 35   
 36 -    def __init__(self, methodName='runTest'): 
 37          """Skip scientific Python tests if not installed. 
 38   
 39          @keyword methodName:    The name of the test. 
 40          @type methodName:       str 
 41          """ 
 42   
 43          # Execute the base class method. 
 44          super(Unit_vectors, self).__init__(methodName) 
 45   
 46   
 47 -    def setUp(self): 
 48          """Set up for all the functional tests.""" 
 49   
 50          # Create the data pipe. 
 51          self.interpreter.pipe.create('mf', 'mf') 
 52   
 53   
 54 -    def test_calc_unit_vectors1(self): 
 55          """Load the PDB file using the Scientific parser and calculate the XH unit vectors.""" 
 56   
 57          # Read the PDB file. 
 58          self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures', read_model=1, parser='scientific') 
 59   
 60          # Load the spins. 
 61          self.interpreter.structure.load_spins(spin_id='@N') 
 62   
 63          # Calculate the unit vectors. 
 64          self.interpreter.structure.vectors(attached='H') 
 65   
 66          # Leu 3. 
 67          self.assert_(hasattr(cdp.mol[0].res[2].spin[0], 'xh_vect')) 
 68          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 28) 
 69          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
 70          self.assertNotEqual(cdp.mol[0].res[2].spin[0].xh_vect, None) 
 71          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[0], 0.40899187) 
 72          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[1], -0.80574458) 
 73          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[2], 0.42837054) 
 74   
 75   
 76 -    def test_calc_unit_vectors2(self): 
 77          """Load the PDB file using the Scientific parser and calculate the XH unit vectors (with spin numbers removed).""" 
 78   
 79          # Read the PDB file. 
 80          self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures', read_model=1, parser='scientific') 
 81   
 82          # Load the spins. 
 83          self.interpreter.structure.load_spins(spin_id='@N') 
 84   
 85          # Remove the spin numbers. 
 86          self.interpreter.spin.number(force=True) 
 87   
 88          # Calculate the unit vectors. 
 89          self.interpreter.structure.vectors(attached='H') 
 90   
 91          # Leu 3. 
 92          self.assert_(hasattr(cdp.mol[0].res[2].spin[0], 'xh_vect')) 
 93          self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 
 94          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
 95          self.assertNotEqual(cdp.mol[0].res[2].spin[0].xh_vect, None) 
 96          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[0], 0.40899187) 
 97          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[1], -0.80574458) 
 98          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[2], 0.42837054) 
 99   
100   
101 -    def test_calc_unit_vectors3(self): 
102          """Load the PDB file using the internal parser and calculate the XH unit vectors.""" 
103   
104          # Read the PDB file. 
105          self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures', read_model=1, parser='internal') 
106   
107          # Load the spins. 
108          self.interpreter.structure.load_spins(spin_id='@N') 
109   
110          # Calculate the unit vectors. 
111          self.interpreter.structure.vectors(attached='H') 
112   
113          # Leu 3. 
114          self.assert_(hasattr(cdp.mol[0].res[2].spin[0], 'xh_vect')) 
115          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 28) 
116          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
117          self.assertNotEqual(cdp.mol[0].res[2].spin[0].xh_vect, None) 
118          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[0], 0.40899187) 
119          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[1], -0.80574458) 
120          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[2], 0.42837054) 
121   
122   
123 -    def test_calc_unit_vectors4(self): 
124          """Load the PDB file using the internal parser and calculate the XH unit vectors from it (with spin numbers removed).""" 
125   
126          # Read the PDB file. 
127          self.interpreter.structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures', read_model=1, parser='internal') 
128   
129          # Load the spins. 
130          self.interpreter.structure.load_spins(spin_id='@N') 
131   
132          # Remove the spin numbers. 
133          self.interpreter.spin.number(force=True) 
134   
135          # Calculate the unit vectors. 
136          self.interpreter.structure.vectors(attached='H') 
137   
138          # Leu 3. 
139          self.assert_(hasattr(cdp.mol[0].res[2].spin[0], 'xh_vect')) 
140          self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 
141          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
142          self.assertNotEqual(cdp.mol[0].res[2].spin[0].xh_vect, None) 
143          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[0], 0.40899187) 
144          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[1], -0.80574458) 
145          self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].xh_vect[2], 0.42837054) 
146