Author: bugman
Date: Fri Feb 13 17:33:19 2015
New Revision: 27638
URL: http://svn.gna.org/viewcvs/relax?rev=27638&view=rev
Log:
Expanded the checking in all the Structure.test_mean* system tests to cover all
atomic information.
This includes the Structure.test_mean, Structure.test_mean_models, and
Structure.test_mean_molecules
system tests. All structural data is now carefully checked to make sure that
the structure.mean
user function operates correctly.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27638&r1=27637&r2=27638&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Fri Feb 13 17:33:19 2015
@@ -3708,12 +3708,18 @@
self.assertEqual(cdp.structure.structural_data[0].num, None)
mol = cdp.structure.structural_data[0].mol[0]
self.assertEqual(len(mol.atom_name), 2)
- self.assertEqual(mol.x[0], 0.5)
- self.assertEqual(mol.y[0], 1.0)
- self.assertEqual(mol.z[0], -1.0)
- self.assertEqual(mol.x[1], 0.0)
- self.assertEqual(mol.y[1], 0.0)
- self.assertEqual(mol.z[1], 0.0)
+ self.assertEqual(mol.atom_name, ['N', 'N'])
+ self.assertEqual(mol.atom_num, [None, None])
+ self.assertEqual(mol.bonded, [[], []])
+ self.assertEqual(mol.chain_id, [None, None])
+ self.assertEqual(mol.element, ['N', 'N'])
+ self.assertEqual(mol.pdb_record, [None, None])
+ self.assertEqual(mol.res_name, ['Tyr', 'Phe'])
+ self.assertEqual(mol.res_num, [2, 3])
+ self.assertEqual(mol.seg_id, [None, None])
+ self.assertEqual(mol.x, [0.5, 0.0])
+ self.assertEqual(mol.y, [1.0, 0.0])
+ self.assertEqual(mol.z, [-1.0, 0.0])
def test_mean_models(self):
@@ -3740,23 +3746,39 @@
# Calculate the mean structure and store it as model 3.
self.interpreter.structure.mean(models=[[1, 2, 4]], set_model_num=3)
+ # The expected data.
+ model_num = [1, 2, 4, 3]
+ x = [
+ [1., 1., 1.],
+ [0., 0., 0.],
+ [-1., -1., -1.],
+ [0., 0., 0.]
+ ]
+ y = [0., 2., 20.]
+ z = [
+ [-1., -1., -1.],
+ [0., 0., 0.],
+ [1., 1., 1.],
+ [0., 0., 0.]
+ ]
+
# Check the internal atomic info.
- self.assertEqual(cdp.structure.structural_data[0].num, 1)
- self.assertEqual(cdp.structure.structural_data[0].mol[0].x, [1., 1.,
1.])
- self.assertEqual(cdp.structure.structural_data[0].mol[0].y, [0., 2.,
20.])
- self.assertEqual(cdp.structure.structural_data[0].mol[0].z, [-1., -1.,
-1.])
- self.assertEqual(cdp.structure.structural_data[1].num, 2)
- self.assertEqual(cdp.structure.structural_data[1].mol[0].x, [0., 0.,
0.])
- self.assertEqual(cdp.structure.structural_data[1].mol[0].y, [0., 2.,
20.])
- self.assertEqual(cdp.structure.structural_data[1].mol[0].z, [0., 0.,
0.])
- self.assertEqual(cdp.structure.structural_data[2].num, 4)
- self.assertEqual(cdp.structure.structural_data[2].mol[0].x, [-1., -1.,
-1.])
- self.assertEqual(cdp.structure.structural_data[2].mol[0].y, [0., 2.,
20.])
- self.assertEqual(cdp.structure.structural_data[2].mol[0].z, [1., 1.,
1.])
- self.assertEqual(cdp.structure.structural_data[3].num, 3)
- self.assertEqual(cdp.structure.structural_data[3].mol[0].x, [0., 0.,
0.])
- self.assertEqual(cdp.structure.structural_data[3].mol[0].y, [0., 2.,
20.])
- self.assertEqual(cdp.structure.structural_data[3].mol[0].z, [0., 0.,
0.])
