Source Code for Module test_suite.system_tests.interatomic

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  2  #                                                                             # 
  3  # Copyright (C) 2012-2013 Edward d'Auvergne                                        # 
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 21   
 22  # Module docstring. 
 23  """System tests of the interatomic data container operations.""" 
 24   
 25   
 26  # Python module imports. 
 27  from os import sep 
 28   
 29  # relax module imports. 
 30  from data_store import Relax_data_store; ds = Relax_data_store() 
 31  from lib.errors import RelaxNoSpinError 
 32  from status import Status; status = Status() 
 33  from test_suite.system_tests.base_classes import SystemTestCase 
 34   
 35   
 36 -class Interatomic(SystemTestCase): 
 37      """Class for testing the interatomic functions.""" 
 38   
 39 -    def test_copy(self): 
 40          """Test the operation of the interatom.copy user function.""" 
 41   
 42          # Create an initial data pipe. 
 43          self.interpreter.pipe.create(pipe_name="orig", pipe_type='N-state') 
 44   
 45          # Create some sequence data. 
 46          self.interpreter.molecule.create(mol_name='Test mol') 
 47          self.interpreter.residue.create(mol_name='Test mol', res_name='His', res_num=1) 
 48          self.interpreter.residue.create(mol_name='Test mol', res_name='His', res_num=2) 
 49          self.interpreter.spin.create(res_num=1, spin_name='N') 
 50          self.interpreter.spin.create(res_num=1, spin_name='H') 
 51          self.interpreter.spin.create(res_num=2, spin_name='N') 
 52          self.interpreter.spin.create(res_num=2, spin_name='H') 
 53   
 54          # Define the interatomic interaction. 
 55          self.interpreter.interatom.define(spin_id1=':1@N', spin_id2=':1@H', direct_bond=False) 
 56          self.interpreter.interatom.define(spin_id1=':2@N', spin_id2=':2@H', direct_bond=False) 
 57   
 58          # Add some test data. 
 59          cdp.interatomic[0].x = 1 
 60          cdp.interatomic[1].y = 2 
 61   
 62          # Create a new data pipe to copy the data to. 
 63          self.interpreter.pipe.create(pipe_name="new", pipe_type='N-state') 
 64   
 65          # Copy the data. 
 66          self.interpreter.sequence.copy(pipe_from='orig') 
 67          self.interpreter.interatom.copy(pipe_from='orig', spin_id1=':2@N', spin_id2=':2@H') 
 68          self.interpreter.interatom.copy(pipe_from='orig', spin_id1=':1@H', spin_id2=':1@N') 
 69   
 70          # Create a new data pipe to copy the data to. 
 71          self.interpreter.pipe.create(pipe_name="new 2", pipe_type='N-state') 
 72   
 73          # Copy the data. 
 74          try: 
 75              self.interpreter.interatom.copy(pipe_from='orig') 
 76          except RelaxNoSpinError: 
 77              print("Correct RelaxError encountered.") 
 78          self.interpreter.sequence.copy(pipe_from='orig') 
 79          self.interpreter.interatom.copy(pipe_from='orig') 
 80   
 81          # Loop over the two new pipes. 
 82          interatom_index = [[0, 1], [1, 0]] 
 83          pipes = ['new', 'new 2'] 
 84          for i in range(len(pipes)): 
 85              # Switch pipes. 
 86              self.interpreter.pipe.switch(pipes[i]) 
 87   
 88              # Check the sequence data. 
 89              self.assertEqual(cdp.mol[0].name, 'Test mol') 
 90              self.assertEqual(cdp.mol[0].res[0].name, 'His') 
 91              self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
 92              self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'H') 
 93              self.assertEqual(cdp.mol[0].res[1].name, 'His') 
 94              self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
 95              self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'H') 
 96   
 97              # Check the interatomic data. 
 98              self.assertEqual(cdp.interatomic[interatom_index[i][0]].spin_id1, '#Test mol:2@N') 
 99              self.assertEqual(cdp.interatomic[interatom_index[i][0]].spin_id2, '#Test mol:2@H') 
100              self.assertEqual(cdp.interatomic[interatom_index[i][0]].y, 2) 
101              self.assertEqual(cdp.interatomic[interatom_index[i][1]].spin_id1, '#Test mol:1@N') 
102              self.assertEqual(cdp.interatomic[interatom_index[i][1]].spin_id2, '#Test mol:1@H') 
103              self.assertEqual(cdp.interatomic[interatom_index[i][1]].x, 1) 
104   
105   
106 -    def test_manipulation(self): 
107          """Test the manipulation of interatomic data containers.""" 
108   
109          # Execute the script. 
110          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'interatomic_tests.py') 
111   
112          # The data. 
113          select = [True, False] + [True]*3 + [False]*2 + [True]*5 + [False]*2 + [True, False] 
114   
115          # Check the data. 
116          self.assertEqual(len(cdp.interatomic), 16) 
117          for i in range(len(cdp.interatomic)): 
118              # A printout to know where the problem is. 
119              print("Checking container:  %-30s %-30s" % (cdp.interatomic[i].spin_id1, cdp.interatomic[i].spin_id2)) 
120   
121              # The container checks. 
122              self.assertEqual(cdp.interatomic[i].select, select[i]) 
123