Source Code for Module test_suite.system_tests.sequence

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006-2013 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2013 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 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 status import Status; status = Status() 
 29  from test_suite.system_tests.base_classes import SystemTestCase 
 30   
 31   
 32 -class Sequence(SystemTestCase): 
 33      """Class for testing the sequence functions.""" 
 34   
 35 -    def setUp(self): 
 36          """Set up for all the functional tests.""" 
 37   
 38          # Create the data pipe. 
 39          self.interpreter.pipe.create('mf', 'mf') 
 40   
 41   
 42 -    def test_load_protein_asp_atoms_from_pdb(self): 
 43          """Load all aspartic acid atoms from the single residue in a loaded protein PDB file.""" 
 44   
 45          # Read the PDB file. 
 46          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) 
 47   
 48          # Load all the ASP atoms (1 molecule, 1 ASP residue, and all atoms). 
 49          self.interpreter.structure.load_spins(spin_id=':ASP') 
 50   
 51          # Test some of the sequence. 
 52          self.assertEqual(len(cdp.mol), 1) 
 53          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
 54          self.assertEqual(len(cdp.mol[0].res), 1) 
 55   
 56          # 1st residue. 
 57          self.assertEqual(cdp.mol[0].res[0].num, 7) 
 58          self.assertEqual(cdp.mol[0].res[0].name, 'ASP') 
 59          self.assertEqual(len(cdp.mol[0].res[0].spin), 12) 
 60          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 78) 
 61          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
 62          self.assertEqual(cdp.mol[0].res[0].spin[1].num, 79) 
 63          self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'H') 
 64          self.assertEqual(cdp.mol[0].res[0].spin[2].num, 80) 
 65          self.assertEqual(cdp.mol[0].res[0].spin[2].name, 'CA') 
 66          self.assertEqual(cdp.mol[0].res[0].spin[3].num, 81) 
 67          self.assertEqual(cdp.mol[0].res[0].spin[3].name, 'HA') 
 68          self.assertEqual(cdp.mol[0].res[0].spin[4].num, 82) 
 69          self.assertEqual(cdp.mol[0].res[0].spin[4].name, 'CB') 
 70          self.assertEqual(cdp.mol[0].res[0].spin[5].num, 83) 
 71          self.assertEqual(cdp.mol[0].res[0].spin[5].name, '1HB') 
 72          self.assertEqual(cdp.mol[0].res[0].spin[6].num, 84) 
 73          self.assertEqual(cdp.mol[0].res[0].spin[6].name, '2HB') 
 74          self.assertEqual(cdp.mol[0].res[0].spin[7].num, 85) 
 75          self.assertEqual(cdp.mol[0].res[0].spin[7].name, 'CG') 
 76          self.assertEqual(cdp.mol[0].res[0].spin[8].num, 86) 
 77          self.assertEqual(cdp.mol[0].res[0].spin[8].name, 'OD1') 
 78          self.assertEqual(cdp.mol[0].res[0].spin[9].num, 87) 
 79          self.assertEqual(cdp.mol[0].res[0].spin[9].name, 'OD2') 
 80          self.assertEqual(cdp.mol[0].res[0].spin[10].num, 88) 
 81          self.assertEqual(cdp.mol[0].res[0].spin[10].name, 'C') 
 82          self.assertEqual(cdp.mol[0].res[0].spin[11].num, 89) 
 83          self.assertEqual(cdp.mol[0].res[0].spin[11].name, 'O') 
 84   
 85   
 86 -    def test_load_protein_gly_N_Ca_spins_from_pdb(self): 
 87          """Load the glycine backbone amide N and Ca spins from a loaded protein PDB file.""" 
 88   
 89          # Read the PDB file. 
 90          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) 
 91   
 92          # Generate the sequence of nitrogen spins (1 molecule, all GLY residues, and only N spins). 
 93          self.interpreter.structure.load_spins(spin_id=':GLY@N') 
 94   
 95          # Append to the sequence the alpha carbon spins (1 molecule, all GLY residues, and only Ca spins). 
 96          self.interpreter.structure.load_spins(spin_id=':GLY@CA') 
 97   
 98          # Test some of the sequence. 
 99          self.assertEqual(len(cdp.mol), 1) 
100          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
101          self.assertEqual(len(cdp.mol[0].res), 3) 
102   
103          # 1st residue. 
104          self.assertEqual(cdp.mol[0].res[0].num, 1) 
105          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
106          self.assertEqual(len(cdp.mol[0].res[0].spin), 2) 
107          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
108          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
109          self.assertEqual(cdp.mol[0].res[0].spin[1].num, 2) 
110          self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'CA') 
111   
112          # 2nd residue. 
