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Package test_suite :: Package system_tests :: Module sequence
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Source Code for Module test_suite.system_tests.sequence

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006-2015 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2013-2014 Troels E. Linnet                                    # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 16  # GNU General Public License for more details.                                # 
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 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from os import sep 
 25   
 26  # relax module imports. 
 27  from data_store import Relax_data_store; ds = Relax_data_store() 
 28  from pipe_control.mol_res_spin import spin_loop 
 29  from status import Status; status = Status() 
 30  from test_suite.system_tests.base_classes import SystemTestCase 
 31   
 32   

 33 -class Sequence(SystemTestCase): 

 34      """Class for testing the sequence functions.""" 
 35   

 36 -    def setUp(self): 

 37          """Set up for all the functional tests.""" 
 38   
 39          # Create the data pipe. 
 40          self.interpreter.pipe.create('mf', 'mf') 

 41   
 42   

 43 -    def test_bug_23372_read_csv(self): 

 44          """Catch U{bug #23372<https://web.archive.org/web/https://gna.org/bugs/?23372>}, the sequence.read failure with CSV files.""" 
 45   
 46          # Load the sequence. 
 47          self.interpreter.sequence.read('Sam.csv', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', res_num_col=1, sep=',') 
 48   
 49          # Check the sequence. 
 50          seq = [":330", ":331"] 
 51          i = 0 
 52          self.assertEqual(len(cdp.mol[0].res), 2) 
 53          for spin, spin_id in spin_loop(return_id=True): 
 54              self.assertEqual(spin_id, seq[i]) 
 55              i += 1 

 56   
 57   

 59          """Load all aspartic acid atoms from the single residue in a loaded protein PDB file.""" 
 60   
 61          # Read the PDB file. 
 62          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) 
 63   
 64          # Load all the ASP atoms (1 molecule, 1 ASP residue, and all atoms). 
 65          self.interpreter.structure.load_spins(spin_id=':ASP') 
 66   
 67          # Test some of the sequence. 
 68          self.assertEqual(len(cdp.mol), 1) 
 69          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
 70          self.assertEqual(len(cdp.mol[0].res), 1) 
 71   
 72          # 1st residue. 
 73          self.assertEqual(cdp.mol[0].res[0].num, 7) 
 74          self.assertEqual(cdp.mol[0].res[0].name, 'ASP') 
 75          self.assertEqual(len(cdp.mol[0].res[0].spin), 12) 
 76          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 78) 
 77          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
 78          self.assertEqual(cdp.mol[0].res[0].spin[1].num, 79) 
 79          self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'H') 
 80          self.assertEqual(cdp.mol[0].res[0].spin[2].num, 80) 
 81          self.assertEqual(cdp.mol[0].res[0].spin[2].name, 'CA') 
 82          self.assertEqual(cdp.mol[0].res[0].spin[3].num, 81) 
 83          self.assertEqual(cdp.mol[0].res[0].spin[3].name, 'HA') 
 84          self.assertEqual(cdp.mol[0].res[0].spin[4].num, 82) 
 85          self.assertEqual(cdp.mol[0].res[0].spin[4].name, 'CB') 
 86          self.assertEqual(cdp.mol[0].res[0].spin[5].num, 83) 
 87          self.assertEqual(cdp.mol[0].res[0].spin[5].name, '1HB') 
 88          self.assertEqual(cdp.mol[0].res[0].spin[6].num, 84) 
 89          self.assertEqual(cdp.mol[0].res[0].spin[6].name, '2HB') 
 90          self.assertEqual(cdp.mol[0].res[0].spin[7].num, 85) 
 91          self.assertEqual(cdp.mol[0].res[0].spin[7].name, 'CG') 
 92          self.assertEqual(cdp.mol[0].res[0].spin[8].num, 86) 
 93          self.assertEqual(cdp.mol[0].res[0].spin[8].name, 'OD1') 
 94          self.assertEqual(cdp.mol[0].res[0].spin[9].num, 87) 
 95          self.assertEqual(cdp.mol[0].res[0].spin[9].name, 'OD2') 
 96          self.assertEqual(cdp.mol[0].res[0].spin[10].num, 88) 
 97          self.assertEqual(cdp.mol[0].res[0].spin[10].name, 'C') 
 98          self.assertEqual(cdp.mol[0].res[0].spin[11].num, 89) 
 99          self.assertEqual(cdp.mol[0].res[0].spin[11].name, 'O') 

