Author: bugman
Date: Wed Oct 1 19:44:20 2014
New Revision: 26110
URL: http://svn.gna.org/viewcvs/relax?rev=26110&view=rev
Log:
Extended the Structure.test_align system test to throughly check the structural
data.
This includes changing the structure.align user function call to use 'fit to
first' and carefully
checking the new atomic coordinates.
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=26110&r1=26109&r2=26110&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Oct 1 19:44:20 2014
@@ -97,7 +97,78 @@
self.interpreter.structure.rotate(R=R, model=2)
# The alignment.
- self.interpreter.structure.align(pipes=['ref', 'align'], method='fit
to mean', atom_id='@N,H')
+ self.interpreter.structure.align(pipes=['ref', 'align'], method='fit
to first', atom_id='@N,H')
+
+ # The atomic data.
+ data = [
+ ["N", "NH", 1, 0.000, 0.000, 0.000],
+ ["H", "NH", 1, 0.000, 0.000, -1.020],
+ ["N", "NH", 2, 0.000, 0.000, 0.000],
+ ["H", "NH", 2, 0.883, 0.000, -0.510],
+ ["N", "NH", 3, 0.000, 0.000, 0.000],
+ ["H", "NH", 3, 0.883, 0.000, 0.510],
+ ["N", "NH", 4, 0.000, 0.000, 0.000],
+ ["H", "NH", 4, 0.000, 0.000, 1.020],
+ ["N", "NH", 5, 0.000, 0.000, 0.000],
+ ["H", "NH", 5, 0.000, 0.000, -1.020],
+ ["N", "NH", 6, 0.000, 0.000, 0.000],
+ ["H", "NH", 6, 0.273, 0.840, -0.510],
+ ["N", "NH", 7, 0.000, 0.000, 0.000],
+ ["H", "NH", 7, 0.273, 0.840, 0.510],
+ ["N", "NH", 8, 0.000, 0.000, 0.000],
+ ["H", "NH", 8, 0.000, 0.000, 1.020],
+ ["N", "NH", 9, 0.000, 0.000, 0.000],
+ ["H", "NH", 9, -0.000, 0.000, -1.020],
+ ["N", "NH", 10, 0.000, 0.000, 0.000],
+ ["H", "NH", 10, -0.715, 0.519, -0.510],
+ ["N", "NH", 11, 0.000, 0.000, 0.000],
+ ["H", "NH", 11, -0.715, 0.519, 0.510],
+ #["N", "NH", 12, 0.000, 0.000, 0.000],
+ #["H", "NH", 12, -0.000, 0.000, 1.020],
+ ["N", "NH", 13, 0.000, 0.000, 0.000],
+ ["H", "NH", 13, -0.000, -0.000, -1.020],
+ ["N", "NH", 14, 0.000, 0.000, 0.000],
+ ["H", "NH", 14, -0.715, -0.519, -0.510],
+ ["N", "NH", 15, 0.000, 0.000, 0.000],
+ ["H", "NH", 15, -0.715, -0.519, 0.510],
+ ["N", "NH", 16, 0.000, 0.000, 0.000],
+ ["H", "NH", 16, -0.000, -0.000, 1.020],
+ ["N", "NH", 17, 0.000, 0.000, 0.000],
+ ["H", "NH", 17, 0.000, -0.000, -1.020],
+ ["N", "NH", 18, 0.000, 0.000, 0.000],
+ ["H", "NH", 18, 0.273, -0.840, -0.510],
+ ["N", "NH", 19, 0.000, 0.000, 0.000],
+ ["H", "NH", 19, 0.273, -0.840, 0.510],
+ ["N", "NH", 20, 0.000, 0.000, 0.000],
+ #["H", "NH", 20, 0.000, -0.000, 1.020]
+ ]
+
+ # The selection object.
+ selection = cdp.structure.selection()
+
+ # Check the first model.
+ self.assertEqual(len(data),
len(cdp.structure.structural_data[0].mol[0].atom_name))
+ i = 0
+ for res_num, res_name, atom_name, pos in
cdp.structure.atom_loop(selection=selection, model_num=1, res_num_flag=True,
res_name_flag=True, atom_name_flag=True, pos_flag=True):
+ self.assertEqual(atom_name, data[i][0])
+ self.assertEqual(res_name, data[i][1])
+ self.assertEqual(res_num, data[i][2])
+ self.assertEqual(pos[0][0], data[i][3])
+ self.assertEqual(pos[0][1], data[i][4])
+ self.assertEqual(pos[0][2], data[i][5])
+ i += 1
+
+ # Check the second model.
+ self.assertEqual(len(data),
len(cdp.structure.structural_data[1].mol[0].atom_name))
+ i = 0
+ for res_num, res_name, atom_name, pos in
cdp.structure.atom_loop(selection=selection, model_num=2, res_num_flag=True,
res_name_flag=True, atom_name_flag=True, pos_flag=True):
+ self.assertEqual(atom_name, data[i][0])
+ self.assertEqual(res_name, data[i][1])
+ self.assertEqual(res_num, data[i][2])
+ self.assertEqual(pos[0][0], data[i][3])
+ self.assertEqual(pos[0][1], data[i][4])
+ self.assertEqual(pos[0][2], data[i][5])
+ i += 1
def test_alt_loc_missing(self):
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