Author: bugman
Date: Wed Oct 1 19:44:34 2014
New Revision: 26118
URL: http://svn.gna.org/viewcvs/relax?rev=26118&view=rev
Log:
Created the Structure.test_delete_atom system test.
This is used to test the deletion of a single atom using the structure.delete
user function.
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=26118&r1=26117&r2=26118&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Oct 1 19:44:34 2014
@@ -2577,6 +2577,74 @@
self.assertEqual(real_data[i], lines[i])
+ def test_delete_atom(self):
+ """Test the deletion of a single atom using the U{structure.delete
user function<http://www.nmr-relax.com/manual/structure_delete.html>}"""
+
+ # Load the test structure.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+'spheroid'
+ self.interpreter.structure.read_pdb(file='uniform.pdb', dir=path)
+
+ # Delete some atoms, testing different combinations.
+ self.interpreter.structure.delete(atom_id=':4@N', verbosity=1)
+ self.interpreter.structure.delete(atom_id=':19', verbosity=1)
+ self.interpreter.structure.delete(atom_id=':16@H', verbosity=1)
+
+ # The expected atomic data after deletion.
+ data = [
+ ["N", "NH", 1, 0.000, 0.000, 0.000, 0, [1]],
+ ["H", "NH", 1, 0.000, 0.000, -1.020, 1, [0]],
+ ["N", "NH", 2, 0.000, 0.000, 0.000, 2, [3]],
+ ["H", "NH", 2, 0.883, 0.000, -0.510, 3, [2]],
+ ["N", "NH", 3, 0.000, 0.000, 0.000, 4, [5]],
+ ["H", "NH", 3, 0.883, 0.000, 0.510, 5, [4]],
+ ["H", "NH", 4, 0.000, 0.000, 1.020, 6, []],
+ ["N", "NH", 5, 0.000, 0.000, 0.000, 7, [8]],
+ ["H", "NH", 5, 0.000, 0.000, -1.020, 8, [7]],
+ ["N", "NH", 6, 0.000, 0.000, 0.000, 9, [10]],
+ ["H", "NH", 6, 0.273, 0.840, -0.510, 10, [9]],
+ ["N", "NH", 7, 0.000, 0.000, 0.000, 11, [12]],
+ ["H", "NH", 7, 0.273, 0.840, 0.510, 12, [11]],
+ ["N", "NH", 8, 0.000, 0.000, 0.000, 13, [14]],
+ ["H", "NH", 8, 0.000, 0.000, 1.020, 14, [13]],
+ ["N", "NH", 9, 0.000, 0.000, 0.000, 15, [16]],
+ ["H", "NH", 9, -0.000, 0.000, -1.020, 16, [15]],
+ ["N", "NH", 10, 0.000, 0.000, 0.000, 17, [18]],
+ ["H", "NH", 10, -0.715, 0.519, -0.510, 18, [17]],
+ ["N", "NH", 11, 0.000, 0.000, 0.000, 19, [20]],
+ ["H", "NH", 11, -0.715, 0.519, 0.510, 20, [19]],
+ ["N", "NH", 12, 0.000, 0.000, 0.000, 21, [22]],
+ ["H", "NH", 12, -0.000, 0.000, 1.020, 22, [21]],
+ ["N", "NH", 13, 0.000, 0.000, 0.000, 23, [24]],
+ ["H", "NH", 13, -0.000, -0.000, -1.020, 24, [23]],
+ ["N", "NH", 14, 0.000, 0.000, 0.000, 25, [26]],
+ ["H", "NH", 14, -0.715, -0.519, -0.510, 26, [25]],
+ ["N", "NH", 15, 0.000, 0.000, 0.000, 27, [28]],
+ ["H", "NH", 15, -0.715, -0.519, 0.510, 28, [27]],
+ ["N", "NH", 16, 0.000, 0.000, 0.000, 29, []],
+ ["N", "NH", 17, 0.000, 0.000, 0.000, 30, [31]],
+ ["H", "NH", 17, 0.000, -0.000, -1.020, 31, [30]],
+ ["N", "NH", 18, 0.000, 0.000, 0.000, 32, [33]],
+ ["H", "NH", 18, 0.273, -0.840, -0.510, 33, [32]],
+ ["N", "NH", 20, 0.000, 0.000, 0.000, 34, [35]],
+ ["H", "NH", 20, 0.000, -0.000, 1.020, 35, [34]]
+ ]
+
+ # The selection object.
+ selection = cdp.structure.selection()
+
+ # Check the structural object.
+ mol = cdp.structure.structural_data[0].mol[0]
+ self.assertEqual(len(data), len(mol.atom_name))
+ for i in range(len(mol.atom_name)):
+ self.assertEqual(mol.atom_name[i], data[i][0])
+ self.assertEqual(mol.res_name[i], data[i][1])
+ self.assertEqual(mol.res_num[i], data[i][2])
+ self.assertEqual(mol.x[i], data[i][3])
+ self.assertEqual(mol.y[i], data[i][4])
+ self.assertEqual(mol.z[i], data[i][5])
+ self.assertEqual(mol.bonded[i], data[i][7])
+
+
def test_delete_empty(self):
"""Test the deletion of non-existent structural data."""
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