test_suite.system

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 # Create a temporary directory for dumping files. 46 ds.tmpdir = mkdtemp() 47 self.tmpdir = ds.tmpdir

48 49

50 - def test_bug_21562_noe_replicate_fail(self):

51 """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.""" 52 53 # Execute the script. 54 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'noe'+sep+'bug_21562_noe_replicate_fail.py') 55 56 # Open the NOE output file. 57 file = open(ds.tmpfile) 58 lines = file.readlines() 59 file.close() 60 61 # How the file should look like. 62 data = [ 63 "# Parameter description: The steady-state NOE value.\n", 64 "#\n", 65 "# mol_name res_num res_name spin_num spin_name value error \n", 66 "2AT7_fmf_mol1 12 PHE 150 N 0.803029108487728 0.0199040298831904 \n", 67 "2AT7_fmf_mol1 13 ASN 170 N 0.829415981681132 0.0339996453012768 \n", 68 "2AT7_fmf_mol1 14 LYS 184 N 0.755789564728523 0.0250941717735858 \n" 69 ] 70 71 # Printout of the real and generated data. 72 print("\n\nThe real data:") 73 for i in range(len(lines)): 74 print(repr(data[i])) 75 print("\nThe generated data:") 76 for i in range(len(lines)): 77 print(repr(lines[i])) 78 print("\n") 79 80 # Check each line. 81 for i in range(len(lines)): 82 self.assertEqual(data[i], lines[i])

83 84

85 - def test_bug_21591_noe_calculation_fail(self):

86 """Catch U{bug #21591<https://web.archive.org/web/https://gna.org/bugs/?21591>}, the failure of the NOE analysis.""" 87 88 # Generate the sequence. 89 self.interpreter.spin.create(mol_name='XYZ_mol1', res_num=120, res_name='GLY', spin_num=1865, spin_name='N') 90 91 # Load the reference spectrum and saturated spectrum peak intensities. 92 path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists' 93 self.interpreter.spectrum.read_intensities(file='noe.140109.8.001.list', dir=path, spectrum_id='ref_ave') 94 self.interpreter.spectrum.read_intensities(file='noe.140109.8.002.list', dir=path, spectrum_id='sat_ave') 95 96 # Set the spectrum types. 97 self.interpreter.noe.spectrum_type('ref', 'ref_ave') 98 self.interpreter.noe.spectrum_type('sat', 'sat_ave') 99 100 # Set the errors. 101 self.interpreter.spectrum.baseplane_rmsd(error=1.3e06, spectrum_id='ref_ave') 102 self.interpreter.spectrum.baseplane_rmsd(error=1.4e06, spectrum_id='sat_ave') 103 104 # Peak intensity error analysis. 105 self.interpreter.spectrum.error_analysis() 106 107 # Calculate the NOEs. 108 self.interpreter.calc() 109 110 # Save the NOEs. 111 self.interpreter.value.write(param='noe', file=ds.tmpfile) 112 113 # Open the NOE output file. 114 file = open(ds.tmpfile) 115 lines = file.readlines() 116 file.close() 117 118 # How the file should look like. 119 data = [ 120 "# Parameter description: The steady-state NOE value.\n", 121 "#\n", 122 "# mol_name res_num res_name spin_num spin_name value error \n", 123 "XYZ_mol1 120 GLY 1865 N 0.520373965716017 0.208104738641507 \n", 124 ] 125 126 # Printout of the real and generated data. 127 print("\n\nThe real data:") 128 for i in range(len(lines)): 129 print(repr(data[i])) 130 print("\nThe generated data:") 131 for i in range(len(lines)): 132 print(repr(lines[i])) 133 print("\n") 134 135 # Check each line. 136 for i in range(len(lines)): 137 self.assertEqual(data[i], lines[i])

138 139

140 - def test_noe_analysis(self):

