Author: bugman
Date: Tue Feb 19 17:51:06 2013
New Revision: 18500
URL: http://svn.gna.org/viewcvs/relax?rev=18500&view=rev
Log:
Fix for the unit tests of the generic_fns.structure package.
The _parse_pdb_record() is now covered by the new pdb_read module, so its
unit tests have also been
shifted into a new module.
Added:
trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py
- copied, changed from r18496,
trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
Modified:
trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
Modified: trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py?rev=18500&r1=18499&r2=18500&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
(original)
+++ trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py Tue
Feb 19 17:51:06 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2012 Edward d'Auvergne
#
+# Copyright (C) 2008-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -60,31 +60,6 @@
# Reset relax.
reset()
-
-
- def test__parse_pdb_record(self):
- """Test the private MolContainer._parse_pdb_record() method."""
-
- # Parse a PDB record.
- record = self.mol_cont._parse_pdb_record('ATOM 158 CG GLU 11
9.590 -1.041 -11.596 1.00 0.00 C')
-
- # Test the elements.
- self.assertEqual(record[0], 'ATOM')
- self.assertEqual(record[1], 158)
- self.assertEqual(record[2], 'CG')
- self.assertEqual(record[3], None)
- self.assertEqual(record[4], 'GLU')
- self.assertEqual(record[5], None)
- self.assertEqual(record[6], 11)
- self.assertEqual(record[7], None)
- self.assertEqual(record[8], 9.59)
- self.assertEqual(record[9], -1.041)
- self.assertEqual(record[10], -11.596)
- self.assertEqual(record[11], 1.0)
- self.assertEqual(record[12], 0.0)
- self.assertEqual(record[13], None)
- self.assertEqual(record[14], 'C')
- self.assertEqual(record[15], None)
def test_atom_loop(self):
Copied: trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py
(from r18496,
trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py?p2=trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py&p1=trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py&r1=18496&r2=18500&rev=18500&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
(original)
+++ trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py Tue
Feb 19 17:51:06 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2012 Edward d'Auvergne
#
+# Copyright (C) 2008-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -19,54 +19,19 @@
#
#
###############################################################################
-# Python module imports.
-from os import path, sep
-import sys
-
# relax module imports.
-from data import Relax_data_store; ds = Relax_data_store()
-from generic_fns.reset import reset
-from generic_fns.structure.internal import Internal, MolContainer
-from relax_io import file_root
-from status import Status; status = Status()
+from generic_fns.structure import pdb_read
from test_suite.unit_tests.base_classes import UnitTestCase
-class Test_internal(UnitTestCase):
- """Unit tests for the functions of the 'generic_fns.structure.internal'
module."""
+class Test_pdb_read(UnitTestCase):
+ """Unit tests for the functions of the 'generic_fns.structure.pdb_read'
module."""
- def setUp(self):
- """Set up for all the internal relax structural object unit tests."""
-
- # The path to a PDB file.
- self.test_pdb_path =
status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'Ap4Aase_res1-12.pdb'
- expanded = path.split(self.test_pdb_path)
- self.test_pdb_dir = expanded[0]
- self.test_pdb_file_name = expanded[1]
- self.test_pdb_root = file_root(self.test_pdb_path)
-
- # Instantiate the structural data object.
- self.data = Internal()
-
- # Instantiate a MolContainer object.
- self.mol_cont = MolContainer()
-
-
- def tearDown(self):
- """Reset the relax data storage object."""
-
- # Delete the structural data object.
- del self.data
-
- # Reset relax.
- reset()
-
-
- def test__parse_pdb_record(self):
- """Test the private MolContainer._parse_pdb_record() method."""
+ def test_atom(self):
+ """Test the pdb_read.atom() function."""
# Parse a PDB record.
- record = self.mol_cont._parse_pdb_record('ATOM 158 CG GLU 11
9.590 -1.041 -11.596 1.00 0.00 C')
+ record = pdb_read.atom('ATOM 158 CG GLU 11 9.590
-1.041 -11.596 1.00 0.00 C')
# Test the elements.
self.assertEqual(record[0], 'ATOM')
@@ -82,170 +47,5 @@
self.assertEqual(record[10], -11.596)
self.assertEqual(record[11], 1.0)
self.assertEqual(record[12], 0.0)
- self.assertEqual(record[13], None)
- self.assertEqual(record[14], 'C')
- self.assertEqual(record[15], None)
-
-
- def test_atom_loop(self):
- """Test the Internal.atom_loop() method."""
-
- # Load the PDB file.
- self.data.load_pdb(self.test_pdb_path)
-
- # Loop over the atoms.
- atom_count = 0
- for atom in self.data.atom_loop():
- atom_count = atom_count + 1
-
- # Test the number of atoms looped over.
- self.assertEqual(atom_count, 150)
-
-
- def test_atom_loop_mol_selection(self):
- """Test the Internal.atom_loop() method with the '#XXX' mol
selection."""
-
- # Load the PDB file.
- self.data.load_pdb(self.test_pdb_path)
-
- # Loop over the atoms.
