Source Code for Module test_suite.unit_tests._lib._structure._internal.test_object

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 2  #                                                                             # 
 3  # Copyright (C) 2015 Edward d'Auvergne                                        # 
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 5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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21   
22  # relax module imports. 
23  from lib.structure.internal import object 
24  from test_suite.unit_tests.base_classes import UnitTestCase 
25   
26   
27 -class Test_object(UnitTestCase): 
28      """Unit tests for the lib.structure.internal.object internal structural object module.""" 
29   
30 -    def test_add_atom_sort(self): 
31          """Test for automated atom sequence sorting of the add_atom() method.""" 
32   
33          # Initialise a structural object and add some atoms. 
34          struct = object.Internal() 
35   
36          # Create three molecules 'X', 'Y', and 'Z' with some connected atoms. 
37          struct.add_atom(atom_name='A', res_name='UNK', res_num=1, mol_name='X', pos=[1., 0., -1.], element='S', sort=True) 
38          struct.add_atom(atom_name='A', res_name='UNK', res_num=1, mol_name='Y', pos=[0., 0., 0.], element='S', sort=True) 
39          struct.add_atom(atom_name='A', res_name='UNK', res_num=1, mol_name='Z', pos=[-1., 0., 1.], element='S', sort=True) 
40          struct.add_atom(atom_name='A', res_name='UNK', res_num=3, mol_name='X', pos=[1., 2., -1.], element='S', sort=True) 
41          struct.add_atom(atom_name='A', res_name='UNK', res_num=3, mol_name='Y', pos=[0., 2., 0.], element='S', sort=True) 
42          struct.add_atom(atom_name='A', res_name='UNK', res_num=3, mol_name='Z', pos=[-1., 2., 1.], element='S', sort=True) 
43          struct.connect_atom(mol_name='X', index1=0, index2=1) 
44          struct.connect_atom(mol_name='Y', index1=0, index2=1) 
45          struct.connect_atom(mol_name='Z', index1=0, index2=1) 
46          struct.add_atom(atom_name='A', res_name='UNK', res_num=2, mol_name='X', pos=[1., 20., -1.], element='S', sort=True) 
47          struct.add_atom(atom_name='A', res_name='UNK', res_num=2, mol_name='Y', pos=[0., 20., 0.], element='S', sort=True) 
48          struct.add_atom(atom_name='A', res_name='UNK', res_num=2, mol_name='Z', pos=[-1., 20., 1.], element='S', sort=True) 
49   
50          # The sorted data. 
51          data = [[ 
52              ['A', 'UNK', 1, [1., 0., -1.], 'S', [2]], 
53              ['A', 'UNK', 2, [1., 20., -1.], 'S', []], 
54              ['A', 'UNK', 3, [1., 2., -1.], 'S', [0]] 
55          ], [ 
56              ['A', 'UNK', 1, [0., 0., 0.], 'S', [2]], 
57              ['A', 'UNK', 2, [0., 20., 0.], 'S', []], 
58              ['A', 'UNK', 3, [0., 2., 0.], 'S', [0]] 
59          ], [ 
60              ['A', 'UNK', 1, [-1., 0., 1.], 'S', [2]], 
61              ['A', 'UNK', 2, [-1., 20., 1.], 'S', []], 
62              ['A', 'UNK', 3, [-1., 2., 1.], 'S', [0]] 
63          ]] 
64          mol_names = ['X', 'Y', 'Z'] 
65   
66          # Test the object. 
67          self.assertEqual(len(struct.structural_data), 1) 
68          for i in range(len(struct.structural_data[0].mol)): 
69              # Alias. 
70              mol = struct.structural_data[0].mol[i] 
71   
72              # Check the molecule data. 
73              self.assertEqual(mol.mol_name, mol_names[i]) 
74   
75              # Loop over the atoms. 
76              for j in range(len(mol.atom_name)): 
77                  self.assertEqual(mol.atom_name[j], data[i][j][0]) 
78                  self.assertEqual(mol.res_name[j], data[i][j][1]) 
79                  self.assertEqual(mol.res_num[j], data[i][j][2]) 
80                  self.assertEqual(mol.x[j], data[i][j][3][0]) 
81                  self.assertEqual(mol.y[j], data[i][j][3][1]) 
82                  self.assertEqual(mol.z[j], data[i][j][3][2]) 
83                  self.assertEqual(mol.element[j], data[i][j][4]) 
84                  self.assertEqual(mol.bonded[j], data[i][j][5]) 
85