Source Code for Module test_suite.system_tests.unit_vectors

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2012 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from os import sep 
 24   
 25  # relax module imports. 
 26  from data import Relax_data_store; ds = Relax_data_store() 
 27  import dep_check 
 28  from status import Status; status = Status() 
 29  from test_suite.system_tests.base_classes import SystemTestCase 
 30   
 31   
 32 -class Unit_vectors(SystemTestCase): 
 33      """Class for testing the calculation of unit vectors.""" 
 34   
 35 -    def __init__(self, methodName='runTest'): 
 36          """Skip scientific Python tests if not installed. 
 37   
 38          @keyword methodName:    The name of the test. 
 39          @type methodName:       str 
 40          """ 
 41   
 42          # Execute the base class method. 
 43          super(Unit_vectors, self).__init__(methodName) 
 44   
 45   
 46 -    def setUp(self): 
 47          """Set up for all the functional tests.""" 
 48   
 49          # Create the data pipe. 
 50          self.interpreter.pipe.create('mf', 'mf') 
 51   
 52   
 53 -    def test_calc_unit_vectors1(self): 
 54          """Load the PDB file using the Scientific parser and calculate the XH unit vectors.""" 
 55   
 56          # Read the PDB file. 
 57          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') 
 58   
 59          # Load the spins. 
 60          self.interpreter.structure.load_spins(spin_id='@N') 
 61          self.interpreter.structure.load_spins(spin_id='@H') 
 62   
 63          # Calculate the unit vectors. 
 64          self.interpreter.dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True) 
 65          self.interpreter.dipole_pair.unit_vectors() 
 66   
 67          # Leu 3. 
 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.assert_(hasattr(cdp.interatomic[0], 'vector')) 
 71          self.assertNotEqual(cdp.interatomic[0].vector, None) 
 72          self.assertAlmostEqual(cdp.interatomic[0].vector[0], 0.40899187) 
 73          self.assertAlmostEqual(cdp.interatomic[0].vector[1], -0.80574458) 
 74          self.assertAlmostEqual(cdp.interatomic[0].vector[2], 0.42837054) 
 75   
 76   
 77 -    def test_calc_unit_vectors2(self): 
 78          """Load the PDB file using the Scientific parser and calculate the XH unit vectors (with spin numbers removed).""" 
 79   
 80          # Read the PDB file. 
 81          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') 
 82   
 83          # Load the spins. 
 84          self.interpreter.structure.load_spins(spin_id='@N') 
 85          self.interpreter.structure.load_spins(spin_id='@H') 
 86   
 87          # Remove the spin numbers. 
 88          self.interpreter.spin.number(force=True) 
 89   
 90          # Calculate the unit vectors. 
 91          self.interpreter.dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True) 
 92          self.interpreter.dipole_pair.unit_vectors() 
 93   
 94          # Leu 3. 
 95          self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 
 96          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
 97          self.assert_(hasattr(cdp.interatomic[0], 'vector')) 
 98          self.assertNotEqual(cdp.interatomic[0].vector, None) 
 99          self.assertAlmostEqual(cdp.interatomic[0].vector[0], 0.40899187) 
100          self.assertAlmostEqual(cdp.interatomic[0].vector[1], -0.80574458) 
101          self.assertAlmostEqual(cdp.interatomic[0].vector[2], 0.42837054) 
102   
103   
104 -    def test_calc_unit_vectors3(self): 
105          """Load the PDB file using the internal parser and calculate the XH unit vectors.""" 
106   
107          # Read the PDB file. 
108          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') 
109   
110          # Load the spins. 
111          self.interpreter.structure.load_spins(spin_id='@N') 
112          self.interpreter.structure.load_spins(spin_id='@H') 
113   
114          # Calculate the unit vectors. 
115          self.interpreter.dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True) 
116          self.interpreter.dipole_pair.unit_vectors() 
117   
118          # Leu 3. 
119          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 28) 
120          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
121          self.assert_(hasattr(cdp.interatomic[0], 'vector')) 
122          self.assertNotEqual(cdp.interatomic[0].vector, None) 
123          self.assertAlmostEqual(cdp.interatomic[0].vector[0], 0.40899187) 
124          self.assertAlmostEqual(cdp.interatomic[0].vector[1], -0.80574458) 
125          self.assertAlmostEqual(cdp.interatomic[0].vector[2], 0.42837054) 
126   
127   
128 -    def test_calc_unit_vectors4(self): 
129          """Load the PDB file using the internal parser and calculate the XH unit vectors from it (with spin numbers removed).""" 
130   
131          # Read the PDB file. 
132          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') 
133   
134          # Load the spins. 
135          self.interpreter.structure.load_spins(spin_id='@N') 
136          self.interpreter.structure.load_spins(spin_id='@H') 
137   
138          # Remove the spin numbers. 
139          self.interpreter.spin.number(force=True) 
140   
141          # Calculate the unit vectors. 
142          self.interpreter.dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True) 
143          self.interpreter.dipole_pair.unit_vectors() 
144   
145          # Leu 3. 
146          self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) 
147          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
148          self.assert_(hasattr(cdp.interatomic[0], 'vector')) 
149          self.assertNotEqual(cdp.interatomic[0].vector, None) 
150          self.assertAlmostEqual(cdp.interatomic[0].vector[0], 0.40899187) 
151          self.assertAlmostEqual(cdp.interatomic[0].vector[1], -0.80574458) 
152          self.assertAlmostEqual(cdp.interatomic[0].vector[2], 0.42837054) 
153