- atom_count = 0
- for atom in self.data.atom_loop(atom_id='#XXX'):
- atom_count = atom_count + 1
-
- # Test the number of atoms looped over.
- self.assertEqual(atom_count, 0)
-
-
- def test_atom_loop_res_selection1(self):
- """Test the Internal.atom_loop() method with the ':8' res
selection."""
-
- # Load the PDB file.
- self.data.load_pdb(self.test_pdb_path)
-
- # Loop over the atoms.
- atom_count = 0
- for res_num, res_name in self.data.atom_loop(atom_id=':8',
res_num_flag=True, res_name_flag=True):
- # Test the residue name and number.
- self.assertEqual(res_num, 8)
- self.assertEqual(res_name, 'SER')
-
- # Increment the atom count.
- atom_count = atom_count + 1
-
- # Test the number of atoms looped over.
- self.assertEqual(atom_count, 11)
-
-
- def test_atom_loop_res_selection2(self):
- """Test the Internal.atom_loop() method with the ':PRO' res
selection."""
-
- # Load the PDB file.
- self.data.load_pdb(self.test_pdb_path)
-
- # Loop over the atoms.
- atom_count = 0
- for atom in self.data.atom_loop(atom_id=':PRO', res_name_flag=True):
- # Test the residue name.
- self.assertEqual(atom[0], 'PRO')
-
- # Increment the atom count.
- atom_count = atom_count + 1
-
- # Test the number of atoms looped over.
- self.assertEqual(atom_count, 42)
-
-
- def test_atom_loop_spin_selection1(self):
- """Test the Internal.atom_loop() method with the '@CA' spin
selection."""
-
- # Load the PDB file.
- self.data.load_pdb(self.test_pdb_path)
-
- # Loop over the atoms.
- atom_count = 0
- for spin_name in self.data.atom_loop(atom_id='@CA',
atom_name_flag=True):
- # Test the spin name.
- self.assertEqual(spin_name[0], 'CA')
-
- # Increment the atom count.
- atom_count = atom_count + 1
-
- # Test the number of atoms looped over.
- self.assertEqual(atom_count, 12)
-
-
- def test_atom_loop_spin_selection2(self):
- """Test the Internal.atom_loop() method with the '@163' spin
selection."""
-
- # Load the PDB file.
- self.data.load_pdb(self.test_pdb_path)
-
- # Loop over the atoms.
- atom_count = 0
- 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):
- # Test the spin info.
- self.assertEqual(model_num, 1)
- self.assertEqual(mol_name, self.test_pdb_root+'_mol1')
- self.assertEqual(res_num, 11)
- self.assertEqual(res_name, 'GLU')
- self.assertEqual(spin_num, 163)
- self.assertEqual(spin_name, 'OE1')
- self.assertEqual(element, 'O')
- self.assertEqual(pos[0], float('10.055'))
- self.assertEqual(pos[1], float('-2.74'))
- self.assertEqual(pos[2], float('-13.193'))
-
- # Increment the atom count.
- atom_count = atom_count + 1
-
- # Test the number of atoms looped over.
- self.assertEqual(atom_count, 1)
-
-
- def test_load_pdb(self):
- """Load a PDB file using Internal.load_pdb()."""
-
- # Load the PDB file.
- self.data.load_pdb(self.test_pdb_path)
-
- # The ModelContainer and MolContainer.
- model = self.data.structural_data[0]
- mol = model.mol[0]
-
- # Test the structural data.
- self.assertEqual(len(self.data.structural_data), 1)
- self.assertEqual(len(model.mol), 1)
- self.assertEqual(model.num, 1)
- self.assertEqual(mol.mol_name, self.test_pdb_root+'_mol1')
- self.assertEqual(mol.file_name, self.test_pdb_file_name)
- self.assertEqual(mol.file_path, self.test_pdb_dir)
- self.assertEqual(mol.file_model, 1)
- self.assertEqual(mol.file_mol_num, 1)
-
- # The real atomic data.
- 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']
- bonded = [[]]*174
- chain_id = [None]*174
- 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']
- pdb_record = ['ATOM']*174
- 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']
- 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]
- seg_id = [None]*174
- 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]
- 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]
- 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]
-
- # Test the atomic data.
- for i in range(len(mol.atom_name)):
- self.assertEqual(mol.atom_name[i], atom_name[i])
- self.assertEqual(mol.bonded[i], bonded[i])
- self.assertEqual(mol.chain_id[i], chain_id[i])
- self.assertEqual(mol.element[i], element[i])
- self.assertEqual(mol.pdb_record[i], pdb_record[i])
- self.assertEqual(mol.res_name[i], res_name[i])
- self.assertEqual(mol.res_num[i], res_num[i])
- self.assertEqual(mol.seg_id[i], seg_id[i])
- self.assertEqual(mol.x[i], x[i])
- self.assertEqual(mol.y[i], y[i])
- self.assertEqual(mol.z[i], z[i])
+ self.assertEqual(record[13], 'C')
+ self.assertEqual(record[14], None)
r18500 - in /trunk/test_suite/unit_tests/_generic_fns/_structure: test_internal.py test_pdb_read.py