Source Code for Module test_suite.system_tests.pcs

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  3  # Copyright (C) 2011-2013 Edward d'Auvergne                                   # 
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 21   
 22  # Module docstring. 
 23  """PCS-based system tests.""" 
 24   
 25   
 26  # Python module imports. 
 27  from os import sep 
 28  from re import search 
 29  from tempfile import mkdtemp 
 30   
 31  # relax module imports. 
 32  from pipe_control.mol_res_spin import count_spins, spin_loop 
 33  from status import Status; status = Status() 
 34  from test_suite.system_tests.base_classes import SystemTestCase 
 35   
 36   
 37 -class Pcs(SystemTestCase): 
 38      """Class for testing PCS operations.""" 
 39   
 40 -    def test_grace_plot(self): 
 41          """Test the creation of Grace plots of PCS data.""" 
 42   
 43          # Create a data pipe for all the data. 
 44          self.interpreter.pipe.create('CaM N-dom', 'N-state') 
 45   
 46          # Create some spins. 
 47          self.interpreter.spin.create(spin_name='N', spin_num=1, res_name='Gly', res_num=3) 
 48          self.interpreter.spin.create(spin_name='H', spin_num=2, res_name='Gly', res_num=3) 
 49          self.interpreter.spin.create(spin_name='N', spin_num=3, res_name='Gly', res_num=4) 
 50          self.interpreter.spin.create(spin_name='H', spin_num=4, res_name='Gly', res_num=4) 
 51          self.interpreter.sequence.display() 
 52   
 53          # Set the element type. 
 54          self.interpreter.spin.element(element='N', spin_id='@N') 
 55          self.interpreter.spin.element(element='H', spin_id='@H') 
 56   
 57          # Data directory. 
 58          dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep 
 59   
 60          # PCSs. 
 61          self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt', dir=dir, res_num_col=1, data_col=2, error_col=4, spin_id='@N') 
 62          self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt', dir=dir, res_num_col=1, data_col=3, error_col=4, spin_id='@H') 
 63   
 64          # Fudge the back-calculated PCS data. 
 65          for spin in spin_loop(): 
 66              spin.pcs_bc = {} 
 67              spin.pcs_bc['dy'] = spin.pcs['dy'] + 0.1 
 68   
 69          # Create the grace plot. 
 70          self.tmpdir = mkdtemp() 
 71          self.interpreter.pcs.corr_plot(format='grace', file='pcs_corr.agr', dir=self.tmpdir, force=True) 
 72   
 73          # Read the file data. 
 74          file = open(self.tmpdir+sep+'pcs_corr.agr') 
 75          lines = file.readlines() 
 76          file.close() 
 77   
 78          # Check the diagonal data. 
 79          for i in range(len(lines)): 
 80              if search('G0.S0', lines[i]): 
 81                  point1 = lines[i+2].split() 
 82                  point2 = lines[i+3].split() 
 83                  self.assertAlmostEqual(float(point1[0]), -100.0) 
 84                  self.assertAlmostEqual(float(point1[1]), -100.0) 
 85                  self.assertAlmostEqual(float(point2[0]), 100.0) 
 86                  self.assertAlmostEqual(float(point2[1]), 100.0) 
 87   
 88          # Check the 15N data. 
 89          for i in range(len(lines)): 
 90              if search('G0.S1', lines[i]): 
 91                  point1 = lines[i+2].split() 
 92                  point2 = lines[i+3].split() 
 93                  self.assertAlmostEqual(float(point1[0]), 0.917+0.1) 
 94                  self.assertAlmostEqual(float(point1[1]), 0.917) 
 95                  self.assertAlmostEqual(float(point1[2]), 0.1) 
 96                  self.assertAlmostEqual(float(point2[0]), 1.131+0.1) 
 97                  self.assertAlmostEqual(float(point2[1]), 1.131) 
 98                  self.assertAlmostEqual(float(point2[2]), 0.1) 
 99   
100          # Check the 1H data. 
