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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) 2006-2013 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
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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_store import Relax_data_store; ds = Relax_data_store() 
 27  from status import Status; status = Status() 
 28  from test_suite.system_tests.base_classes import SystemTestCase 
 29   
 30   

 31 -class Sequence(SystemTestCase): 

 32      """Class for testing the sequence functions.""" 
 33   

 34 -    def setUp(self): 

 35          """Set up for all the functional tests.""" 
 36   
 37          # Create the data pipe. 
 38          self.interpreter.pipe.create('mf', 'mf') 

 39   
 40   

 42          """Load all aspartic acid atoms from the single residue in a loaded protein PDB file.""" 
 43   
 44          # Read the PDB file. 
 45          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) 
 46   
 47          # Load all the ASP atoms (1 molecule, 1 ASP residue, and all atoms). 
 48          self.interpreter.structure.load_spins(spin_id=':ASP') 
 49   
 50          # Test some of the sequence. 
 51          self.assertEqual(len(cdp.mol), 1) 
 52          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
 53          self.assertEqual(len(cdp.mol[0].res), 1) 
 54   
 55          # 1st residue. 
 56          self.assertEqual(cdp.mol[0].res[0].num, 7) 
 57          self.assertEqual(cdp.mol[0].res[0].name, 'ASP') 
 58          self.assertEqual(len(cdp.mol[0].res[0].spin), 12) 
 59          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 78) 
 60          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
 61          self.assertEqual(cdp.mol[0].res[0].spin[1].num, 79) 
 62          self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'H') 
 63          self.assertEqual(cdp.mol[0].res[0].spin[2].num, 80) 
 64          self.assertEqual(cdp.mol[0].res[0].spin[2].name, 'CA') 
 65          self.assertEqual(cdp.mol[0].res[0].spin[3].num, 81) 
 66          self.assertEqual(cdp.mol[0].res[0].spin[3].name, 'HA') 
 67          self.assertEqual(cdp.mol[0].res[0].spin[4].num, 82) 
 68          self.assertEqual(cdp.mol[0].res[0].spin[4].name, 'CB') 
 69          self.assertEqual(cdp.mol[0].res[0].spin[5].num, 83) 
 70          self.assertEqual(cdp.mol[0].res[0].spin[5].name, '1HB') 
 71          self.assertEqual(cdp.mol[0].res[0].spin[6].num, 84) 
 72          self.assertEqual(cdp.mol[0].res[0].spin[6].name, '2HB') 
 73          self.assertEqual(cdp.mol[0].res[0].spin[7].num, 85) 
 74          self.assertEqual(cdp.mol[0].res[0].spin[7].name, 'CG') 
 75          self.assertEqual(cdp.mol[0].res[0].spin[8].num, 86) 
 76          self.assertEqual(cdp.mol[0].res[0].spin[8].name, 'OD1') 
 77          self.assertEqual(cdp.mol[0].res[0].spin[9].num, 87) 
 78          self.assertEqual(cdp.mol[0].res[0].spin[9].name, 'OD2') 
 79          self.assertEqual(cdp.mol[0].res[0].spin[10].num, 88) 
 80          self.assertEqual(cdp.mol[0].res[0].spin[10].name, 'C') 
 81          self.assertEqual(cdp.mol[0].res[0].spin[11].num, 89) 
 82          self.assertEqual(cdp.mol[0].res[0].spin[11].name, 'O') 

 83   
 84   

 86          """Load the glycine backbone amide N and Ca spins from a loaded protein PDB file.""" 
 87   
 88          # Read the PDB file. 
 89          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) 
 90   
 91          # Generate the sequence of nitrogen spins (1 molecule, all GLY residues, and only N spins). 
 92          self.interpreter.structure.load_spins(spin_id=':GLY@N') 
 93   
 94          # Append to the sequence the alpha carbon spins (1 molecule, all GLY residues, and only Ca spins). 
 95          self.interpreter.structure.load_spins(spin_id=':GLY@CA') 
 96   
 97          # Test some of the sequence. 
 98          self.assertEqual(len(cdp.mol), 1) 
 99          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
100          self.assertEqual(len(cdp.mol[0].res), 3) 
101   
102          # 1st residue. 
103          self.assertEqual(cdp.mol[0].res[0].num, 1) 
104          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
105          self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 
106          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
107          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
108          self.assertEqual(cdp.mol[0].res[0].spin[1].num, 2) 
109          self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'CA') 
110   
111          # 2nd residue. 
112          self.assertEqual(cdp.mol[0].res[1].num, 4) 
113          self.assertEqual(cdp.mol[0].res[1].name, 'GLY') 
114          self.assertEqual(len(cdp.mol[0].res[1].spin), 2) 
115          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 43) 
116          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
117          self.assertEqual(cdp.mol[0].res[1].spin[1].num, 45) 
118          self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'CA') 
119   
120          # 3rd residue. 
121          self.assertEqual(cdp.mol[0].res[2].num, 12) 
122          self.assertEqual(cdp.mol[0].res[2].name, 'GLY') 
123          self.assertEqual(len(cdp.mol[0].res[2].spin), 2) 
124          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 144) 
125          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
126          self.assertEqual(cdp.mol[0].res[2].spin[1].num, 146) 
127          self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'CA') 

