remove sphinx bootstrap theme, for readthedocs

ekwan · Feb 4, 2020 · 31f2680 · 31f2680
1 parent 7e2d66e
commit 31f2680
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Showing 3 changed files with 30 additions and 6 deletions.
diff --git a/cctk/ensemble.py b/cctk/ensemble.py
@@ -217,7 +217,7 @@ def align(self, align_to=1, atoms=None):
         Args:
             align_to (int): which geometry to align to (1-indexed)
             atoms (list): which atoms to align in each molecule (1-indexed; must be at least 3)
-                alternatively, specify "None" for all atoms or "heavy" for all heavy atoms
+                alternatively, specify ``None`` for all atoms or "heavy" for all heavy atoms
 
         Returns:
             a new Ensemble() object with the objects aligned

diff --git a/docs/conf.py b/docs/conf.py
@@ -75,6 +75,6 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
 
-html_theme = 'bootstrap'
-import sphinx_bootstrap_theme
-html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+#html_theme = 'bootstrap'
+#import sphinx_bootstrap_theme
+#html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
diff --git a/test/core_tests.py b/test/core_tests.py
@@ -267,23 +267,47 @@ def generate_test_ensemble(self):
         ensemble.add_molecule(mol_trans)
         self.assertEqual(len(ensemble.molecules), 3)
 
-        mol_trans_rot = ensemble.molecules[1].translate_molecule(e2)
+        mol_trans_rot = copy.deepcopy(ensemble.molecules[1].translate_molecule(e2))
         ensemble.add_molecule(mol_trans_rot)
         self.assertEqual(len(ensemble.molecules), 4)
 
-        mol_rot_trans = ensemble.molecules[2].rotate_molecule(e1, 90)
+        mol_rot_trans = copy.deepcopy(ensemble.molecules[2].rotate_molecule(e1, 90))
         ensemble.add_molecule(mol_rot_trans)
         self.assertEqual(len(ensemble.molecules), 5)
 
+        ensemble.add_molecule(copy.deepcopy(ensemble.molecules[4].rotate_molecule(e3, 20)))
+        ensemble.add_molecule(copy.deepcopy(ensemble.molecules[5].rotate_molecule(e3, 20)))
+        ensemble.add_molecule(copy.deepcopy(ensemble.molecules[6].rotate_molecule(e3, 20)))
+        ensemble.add_molecule(copy.deepcopy(ensemble.molecules[7].rotate_molecule(e3, 20)))
+        ensemble.add_molecule(copy.deepcopy(ensemble.molecules[4].rotate_molecule(e3, -20)))
+        ensemble.add_molecule(copy.deepcopy(ensemble.molecules[5].rotate_molecule(e3, -20)))
+        ensemble.add_molecule(copy.deepcopy(ensemble.molecules[6].rotate_molecule(e3, -20)))
+        ensemble.add_molecule(copy.deepcopy(ensemble.molecules[7].rotate_molecule(e3, -20)))
         return ensemble
 
     def test_align(self):
+        #### since all the molecules are identical, every way we do this should be totally fine
         ensemble = self.generate_test_ensemble()
         ensemble.align()
         template = ensemble.molecules[0].geometry
         for molecule in ensemble.molecules:
             for i in range(0,len(template)):
                 self.assertTrue(cctk.helper_functions.compute_distance_between(molecule.geometry[i],template[i]) < 0.0001)
 
+        ensemble2 = self.generate_test_ensemble()
+        ensemble2.align(atoms="heavy")
+        template = ensemble2.molecules[0].geometry
+        for molecule in ensemble2.molecules:
+            for i in range(0,len(template)):
+                self.assertTrue(cctk.helper_functions.compute_distance_between(molecule.geometry[i],template[i]) < 0.0001)
+
+        ensemble3 = self.generate_test_ensemble()
+        ensemble3.align(atoms=[13, 4, 27, 6, 9, 14])
+        template = ensemble3.molecules[0].geometry
+        for molecule in ensemble3.molecules:
+            for i in range(0,len(template)):
+                self.assertTrue(cctk.helper_functions.compute_distance_between(molecule.geometry[i],template[i]) < 0.0001)
+
+
 if __name__ == '__main__':
     unittest.main()