Merge pull request #28 from pckroon/fix_27

Fix 27
pckroon · Jul 27, 2023 · 077f254 · 077f254
2 parents d4813a7 + b1052eb
commit 077f254
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diff --git a/pysmiles/smiles_helper.py b/pysmiles/smiles_helper.py
@@ -141,8 +141,8 @@ def format_atom(molecule, node_key, default_element='*'):
     if aromatic:
         name = name.lower()
 
-    if (stereo is None and isotope == '' and charge == 0 and default_h and
-            class_ == '' and name.lower() in 'b c n o p s se as *'.split()):
+    if (stereo is None and isotope == '' and charge == 0 and default_h and class_ == '' and
+            (name.lower() in 'b c n o p s *'.split() or name in 'F Cl Br I'.split())):
         return name
 
     if hcount:

diff --git a/tests/test_write_smiles.py b/tests/test_write_smiles.py
@@ -142,6 +142,16 @@
         [],
         dict(explicit_hydrogen=False, zero_order_bonds=False, reinterpret_aromatic=True),
     ),
+    (
+      [(0, {'element': 'Se', 'charge': 0, 'aromatic': False, 'hcount': 0})],
+      [],
+      False
+    ),
+    (
+      [(0, {'element': 'As', 'charge': 0, 'aromatic': False, 'hcount': 0})],
+      [],
+      False
+    ),
 ))
 def test_write_smiles(node_data, edge_data, kwargs):
     mol = make_mol(node_data, edge_data)