Source Code for Module test_suite.system_tests.noe

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006-2014 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.                                # 
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 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from os import sep 
 24  from tempfile import mktemp 
 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 Noe(SystemTestCase): 
 34      """Class for testing various aspects specific to the NOE analysis.""" 
 35   
 36 -    def setUp(self): 
 37          """Set up for all the functional tests.""" 
 38   
 39          # Create the data pipe. 
 40          self.interpreter.pipe.create('noe', 'noe') 
 41   
 42          # Create a temporary file. 
 43          ds.tmpfile = mktemp() 
 44   
 45   
 46 -    def test_bug_21562_noe_replicate_fail(self): 
 47          """Catch U{bug #21562<https://web.archive.org/web/https://gna.org/bugs/?21562>}, the failure of the NOE analysis when replicated spectra are used.""" 
 48   
 49          # Execute the script. 
 50          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'noe'+sep+'bug_21562_noe_replicate_fail.py') 
 51   
 52          # Open the NOE output file. 
 53          file = open(ds.tmpfile) 
 54          lines = file.readlines() 
 55          file.close() 
 56   
 57          # How the file should look like. 
 58          data = [ 
 59              "# Parameter description:  The NOE.\n", 
 60              "#\n", 
 61              "# mol_name       res_num    res_name    spin_num    spin_name    value                   error                   \n", 
 62              "2AT7_fmf_mol1    12         PHE         150         N               0.803029108487728      0.0199040298831904    \n", 
 63              "2AT7_fmf_mol1    13         ASN         170         N               0.829415981681132      0.0339996453012768    \n", 
 64              "2AT7_fmf_mol1    14         LYS         184         N               0.755789564728523      0.0250941717735858    \n" 
 65          ] 
 66   
 67          # Printout of the real and generated data. 
 68          print("\n\nThe real data:") 
 69          for i in range(len(lines)): 
 70              print(repr(data[i])) 
 71          print("\nThe generated data:") 
 72          for i in range(len(lines)): 
 73              print(repr(lines[i])) 
 74          print("\n") 
 75   
 76          # Check each line. 
 77          for i in range(len(lines)): 
 78              self.assertEqual(data[i], lines[i]) 
 79   
 80   
 81 -    def test_bug_21591_noe_calculation_fail(self): 
 82          """Catch U{bug #21591<https://web.archive.org/web/https://gna.org/bugs/?21591>}, the failure of the NOE analysis.""" 
 83   
 84          # Generate the sequence. 
 85          self.interpreter.spin.create(mol_name='XYZ_mol1', res_num=120, res_name='GLY', spin_num=1865, spin_name='N') 
 86   
 87          # Load the reference spectrum and saturated spectrum peak intensities. 
 88          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists' 
 89          self.interpreter.spectrum.read_intensities(file='noe.140109.8.001.list', dir=path, spectrum_id='ref_ave') 
 90          self.interpreter.spectrum.read_intensities(file='noe.140109.8.002.list', dir=path, spectrum_id='sat_ave') 
 91   
 92          # Set the spectrum types. 
 93          self.interpreter.noe.spectrum_type('ref', 'ref_ave') 
 94          self.interpreter.noe.spectrum_type('sat', 'sat_ave') 
 95   
 96          # Set the errors. 
 97          self.interpreter.spectrum.baseplane_rmsd(error=1.3e06, spectrum_id='ref_ave') 
 98          self.interpreter.spectrum.baseplane_rmsd(error=1.4e06, spectrum_id='sat_ave') 
 99   
100          # Peak intensity error analysis. 
101          self.interpreter.spectrum.error_analysis() 
102   
103          # Calculate the NOEs. 
104          self.interpreter.calc() 
105   
106          # Save the NOEs. 
107          self.interpreter.value.write(param='noe', file=ds.tmpfile) 
108   
109          # Open the NOE output file. 
110          file = open(ds.tmpfile) 
111          lines = file.readlines() 
112          file.close() 
113   
114          # How the file should look like. 
115          data = [ 
116              "# Parameter description:  The NOE.\n", 
117              "#\n", 
118              "# mol_name    res_num    res_name    spin_num    spin_name    value                   error                   \n", 
119              "XYZ_mol1      120        GLY         1865        N               0.520373965716017       0.208104738641507    \n", 
120          ] 
121   
122          # Printout of the real and generated data. 
123          print("\n\nThe real data:") 
124          for i in range(len(lines)): 
125              print(repr(data[i])) 
126          print("\nThe generated data:") 
127          for i in range(len(lines)): 
128              print(repr(lines[i])) 
129          print("\n") 
130   
131          # Check each line. 
