Source Code for Module test_suite.unit_tests.molecule_testing_base

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  3  # Copyright (C) 2007-2008,2012 Edward d'Auvergne                              # 
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 21   
 22  # relax module imports. 
 23  from data_store import Relax_data_store; ds = Relax_data_store() 
 24  from pipe_control.mol_res_spin import copy_residue, create_residue, metadata_update 
 25  from pipe_control import pipes 
 26  from lib.errors import RelaxError, RelaxMultiMolIDError, RelaxNoPipeError, RelaxResSelectDisallowError, RelaxSpinSelectDisallowError 
 27  from test_suite.unit_tests.base_classes import UnitTestCase 
 28   
 29   
 30 -class Molecule_base_class(UnitTestCase): 
 31      """Testing base class for 'prompt.molecule' and corresponding 'pipe_control.mol_spin_res' fns. 
 32   
 33      This base class also contains many shared unit tests. 
 34      """ 
 35   
 36 -    def setUp(self): 
 37          """Set up for all the molecule unit tests.""" 
 38   
 39          # Add a data pipe to the data store. 
 40          ds.add(pipe_name='orig', pipe_type='mf') 
 41   
 42          # Add a second data pipe for copying tests. 
 43          ds.add(pipe_name='test', pipe_type='mf') 
 44   
 45          # Set the current data pipe to 'orig'. 
 46          pipes.switch('orig') 
 47   
 48   
 49 -    def setup_data(self): 
 50          """Function for setting up some data for the unit tests.""" 
 51   
 52          # Get the data pipe. 
 53          dp = pipes.get_pipe('orig') 
 54   
 55          # Create the first residue and add some data to its spin container. 
 56          create_residue(1, 'Ala') 
 57          dp.mol[0].res[0].spin[0].num = 111 
 58          dp.mol[0].res[0].spin[0].x = 1 
 59          dp.mol[0].name = 'Old mol' 
 60   
 61          # Create a second molecule. 
 62          dp.mol.add_item('New mol') 
 63   
 64          # Copy the residue to the new molecule. 
 65          copy_residue(res_from=':1', res_to='#New mol') 
 66          copy_residue(res_from='#Old mol:1', res_to='#New mol:5') 
 67   
 68          # Change the first residue's data. 
 69          dp.mol[0].res[0].spin[0].num = 222 
 70          dp.mol[0].res[0].spin[0].x = 2 
 71   
 72          # Update the metadata. 
 73          metadata_update() 
 74   
 75   
 76 -    def test_copy_molecule_between_pipes(self): 
 77          """Test the copying of the molecule data between different data pipes. 
 78   
 79          The function tested is both pipe_control.mol_res_spin.copy_molecule() and 
 80          prompt.molecule.copy(). 
 81          """ 
 82   
 83          # Get the data pipes. 
 84          dp = pipes.get_pipe('orig') 
 85          dp_test = pipes.get_pipe('test') 
 86   
 87          # Create the first molecule and residue and add some data to its spin container. 
 88          self.molecule_fns.create('Old mol') 
 89          create_residue(1, 'Ala') 
 90          dp.mol[0].res[0].spin[0].num = 111 
 91          dp.mol[0].res[0].spin[0].x = 1 
 92   
 93          # Update the metadata. 
 94          metadata_update() 
 95   
 96          # Copy the molecule to the second data pipe. 
 97          self.molecule_fns.copy(mol_from='#Old mol', pipe_to='test') 
 98          self.molecule_fns.copy(pipe_from='orig', mol_from='#Old mol', pipe_to='test', mol_to='#New mol') 
 99   
100          # Change the first molecule's data. 
101          dp.mol[0].res[0].spin[0].num = 222 
102          dp.mol[0].res[0].spin[0].x = 2 
103   
104          # Update the metadata. 
105          metadata_update() 
106   
107          # Test the original molecule. 
108          self.assertEqual(dp.mol[0].name, 'Old mol') 
109          self.assertEqual(dp.mol[0].res[0].num, 1) 
110          self.assertEqual(dp.mol[0].res[0].name, 'Ala') 
111          self.assertEqual(dp.mol[0].res[0].spin[0].num, 222) 
112          self.assertEqual(dp.mol[0].res[0].spin[0].x, 2) 
113   
114          # Test the new molecule. 