100   
101   

103          """Load the glycine backbone amide N and Ca spins from a loaded protein PDB file.""" 
104   
105          # Read the PDB file. 
106          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) 
107   
108          # Generate the sequence of nitrogen spins (1 molecule, all GLY residues, and only N spins). 
109          self.interpreter.structure.load_spins(spin_id=':GLY@N') 
110   
111          # Append to the sequence the alpha carbon spins (1 molecule, all GLY residues, and only Ca spins). 
112          self.interpreter.structure.load_spins(spin_id=':GLY@CA') 
113   
114          # Test some of the sequence. 
115          self.assertEqual(len(cdp.mol), 1) 
116          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
117          self.assertEqual(len(cdp.mol[0].res), 3) 
118   
119          # 1st residue. 
120          self.assertEqual(cdp.mol[0].res[0].num, 1) 
121          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
122          self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 
123          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
124          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
125          self.assertEqual(cdp.mol[0].res[0].spin[1].num, 2) 
126          self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'CA') 
127   
128          # 2nd residue. 
129          self.assertEqual(cdp.mol[0].res[1].num, 4) 
130          self.assertEqual(cdp.mol[0].res[1].name, 'GLY') 
131          self.assertEqual(len(cdp.mol[0].res[1].spin), 2) 
132          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 43) 
133          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
134          self.assertEqual(cdp.mol[0].res[1].spin[1].num, 45) 
135          self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'CA') 
136   
137          # 3rd residue. 
138          self.assertEqual(cdp.mol[0].res[2].num, 12) 
139          self.assertEqual(cdp.mol[0].res[2].name, 'GLY') 
140          self.assertEqual(len(cdp.mol[0].res[2].spin), 2) 
141          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 144) 
142          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
143          self.assertEqual(cdp.mol[0].res[2].spin[1].num, 146) 
144          self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'CA') 

145   
146   

148          """Load the glycine backbone amide N spins from a loaded protein PDB file.""" 
149   
150          # Read the PDB file. 
151          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) 
152   
153          # Generate the sequence (1 molecule, all GLY residues, and only N spins). 
154          self.interpreter.structure.load_spins(spin_id=':GLY@N') 
155   
156          # Test some of the sequence. 
157          self.assertEqual(len(cdp.mol), 1) 
158          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
159          self.assertEqual(len(cdp.mol[0].res), 3) 
160   
161          # 1st residue. 
162          self.assertEqual(cdp.mol[0].res[0].num, 1) 
163          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
164          self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 
165          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
166          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
167   
168          # 2nd residue. 
169          self.assertEqual(cdp.mol[0].res[1].num, 4) 
170          self.assertEqual(cdp.mol[0].res[1].name, 'GLY') 
171          self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 
172          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 43) 
173          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
174   
175          # 3rd residue. 
176          self.assertEqual(cdp.mol[0].res[2].num, 12) 
177          self.assertEqual(cdp.mol[0].res[2].name, 'GLY') 
178          self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 
179          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 144) 
180          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 