132          for i in range(len(lines)): 
133              self.assertEqual(data[i], lines[i]) 
134   
135   
136 -    def test_noe_analysis(self): 
137          """Test the NOE analysis.""" 
138   
139          # Execute the script. 
140          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'noe'+sep+'noe.py') 
141   
142          # The real data. 
143          sat = [5050.0, 51643.0, 53663.0, -65111.0, -181131.0, -105322.0] 
144          ref = [148614.0, 166842.0, 128690.0, 99566.0, 270047.0, 130959.0] 
145          noe = [0.033980647852826784, 0.30953237194471417, 0.4169943274535706, -0.6539481349054899, -0.6707387973204665, -0.8042364404126482] 
146          noe_err = [0.02020329903276632, 0.2320024671657343, 0.026067523940084526, 0.038300618865378507, 0.014260663438353431, 0.03183614777183591] 
147   
148          # Check the data. 
149          i = 0 
150          for spin in spin_loop(): 
151              # Skip deselected spins. 
152              if not spin.select: 
153                  continue 
154   
155              # Check the intensity data. 
156              self.assertEqual(sat[i], spin.intensities['sat_ave']) 
157              self.assertEqual(ref[i], spin.intensities['ref_ave']) 
158   
159              # Check the NOE data. 
160              self.assertEqual(noe[i], spin.noe) 
161              self.assertAlmostEqual(noe_err[i], spin.noe_err) 
162   
163              # Increment the spin index. 
164              i += 1 
165   
166          # The real Grace file data. 
167          data = [ 
168              '@version 50121\n', 
169              '@page size 842, 595\n', 
170              '@with g0\n', 
171              '@    view 0.15, 0.15, 1.28, 0.85\n', 
172              '@    xaxis  label "Residue number"\n', 
173              '@    xaxis  label char size 1.00\n', 
174              '@    xaxis  tick major size 0.50\n', 
175              '@    xaxis  tick major linewidth 0.5\n', 
176              '@    xaxis  tick minor linewidth 0.5\n', 
177              '@    xaxis  tick minor size 0.25\n', 
178              '@    xaxis  ticklabel char size 0.70\n', 
179              '@    yaxis  label "\\qNOE\\Q"\n', 
180              '@    yaxis  label char size 1.00\n', 
181              '@    yaxis  tick major size 0.50\n', 
182              '@    yaxis  tick major linewidth 0.5\n', 
183              '@    yaxis  tick minor linewidth 0.5\n', 
184              '@    yaxis  tick minor size 0.25\n', 
185              '@    yaxis  ticklabel char size 0.70\n', 
186              '@    legend off\n', 
187              '@    legend box fill pattern 1\n', 
188              '@    legend char size 1.0\n', 
189              '@    frame linewidth 0.5\n', 
190              '@    s0 symbol 1\n', 
191              '@    s0 symbol size 0.45\n', 
192              '@    s0 symbol linewidth 0.5\n', 
193              '@    s0 errorbar size 0.5\n', 
194              '@    s0 errorbar linewidth 0.5\n', 
195              '@    s0 errorbar riser linewidth 0.5\n', 
196              '@    s0 legend "N spins"\n', 
197              '@    s1 symbol 2\n', 
198              '@    s1 symbol size 0.45\n', 
199              '@    s1 symbol linewidth 0.5\n', 
200              '@    s1 errorbar size 0.5\n', 
201              '@    s1 errorbar linewidth 0.5\n', 
202              '@    s1 errorbar riser linewidth 0.5\n', 
203              '@    s1 legend "NE1 spins"\n', 
204              '@target G0.S0\n', 
205              '@type xydy\n', 
206              '4                              0.033980647852827              0.020203299032766             \n', 
207              '5                              0.309532371944714              0.232002467165734             \n', 
208              '6                              0.416994327453571              0.026067523940085             \n', 
209              '40                             -0.653948134905490             0.038300618865379             \n', 
210              '55                             -0.804236440412648             0.031836147771836             \n', 
211              '&\n', 
212              '@target G0.S1\n', 
213              '@type xydy\n', 
214              '40                             -0.670738797320466             0.014260663438353             \n', 
215              '&\n', 
216              '@with g0\n', 
217              '@autoscale\n' 
218          ] 
219   
220          # Check the Grace file. 
221          file = open(ds.tmpfile) 
222          lines = file.readlines() 
223          file.close() 
224          for i in range(len(lines)): 
225              print("            '%s\\n'," % lines[i][:-1].replace('"', "\\\"")) 
226          for i in range(len(lines)): 
227              self.assertEqual(data[i], lines[i]) 
228