115          self.assertEqual(dp_test.mol[0].name, 'Old mol') 
116          self.assertEqual(dp_test.mol[0].res[0].num, 1) 
117          self.assertEqual(dp_test.mol[0].res[0].name, 'Ala') 
118          self.assertEqual(dp_test.mol[0].res[0].spin[0].num, 111) 
119          self.assertEqual(dp_test.mol[0].res[0].spin[0].x, 1) 
120   
121          # Test the second new molecule. 
122          self.assertEqual(dp_test.mol[1].name, 'New mol') 
123          self.assertEqual(dp_test.mol[1].res[0].num, 1) 
124          self.assertEqual(dp_test.mol[1].res[0].name, 'Ala') 
125          self.assertEqual(dp_test.mol[1].res[0].spin[0].num, 111) 
126          self.assertEqual(dp_test.mol[1].res[0].spin[0].x, 1) 
127   
128   
129 -    def test_copy_molecule_between_pipes_fail_no_pipe(self): 
130          """Test the failure of copying of the molecule data between different data pipes. 
131   
132          The function tested is both pipe_control.mol_res_spin.copy_molecule() and 
133          prompt.molecule.copy(). 
134          """ 
135   
136          # Get the data pipe. 
137          dp = pipes.get_pipe('orig') 
138   
139          # Create the first molecule and residue and add some data to its spin container. 
140          self.molecule_fns.create('Old mol') 
141          create_residue(1, 'Ala') 
142          dp.mol[0].res[0].spin[0].num = 111 
143          dp.mol[0].res[0].spin[0].x = 1 
144   
145          # Update the metadata. 
146          metadata_update() 
147   
148          # Copy the molecule to the second data pipe. 
149          self.assertRaises(RelaxNoPipeError, self.molecule_fns.copy, mol_from='#Old mol', pipe_to='test2') 
150   
151   
152 -    def test_copy_molecule_within_pipe(self): 
153          """Test the copying of the molecule data within a single data pipe. 
154   
155          The function tested is both pipe_control.mol_res_spin.copy_molecule() and 
156          prompt.molecule.copy(). 
157          """ 
158   
159          # Get the data pipe. 
160          dp = pipes.get_pipe('orig') 
161   
162          # Create the first molecule and residue and add some data to its spin container. 
163          self.molecule_fns.create('Old mol') 
164          create_residue(1, 'Ala') 
165          dp.mol[0].res[0].spin[0].num = 111 
166          dp.mol[0].res[0].spin[0].x = 1 
167   
168          # Update the metadata. 
169          metadata_update() 
170   
171          # Copy the molecule a few times. 
172          self.molecule_fns.copy(mol_from='#Old mol', mol_to='#2') 
173          self.molecule_fns.copy(mol_from='#Old mol', pipe_to='orig', mol_to='#3') 
174   
175          # Change the first molecule's data. 
176          dp.mol[0].res[0].spin[0].num = 222 
177          dp.mol[0].res[0].spin[0].x = 2 
178   
179          # Update the metadata. 
180          metadata_update() 
181   
182          # Copy the molecule once more. 
183          self.molecule_fns.copy(mol_from='#Old mol', mol_to='#4') 
184   
185          # Test the original molecule. 
186          self.assertEqual(dp.mol[0].name, 'Old mol') 
187          self.assertEqual(dp.mol[0].res[0].num, 1) 
188          self.assertEqual(dp.mol[0].res[0].name, 'Ala') 
189          self.assertEqual(dp.mol[0].res[0].spin[0].num, 222) 
190          self.assertEqual(dp.mol[0].res[0].spin[0].x, 2) 
191   
192          # Test the new molecule 2. 
193          self.assertEqual(dp.mol[1].name, '2') 
194          self.assertEqual(dp.mol[1].res[0].num, 1) 
195          self.assertEqual(dp.mol[1].res[0].name, 'Ala') 
196          self.assertEqual(dp.mol[1].res[0].spin[0].num, 111) 
197          self.assertEqual(dp.mol[1].res[0].spin[0].x, 1) 
198   
199          # Test the new molecule 3. 
