Source Code for Module test_suite.consistency_tests

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006 Chris MacRaild                                           # 
  4  # Copyright (C) 2007 Sebastien Morin                                          # 
  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  import sys 
 25   
 26   
 27 -class Consistent: 
 28 -    def __init__(self, relax, test_name): 
 29          """Class for testing various aspects specific to consistency tests.""" 
 30   
 31          self.relax = relax 
 32   
 33          # Results reading test. 
 34          if test_name == 'set': 
 35   
 36              # The name of the test. 
 37              self.name = "The user function value.set()" 
 38   
 39              # The test. 
 40              self.test = self.set_value 
 41   
 42          # Consistency tests calculation test. 
 43          if test_name == 'calc': 
 44   
 45              # The name of the test. 
 46              self.name = "Consistency tests calculation" 
 47   
 48              # The test. 
 49              self.test = self.calc 
 50   
 51   
 52 -    def calc(self, run): 
 53          """The consistency tests calculation test.""" 
 54   
 55          # Arguments. 
 56          self.run = run 
 57   
 58          # Setup. 
 59          self.calc_setup() 
 60   
 61          # Try the consistency testing. 
 62          self.relax.interpreter._Minimisation.calc(self.run) 
 63   
 64          # Success. 
 65          return self.calc_integrity() 
 66   
 67   
 68 -    def calc_integrity(self): 
 69          """The consistency tests calculation sub-routine.""" 
 70   
 71          # Correct consistency functions values: 
 72          j0 = [4.0958793960056238e-09, 3.7976266046729745e-09] 
 73          f_eta = [0.20302515844782615, 0.18796462392813956] 
 74          f_r2 = [2.0611470814962761e-09, 1.9117396355237641e-09] 
 75   
 76          # Loop over residues. 
 77          for index,residue in enumerate(self.relax.data.res[self.run]): 
 78              # Residues -2 and -1 have data. 
 79              if index == 0 or index == 1: 
 80                  if not self.relax.data.res[self.run][index].select: 
 81                      print 'Residue', self.relax.data.res[self.run][index].num, 'unexpectedly not selected' 
 82                      return 
 83   
 84                  if abs(self.relax.data.res[self.run][index].j0 - j0[index]) > j0[index]/1e6: 
 85                      print 'Error in residue', self.relax.data.res[self.run][index].num, 'j0 calculated value' 
 86                      return 
 87                  if abs(self.relax.data.res[self.run][index].f_eta - f_eta[index]) > f_eta[index]/1e6: 
 88                      print 'Error in residue', self.relax.data.res[self.run][index].num, 'f_eta calculated value' 
 89                      return 
 90                  if abs(self.relax.data.res[self.run][index].f_r2 - f_r2[index]) > f_r2[index]/1e6: 
 91                      print 'Error in residue', self.relax.data.res[self.run][index].num, 'f_r2 calculated value' 
 92                      return 
 93   
 94              # Other residues have insufficient data. 
 95              else: 
 96                  if self.relax.data.res[self.run][index].select: 
 97                      print 'Residue', self.relax.data.res[self.run][index].num, 'unexpectedly selected' 
 98                      return 
 99   
100          # Success. 
101          return 1 
102   
103   
104 -    def calc_setup(self): 
105          """Setup for the calculation test.""" 
106   
107          # Locate and describe the data. 
108          dir = sys.path[-1] + '/test_suite/data/jw_mapping/' 
109   
110          dataPaths = [dir + 'noe.dat', 
111                       dir + 'R1.dat', 
112                       dir + 'R2.dat'] 
113   
114          dataTypes = [('NOE', '600', 600.0e6), 
115                       ('R1', '600', 600.0e6), 
116                       ('R2', '600', 600.0e6)] 
117   
118          # Create the run. 
119          self.relax.generic.runs.create(self.run, 'ct') 
120   
121          # Read the sequence. 
122          self.relax.interpreter._Sequence.read(self.run, file='test_seq', dir=sys.path[-1] + '/test_suite/data') 
123   
124          # Read the data. 
125          for dataSet in xrange(len(dataPaths)): 
126              self.relax.interpreter._Relax_data.read(self.run, dataTypes[dataSet][0], dataTypes[dataSet][1], dataTypes[dataSet][2], dataPaths[dataSet]) 
127   
128          # Nuclei type. 
129          self.relax.interpreter._Nuclei.nuclei('N') 
130   
131          # Set r and csa. 
132          self.relax.interpreter._Value.set(self.run, 1.02 * 1e-10, 'bond_length') 
133          self.relax.interpreter._Value.set(self.run, -170 * 1e-6, 'csa') 
134   
135          # Set the angle between the 15N-1H vector and the principal axis of the 15N chemical shift tensor 
136          self.relax.interpreter._Value.set(self.run, 15.7, 'orientation') 
137   
138          # Set the approximate correlation time. 
139          self.relax.interpreter._Value.set(self.run, 13 * 1e-9, 'tc') 
140   
141          # Set the frequency. 
142          self.relax.interpreter._Consistency_tests.set_frq(self.run, frq=600.0 * 1e6) 
143   
144   
145 -    def set_value(self, run): 
146          """The value.set test.""" 
147   
148          # Arguments. 
149          self.run = run 
150   
151          # Create the run. 
152          self.relax.generic.runs.create(self.run, 'ct') 
153   
154          # Read the sequence. 
155          self.relax.interpreter._Sequence.read(self.run, file='test_seq', dir=sys.path[-1] + '/test_suite/data') 
156   
157          # Try to set the values. 
158          bond_length = 1.02 * 1e-10 
159          csa = -170 * 1e-6 
160          orientation = 15.7 
161          tc = 13 * 1e-9 
162          self.relax.interpreter._Value.set(self.run, bond_length, 'bond_length') 
163          self.relax.interpreter._Value.set(self.run, csa, 'csa') 
164          self.relax.interpreter._Value.set(self.run, orientation, 'orientation') 
165          self.relax.interpreter._Value.set(self.run, tc, 'tc') 
166   
167          # Test values. 
168          for i in xrange( len(self.relax.data.res[self.run]) ): 
169              if self.relax.data.res[self.run][i].r != bond_length: 
170                  print 'Value of bond_length has not been set correctly' 
171                  return 
172              if self.relax.data.res[self.run][i].csa != csa: 
173                  print 'Value of csa has not been set correctly' 
174                  return 
175              if self.relax.data.res[self.run][i].orientation != orientation: 
176                  print 'Value of orientation has not been set correctly' 
177                  return 
178              if self.relax.data.res[self.run][i].tc != tc: 
179                  print 'Value of tc has not been set correctly' 
180                  return 
181   
182          # Success. 
183          return 1 
184