Source Code for Module test_suite.jw_mapping

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006 Chris MacRaild                                           # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax 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 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax 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 relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  import sys 
 24   
 25   
 26 -class Jw: 
 27 -    def __init__(self, relax, test_name): 
 28          """Class for testing various aspects specific to reduced spectral density mapping.""" 
 29   
 30          self.relax = relax 
 31   
 32          # Results reading test. 
 33          if test_name == 'set': 
 34               
 35              # The name of the test. 
 36              self.name = "The user function value.set()" 
 37   
 38              # The test. 
 39              self.test = self.set_value 
 40   
 41          # Spectral density calculation test. 
 42          if test_name == 'calc': 
 43               
 44              # The name of the test. 
 45              self.name = "Spectral density calculation" 
 46   
 47              # The test. 
 48              self.test = self.calc 
 49   
 50   
 51 -    def calc(self, run): 
 52          """The spectral density calculation test.""" 
 53   
 54          # Arguments. 
 55          self.run = run 
 56   
 57          # Setup. 
 58          self.calc_setup() 
 59           
 60          # Try the reduced spectral density mapping. 
 61          self.relax.interpreter._Minimisation.calc(self.run) 
 62           
 63          # Success. 
 64          return self.calc_integrity() 
 65           
 66   
 67 -    def calc_integrity(self): 
 68           
 69          # Correct jw values: 
 70          j0 = [4.0703318681008998e-09, 3.7739393907014834e-09] 
 71          jwx = [1.8456254300773903e-10, 1.6347516082378241e-10] 
 72          jwh = [1.5598167512718012e-12, 2.9480536599037041e-12] 
 73   
 74          # Loop over residues. 
 75          for index,residue in enumerate(self.relax.data.res[self.run]): 
 76              # Residues -2 and -1 have data. 
 77              if index == 0 or index == 1: 
 78                  if not self.relax.data.res[self.run][index].select: 
 79                      print 'Residue', self.relax.data.res[self.run][index].num, 'unexpectedly not selected' 
 80                      return 
 81   
 82                  if abs(self.relax.data.res[self.run][index].j0 - j0[index]) > j0[index]/1e6: 
 83                      print 'Error in residue', self.relax.data.res[self.run][index].num, 'j0 calculated value' 
 84                      return 
 85                  if abs(self.relax.data.res[self.run][index].jwh - jwh[index]) > jwh[index]/1e6: 
 86                      print 'Error in residue', self.relax.data.res[self.run][index].num, 'jwh calculated value' 
 87                      return 
 88                  if abs(self.relax.data.res[self.run][index].jwx - jwx[index]) > jwx[index]/1e6: 
 89                      print 'Error in residue', self.relax.data.res[self.run][index].num, 'jwx calculated value' 
 90                      return 
 91   
 92              # Other residues have insufficient data. 
 93              else: 
 94                  if self.relax.data.res[self.run][index].select: 
 95                      print 'Residue', self.relax.data.res[self.run][index].num, 'unexpectedly selected' 
 96                      return 
 97   
 98          # Success. 
 99          return 1 
100   
101   
102 -    def calc_setup(self): 
103          """Setup for the calculation test.""" 
104   
105          dir = sys.path[-1] + '/test_suite/data/jw_mapping/' 
106   
107          dataPaths = [dir + 'noe.dat', 
108                       dir + 'R1.dat', 
109                       dir + 'R2.dat'] 
110   
111          dataTypes = [('NOE', '600', 600.0e6), 
112                       ('R1', '600', 600.0e6), 
113                       ('R2', '600', 600.0e6)] 
114           
115          # Create the run. 
116          self.relax.generic.runs.create(self.run, 'jw') 
117   
118          # Read the sequence. 
119          self.relax.interpreter._Sequence.read(self.run, file='test_seq', dir=sys.path[-1] + '/test_suite/data') 
120   
121          # Read the data. 
122          for dataSet in xrange(len(dataPaths)): 
123              self.relax.interpreter._Relax_data.read(self.run, dataTypes[dataSet][0], dataTypes[dataSet][1], dataTypes[dataSet][2], dataPaths[dataSet]) 
124   
125          # Nuclei type. 
126          self.relax.interpreter._Nuclei.nuclei('N') 
127   
128          # Set r and csa. 
129          self.relax.interpreter._Value.set(self.run, 1.02 * 1e-10, 'bond_length') 
130          self.relax.interpreter._Value.set(self.run, -172 * 1e-6, 'csa') 
131   
132          # Select the frequency. 
133          self.relax.interpreter._Jw_mapping.set_frq(self.run, frq=600.0 * 1e6) 
134   
135   
136 -    def set_value(self, run): 
137          """The value.set test.""" 
138   
139          # Arguments. 
140          self.run = run 
141   
142          # Create the run. 
143          self.relax.generic.runs.create(self.run, 'jw') 
144   
145          # Read the sequence. 
146          self.relax.interpreter._Sequence.read(self.run, file='test_seq', dir=sys.path[-1] + '/test_suite/data') 
147   
148          # Try to set the values. 
149          bond_length = 1.02 * 1e-10 
150          csa = -172 * 1e-6 
151          self.relax.interpreter._Value.set(self.run, bond_length, 'bond_length') 
152          self.relax.interpreter._Value.set(self.run, csa, 'csa') 
153   
154          # Test values. 
155          for i in xrange( len(self.relax.data.res[self.run]) ): 
156              if self.relax.data.res[self.run][i].r != bond_length: 
157                  print 'Value of bond_length has not been set correctly' 
158                  return 
159              if self.relax.data.res[self.run][i].csa != csa: 
160                  print 'Value of csa has not been set correctly' 
161                  return 
162   
163          # Success. 
164          return 1 
165