Source Code for Module test_suite.system_tests.dasha

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008 Sebastien Morin                                          # 
  4  # Copyright (C) 2010-2014 Edward d'Auvergne                                   # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  7  #                                                                             # 
  8  # This program is free software: you can redistribute it and/or modify        # 
  9  # it under the terms of the GNU General Public License as published by        # 
 10  # the Free Software Foundation, either version 3 of the License, or           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 13  # This program is distributed in the hope that it will be useful,             # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 16  # GNU General Public License for more details.                                # 
 17  #                                                                             # 
 18  # You should have received a copy of the GNU General Public License           # 
 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from math import pi 
 25  from os import sep 
 26  from tempfile import mkdtemp 
 27   
 28  # relax module imports. 
 29  from data_store import Relax_data_store; ds = Relax_data_store() 
 30  import dep_check 
 31  from pipe_control.interatomic import interatomic_loop 
 32  from pipe_control.mol_res_spin import spin_loop 
 33  from lib.io import test_binary 
 34  from status import Status; status = Status() 
 35  from test_suite.system_tests.base_classes import SystemTestCase 
 36   
 37   
 38 -class Dasha(SystemTestCase): 
 39      """Class for testing various aspects specific to model-free analysis using the program 'Dasha'.""" 
 40   
 41 -    def __init__(self, methodName='runTest'): 
 42          """Skip the tests if the subprocess module is not available (Python 2.3 and earlier). 
 43   
 44          @keyword methodName:    The name of the test. 
 45          @type methodName:       str 
 46          """ 
 47   
 48          # Execute the base class method. 
 49          super(Dasha, self).__init__(methodName) 
 50   
 51          # Missing module. 
 52          if not dep_check.subprocess_module: 
 53              # Store in the status object.  
 54              status.skipped_tests.append([methodName, 'subprocess', self._skip_type]) 
 55   
 56          # Test for the presence of the Dasha binary (skip the test if not present). 
 57          try: 
 58              test_binary('dasha') 
 59          except: 
 60              status.skipped_tests.append([methodName, 'Dasha model-free software', self._skip_type]) 
 61   
 62   
 63 -    def setUp(self): 
 64          """Set up for all the functional tests.""" 
 65   
 66          # Create the data pipe. 
 67          self.interpreter.pipe.create('dasha', 'mf') 
 68   
 69          # Create a temporary directory for Dasha outputs. 
 70          ds.tmpdir = mkdtemp() 
 71   
 72   
 73 -    def test_dasha(self): 
 74          """Test a complete model-free analysis using the program 'Dasha'.""" 
 75   
 76          # Execute the script. 
 77          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'dasha.py') 
 78   
 79          # Check the global data. 
 80          self.assertEqual(len(cdp.ri_ids), 3) 
 81          for ri_id in cdp.ri_ids: 
 82              self.assertEqual(cdp.spectrometer_frq[ri_id], 600000000.0) 
 83          self.assertEqual(cdp.ri_type['R1_600'], 'R1') 
 84          self.assertEqual(cdp.ri_type['R2_600'], 'R2') 
 85          self.assertEqual(cdp.ri_type['NOE_600'], 'NOE') 
 86   
 87          # The spin data. 
 88          select = [True, True, False, False] 
 89          fixed = [False, False, False, False] 
 90          isotope = ['15N', '15N', '15N', '15N'] 
 91          model = ['m3', 'm3', 'm3', 'm3'] 
 92          equation = ['mf_orig', 'mf_orig', 'mf_orig', 'mf_orig'] 
 93          params = [['s2', 'rex'], ['s2', 'rex'], ['s2', 'rex'], ['s2', 'rex']] 
 94          s2 = [0.71510, 0.64359, None, None] 
 95          s2f = [None, None, None, None] 
 96          s2s = [None, None, None, None] 
 97          local_tm = [None, None, None, None] 
 98          te = [None, None, None, None] 
 99          tf = [None, None, None, None] 
100          ts = [None, None, None, None] 
101          rex_scale = 1.0 / (2.0 * pi * cdp.spectrometer_frq[cdp.ri_ids[0]]) ** 2 
102          rex = [4.32701*rex_scale, 4.29432*rex_scale, None, None] 
103          csa = [-172e-6, -172e-6, -172e-6, -172e-6] 
104          chi2 = [1.9657, 0.63673, None, None] 
105          ri_data = [{'R1_600': 1.0, 'R2_600': 15.0, 'NOE_600': 0.9}, 
106                     {'R1_600': 0.9, 'R2_600': 13.9, 'NOE_600': 0.79}, 
107                     {'R2_600': 12.0, 'NOE_600': 0.6}, 
108                     None] 
109          ri_data_err = [{'R1_600': 0.05, 'R2_600': 0.5, 'NOE_600': 0.05}, 
110                         {'R1_600': 0.05, 'R2_600': 0.8, 'NOE_600': 0.05}, 
111                         {'R2_600': 0.5, 'NOE_600': 0.05}, 
112                         None] 
113   
114          # Check the spin data. 
115          i = 0 
116          for spin in spin_loop(): 
117              # Protons. 
118              if spin.isotope == '1H': 
119                  self.assertEqual(spin.select, False) 
120                  continue 
121   
122              # Check the data. 
123              self.assertEqual(spin.select, select[i]) 
124              self.assertEqual(spin.fixed, fixed[i]) 
125              self.assertEqual(spin.isotope, isotope[i]) 
126              self.assertEqual(spin.model, model[i]) 
127              self.assertEqual(spin.equation, equation[i]) 
128              self.assertEqual(spin.params, params[i]) 
129              self.assertEqual(spin.s2, s2[i]) 
130              self.assertEqual(spin.s2f, s2f[i]) 
131              self.assertEqual(spin.s2s, s2s[i]) 
132              self.assertEqual(spin.local_tm, local_tm[i]) 
133              self.assertEqual(spin.te, te[i]) 
134              self.assertEqual(spin.tf, tf[i]) 
135              self.assertEqual(spin.ts, ts[i]) 
136              self.assertEqual(spin.rex, rex[i]) 
137              self.assertAlmostEqual(spin.csa, csa[i]) 
138              self.assertEqual(spin.chi2, chi2[i]) 
139              if ri_data[i] == None: 
140                  self.assert_(not hasattr(spin, 'ri_data')) 
141              else: 
142                  for ri_id in cdp.ri_ids: 
143                      if ri_id in ri_data[i]: 
144                          self.assertEqual(spin.ri_data[ri_id], ri_data[i][ri_id]) 
145   
146              # Increment the spin index. 
147              i += 1 
148   
149          # Check the interatomic data. 
150          r = [1.02e-10, 1.02e-10, 1.02e-10, 1.02e-10] 
151          i = 0 
152          for interatom in interatomic_loop(): 
153              self.assertAlmostEqual(interatom.r, r[i]) 
154              i += 1 
155