Source Code for Module test_suite.system_tests.consistency_tests

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006 Chris MacRaild                                           # 
  4  # Copyright (C) 2007-2008 Sebastien Morin                                     # 
  5  # Copyright (C) 2010-2012 Edward d'Auvergne                                   # 
  6  #                                                                             # 
  7  # This file is part of the program relax.                                     # 
  8  #                                                                             # 
  9  # relax is free software; you can redistribute it and/or modify               # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation; either version 2 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # relax is distributed in the hope that it will be useful,                    # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with relax; if not, write to the Free Software                        # 
 21  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 22  #                                                                             # 
 23  ############################################################################### 
 24   
 25  # Python module imports. 
 26  from os import sep 
 27  import sys 
 28   
 29  # relax module imports. 
 30  from base_classes import SystemTestCase 
 31  from data import Relax_data_store; ds = Relax_data_store() 
 32  from generic_fns.mol_res_spin import residue_loop 
 33  from physical_constants import N15_CSA, NH_BOND_LENGTH 
 34  from status import Status; status = Status() 
 35   
 36   
 37 -class Ct(SystemTestCase): 
 38      """Class for testing various aspects specific to consistency testing.""" 
 39   
 40   
 41 -    def setUp(self): 
 42          """Set up for all the functional tests.""" 
 43   
 44          # Create the data pipe. 
 45          self.interpreter.pipe.create('ct', 'ct') 
 46   
 47   
 48 -    def test_calc(self): 
 49          """The consistency testing calculation test.""" 
 50   
 51          # Data directory. 
 52          dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep 
 53   
 54          # The data. 
 55          ri_ids = ['NOE_600', 'R1_600', 'R2_600'] 
 56          ri_type = ['NOE', 'R1', 'R2'] 
 57          frq = [600e6]*3 
 58          data_paths = [dir + 'noe.dat', dir + 'R1.dat', dir + 'R2.dat'] 
 59   
 60          # Correct consistency functions values: 
 61          j0 = [4.0703318681008998e-09, 3.7739393907014834e-09] 
 62          f_eta = [0.20413244790407614, 0.18898977395296815] 
 63          f_r2 = [2.0482909381655862e-09, 1.8998154021753067e-09] 
 64   
 65          # Read the sequence. 
 66          self.interpreter.sequence.read(file='test_seq', dir=status.install_path + sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2) 
 67   
 68          # Read the data. 
 69          for i in xrange(len(ri_ids)): 
 70              self.interpreter.relax_data.read(ri_id=ri_ids[i], ri_type=ri_type[i], frq=frq[i], file=data_paths[i], res_num_col=1, res_name_col=2, data_col=3, error_col=4) 
 71   
 72          # Set r, csa, heteronucleus type, and proton type. 
 73          self.interpreter.value.set(NH_BOND_LENGTH, 'r') 
 74          self.interpreter.value.set(N15_CSA, 'csa') 
 75          self.interpreter.value.set('15N', 'heteronuc_type') 
 76          self.interpreter.value.set('1H', 'proton_type') 
 77   
 78          # Set the angle between the 15N-1H vector and the principal axis of the 15N chemical shift tensor 
 79          self.interpreter.value.set(15.7, 'orientation') 
 80   
 81          # Set the approximate correlation time. 
 82          self.interpreter.value.set(13 * 1e-9, 'tc') 
 83   
 84          # Select the frequency. 
 85          self.interpreter.consistency_tests.set_frq(frq=600.0 * 1e6) 
 86   
 87          # Try the consistency testing. 
 88          self.interpreter.calc() 
 89   
 90          # Loop over residues. 
 91          index = 0 
 92          for res in residue_loop(): 
 93              # Residues -2 and -1 have data. 
 94              if res.num == -2 or res.num == -1: 
 95                  self.assert_(res.spin[0].select) 
 96                  self.assertAlmostEqual(res.spin[0].j0, j0[index]) 
 97                  self.assertAlmostEqual(res.spin[0].f_eta, f_eta[index]) 
 98                  self.assertAlmostEqual(res.spin[0].f_r2, f_r2[index]) 
 99                  index = index + 1 
100   
101              # Other residues have insufficient data. 
102              else: 
103                  self.assert_(not res.spin[0].select) 
104   
105   
106 -    def test_set_value(self): 
107          """The user function value.set().""" 
108   
109          # Read the sequence. 
110          self.interpreter.sequence.read(file='test_seq', dir=status.install_path + sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2) 
111   
112          # Try to set the values. 
113          bond_length = NH_BOND_LENGTH 
114          csa = N15_CSA 
115          self.interpreter.value.set(bond_length, 'r') 
116          self.interpreter.value.set(csa, 'csa') 
117   
118          # Loop over residues. 
119          for res in residue_loop(): 
120              self.assertEqual(res.spin[0].r, NH_BOND_LENGTH) 
121              self.assertEqual(res.spin[0].csa, N15_CSA) 
122   
123   
124 -    def test_consistency(self): 
125          """Test a complete consistency tests run using a script.""" 
126   
127          # Execute the script. 
128          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'consistency_tests.py') 
129