Source Code for Module test_suite.unit_tests.sequence_testing_base

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2007-2012 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program 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 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from os import sep 
 24  import sys 
 25  from tempfile import mktemp 
 26  try: 
 27      from hashlib import md5 
 28  except ImportError: 
 29      from md5 import new as md5 
 30   
 31  # relax module imports. 
 32  from data import Relax_data_store; ds = Relax_data_store() 
 33  from generic_fns import pipes 
 34  from relax_io import delete 
 35  from status import Status; status = Status() 
 36  from test_suite.unit_tests.base_classes import UnitTestCase 
 37   
 38   
 39 -class Sequence_base_class(UnitTestCase): 
 40      """Base class for the tests of both the 'prompt.sequence' and 'generic_fns.sequence' modules. 
 41   
 42      This base class also contains many shared unit tests. 
 43      """ 
 44   
 45 -    def setUp(self): 
 46          """Set up for all the molecule unit tests.""" 
 47   
 48          # Add a data pipe to the data store. 
 49          ds.add(pipe_name='orig', pipe_type='mf') 
 50   
 51          # Get a temporary file name. 
 52          ds.tmpfile = mktemp() 
 53   
 54          # Ap4Aase residue sequence data. 
 55          self.Ap4Aase_res_num = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165] 
 56          self.Ap4Aase_res_name = ['GLY', 'PRO', 'LEU', 'GLY', 'SER', 'MET', 'ASP', 'SER', 'PRO', 'PRO', 'GLU', 'GLY', 'TYR', 'ARG', 'ARG', 'ASN', 'VAL', 'GLY', 'ILE', 'CYS', 'LEU', 'MET', 'ASN', 'ASN', 'ASP', 'LYS', 'LYS', 'ILE', 'PHE', 'ALA', 'ALA', 'SER', 'ARG', 'LEU', 'ASP', 'ILE', 'PRO', 'ASP', 'ALA', 'TRP', 'GLN', 'MET', 'PRO', 'GLN', 'GLY', 'GLY', 'ILE', 'ASP', 'GLU', 'GLY', 'GLU', 'ASP', 'PRO', 'ARG', 'ASN', 'ALA', 'ALA', 'ILE', 'ARG', 'GLU', 'LEU', 'ARG', 'GLU', 'GLU', 'THR', 'GLY', 'VAL', 'THR', 'SER', 'ALA', 'GLU', 'VAL', 'ILE', 'ALA', 'GLU', 'VAL', 'PRO', 'TYR', 'TRP', 'LEU', 'THR', 'TYR', 'ASP', 'PHE', 'PRO', 'PRO', 'LYS', 'VAL', 'ARG', 'GLU', 'LYS', 'LEU', 'ASN', 'ILE', 'GLN', 'TRP', 'GLY', 'SER', 'ASP', 'TRP', 'LYS', 'GLY', 'GLN', 'ALA', 'GLN', 'LYS', 'TRP', 'PHE', 'LEU', 'PHE', 'LYS', 'PHE', 'THR', 'GLY', 'GLN', 'ASP', 'GLN', 'GLU', 'ILE', 'ASN', 'LEU', 'LEU', 'GLY', 'ASP', 'GLY', 'SER', 'GLU', 'LYS', 'PRO', 'GLU', 'PHE', 'GLY', 'GLU', 'TRP', 'SER', 'TRP', 'VAL', 'THR', 'PRO', 'GLU', 'GLN', 'LEU', 'ILE', 'ASP', 'LEU', 'THR', 'VAL', 'GLU', 'PHE', 'LYS', 'LYS', 'PRO', 'VAL', 'TYR', 'LYS', 'GLU', 'VAL', 'LEU', 'SER', 'VAL', 'PHE', 'ALA', 'PRO', 'HIS', 'LEU'] 
 57   
 58   
 59 -    def test_copy_protein_sequence(self): 
 60          """Test the copying of an amino acid sequence. 
 61   
 62          The functions tested are generic_fns.sequence.copy() and prompt.sequence.copy(). 
 63          """ 
 64   
 65          # Get the data pipe. 
 66          dp_orig = pipes.get_pipe('orig') 
 67   
 68          # Create a simple animo acid sequence. 
 69          dp_orig.mol[0].res[0].num = 1 
 70          dp_orig.mol[0].res[0].name = 'GLY' 
 71          dp_orig.mol[0].res.add_item('PRO', 2) 
 72          dp_orig.mol[0].res.add_item('LEU', 3) 
 73          dp_orig.mol[0].res.add_item('GLY', 4) 
 74          dp_orig.mol[0].res.add_item('SER', 5) 
 75   
 76          # Add an object which should not be copied. 
 77          dp_orig.mol[0].res[2].spin[0].test = True 
 78   
 79          # Add a new data pipe to the data store. 