128   
129   

131          """Load the glycine backbone amide N spins from a loaded protein PDB file.""" 
132   
133          # Read the PDB file. 
134          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) 
135   
136          # Generate the sequence (1 molecule, all GLY residues, and only N spins). 
137          self.interpreter.structure.load_spins(spin_id=':GLY@N') 
138   
139          # Test some of the sequence. 
140          self.assertEqual(len(cdp.mol), 1) 
141          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
142          self.assertEqual(len(cdp.mol[0].res), 3) 
143   
144          # 1st residue. 
145          self.assertEqual(cdp.mol[0].res[0].num, 1) 
146          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
147          self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 
148          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
149          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
150   
151          # 2nd residue. 
152          self.assertEqual(cdp.mol[0].res[1].num, 4) 
153          self.assertEqual(cdp.mol[0].res[1].name, 'GLY') 
154          self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 
155          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 43) 
156          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
157   
158          # 3rd residue. 
159          self.assertEqual(cdp.mol[0].res[2].num, 12) 
160          self.assertEqual(cdp.mol[0].res[2].name, 'GLY') 
161          self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 
162          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 144) 
163          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 

164   
165   

167          """Load the protein backbone amide N spins from a loaded PDB file.""" 
168   
169          # Read the PDB file. 
170          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) 
171   
172          # Generate the sequence (1 molecule, all residues, and only N spins). 
173          self.interpreter.structure.load_spins(spin_id='@N') 
174   
175          # Test some of the sequence. 
176          self.assertEqual(len(cdp.mol), 1) 
177          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
178          self.assertEqual(len(cdp.mol[0].res), 12) 
179   
180          # 1st residue. 
181          self.assertEqual(cdp.mol[0].res[0].num, 1) 
182          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
183          self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 
184          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
185          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
186   
187          # 2nd residue. 
188          self.assertEqual(cdp.mol[0].res[1].num, 2) 
189          self.assertEqual(cdp.mol[0].res[1].name, 'PRO') 
190          self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 
191          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 10) 
192          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
193   
194          # 3rd residue. 
195          self.assertEqual(cdp.mol[0].res[2].num, 3) 
196          self.assertEqual(cdp.mol[0].res[2].name, 'LEU') 
197          self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 
198          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 24) 
199          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
200   
201          # 4th residue. 
202          self.assertEqual(cdp.mol[0].res[3].num, 4) 
203          self.assertEqual(cdp.mol[0].res[3].name, 'GLY') 
204          self.assertEqual(len(cdp.mol[0].res[3].spin), 1) 
205          self.assertEqual(cdp.mol[0].res[3].spin[0].num, 43) 
206          self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') 
207   
208          # 5th residue. 
209          self.assertEqual(cdp.mol[0].res[4].num, 5) 
210          self.assertEqual(cdp.mol[0].res[4].name, 'SER') 
211          self.assertEqual(len(cdp.mol[0].res[4].spin), 1) 
212          self.assertEqual(cdp.mol[0].res[4].spin[0].num, 50) 
213          self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N') 
214   
215          # 6th residue. 