141 """Test the NOE analysis. 142 143 The test has been modified to also catch U{bug #21863<https://web.archive.org/web/https://gna.org/bugs/?21863>}. 144 """ 145 146 # Execute the script. 147 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'noe'+sep+'noe.py') 148 149 # The real data. 150 sat = [5050.0, 51643.0, 53663.0, -65111.0, -181131.0, -105322.0] 151 ref = [148614.0, 166842.0, 128690.0, 99566.0, 270047.0, 130959.0] 152 noe = [0.033980647852826784, 0.30953237194471417, 0.4169943274535706, -0.6539481349054899, -0.6707387973204665, -0.8042364404126482] 153 noe_err = [0.02020329903276632, 0.2320024671657343, 0.026067523940084526, 0.038300618865378507, 0.014260663438353431, 0.03183614777183591] 154 155 # Check the data. 156 i = 0 157 for spin in spin_loop(): 158 # Skip deselected spins. 159 if not spin.select: 160 continue 161 162 # Check the intensity data. 163 self.assertEqual(sat[i], spin.peak_intensity['sat_ave']) 164 self.assertEqual(ref[i], spin.peak_intensity['ref_ave']) 165 166 # Check the NOE data. 167 self.assertEqual(noe[i], spin.noe) 168 self.assertAlmostEqual(noe_err[i], spin.noe_err) 169 170 # Increment the spin index. 171 i += 1 172 173 # The real Grace file data. 174 data = [[ 175 '@version 50121\n', 176 '@page size 842, 595\n', 177 '@with g0\n', 178 '@ view 0.15, 0.15, 1.28, 0.85\n', 179 '@ xaxis label "Residue number"\n', 180 '@ xaxis label char size 1.00\n', 181 '@ xaxis tick major size 0.50\n', 182 '@ xaxis tick major linewidth 0.5\n', 183 '@ xaxis tick minor linewidth 0.5\n', 184 '@ xaxis tick minor size 0.25\n', 185 '@ xaxis ticklabel char size 0.70\n', 186 '@ yaxis label "\\qPeak intensities\\Q"\n', 187 '@ yaxis label char size 1.00\n', 188 '@ yaxis tick major size 0.50\n', 189 '@ yaxis tick major linewidth 0.5\n', 190 '@ yaxis tick minor linewidth 0.5\n', 191 '@ yaxis tick minor size 0.25\n', 192 '@ yaxis ticklabel char size 0.70\n', 193 '@ legend on\n', 194 '@ legend box fill pattern 1\n', 195 '@ legend char size 1.0\n', 196 '@ frame linewidth 0.5\n', 197 '@ s0 symbol 1\n', 198 '@ s0 symbol size 0.45\n', 199 '@ s0 symbol linewidth 0.5\n', 200 '@ s0 errorbar size 0.5\n', 201 '@ s0 errorbar linewidth 0.5\n', 202 '@ s0 errorbar riser linewidth 0.5\n', 203 '@ s0 legend "ref_ave"\n', 204 '@ s1 symbol 2\n', 205 '@ s1 symbol size 0.45\n', 206 '@ s1 symbol linewidth 0.5\n', 207 '@ s1 errorbar size 0.5\n', 208 '@ s1 errorbar linewidth 0.5\n', 209 '@ s1 errorbar riser linewidth 0.5\n', 210 '@ s1 legend "sat_ave"\n', 211 '@target G0.S0\n', 212 '@type xydy\n', 213 '4 148614.000000000000000 3600.000000000000000 \n', 214 '5 166842.000000000000000 122000.000000000000000 \n', 215 '6 128690.000000000000000 3600.000000000000000 \n', 216 '40 99566.000000000000000 3600.000000000000000 \n', 217 '40 270047.000000000000000 3600.000000000000000 \n', 218 '55 130959.000000000000000 