Source Code for Module test_suite.unit_tests._generic_fns._structure.test_internal

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2012 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 path, sep 
 24  import sys 
 25   
 26  # relax module imports. 
 27  from data import Relax_data_store; ds = Relax_data_store() 
 28  from generic_fns.reset import reset 
 29  from generic_fns.structure.internal import Internal, MolContainer 
 30  from relax_io import file_root 
 31  from status import Status; status = Status() 
 32  from test_suite.unit_tests.base_classes import UnitTestCase 
 33   
 34   
 35 -class Test_internal(UnitTestCase): 
 36      """Unit tests for the functions of the 'generic_fns.structure.internal' module.""" 
 37   
 38 -    def setUp(self): 
 39          """Set up for all the internal relax structural object unit tests.""" 
 40   
 41          # The path to a PDB file. 
 42          self.test_pdb_path = status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'Ap4Aase_res1-12.pdb' 
 43          expanded = path.split(self.test_pdb_path) 
 44          self.test_pdb_dir = expanded[0] 
 45          self.test_pdb_file_name = expanded[1] 
 46          self.test_pdb_root = file_root(self.test_pdb_path) 
 47   
 48          # Instantiate the structural data object. 
 49          self.data = Internal() 
 50   
 51          # Instantiate a MolContainer object. 
 52          self.mol_cont = MolContainer() 
 53   
 54   
 55 -    def tearDown(self): 
 56          """Reset the relax data storage object.""" 
 57   
 58          # Delete the structural data object. 
 59          del self.data 
 60   
 61          # Reset relax. 
 62          reset() 
 63   
 64   
 65 -    def test__parse_pdb_record(self): 
 66          """Test the private MolContainer._parse_pdb_record() method.""" 
 67   
 68          # Parse a PDB record. 
 69          record = self.mol_cont._parse_pdb_record('ATOM    158  CG  GLU    11       9.590  -1.041 -11.596  1.00  0.00           C') 
 70   
 71          # Test the elements. 
 72          self.assertEqual(record[0], 'ATOM') 
 73          self.assertEqual(record[1], 158) 
 74          self.assertEqual(record[2], 'CG') 
 75          self.assertEqual(record[3], None) 
 76          self.assertEqual(record[4], 'GLU') 
 77          self.assertEqual(record[5], None) 
 78          self.assertEqual(record[6], 11) 
 79          self.assertEqual(record[7], None) 
 80          self.assertEqual(record[8], 9.59) 
 81          self.assertEqual(record[9], -1.041) 
 82          self.assertEqual(record[10], -11.596) 
 83          self.assertEqual(record[11], 1.0) 
 84          self.assertEqual(record[12], 0.0) 
 85          self.assertEqual(record[13], None) 
 86          self.assertEqual(record[14], 'C') 
 87          self.assertEqual(record[15], None) 
 88   
 89   
 90 -    def test_atom_loop(self): 
 91          """Test the Internal.atom_loop() method.""" 
 92   
 93          # Load the PDB file. 
 94          self.data.load_pdb(self.test_pdb_path) 
 95   
 96          # Loop over the atoms. 
 97          atom_count = 0 
 98          for atom in self.data.atom_loop(): 
 99              atom_count = atom_count + 1 
100   
101          # Test the number of atoms looped over. 
102          self.assertEqual(atom_count, 150) 
103   
104   
105 -    def test_atom_loop_mol_selection(self): 
106          """Test the Internal.atom_loop() method with the '#XXX' mol selection.""" 
107   
108          # Load the PDB file. 
109          self.data.load_pdb(self.test_pdb_path) 
110   
111          # Loop over the atoms. 
112          atom_count = 0 
113          for atom in self.data.atom_loop(atom_id='#XXX'): 
114              atom_count = atom_count + 1 
115   
116          # Test the number of atoms looped over. 
117          self.assertEqual(atom_count, 0) 
118   
119   
120 -    def test_atom_loop_res_selection1(self): 
121          """Test the Internal.atom_loop() method with the ':8' res selection.""" 
122   
123          # Load the PDB file. 
124          self.data.load_pdb(self.test_pdb_path) 
125   
126          # Loop over the atoms. 
