Fixes error with several ring double bonds (duartegroup#87)

* Add fix for ring building

* Correct typo in ReactionFormationFalied 

* Add tests

autode/__init__.py

@@ -33,7 +33,7 @@
   - Merge when tests pass
 """
 
-__version__ = '1.1.1'
+__version__ = '1.1.2'
 
 
 __all__ = [

autode/exceptions.py

@@ -59,7 +59,7 @@ class XYZfileWrongFormat(Exception):
     pass
 
 
-class ReactionFormationFalied(Exception):
+class ReactionFormationFailed(Exception):
     pass
 
 

autode/reactions/reaction_types.py

@@ -1,4 +1,4 @@
-from autode.exceptions import ReactionFormationFalied
+from autode.exceptions import ReactionFormationFailed
 from autode.log import logger
 
 
@@ -43,11 +43,11 @@ def classify(reactants, products):
 
     elif len(reactants) == 0:
         logger.critical('Reaction had no reactants – cannot form a reaction')
-        raise ReactionFormationFalied
+        raise ReactionFormationFailed
 
     elif len(products) == 0:
         logger.critical('Reaction had no products – cannot form a reaction')
-        raise ReactionFormationFalied
+        raise ReactionFormationFailed
 
     else:
         logger.critical('Unsupported reaction type')

autode/smiles/atom_types.py

@@ -52,7 +52,7 @@ def reset_onto(self, points, coord):
         # Take a copy of the template coordinates to rotate and delete
         site_coords = np.copy(self.template_site_coords)
 
-        if len(site_coords) == len(points):
+        if len(site_coords) == len(points) or len(points) == 0:
             logger.info('No reset needed - sites were all occupied')
             return
 

doc/changelog.rst

@@ -1,6 +1,24 @@
 Changelog
 =========
 
+1.1.2
+--------
+----------
+
+Bugfixes
+
+Usability improvements/Changes
+******************************
+- Fixes typo in :code:`autode.exceptions.ReactionFormationFalied`
+
+Bug Fixes
+*********
+
+- Fixes a bug where rings containing mostly double bonds failed to build with :code:`autode.smiles.builder.Builder`
+- Fixes using XTB as a high-level method with the xtb-gaussian wrapper (thanks @kjelljorner)
+
+
+
 1.1.1
 --------
 ----------

setup.py

@@ -20,7 +20,7 @@
                         extra_link_args=["-std=c++11"])]
 
 setup(name='autode',
-      version='1.1.1',
+      version='1.1.2',
       packages=['autode',
                 'autode.conformers',
                 'autode.pes',

tests/test_reactions.py

@@ -1,5 +1,5 @@
-from autode.reactions.reaction_types import classify
-from autode.exceptions import ReactionFormationFalied
+from autode.reactions.reaction_types import classify, Addition
+from autode.exceptions import ReactionFormationFailed
 import pytest
 
 
@@ -23,11 +23,20 @@ def test_classify():
     assert rearrangement.name == 'rearrangement'
 
     # Needs to have at least some reactants and products
-    with pytest.raises(ReactionFormationFalied):
+    with pytest.raises(ReactionFormationFailed):
         _ = classify([], [])
+
+    with pytest.raises(ReactionFormationFailed):
         _ = classify([0], [])
+
+    with pytest.raises(ReactionFormationFailed):
         _ = classify([], [0])
 
     # 3 -> 3 reactions are not currently supported
     with pytest.raises(NotImplementedError):
         _ = classify([0, 1, 2], [3, 4, 5])
+
+
+def test_equality():
+
+    assert Addition == Addition

tests/test_smiles_builder.py

@@ -659,3 +659,9 @@ def test_cis_dihedral_force():
 
     # Distance between the end carbons needs to be smaller than the trans
     assert 2.0 < builder.distance(0, 3) < 3.1
+
+
+def test_many_ring_double_bonds():
+
+    assert built_molecule_is_reasonable(smiles=r'C1=C\N=C/C=N\C=C/C/1')
+    assert built_molecule_is_reasonable(smiles=r'C1=CC=C/N=N\C=C1')