200          self.assertEqual(dp.mol[2].name, '3') 
201          self.assertEqual(dp.mol[2].res[0].num, 1) 
202          self.assertEqual(dp.mol[2].res[0].name, 'Ala') 
203          self.assertEqual(dp.mol[2].res[0].spin[0].num, 111) 
204          self.assertEqual(dp.mol[2].res[0].spin[0].x, 1) 
205   
206          # Test the new molecule 4. 
207          self.assertEqual(dp.mol[3].name, '4') 
208          self.assertEqual(dp.mol[3].res[0].num, 1) 
209          self.assertEqual(dp.mol[3].res[0].name, 'Ala') 
210          self.assertEqual(dp.mol[3].res[0].spin[0].num, 222) 
211          self.assertEqual(dp.mol[3].res[0].spin[0].x, 2) 
212   
213   
214 -    def test_copy_molecule_within_pipe_fail(self): 
215          """Test the failure of the copying of the molecule data within a molecule. 
216   
217          The function tested is both pipe_control.mol_res_spin.copy_molecule() and 
218          prompt.molecule.copy(). 
219          """ 
220   
221          # Create a few molecules. 
222          self.molecule_fns.create('GST') 
223          self.molecule_fns.create('GB1') 
224   
225          # Copy a non-existent molecule (MBP). 
226          self.assertRaises(RelaxError, self.molecule_fns.copy, mol_from='#MBP', mol_to='#IL4') 
227   
228          # Copy a molecule to one which already exists. 
229          self.assertRaises(RelaxError, self.molecule_fns.copy, mol_from='#GST', mol_to='#GB1') 
230   
231   
232 -    def test_create_molecule(self): 
233          """Test the creation of a molecule data structure. 
234   
235          The function tested is both pipe_control.mol_res_spin.create_molecule() and 
236          prompt.molecule.create(). 
237          """ 
238   
239          # Get the data pipe. 
240          dp = pipes.get_pipe('orig') 
241   
242          # Create a few new molecules. 
243          self.molecule_fns.create('Ap4Aase') 
244          self.molecule_fns.create('ATP') 
245          self.molecule_fns.create(mol_name='MgF4') 
246   
247          # Test that the molecule names are correct. 
248          self.assertEqual(dp.mol[0].name, 'Ap4Aase') 
249          self.assertEqual(dp.mol[1].name, 'ATP') 
250          self.assertEqual(dp.mol[2].name, 'MgF4') 
251   
252   
253 -    def test_create_molecule_fail(self): 
254          """Test the failure of molecule creation by supplying two molecules with the same name. 
255   
256          The function tested is both pipe_control.mol_res_spin.create_molecule() and 
257          prompt.molecule.create(). 
258          """ 
259   
260          # Create the first molecule. 
261          self.molecule_fns.create('CaM') 
262   
263          # Assert that a RelaxError occurs when the next added molecule has the same name as the first. 
264          self.assertRaises(RelaxError, self.molecule_fns.create, 'CaM') 
265   
266   
267 -    def test_delete_molecule(self): 
268          """Test molecule deletion. 
269   
270          The function tested is both pipe_control.mol_res_spin.delete_molecule() and 
271          prompt.molecule.delete(). 
272          """ 
273   
274          # Set up some data. 
275          self.setup_data() 
276   
277          # Get the data pipe. 
278          dp = pipes.get_pipe('orig') 
279   
280          # Delete the first molecule. 
281          self.molecule_fns.delete(mol_id='#Old mol') 
282   
283          # Test that the first molecule is now 'New mol'. 
284          self.assertEqual(dp.mol[0].name, 'New mol') 
285          self.assertEqual(dp.mol[0].res[0].num, 1) 
286          self.assertEqual(dp.mol[0].res[0].name, 'Ala') 
287          self.assertEqual(dp.mol[0].res[0].spin[0].num, 111) 
288          self.assertTrue(hasattr(dp.mol[0].res[0].spin[0], 'x')) 
289          self.assertEqual(dp.mol[0].res[1].num, 5) 
290          self.assertEqual(dp.mol[0].res[1].name, 'Ala') 
291          self.assertEqual(dp.mol[0].res[1].spin[0].num, 111) 
292          self.assertTrue(hasattr(dp.mol[0].res[1].spin[0], 'x')) 
293   
294   
295 -    def test_delete_molecule_all(self): 
296          """Test the deletion of all molecules. 