113          self.assertEqual(cdp.mol[0].res[1].num, 4) 
114          self.assertEqual(cdp.mol[0].res[1].name, 'GLY') 
115          self.assertEqual(len(cdp.mol[0].res[1].spin), 2) 
116          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 43) 
117          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
118          self.assertEqual(cdp.mol[0].res[1].spin[1].num, 45) 
119          self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'CA') 
120   
121          # 3rd residue. 
122          self.assertEqual(cdp.mol[0].res[2].num, 12) 
123          self.assertEqual(cdp.mol[0].res[2].name, 'GLY') 
124          self.assertEqual(len(cdp.mol[0].res[2].spin), 2) 
125          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 144) 
126          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
127          self.assertEqual(cdp.mol[0].res[2].spin[1].num, 146) 
128          self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'CA') 
129   
130   
131 -    def test_load_protein_gly_N_spins_from_pdb(self): 
132          """Load the glycine backbone amide N spins from a loaded protein PDB file.""" 
133   
134          # Read the PDB file. 
135          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) 
136   
137          # Generate the sequence (1 molecule, all GLY residues, and only N spins). 
138          self.interpreter.structure.load_spins(spin_id=':GLY@N') 
139   
140          # Test some of the sequence. 
141          self.assertEqual(len(cdp.mol), 1) 
142          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
143          self.assertEqual(len(cdp.mol[0].res), 3) 
144   
145          # 1st residue. 
146          self.assertEqual(cdp.mol[0].res[0].num, 1) 
147          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
148          self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 
149          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
150          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
151   
152          # 2nd residue. 
153          self.assertEqual(cdp.mol[0].res[1].num, 4) 
154          self.assertEqual(cdp.mol[0].res[1].name, 'GLY') 
155          self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 
156          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 43) 
157          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
158   
159          # 3rd residue. 
160          self.assertEqual(cdp.mol[0].res[2].num, 12) 
161          self.assertEqual(cdp.mol[0].res[2].name, 'GLY') 
162          self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 
163          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 144) 
164          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
165   
166   
167 -    def test_load_protein_N_spins_from_pdb(self): 
168          """Load the protein backbone amide N spins from a loaded PDB file.""" 
169   
170          # Read the PDB file. 
171          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) 
172   
173          # Generate the sequence (1 molecule, all residues, and only N spins). 
174          self.interpreter.structure.load_spins(spin_id='@N') 
175   
176          # Test some of the sequence. 
177          self.assertEqual(len(cdp.mol), 1) 
178          self.assertEqual(cdp.mol[0].name, 'Ap4Aase_res1-12_mol1') 
179          self.assertEqual(len(cdp.mol[0].res), 12) 
180   
181          # 1st residue. 
182          self.assertEqual(cdp.mol[0].res[0].num, 1) 
183          self.assertEqual(cdp.mol[0].res[0].name, 'GLY') 
184          self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 
185          self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1) 
186          self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') 
187   
188          # 2nd residue. 
189          self.assertEqual(cdp.mol[0].res[1].num, 2) 
190          self.assertEqual(cdp.mol[0].res[1].name, 'PRO') 
191          self.assertEqual(len(cdp.mol[0].res[1].spin), 1) 
192          self.assertEqual(cdp.mol[0].res[1].spin[0].num, 10) 
193          self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') 
194   
195          # 3rd residue. 
196          self.assertEqual(cdp.mol[0].res[2].num, 3) 
197          self.assertEqual(cdp.mol[0].res[2].name, 'LEU') 
198          self.assertEqual(len(cdp.mol[0].res[2].spin), 1) 
199          self.assertEqual(cdp.mol[0].res[2].spin[0].num, 24) 
200          self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') 
201   
202          # 4th residue. 
203          self.assertEqual(cdp.mol[0].res[3].num, 4) 
204          self.assertEqual(cdp.mol[0].res[3].name, 'GLY') 
205          self.assertEqual(len(cdp.mol[0].res[3].spin), 1) 
206          self.assertEqual(cdp.mol[0].res[3].spin[0].num, 43) 
207          self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') 
208   
209          # 5th residue. 
210          self.assertEqual(cdp.mol[0].res[4].num, 5) 
211          self.assertEqual(cdp.mol[0].res[4].name, 'SER') 
212          self.assertEqual(len(cdp.mol[0].res[4].spin), 1) 
213          self.assertEqual(cdp.mol[0].res[4].spin[0].num, 50) 
214          self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N') 
215   
216          # 6th residue. 
217          self.assertEqual(cdp.mol[0].res[5].num, 6) 
218          self.assertEqual(cdp.mol[0].res[5].name, 'MET') 
219          self.assertEqual(len(cdp.mol[0].res[5].spin), 1) 
220          self.assertEqual(cdp.mol[0].res[5].spin[0].num, 61) 
221          self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') 
222   
223          # 7th residue. 