127          atom_count = 0 
128          for res_num, res_name in self.data.atom_loop(atom_id=':8', res_num_flag=True, res_name_flag=True): 
129              # Test the residue name and number. 
130              self.assertEqual(res_num, 8) 
131              self.assertEqual(res_name, 'SER') 
132   
133              # Increment the atom count. 
134              atom_count = atom_count + 1 
135   
136          # Test the number of atoms looped over. 
137          self.assertEqual(atom_count, 11) 
138   
139   
140 -    def test_atom_loop_res_selection2(self): 
141          """Test the Internal.atom_loop() method with the ':PRO' res selection.""" 
142   
143          # Load the PDB file. 
144          self.data.load_pdb(self.test_pdb_path) 
145   
146          # Loop over the atoms. 
147          atom_count = 0 
148          for atom in self.data.atom_loop(atom_id=':PRO', res_name_flag=True): 
149              # Test the residue name. 
150              self.assertEqual(atom[0], 'PRO') 
151   
152              # Increment the atom count. 
153              atom_count = atom_count + 1 
154   
155          # Test the number of atoms looped over. 
156          self.assertEqual(atom_count, 42) 
157   
158   
159 -    def test_atom_loop_spin_selection1(self): 
160          """Test the Internal.atom_loop() method with the '@CA' spin selection.""" 
161   
162          # Load the PDB file. 
163          self.data.load_pdb(self.test_pdb_path) 
164   
165          # Loop over the atoms. 
166          atom_count = 0 
167          for spin_name in self.data.atom_loop(atom_id='@CA', atom_name_flag=True): 
168              # Test the spin name. 
169              self.assertEqual(spin_name[0], 'CA') 
170   
171              # Increment the atom count. 
172              atom_count = atom_count + 1 
173   
174          # Test the number of atoms looped over. 
175          self.assertEqual(atom_count, 12) 
176   
177   
178 -    def test_atom_loop_spin_selection2(self): 
179          """Test the Internal.atom_loop() method with the '@163' spin selection.""" 
180   
181          # Load the PDB file. 
182          self.data.load_pdb(self.test_pdb_path) 
183   
184          # Loop over the atoms. 
185          atom_count = 0 
186          for model_num, mol_name, res_num, res_name, spin_num, spin_name, element, pos in self.data.atom_loop(atom_id='@163', model_num_flag=True, mol_name_flag=True, res_num_flag=True, res_name_flag=True, atom_num_flag=True, atom_name_flag=True, element_flag=True, pos_flag=True): 
187              # Test the spin info. 
188              self.assertEqual(model_num, 1) 
189              self.assertEqual(mol_name, self.test_pdb_root+'_mol1') 
190              self.assertEqual(res_num, 11) 
191              self.assertEqual(res_name, 'GLU') 
192              self.assertEqual(spin_num, 163) 
193              self.assertEqual(spin_name, 'OE1') 
194              self.assertEqual(element, 'O') 
195              self.assertEqual(pos[0], float('10.055')) 
196              self.assertEqual(pos[1], float('-2.74')) 
197              self.assertEqual(pos[2], float('-13.193')) 
198   
199              # Increment the atom count. 
200              atom_count = atom_count + 1 
201   
202          # Test the number of atoms looped over. 
203          self.assertEqual(atom_count, 1) 
204   
205   
206 -    def test_load_pdb(self): 
207          """Load a PDB file using Internal.load_pdb().""" 
208   
209          # Load the PDB file. 
210          self.data.load_pdb(self.test_pdb_path) 
211   
212          # The ModelContainer and MolContainer. 
213          model = self.data.structural_data[0] 
214          mol = model.mol[0] 
215   
216          # Test the structural data. 
217          self.assertEqual(len(self.data.structural_data), 1) 
218          self.assertEqual(len(model.mol), 1) 
219          self.assertEqual(model.num, 1) 
220          self.assertEqual(mol.mol_name, self.test_pdb_root+'_mol1') 
221          self.assertEqual(mol.file_name, self.test_pdb_file_name) 
222          self.assertEqual(mol.file_path, self.test_pdb_dir) 
223          self.assertEqual(mol.file_model, 1) 
224          self.assertEqual(mol.file_mol_num, 1) 
225   
226          # The real atomic data. 