216          self.assertEqual(cdp.mol[0].res[5].num, 6) 
217          self.assertEqual(cdp.mol[0].res[5].name, 'MET') 
218          self.assertEqual(len(cdp.mol[0].res[5].spin), 1) 
219          self.assertEqual(cdp.mol[0].res[5].spin[0].num, 61) 
220          self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') 
221   
222          # 7th residue. 
223          self.assertEqual(cdp.mol[0].res[6].num, 7) 
224          self.assertEqual(cdp.mol[0].res[6].name, 'ASP') 
225          self.assertEqual(len(cdp.mol[0].res[6].spin), 1) 
226          self.assertEqual(cdp.mol[0].res[6].spin[0].num, 78) 
227          self.assertEqual(cdp.mol[0].res[6].spin[0].name, 'N') 
228   
229          # 8th residue. 
230          self.assertEqual(cdp.mol[0].res[7].num, 8) 
231          self.assertEqual(cdp.mol[0].res[7].name, 'SER') 
232          self.assertEqual(len(cdp.mol[0].res[7].spin), 1) 
233          self.assertEqual(cdp.mol[0].res[7].spin[0].num, 90) 
234          self.assertEqual(cdp.mol[0].res[7].spin[0].name, 'N') 
235   
236          # 9th residue. 
237          self.assertEqual(cdp.mol[0].res[8].num, 9) 
238          self.assertEqual(cdp.mol[0].res[8].name, 'PRO') 
239          self.assertEqual(len(cdp.mol[0].res[8].spin), 1) 
240          self.assertEqual(cdp.mol[0].res[8].spin[0].num, 101) 
241          self.assertEqual(cdp.mol[0].res[8].spin[0].name, 'N') 
242   
243          # 10th residue. 
244          self.assertEqual(cdp.mol[0].res[9].num, 10) 
245          self.assertEqual(cdp.mol[0].res[9].name, 'PRO') 
246          self.assertEqual(len(cdp.mol[0].res[9].spin), 1) 
247          self.assertEqual(cdp.mol[0].res[9].spin[0].num, 115) 
248          self.assertEqual(cdp.mol[0].res[9].spin[0].name, 'N') 
249   
250          # 11th residue. 
251          self.assertEqual(cdp.mol[0].res[10].num, 11) 
252          self.assertEqual(cdp.mol[0].res[10].name, 'GLU') 
253          self.assertEqual(len(cdp.mol[0].res[10].spin), 1) 
254          self.assertEqual(cdp.mol[0].res[10].spin[0].num, 129) 
255          self.assertEqual(cdp.mol[0].res[10].spin[0].name, 'N') 
256   
257          # 12th residue. 
258          self.assertEqual(cdp.mol[0].res[11].num, 12) 
259          self.assertEqual(cdp.mol[0].res[11].name, 'GLY') 
260          self.assertEqual(len(cdp.mol[0].res[11].spin), 1) 
261          self.assertEqual(cdp.mol[0].res[11].spin[0].num, 144) 
262          self.assertEqual(cdp.mol[0].res[11].spin[0].name, 'N') 

263   
264   

265 -    def test_read(self): 

266          """The sequence.read() test.""" 
267   
268          # Read the sequence. 
269          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) 

270   
271   

272 -    def test_sequence_copy(self): 

273          """Test the sequence.copy user function.""" 
274   
275          # First create some spins. 
276          self.interpreter.spin.create(spin_name='A', spin_num=1, res_num=1) 
277          self.interpreter.spin.create(spin_name='A', spin_num=2, res_num=1) 
278          self.interpreter.spin.create(spin_name='B', spin_num=3, res_num=1) 
279          self.interpreter.spin.create(spin_name='B2', spin_num=4, res_num=1) 
280          self.interpreter.spin.create(spin_name='A', spin_num=1, res_num=2) 
281          self.interpreter.spin.create(spin_name='A', spin_num=2, res_num=2) 
282          self.interpreter.spin.create(spin_name='B', spin_num=3, res_num=2) 
283          self.interpreter.spin.create(spin_name='B2', spin_num=4, res_num=2) 
284   
285          # Create a new data pipe to copy to. 
286          self.interpreter.pipe.create('seq copy test', 'mf') 
287   
288          # Copy the sequence. 
289          self.interpreter.sequence.copy(pipe_from='mf') 
290   
291          # Alias the data pipes. 
292          pipe1 = ds['mf'] 
293          pipe2 = ds['seq copy test'] 
294   
295          # Check the residue count. 
296          self.assertEqual(len(pipe1.mol[0].res), len(pipe2.mol[0].res)) 
297   
298          # Check the spin counts. 
299          for i in range(len(pipe1.mol[0].res)): 
300              self.assertEqual(len(pipe1.mol[0].res[i].spin), len(pipe2.mol[0].res[i].spin)) 

301

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