101          for i in range(len(lines)): 
102              if search('G0.S2', lines[i]): 
103                  point1 = lines[i+2].split() 
104                  point2 = lines[i+3].split() 
105                  self.assertAlmostEqual(float(point1[0]), 0.843+0.1) 
106                  self.assertAlmostEqual(float(point1[1]), 0.843) 
107                  self.assertAlmostEqual(float(point1[2]), 0.1) 
108                  self.assertAlmostEqual(float(point2[0]), 1.279+0.1) 
109                  self.assertAlmostEqual(float(point2[1]), 1.279) 
110                  self.assertAlmostEqual(float(point2[2]), 0.1) 
111   
112   
113 -    def test_load_multi_col_data(self): 
114          """Test the loading of PCS data from a file with different columns for each spin type.""" 
115   
116          # Create a data pipe for all the data. 
117          self.interpreter.pipe.create('CaM N-dom', 'N-state') 
118   
119          # Create some spins. 
120          self.interpreter.spin.create(spin_name='N', spin_num=1, res_name='Gly', res_num=3) 
121          self.interpreter.spin.create(spin_name='H', spin_num=2, res_name='Gly', res_num=3) 
122          self.interpreter.spin.create(spin_name='N', spin_num=3, res_name='Gly', res_num=4) 
123          self.interpreter.spin.create(spin_name='H', spin_num=4, res_name='Gly', res_num=4) 
124          self.interpreter.sequence.display() 
125   
126          # Data directory. 
127          dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep 
128   
129          # PCSs. 
130          self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt', dir=dir, res_num_col=1, data_col=2, error_col=4, spin_id='@N') 
131          self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt', dir=dir, res_num_col=1, data_col=3, error_col=4, spin_id='@H') 
132   
133          # The data. 
134          pcs_data = { 
135              ':3@N': 0.917, 
136              ':3@H': 0.843, 
137              ':4@N': 1.131, 
138              ':4@H': 1.279, 
139          } 
140   
141          # Check the PCS data. 
142          print("\n") 
143          for spin, spin_id in spin_loop(return_id=True): 
144              print("Checking the PCS data of spin '%s'." % spin_id) 
145              self.assert_(hasattr(spin, 'pcs')) 
146              self.assertEqual(spin.pcs['dy'], pcs_data[spin_id]) 
147              self.assertEqual(spin.pcs_err['dy'], 0.1) 
148   
149   
150 -    def test_load_multi_col_data2(self): 
151          """Test the loading of PCS data from a file with different columns for each spin type.""" 
152   
153          # Create a data pipe for all the data. 
154          self.interpreter.pipe.create('CaM N-dom', 'N-state') 
155   
156          # Create some spins. 
157          self.interpreter.spin.create(spin_name='N', spin_num=1, res_name='Gly', res_num=3, mol_name='CaM') 
158          self.interpreter.spin.create(spin_name='H', spin_num=2, res_name='Gly', res_num=3, mol_name='CaM') 
159          self.interpreter.spin.create(spin_name='N', spin_num=3, res_name='Gly', res_num=4, mol_name='CaM') 
160          self.interpreter.spin.create(spin_name='H', spin_num=4, res_name='Gly', res_num=4, mol_name='CaM') 
161          self.interpreter.sequence.display() 
162   
163          # Data directory. 
164          dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep 
165   
166          # PCSs. 
167          self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt', dir=dir, res_num_col=1, data_col=2, error_col=4, spin_id='@N') 
168          self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt', dir=dir, res_num_col=1, data_col=3, error_col=4, spin_id='@H') 
169   
170          # The data. 
171          pcs_data = { 
172              '#CaM:3@N': 0.917, 
173              '#CaM:3@H': 0.843, 
174              '#CaM:4@N': 1.131, 
175              '#CaM:4@H': 1.279, 
176          } 
177   
178          # Check the PCS data. 
179          print("\n") 
180          for spin, spin_id in spin_loop(return_id=True): 
181              print("Checking the PCS data of spin '%s'." % spin_id) 
182              self.assert_(hasattr(spin, 'pcs')) 
183              self.assertEqual(spin.pcs['dy'], pcs_data[spin_id]) 
184              self.assertEqual(spin.pcs_err['dy'], 0.1) 
185   
186   
187 -    def test_pcs_copy(self): 
188          """Test the operation of the pcs.copy user function.""" 
189   
190          # Create a data pipe. 
191          self.interpreter.pipe.create('orig', 'N-state') 
192   
193          # Data directory. 