3600.000000000000000 \n', 219 '&\n', 220 '@target G0.S1\n', 221 '@type xydy\n', 222 '4 5050.000000000000000 3000.000000000000000 \n', 223 '5 51643.000000000000000 8500.000000000000000 \n', 224 '6 53663.000000000000000 3000.000000000000000 \n', 225 '40 -65111.000000000000000 3000.000000000000000 \n', 226 '40 -181131.000000000000000 3000.000000000000000 \n', 227 '55 -105322.000000000000000 3000.000000000000000 \n', 228 '&\n', 229 '@with g0\n', 230 '@autoscale\n' 231 ], [ 232 '@version 50121\n', 233 '@page size 842, 595\n', 234 '@with g0\n', 235 '@ view 0.15, 0.15, 1.28, 0.85\n', 236 '@ xaxis label "Residue number"\n', 237 '@ xaxis label char size 1.00\n', 238 '@ xaxis tick major size 0.50\n', 239 '@ xaxis tick major linewidth 0.5\n', 240 '@ xaxis tick minor linewidth 0.5\n', 241 '@ xaxis tick minor size 0.25\n', 242 '@ xaxis ticklabel char size 0.70\n', 243 '@ yaxis label "\\qNOE\\Q"\n', 244 '@ yaxis label char size 1.00\n', 245 '@ yaxis tick major size 0.50\n', 246 '@ yaxis tick major linewidth 0.5\n', 247 '@ yaxis tick minor linewidth 0.5\n', 248 '@ yaxis tick minor size 0.25\n', 249 '@ yaxis ticklabel char size 0.70\n', 250 '@ legend on\n', 251 '@ legend box fill pattern 1\n', 252 '@ legend char size 1.0\n', 253 '@ frame linewidth 0.5\n', 254 '@ s0 symbol 1\n', 255 '@ s0 symbol size 0.45\n', 256 '@ s0 symbol linewidth 0.5\n', 257 '@ s0 errorbar size 0.5\n', 258 '@ s0 errorbar linewidth 0.5\n', 259 '@ s0 errorbar riser linewidth 0.5\n', 260 '@ s0 legend "N spins"\n', 261 '@ s1 symbol 2\n', 262 '@ s1 symbol size 0.45\n', 263 '@ s1 symbol linewidth 0.5\n', 264 '@ s1 errorbar size 0.5\n', 265 '@ s1 errorbar linewidth 0.5\n', 266 '@ s1 errorbar riser linewidth 0.5\n', 267 '@ s1 legend "NE1 spins"\n', 268 '@target G0.S0\n', 269 '@type xydy\n', 270 '4 0.033980647852827 0.020203299032766 \n', 271 '5 0.309532371944714 0.232002467165734 \n', 272 '6 0.416994327453571 0.026067523940085 \n', 273 '40 -0.653948134905490 0.038300618865379 \n', 274 '55 -0.804236440412648 0.031836147771836 \n', 275 '&\n', 276 '@target G0.S1\n', 277 '@type xydy\n', 278 '40 -0.670738797320466 0.014260663438353 \n', 279 '&\n', 280 '@with g0\n', 281 '@autoscale\n' 282 ]] 283 284 # Check the Grace files. 285 ids = ['intensities', 'noe'] 286 for i in range(len(ids)): 287 # The file name. 288 file_name = "%s.agr" % ids[i] 289 290 # Does the file exist? 291 self.assert_(access(ds.tmpdir+sep+file_name, F_OK)) 292 293 # Open the file and extract the contents. 294 file = open(ds.tmpdir + sep + file_name) 295 lines = file.readlines() 296 file.close() 297 298 # Nothing. 299 self.assertNotEqual(lines, []) 300 301 # Check the file contents. 302 for j in range(len(lines)): 303 print(" '%s\\n'," % lines[j][:-1].replace('"', "\\\"")) 304 for j in range(len(lines)): 305 self.assertEqual(data[i][j], lines[j])

Source Code for Module test_suite.system_tests.noe