 80          ds.add(pipe_name='new', pipe_type='mf') 
 81          dp_new = pipes.get_pipe('new') 
 82   
 83          # Copy the residue sequence. 
 84          self.sequence_fns.copy('orig') 
 85   
 86          # Test the sequence. 
 87          self.assertEqual(dp_new.mol[0].res[0].num, 1) 
 88          self.assertEqual(dp_new.mol[0].res[0].name, 'GLY') 
 89          self.assertEqual(dp_new.mol[0].res[1].num, 2) 
 90          self.assertEqual(dp_new.mol[0].res[1].name, 'PRO') 
 91          self.assertEqual(dp_new.mol[0].res[2].num, 3) 
 92          self.assertEqual(dp_new.mol[0].res[2].name, 'LEU') 
 93          self.assertEqual(dp_new.mol[0].res[3].num, 4) 
 94          self.assertEqual(dp_new.mol[0].res[3].name, 'GLY') 
 95          self.assertEqual(dp_new.mol[0].res[4].num, 5) 
 96          self.assertEqual(dp_new.mol[0].res[4].name, 'SER') 
 97   
 98          # Test that the extra object was not copied. 
 99          self.assert_(not hasattr(dp_new.mol[0].res[2].spin[0], 'test')) 
100   
101   
102 -    def test_display_protein_sequence(self): 
103          """Test the display of an amino acid sequence. 
104   
105          The functions tested are generic_fns.sequence.display() and prompt.sequence.display(). 
106          """ 
107   
108          # Get the data pipe. 
109          dp_orig = pipes.get_pipe('orig') 
110   
111          # Create a simple animo acid sequence. 
112          dp_orig.mol[0].res[0].num = 1 
113          dp_orig.mol[0].res[0].name = 'GLY' 
114          dp_orig.mol[0].res.add_item('PRO', 2) 
115          dp_orig.mol[0].res.add_item('LEU', 3) 
116          dp_orig.mol[0].res.add_item('GLY', 4) 
117          dp_orig.mol[0].res.add_item('SER', 5) 
118   
119          # Try displaying the residue sequence. 
120          self.sequence_fns.display(res_num_flag=True, res_name_flag=True) 
121   
122   
123 -    def test_read_protein_noe_data(self): 
124          """Test the reading of the amino acid sequence out of a protein NOE data file. 
125   
126          The functions tested are generic_fns.sequence.read() and prompt.sequence.read(). 
127          """ 
128   
129          # Read the residue sequence out of the Ap4Aase 600 MHz NOE data file. 
130          self.sequence_fns.read(file='Ap4Aase.Noe.600.bz2', dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data', res_num_col=1, res_name_col=2) 
131   
132          # Get the data pipe. 
133          dp = pipes.get_pipe('orig') 
134   
135          # Test the entire sequence. 
136          for i in range(len(self.Ap4Aase_res_num)): 
137              self.assertEqual(dp.mol[0].res[i].num, self.Ap4Aase_res_num[i]) 
138              self.assertEqual(dp.mol[0].res[i].name, self.Ap4Aase_res_name[i]) 
139   
140   
141 -    def test_write_protein_sequence(self): 
142          """Test the writing of an amino acid sequence. 
143   
144          The functions tested are generic_fns.sequence.write() and prompt.sequence.write(). 
145          """ 
146   
147          # Get the data pipe. 
148          dp_orig = pipes.get_pipe('orig') 
149   
150          # Create a simple animo acid sequence. 
151          dp_orig.mol[0].res[0].num = 1 
152          dp_orig.mol[0].res[0].name = 'GLY' 
153          dp_orig.mol[0].res.add_item('PRO', 2) 
154          dp_orig.mol[0].res.add_item('LEU', 3) 
155          dp_orig.mol[0].res.add_item('GLY', 4) 
156          dp_orig.mol[0].res.add_item('SER', 5) 
157   
158          # Write the residue sequence. 
159          self.sequence_fns.write(file=ds.tmpfile, res_num_flag=True, res_name_flag=True) 
160   
161          # Open the temp file. 
162          file = open(ds.tmpfile) 
163   
164          # Get the md5sum of the file. 
165          file_md5 = md5() 
166          text = file.read() 
167          if hasattr(text, 'encode'):    # Python 3 encoding fix. 
168              text = text.encode() 
169          file_md5.update(text) 
170   
171          # Test the md5sum. 
172          digest = file_md5.digest() 
173          if sys.version_info[0] == 3: 
174              self.assertEqual(digest, eval("b'\\xc7\\xa0\\xd0i\\xa54|f\\xcc1\\xd6|\\xe7\\x82#:'")) 
175          else: 
176              self.assertEqual(digest, '\xc7\xa0\xd0i\xa54|f\xcc1\xd6|\xe7\x82#:') 
177   
178          # Close the file. 
179          file.close() 
180