+ self.assertEqual(len(cdp.structure.structural_data), 4)
+ for i in range(4):
+ self.assertEqual(len(cdp.structure.structural_data[i].mol), 1)
+ self.assertEqual(cdp.structure.structural_data[i].num,
model_num[i])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].atom_num,
[None, None, None])
+
self.assertEqual(cdp.structure.structural_data[i].mol[0].atom_name, ['A', 'A',
'A'])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].bonded,
[[], [], []])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].chain_id,
[None, None, None])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].element,
['S', 'S', 'S'])
+
self.assertEqual(cdp.structure.structural_data[i].mol[0].pdb_record, [None,
None, None])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].res_name,
['UNK', 'UNK', 'UNK'])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].res_num,
[1, 2, 3])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].seg_id,
[None, None, None])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].x, x[i])
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].y, y)
+ self.assertEqual(cdp.structure.structural_data[i].mol[0].z, z[i])
def test_mean_molecules(self):
@@ -3779,23 +3801,39 @@
# Calculate the mean structure.
self.interpreter.structure.mean(molecules=[['X', 'Y', 'Z']],
set_mol_name='A')
+ # The expected data.
+ mol_name = ['X', 'Y', 'Z', 'A']
+ x = [
+ [1., 1., 1.],
+ [0., 0., 0.],
+ [-1., -1., -1.],
+ [0., 0., 0.]
+ ]
+ y = [0., 2., 20.]
+ z = [
+ [-1., -1., -1.],
+ [0., 0., 0.],
+ [1., 1., 1.],
+ [0., 0., 0.]
+ ]
+
# Check the internal atomic info.
- self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name, 'X')
- self.assertEqual(cdp.structure.structural_data[0].mol[0].x, [1., 1.,
1.])
- self.assertEqual(cdp.structure.structural_data[0].mol[0].y, [0., 2.,
20.])
- self.assertEqual(cdp.structure.structural_data[0].mol[0].z, [-1., -1.,
-1.])
- self.assertEqual(cdp.structure.structural_data[0].mol[1].mol_name, 'Y')
- self.assertEqual(cdp.structure.structural_data[0].mol[1].x, [0., 0.,
0.])
- self.assertEqual(cdp.structure.structural_data[0].mol[1].y, [0., 2.,
20.])
- self.assertEqual(cdp.structure.structural_data[0].mol[1].z, [0., 0.,
0.])
- self.assertEqual(cdp.structure.structural_data[0].mol[2].mol_name, 'Z')
- self.assertEqual(cdp.structure.structural_data[0].mol[2].x, [-1., -1.,
-1.])
- self.assertEqual(cdp.structure.structural_data[0].mol[2].y, [0., 2.,
20.])
- self.assertEqual(cdp.structure.structural_data[0].mol[2].z, [1., 1.,
1.])
- self.assertEqual(cdp.structure.structural_data[0].mol[3].mol_name, 'A')
- self.assertEqual(cdp.structure.structural_data[0].mol[3].x, [0., 0.,
0.])
- self.assertEqual(cdp.structure.structural_data[0].mol[3].y, [0., 2.,
20.])
- self.assertEqual(cdp.structure.structural_data[0].mol[3].z, [0., 0.,
0.])
+ self.assertEqual(len(cdp.structure.structural_data), 1)
+ for i in range(4):
+ self.assertEqual(len(cdp.structure.structural_data[0].mol), 4)
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].mol_name,
mol_name[i])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].atom_num,
[None, None, None])
+
self.assertEqual(cdp.structure.structural_data[0].mol[i].atom_name, ['A', 'A',
'A'])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].bonded,
[[], [], []])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].chain_id,
[None, None, None])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].element,
['S', 'S', 'S'])
+
self.assertEqual(cdp.structure.structural_data[0].mol[i].pdb_record, [None,
None, None])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].res_name,
['UNK', 'UNK', 'UNK'])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].res_num,
[1, 2, 3])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].seg_id,
[None, None, None])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].x, x[i])
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].y, y)
+ self.assertEqual(cdp.structure.structural_data[0].mol[i].z, z[i])
def test_metadata_xml(self):
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