Author: bugman
Date: Wed Mar 6 17:33:01 2013
New Revision: 18659
URL: http://svn.gna.org/viewcvs/relax?rev=18659&view=rev
Log:
Created the Structure.test_read_xyz_strychnine system test to demonstrate a
bug in the XYZ parser.
This is for the reading of XYZ structure files.
Added:
trunk/test_suite/shared_data/structures/strychnine.xyz
Modified:
trunk/test_suite/system_tests/structure.py
Added: trunk/test_suite/shared_data/structures/strychnine.xyz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/structures/strychnine.xyz?rev=18659&view=auto
==============================================================================
--- trunk/test_suite/shared_data/structures/strychnine.xyz (added)
+++ trunk/test_suite/shared_data/structures/strychnine.xyz Wed Mar 6
17:33:01 2013
@@ -1,0 +1,49 @@
+47
+strychnine molecule
+ O -2.547545 2.139059 0.472310
+ O 2.015408 3.324289 0.213156
+ N 1.207610 1.203922 0.478894
+ N -1.350394 -2.624460 0.301178
+ C -0.258837 -2.073956 -0.558021
+ C -0.824223 -1.406962 -1.808433
+ C -1.741283 -0.250780 -1.378644
+ C -0.819735 0.828965 -0.783392
+ C 0.003153 0.334416 0.415455
+ C 2.358372 0.448322 0.162421
+ C 3.667689 0.888405 -0.010558
+ C 4.632616 -0.056196 -0.360560
+ C 4.303015 -1.398582 -0.525823
+ C 2.988069 -1.825141 -0.331972
+ C 2.015427 -0.899636 0.012625
+ C 0.561728 -1.122705 0.360284
+ C 0.390886 -1.834862 1.723978
+ C -1.067936 -2.282629 1.709808
+ C -2.708975 -2.252045 -0.131301
+ C -2.815469 -0.775379 -0.431910
+ C -3.718174 0.023460 0.134879
+ C -3.726395 1.516213 -0.058936
+ C -1.423939 2.193179 -0.407936
+ C -0.372897 3.059448 0.332496
+ C 1.064718 2.558120 0.325331
+ H 0.399932 -2.896344 -0.855386
+ H -1.364146 -2.140645 -2.409934
+ H -0.007016 -1.035292 -2.430851
+ H -2.229948 0.177326 -2.261725
+ H -0.101863 1.055799 -1.581061
+ H -0.582210 0.470722 1.326014
+ H 3.918694 1.929549 0.116264
+ H 5.656588 0.267474 -0.505165
+ H 5.068478 -2.115052 -0.797816
+ H 2.736463 -2.873299 -0.445917
+ H 1.059165 -2.698455 1.760657
+ H 0.631843 -1.189746 2.570301
+ H -1.243126 -3.142405 2.361743
+ H -1.719677 -1.470258 2.058429
+ H -3.410692 -2.541912 0.651788
+ H -2.971493 -2.840572 -1.016009
+ H -4.455619 -0.395106 0.813636
+ H -3.834304 1.785629 -1.118252
+ H -4.559845 1.966160 0.480526
+ H -1.736135 2.699031 -1.329897
+ H -0.354638 4.078330 -0.048526
+ H -0.690723 3.116119 1.378208
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=18659&r1=18658&r2=18659&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Mar 6 17:33:01 2013
@@ -917,6 +917,31 @@
self.assertAlmostEqual(cdp.interatomic[0].vector[0], -0.4102707)
self.assertAlmostEqual(cdp.interatomic[0].vector[1], 0.62128879)
self.assertAlmostEqual(cdp.interatomic[0].vector[2], -0.6675913)
+
+
+ def test_read_xyz_strychnine(self):
+ """Load the 'strychnine.xyz' XYZ file (using the internal structural
object XYZ reader)."""
+
+ # Path of the files.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+ # Read the XYZ file.
+ self.interpreter.structure.read_xyz(file='strychnine.xyz', dir=path,
set_mol_name='strychnine')
+
+ # Test the molecule data.
+ self.assertEqual(len(cdp.structure.structural_data), 1)
+ self.assertEqual(len(cdp.structure.structural_data[0].mol), 1)
+
+ # Load the carbon atoms and test it.
+ self.interpreter.structure.load_spins('@C')
+ self.assertEqual(count_spins(), 21)
+
+ # Load the protons.
+ self.interpreter.structure.load_spins('@H')
+ self.assertEqual(count_spins(), 43)
+
+ # And now all the rest of the atoms.
+ self.interpreter.structure.load_spins()
def test_rmsd(self):
r18659 - in /trunk/test_suite: shared_data/structures/strychnine.xyz system_tests/structure.py