194          dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep 
195   
196          # Load the spins. 
197          self.interpreter.sequence.read(file='pcs.txt', dir=dir, spin_name_col=1) 
198          self.interpreter.sequence.display() 
199   
200          # Load the PCSs. 
201          self.interpreter.pcs.read(align_id='tb', file='pcs.txt', dir=dir, spin_name_col=1, data_col=2) 
202          self.interpreter.sequence.display() 
203   
204          # The PCSs. 
205          pcs = [0.004, 0.008, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006, 0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054, 0.075, 0.065, None, 0.070, 0.015, 0.098, 0.060, 0.120] 
206   
207          # Create a new data pipe by copying the old, then switch to it. 
208          self.interpreter.pipe.copy(pipe_from='orig', pipe_to='new') 
209          self.interpreter.pipe.switch(pipe_name='new') 
210   
211          # Delete the PCS data. 
212          self.interpreter.pcs.delete() 
213   
214          # Copy the PCSs. 
215          self.interpreter.pcs.copy(pipe_from='orig', align_id='tb') 
216   
217          # Checks. 
218          self.assertEqual(count_spins(), 26) 
219          self.assertEqual(len(cdp.interatomic), 0) 
220          i = 0 
221          for spin in spin_loop(): 
222              self.assertEqual(pcs[i], spin.pcs['tb']) 
223              i += 1 
224   
225   
226 -    def test_pcs_load(self): 
227          """Test for the loading of some PCS data with the spin ID format.""" 
228   
229          # Create a data pipe. 
230          self.interpreter.pipe.create('test', 'N-state') 
231   
232          # Data directory. 
233          dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep 
234   
235          # Load the spins. 
236          self.interpreter.sequence.read(file='pcs.txt', dir=dir, spin_name_col=1) 
237          self.interpreter.sequence.display() 
238   
239          # Load the PCSs. 
240          self.interpreter.pcs.read(align_id='tb', file='pcs.txt', dir=dir, spin_name_col=1, data_col=2) 
241          self.interpreter.sequence.display() 
242   
243          # The PCSs. 
244          pcs = [0.004, 0.008, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006, 0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054, 0.075, 0.065, None, 0.070, 0.015, 0.098, 0.060, 0.120] 
245   
246          # Checks. 
247          self.assertEqual(count_spins(), 26) 
248          self.assertEqual(len(cdp.interatomic), 0) 
249          i = 0 
250          for spin in spin_loop(): 
251              self.assertEqual(pcs[i], spin.pcs['tb']) 
252              i += 1 
253   
254   
255 -    def test_structural_noise(self): 
256          """Test the operation of the pcs.structural_noise user function.""" 
257   
258          # The file. 
259          state = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'saved_states'+sep+'pcs_structural_noise_test.bz2' 
260   
261          # Load the state. 
262          self.interpreter.state.load(state) 
263   
264          # Structural noise (twice to make sure old errors are removed properly from the PCS error). 
265          self.interpreter.pcs.structural_noise(rmsd=200.0, sim_num=100, file='devnull', dir=None, force=True) 
266          self.interpreter.pcs.structural_noise(rmsd=0.2, sim_num=20000, file='devnull', dir=None, force=True) 
267   
268          # The simulated data (from 1,000,000 randomisations of 0.2 Angstrom RMSD). 
269          pcs_struct_err = { 
270              'Dy N-dom': 0.014643633242475744, 
271              'Er N-dom': 0.0047594540182391868, 
272              'Tm N-dom': 0.010454580925459261, 
273              'Tb N-dom': 0.01613972832580988 
274          } 
275          pcs_err = { 
276              'Dy N-dom': 0.1010664929367797, 
277              'Er N-dom': 0.10011319794388618, 
278              'Tm N-dom': 0.1005450061531003, 
279              'Tb N-dom': 0.10129408092495312 
280          } 
281   
282          # Alias the single spin. 
283          spin = cdp.mol[0].res[0].spin[0] 
284   
285          # Test the PCS data. 
286          for id in ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom']: 
287              self.assertAlmostEqual(spin.pcs_struct_err[id], pcs_struct_err[id], 2) 
288              self.assertAlmostEqual(spin.pcs_err[id], pcs_err[id], 2) 
289