Source Code for Module test_suite.system_tests.jw_mapping

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006 Chris MacRaild                                           # 
  4  # Copyright (C) 2007-2012 Edward d'Auvergne                                   # 
  5  #                                                                             # 
  6  # This file is part of the program relax.                                     # 
  7  #                                                                             # 
  8  # relax 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 2 of the License, or           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 13  # relax 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 relax; if not, write to the Free Software                        # 
 20  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Python module imports. 
 25  from os import sep 
 26  import sys 
 27   
 28  # relax module imports. 
 29  from base_classes import SystemTestCase 
 30  from data import Relax_data_store; ds = Relax_data_store() 
 31  from generic_fns.mol_res_spin import residue_loop 
 32  from physical_constants import N15_CSA, NH_BOND_LENGTH 
 33  from status import Status; status = Status() 
 34   
 35   
 36 -class Jw(SystemTestCase): 
 37      """Class for testing various aspects specific to reduced spectral density mapping.""" 
 38   
 39 -    def setUp(self): 
 40          """Set up for all the functional tests.""" 
 41   
 42          # Create the data pipe. 
 43          self.interpreter.pipe.create('jw', 'jw') 
 44   
 45   
 46 -    def test_calc(self): 
 47          """The spectral density calculation test.""" 
 48   
 49          # Data directory. 
 50          dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep 
 51   
 52          # The data. 
 53          ri_ids = ['NOE_600', 'R1_600', 'R2_600'] 
 54          ri_type = ['NOE', 'R1', 'R2'] 
 55          frq = [600e6]*3 
 56          data_paths = [dir + 'noe.dat', dir + 'R1.dat', dir + 'R2.dat'] 
 57   
 58          # Correct jw values: 
 59          j0 = [4.0703318681008998e-09, 3.7739393907014834e-09] 
 60          jwx = [1.8456254300773903e-10, 1.6347516082378241e-10] 
 61          jwh = [1.5598167512718012e-12, 2.9480536599037041e-12] 
 62   
 63          # Read the sequence. 
 64          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) 
 65   
 66          # Read the data. 
 67          for i in xrange(len(ri_ids)): 
 68              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) 
 69   
 70          # Set r, csa, heteronucleus type, and proton type. 
 71          self.interpreter.value.set(NH_BOND_LENGTH, 'r') 
 72          self.interpreter.value.set(N15_CSA, 'csa') 
 73          self.interpreter.value.set('15N', 'heteronuc_type') 
 74          self.interpreter.value.set('1H', 'proton_type') 
 75   
 76          # Select the frequency. 
 77          self.interpreter.jw_mapping.set_frq(frq=600.0 * 1e6) 
 78   
 79          # Try the reduced spectral density mapping. 
 80          self.interpreter.calc() 
 81   
 82          # Loop over residues. 
 83          index = 0 
 84          for res in residue_loop(): 
 85              # Residues -2 and -1 have data. 
 86              if res.num == -2 or res.num == -1: 
 87                  self.assert_(res.spin[0].select) 
 88                  self.assertAlmostEqual(res.spin[0].j0, j0[index]) 
 89                  self.assertAlmostEqual(res.spin[0].jwh, jwh[index]) 
 90                  self.assertAlmostEqual(res.spin[0].jwx, jwx[index]) 
 91                  index = index + 1 
 92   
 93              # Other residues have insufficient data. 
 94              else: 
 95                  self.assert_(not res.spin[0].select) 
 96   
 97   
 98 -    def test_set_value(self): 
 99          """The user function value.set().""" 
100   
101          # Read the sequence. 
102          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) 
103   
104          # Try to set the values. 
105          bond_length = NH_BOND_LENGTH 
106          csa = N15_CSA 
107          self.interpreter.value.set(bond_length, 'r') 
108          self.interpreter.value.set(csa, 'csa') 
109   
110          # Loop over residues. 
111          for res in residue_loop(): 
112              self.assertEqual(res.spin[0].r, NH_BOND_LENGTH) 
113              self.assertEqual(res.spin[0].csa, N15_CSA) 
114   
115   
116 -    def test_mapping(self): 
117          """Test a complete jw mapping run using a script.""" 
118   
119          # Execute the script. 
120          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'jw_mapping.py') 
121