297   
298          The function tested is both pipe_control.mol_res_spin.delete_molecule() and 
299          prompt.molecule.delete(). 
300          """ 
301   
302          # Get the data pipe. 
303          dp = pipes.get_pipe('orig') 
304   
305          # Set up some data. 
306          self.setup_data() 
307   
308          # Delete all molecules. 
309          self.molecule_fns.delete(mol_id='#Old mol') 
310          self.molecule_fns.delete(mol_id='#New mol') 
311   
312          # Test that the first molecule defaults back to the empty container. 
313          self.assertEqual(dp.mol[0].name, None) 
314          self.assertEqual(dp.mol[0].res[0].num, None) 
315          self.assertEqual(dp.mol[0].res[0].name, None) 
316          self.assertEqual(dp.mol[0].res[0].spin[0].num, None) 
317          self.assertEqual(dp.mol[0].res[0].spin[0].name, None) 
318   
319   
320 -    def test_delete_molecule_fail(self): 
321          """Test the failure of molecule deletion when a residue or spin id is supplied. 
322   
323          The function tested is both pipe_control.mol_res_spin.delete_molecule() and 
324          prompt.molecule.delete(). 
325          """ 
326   
327          # Supply a spin id. 
328          self.assertRaises(RelaxSpinSelectDisallowError, self.molecule_fns.delete, mol_id='@2') 
329   
330          # Supply a residue id. 
331          self.assertRaises(RelaxResSelectDisallowError, self.molecule_fns.delete, mol_id=':1') 
332   
333   
334 -    def test_display_molecule(self): 
335          """Test the display of molecular information. 
336   
337          The function tested is both pipe_control.mol_res_spin.display_molecule() and 
338          prompt.molecule.display(). 
339          """ 
340   
341          # Set up some data. 
342          self.setup_data() 
343   
344          # The following should all work without error. 
345          self.molecule_fns.display() 
346          self.molecule_fns.display('#Old mol') 
347          self.molecule_fns.display(mol_id='#New mol') 
348   
349   
350 -    def test_display_molecule_fail(self): 
351          """Test the failure of the display of molecule information. 
352   
353          The function tested is both pipe_control.mol_res_spin.display_molecule() and 
354          prompt.molecule.display(). 
355          """ 
356   
357          # Set up some data. 
358          self.setup_data() 
359   
360          # The following should fail. 
361          self.assertRaises(RelaxSpinSelectDisallowError, self.molecule_fns.display, '@N') 
362          self.assertRaises(RelaxResSelectDisallowError, self.molecule_fns.display, ':1') 
363   
364   
365 -    def test_name_molecule(self): 
366          """Test the renaming of a molecule. 
367   
368          The function tested is both pipe_control.mol_res_spin.name_molecule() and 
369          prompt.molecule.name(). 
370          """ 
371   
372          # Set up some data. 
373          self.setup_data() 
374   
375          # Get the data pipe. 
376          dp = pipes.get_pipe('orig') 
377   
378          # Rename the molecule. 
379          self.molecule_fns.name(mol_id='#New mol', name='K', force=True) 
380   
381          # Test that the molecule has been renamed. 
382          self.assertEqual(dp.mol[1].name, 'K') 
383   
384   
385 -    def test_name_molecule_fail(self): 
386          """Test the failure of naming a molecule when a residue or spin id is given. 
387   
388          The function tested is both pipe_control.mol_res_spin.name_molecule() and 
389          prompt.molecule.name(). 
390          """ 
391   
392          # Try naming using a spin id. 
393          self.assertRaises(RelaxSpinSelectDisallowError, self.molecule_fns.name, mol_id='@111', name='K') 
394   
395          # Try naming using a residue id. 
396          self.assertRaises(RelaxResSelectDisallowError, self.molecule_fns.name, mol_id=':1', name='K') 
397   
398   
399 -    def test_name_molecule_many_fail(self): 
400          """Test the failure of the naming of multiple molecules to the same name. 
401   
402          The function tested is both pipe_control.mol_res_spin.name_molecule() and 
403          prompt.molecule.name(). 
404          """ 
405   
406          # Set up some data. 
407          self.setup_data() 
408   
409          # Test for the failure. 
410          self.assertRaises(RelaxMultiMolIDError, self.molecule_fns.name, mol_id='#Old mol,New mol', name='K') 
411