227          atom_name = ['N', 'CA', '1HA', '2HA', 'C', 'O', '1HT', '2HT', '3HT', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', 'HG', 'CD1', '1HD1', '2HD1', '3HD1', 'CD2', '1HD2', '2HD2', '3HD2', 'C', 'O', 'N', 'H', 'CA', '1HA', '2HA', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'OG', 'HG', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', 'SD', 'CE', '1HE', '2HE', '3HE', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', 'OD1', 'OD2', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'OG', 'HG', 'C', 'O', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'CD', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', '1HD', '2HD', 'C', 'O', 'N', 'H', 'CA', 'HA', 'CB', '1HB', '2HB', 'CG', '1HG', '2HG', 'CD', 'OE1', 'OE2', 'C', 'O', 'N', 'H', 'CA', '1HA', '2HA', 'C', 'O'] 
228          bonded = [[]]*174 
229          chain_id = [None]*174 
230          element = ['N', 'C', 'H', 'H', 'C', 'O', 'H', 'H', 'H', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'O', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'S', 'C', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'O', 'O', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'O', 'H', 'C', 'O', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'O', 'N', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'O', 'O', 'C', 'O', 'N', 'H', 'C', 'H', 'H', 'C', 'O'] 
231          pdb_record = ['ATOM']*174 
232          res_name = ['GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'LEU', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'ASP', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'PRO', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLU', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY', 'GLY'] 
233          res_num = [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12] 
234          seg_id = [None]*174 
235          x = [8.442, 7.469, 8.013, 6.825, 6.610, 6.827, 9.398, 8.180, 8.448, 5.613, 5.281, 4.714, 5.222, 3.646, 3.332, 2.800, 4.319, 4.853, 3.587, 6.162, 4.805, 4.075, 3.593, 4.074, 4.475, 3.498, 3.572, 2.025, 1.965, 1.609, 1.176, 1.823, 0.176, 0.096, 0.509, -0.789, 0.474, 0.809, -0.595, 0.707, 4.264, 4.364, 4.809, 4.697, 5.561, 6.220, 6.156, 4.659, 4.746, 3.786, 3.770, 2.851, 2.368, 1.785, 1.177, 1.165, 2.360, 1.690, 3.546, 3.804, 3.814, 3.563, 4.442, 4.984, 5.411, 6.192, 4.872, 6.068, 6.868, 5.332, 6.747, 6.155, 5.409, 6.977, 5.721, 3.369, 2.255, 3.703, 4.604, 2.753, 1.851, 3.329, 4.182, 3.644, 2.319, 1.992, 1.854, 2.419, 1.251, 3.451, 4.359, 3.267, 2.246, 4.223, 4.054, 4.040, 5.573, 6.142, 3.488, 4.276, 2.795, 1.828, 2.929, 2.810, 1.772, 0.912, 2.067, 1.505, 0.464, 2.138, 0.938, 2.273, 4.268, 4.585, 5.076, 4.776, 6.392, 6.925, 7.120, 7.968, 7.464, 6.130, 6.384, 6.135, 4.210, 4.246, 6.325, 5.263, 7.477, 8.281, 7.587, 7.039, 9.047, 9.133, 9.654, 9.590, 10.670, 9.215, 9.190, 10.055, 8.012, 7.007, 7.361, 6.144, 5.925, 5.555, 6.329, 4.814, 4.894, 4.761] 