224          self.assertEqual(cdp.mol[0].res[6].num, 7) 
225          self.assertEqual(cdp.mol[0].res[6].name, 'ASP') 
226          self.assertEqual(len(cdp.mol[0].res[6].spin), 1) 
227          self.assertEqual(cdp.mol[0].res[6].spin[0].num, 78) 
228          self.assertEqual(cdp.mol[0].res[6].spin[0].name, 'N') 
229   
230          # 8th residue. 
231          self.assertEqual(cdp.mol[0].res[7].num, 8) 
232          self.assertEqual(cdp.mol[0].res[7].name, 'SER') 
233          self.assertEqual(len(cdp.mol[0].res[7].spin), 1) 
234          self.assertEqual(cdp.mol[0].res[7].spin[0].num, 90) 
235          self.assertEqual(cdp.mol[0].res[7].spin[0].name, 'N') 
236   
237          # 9th residue. 
238          self.assertEqual(cdp.mol[0].res[8].num, 9) 
239          self.assertEqual(cdp.mol[0].res[8].name, 'PRO') 
240          self.assertEqual(len(cdp.mol[0].res[8].spin), 1) 
241          self.assertEqual(cdp.mol[0].res[8].spin[0].num, 101) 
242          self.assertEqual(cdp.mol[0].res[8].spin[0].name, 'N') 
243   
244          # 10th residue. 
245          self.assertEqual(cdp.mol[0].res[9].num, 10) 
246          self.assertEqual(cdp.mol[0].res[9].name, 'PRO') 
247          self.assertEqual(len(cdp.mol[0].res[9].spin), 1) 
248          self.assertEqual(cdp.mol[0].res[9].spin[0].num, 115) 
249          self.assertEqual(cdp.mol[0].res[9].spin[0].name, 'N') 
250   
251          # 11th residue. 
252          self.assertEqual(cdp.mol[0].res[10].num, 11) 
253          self.assertEqual(cdp.mol[0].res[10].name, 'GLU') 
254          self.assertEqual(len(cdp.mol[0].res[10].spin), 1) 
255          self.assertEqual(cdp.mol[0].res[10].spin[0].num, 129) 
256          self.assertEqual(cdp.mol[0].res[10].spin[0].name, 'N') 
257   
258          # 12th residue. 
259          self.assertEqual(cdp.mol[0].res[11].num, 12) 
260          self.assertEqual(cdp.mol[0].res[11].name, 'GLY') 
261          self.assertEqual(len(cdp.mol[0].res[11].spin), 1) 
262          self.assertEqual(cdp.mol[0].res[11].spin[0].num, 144) 
263          self.assertEqual(cdp.mol[0].res[11].spin[0].name, 'N') 
264   
265   
266 -    def test_read(self): 
267          """The sequence.read() test.""" 
268   
269          # Read the sequence. 
270          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) 
271           
272          # Test some of the sequence. 
273          self.assertEqual(len(cdp.mol), 1) 
274          self.assertEqual(cdp.mol[0].name, None) 
275          self.assertEqual(len(cdp.mol[0].res), 5) 
276   
277          # 1st residue. 
278          self.assertEqual(cdp.mol[0].res[0].num, -2) 
279          self.assertEqual(cdp.mol[0].res[0].name, 'Gly') 
280          self.assertEqual(len(cdp.mol[0].res[0].spin), 1) 
281          self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) 
282          self.assertEqual(cdp.mol[0].res[0].spin[0].name, None) 
283   
284 -    def test_sequence_copy(self): 
285          """Test the sequence.copy user function.""" 
286   
287          # First create some spins. 
288          self.interpreter.spin.create(spin_name='A', spin_num=1, res_num=1) 
289          self.interpreter.spin.create(spin_name='A', spin_num=2, res_num=1) 
290          self.interpreter.spin.create(spin_name='B', spin_num=3, res_num=1) 
291          self.interpreter.spin.create(spin_name='B2', spin_num=4, res_num=1) 
292          self.interpreter.spin.create(spin_name='A', spin_num=1, res_num=2) 
293          self.interpreter.spin.create(spin_name='A', spin_num=2, res_num=2) 
294          self.interpreter.spin.create(spin_name='B', spin_num=3, res_num=2) 
295          self.interpreter.spin.create(spin_name='B2', spin_num=4, res_num=2) 
296   
297          # Create a new data pipe to copy to. 
298          self.interpreter.pipe.create('seq copy test', 'mf') 
299   
300          # Copy the sequence. 
301          self.interpreter.sequence.copy(pipe_from='mf') 
302   
303          # Alias the data pipes. 
304          pipe1 = ds['mf'] 
305          pipe2 = ds['seq copy test'] 
306   
307          # Check the residue count. 
308          self.assertEqual(len(pipe1.mol[0].res), len(pipe2.mol[0].res)) 
309   
310          # Check the spin counts. 
311          for i in range(len(pipe1.mol[0].res)): 
312              self.assertEqual(len(pipe1.mol[0].res[i].spin), len(pipe2.mol[0].res[i].spin)) 
313