181   
182   

184          """Load the protein backbone amide N spins from a loaded PDB file.""" 
185   
186          # Read the PDB file. 
187          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) 
188   
189          # Generate the sequence (1 molecule, all residues, and only N spins). 
190          self.interpreter.structure.load_spins(spin_id='@N') 
191   
192          # Test some of the sequence. 
193          self.assertEqual(len(cdp.mol), 1) 
194          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
195          self.assertEqual(len(cdp.mol[0].res), 12) 
196   
197          # 1st residue. 
198          self.assertEqual(cdp.mol[0].res[0].num, 1) 
199          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
200          self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 
201          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
202          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
203   
204          # 2nd residue. 
205          self.assertEqual(cdp.mol[0].res[1].num, 2) 
206          self.assertEqual(cdp.mol[0].res[1].name, 'PRO') 
207          self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 
208          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 10) 
209          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
210   
211          # 3rd residue. 
212          self.assertEqual(cdp.mol[0].res[2].num, 3) 
213          self.assertEqual(cdp.mol[0].res[2].name, 'LEU') 
214          self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 
215          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 24) 
216          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
217   
218          # 4th residue. 
219          self.assertEqual(cdp.mol[0].res[3].num, 4) 
220          self.assertEqual(cdp.mol[0].res[3].name, 'GLY') 
221          self.assertEqual(len(cdp.mol[0].res[3].spin), 1) 
222          self.assertEqual(cdp.mol[0].res[3].spin[0].num, 43) 
223          self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') 
224   
225          # 5th residue. 
226          self.assertEqual(cdp.mol[0].res[4].num, 5) 
227          self.assertEqual(cdp.mol[0].res[4].name, 'SER') 
228          self.assertEqual(len(cdp.mol[0].res[4].spin), 1) 
229          self.assertEqual(cdp.mol[0].res[4].spin[0].num, 50) 
230          self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N') 
231   
232          # 6th residue. 
233          self.assertEqual(cdp.mol[0].res[5].num, 6) 
234          self.assertEqual(cdp.mol[0].res[5].name, 'MET') 
235          self.assertEqual(len(cdp.mol[0].res[5].spin), 1) 
236          self.assertEqual(cdp.mol[0].res[5].spin[0].num, 61) 
237          self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') 
238   
239          # 7th residue. 
240          self.assertEqual(cdp.mol[0].res[6].num, 7) 
241          self.assertEqual(cdp.mol[0].res[6].name, 'ASP') 
242          self.assertEqual(len(cdp.mol[0].res[6].spin), 1) 
243          self.assertEqual(cdp.mol[0].res[6].spin[0].num, 78) 
244          self.assertEqual(cdp.mol[0].res[6].spin[0].name, 'N') 
245   
246          # 8th residue. 
247          self.assertEqual(cdp.mol[0].res[7].num, 8) 
248          self.assertEqual(cdp.mol[0].res[7].name, 'SER') 
249          self.assertEqual(len(cdp.mol[0].res[7].spin), 1) 
250          self.assertEqual(cdp.mol[0].res[7].spin[0].num, 90) 
251          self.assertEqual(cdp.mol[0].res[7].spin[0].name, 'N') 
252   
253          # 9th residue. 
254          self.assertEqual(cdp.mol[0].res[8].num, 9) 
255          self.assertEqual(cdp.mol[0].res[8].name, 'PRO') 
256          self.assertEqual(len(cdp.mol[0].res[8].spin), 1) 
257          self.assertEqual(cdp.mol[0].res[8].spin[0].num, 101) 
258          self.assertEqual(cdp.mol[0].res[8].spin[0].name, 'N') 
259   
260          # 10th residue. 
261          self.assertEqual(cdp.mol[0].res[9].num, 10) 
262          self.assertEqual(cdp.mol[0].res[9].name, 'PRO') 
263          self.assertEqual(len(cdp.mol[0].res[9].spin), 1) 
264          self.assertEqual(cdp.mol[0].res[9].spin[0].num, 115) 
265          self.assertEqual(cdp.mol[0].res[9].spin[0].name, 'N') 
266   
267          # 11th residue. 
268          self.assertEqual(cdp.mol[0].res[10].num, 11) 
269          self.assertEqual(cdp.mol[0].res[10].name, 'GLU') 
270          self.assertEqual(len(cdp.mol[0].res[10].spin), 1) 
271          self.assertEqual(cdp.mol[0].res[10].spin[0].num, 129) 
272          self.assertEqual(cdp.mol[0].res[10].spin[0].name, 'N') 
273   
274          # 12th residue. 
275          self.assertEqual(cdp.mol[0].res[11].num, 12) 
276          self.assertEqual(cdp.mol[0].res[11].name, 'GLY') 
277          self.assertEqual(len(cdp.mol[0].res[11].spin), 1) 
278          self.assertEqual(cdp.mol[0].res[11].spin[0].num, 144) 
279          self.assertEqual(cdp.mol[0].res[11].spin[0].name, 'N') 

280   
281   

282 -    def test_read(self): 

283          """The sequence.read() test.""" 
284   
285          # Read the sequence. 
286          self.interpreter.sequence.read(file='test_seq', dir=status.install_path + sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2) 
287           
288          # Test some of the sequence. 
289          self.assertEqual(len(cdp.mol), 1) 
290          self.assertEqual(cdp.mol[0].name, None) 
291          self.assertEqual(len(cdp.mol[0].res), 5) 
292   
293          # 1st residue. 
294          self.assertEqual(cdp.mol[0].res[0].num, -2) 
295          self.assertEqual(cdp.mol[0].res[0].name, 'Gly') 
296          self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 
297          self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 
298          self.assertEqual(cdp.mol[0].res[0].spin[0].name, None) 

299   

300 -    def test_sequence_copy(self): 

301          """Test the sequence.copy user function.""" 
302   
303          # First create some spins. 
304          self.interpreter.spin.create(spin_name='A', spin_num=1, res_num=1) 
305          self.interpreter.spin.create(spin_name='A', spin_num=2, res_num=1) 
306          self.interpreter.spin.create(spin_name='B', spin_num=3, res_num=1) 
307          self.interpreter.spin.create(spin_name='B2', spin_num=4, res_num=1) 
308          self.interpreter.spin.create(spin_name='A', spin_num=1, res_num=2) 
309          self.interpreter.spin.create(spin_name='A', spin_num=2, res_num=2) 
310          self.interpreter.spin.create(spin_name='B', spin_num=3, res_num=2) 
311          self.interpreter.spin.create(spin_name='B2', spin_num=4, res_num=2) 
312   
313          # Create a new data pipe to copy to. 
314          self.interpreter.pipe.create('seq copy test', 'mf') 
315   
316          # Copy the sequence. 
317          self.interpreter.sequence.copy(pipe_from='mf') 
318   
319          # Alias the data pipes. 
320          pipe1 = ds['mf'] 
321          pipe2 = ds['seq copy test'] 
322   
323          # Check the residue count. 
324          self.assertEqual(len(pipe1.mol[0].res), len(pipe2.mol[0].res)) 
325   
326          # Check the spin counts. 
327          for i in range(len(pipe1.mol[0].res)): 
328              self.assertEqual(len(pipe1.mol[0].res[i].spin), len(pipe2.mol[0].res[i].spin)) 

329

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