236          y = [10.188, 9.889, 9.712, 10.745, 8.674, 7.991, 10.291, 11.073, 9.416, 8.385, 9.152, 7.243, 6.302, 7.443, 6.483, 7.963, 8.253, 7.605, 8.842, 9.327, 10.088, 7.251, 8.285, 6.099, 5.309, 5.986, 4.953, 6.396, 7.471, 6.106, 5.775, 5.225, 4.796, 4.954, 3.787, 4.949, 6.853, 7.828, 6.775, 6.720, 6.853, 8.068, 6.222, 5.251, 6.956, 6.273, 7.706, 7.634, 8.841, 6.847, 5.889, 7.360, 6.511, 8.230, 7.620, 8.669, 9.269, 9.652, 8.174, 9.362, 7.546, 6.604, 8.253, 9.095, 7.354, 7.976, 6.886, 6.258, 5.824, 5.499, 6.846, 5.570, 5.985, 5.190, 4.766, 8.771, 8.245, 9.789, 10.161, 10.351, 10.605, 11.610, 11.341, 12.287, 12.322, 11.787, 13.410, 9.322, 9.015, 8.776, 9.052, 7.758, 7.826, 7.990, 8.977, 7.248, 7.894, 8.285, 6.370, 6.214, 5.342, 5.431, 3.973, 3.943, 3.230, 3.234, 2.212, 3.991, 3.892, 3.624, 5.960, 5.908, 3.339, 3.179, 2.980, 3.150, 2.375, 2.876, 2.616, 3.262, 1.675, 3.264, 4.305, 2.758, 4.055, 2.299, 0.876, 0.258, 0.312, 0.871, -1.106, -1.253, -1.489, -2.564, -1.049, -1.041, -1.011, -0.052, -1.970, -2.740, -1.931, -2.037, -1.962, -2.949, -2.983, -3.917, -4.588, -4.488, -3.289, -3.932] 
237          z = [6.302, 7.391, 8.306, 7.526, 7.089, 6.087, 6.697, 5.822, 5.604, 7.943, 9.155, 7.752, 7.908, 8.829, 9.212, 8.407, 9.880, 10.560, 10.415, 9.754, 8.900, 6.374, 5.909, 5.719, 6.139, 4.391, 4.081, 4.415, 4.326, 5.367, 3.307, 2.640, 3.889, 4.956, 3.700, 3.430, 2.493, 2.814, 2.633, 1.449, 3.403, 3.572, 2.369, 2.281, 1.371, 0.855, 1.868, 0.359, 0.149, -0.269, -0.055, -1.268, -1.726, -0.608, 0.037, -1.377, 0.162, 0.731, -2.354, -2.175, -3.496, -3.603, -4.606, -4.199, -5.387, -5.803, -6.196, -4.563, -5.146, -4.350, -3.001, -1.895, -1.241, -1.307, -2.472, -5.551, -5.582, -6.328, -6.269, -7.274, -6.735, -7.913, -8.518, -7.133, -8.791, -9.871, -8.395, -8.346, -8.584, -8.977, -8.732, -10.002, -10.355, -11.174, -11.584, -11.936, -10.759, -11.425, -9.403, -8.469, -9.921, -11.030, -9.410, -8.336, -10.080, -9.428, -10.291, -11.333, -11.606, -12.128, -10.723, -11.893, -9.781, -10.959, -8.768, -7.344, -8.971, -9.765, -7.642, -7.816, -7.251, -6.715, -6.584, -5.765, -7.175, -6.955, -9.288, -9.222, -9.654, -9.696, -10.009, -10.928, -10.249, -10.194, -9.475, -11.596, -11.540, -11.813, -12.724, -13.193, -13.137, -8.947, -7.774, -9.383, -10.338, -8.477, -8.138, -9.017, -7.265, -6.226] 
238   
239          # Test the atomic data. 
240          for i in range(len(mol.atom_name)): 
241              self.assertEqual(mol.atom_name[i], atom_name[i]) 
242              self.assertEqual(mol.bonded[i], bonded[i]) 
243              self.assertEqual(mol.chain_id[i], chain_id[i]) 
244              self.assertEqual(mol.element[i], element[i]) 
245              self.assertEqual(mol.pdb_record[i], pdb_record[i]) 
246              self.assertEqual(mol.res_name[i], res_name[i]) 
247              self.assertEqual(mol.res_num[i], res_num[i]) 
248              self.assertEqual(mol.seg_id[i], seg_id[i]) 
249              self.assertEqual(mol.x[i], x[i]) 
250              self.assertEqual(mol.y[i], y[i]) 
251              self.assertEqual(mol.z[i], z[i]) 
252