Source Code for Module test_suite.system_tests.noe

  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).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation, either version 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 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  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_noe_analysis(self): 
 47          """Test the NOE analysis.""" 
 48   
 49          # Execute the script. 
 50          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'noe.py') 
 51   
 52          # The real data. 
 53          sat = [5050.0, 51643.0, 53663.0, -65111.0, -181131.0, -105322.0] 
 54          ref = [148614.0, 166842.0, 128690.0, 99566.0, 270047.0, 130959.0] 
 55          noe = [0.033980647852826784, 0.30953237194471417, 0.4169943274535706, -0.6539481349054899, -0.6707387973204665, -0.8042364404126482] 
 56          noe_err = [0.02020329903276632, 0.2320024671657343, 0.026067523940084526, 0.038300618865378507, 0.014260663438353431, 0.03183614777183591] 
 57   
 58          # Check the data. 
 59          i = 0 
 60          for spin in spin_loop(): 
 61              # Skip deselected spins. 
 62              if not spin.select: 
 63                  continue 
 64   
 65              # Check the intensity data. 
 66              self.assertEqual(sat[i], spin.intensities['sat_ave']) 
 67              self.assertEqual(ref[i], spin.intensities['ref_ave']) 
 68   
 69              # Check the NOE data. 
 70              self.assertEqual(noe[i], spin.noe) 
 71              self.assertAlmostEqual(noe_err[i], spin.noe_err) 
 72   
 73              # Increment the spin index. 
 74              i += 1 
 75   
 76          # The real Grace file data. 
 77          data = [ 
 78              '@version 50121\n', 
 79              '@page size 842, 595\n', 
 80              '@with g0\n', 
 81              '@    view 0.15, 0.15, 1.28, 0.85\n', 
 82              '@    xaxis  label "Residue number"\n', 
 83              '@    xaxis  label char size 1.00\n', 
 84              '@    xaxis  tick major size 0.50\n', 
 85              '@    xaxis  tick major linewidth 0.5\n', 
 86              '@    xaxis  tick minor linewidth 0.5\n', 
 87              '@    xaxis  tick minor size 0.25\n', 
 88              '@    xaxis  ticklabel char size 0.70\n', 
 89              '@    yaxis  label "\\qNOE\\Q"\n', 
 90              '@    yaxis  label char size 1.00\n', 
 91              '@    yaxis  tick major size 0.50\n', 
 92              '@    yaxis  tick major linewidth 0.5\n', 
 93              '@    yaxis  tick minor linewidth 0.5\n', 
 94              '@    yaxis  tick minor size 0.25\n', 
 95              '@    yaxis  ticklabel char size 0.70\n', 
 96              '@    legend off\n', 
 97              '@    frame linewidth 0.5\n', 
 98              '@    s0 symbol 1\n', 
 99              '@    s0 symbol size 0.45\n', 
100              '@    s0 symbol linewidth 0.5\n', 
101              '@    s0 errorbar size 0.5\n', 
102              '@    s0 errorbar linewidth 0.5\n', 
103              '@    s0 errorbar riser linewidth 0.5\n', 
104              '@    s0 legend "N spins"\n', 
105              '@    s1 symbol 2\n', 
106              '@    s1 symbol size 0.45\n', 
107              '@    s1 symbol linewidth 0.5\n', 
108              '@    s1 errorbar size 0.5\n', 
109              '@    s1 errorbar linewidth 0.5\n', 
110              '@    s1 errorbar riser linewidth 0.5\n', 
111              '@    s1 legend "NE1 spins"\n', 
112              '@target G0.S0\n', 
113              '@type xydy\n', 
114              '4                              0.033980647852827              0.020203299032766             \n', 
115              '5                              0.309532371944714              0.232002467165734             \n', 
116              '6                              0.416994327453571              0.026067523940085             \n', 
117              '40                             -0.653948134905490             0.038300618865379             \n', 
118              '55                             -0.804236440412648             0.031836147771836             \n', 
119              '&\n', 
120              '@target G0.S1\n', 
121              '@type xydy\n', 
122              '40                             -0.670738797320466             0.014260663438353             \n', 
123              '&\n', 
124              '@with g0\n', 
125              '@autoscale\n' 
126          ] 
127   
128          # Check the Grace file. 
129          file = open(ds.tmpfile) 
130          lines = file.readlines() 
131          file.close() 
132          for i in range(len(lines)): 
133              print("            '%s\\n'," % lines[i][:-1].replace('"', "\\\"")) 
134          for i in range(len(lines)): 
135              self.assertEqual(data[i], lines[i]) 
136