Merge branch 'master' into bugfix-120-radical-kekulization

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.9]
 
     steps:
       - uses: actions/checkout@v2

README.md

@@ -221,11 +221,10 @@ By default, `selfies` is tested against a random subset
  * 130K molecules from [QM9](https://www.nature.com/articles/sdata201422)
  * 250K molecules from [ZINC](https://en.wikipedia.org/wiki/ZINC_database)
  * 50K molecules from a dataset of [non-fullerene acceptors for organic solar cells](https://www.sciencedirect.com/science/article/pii/S2542435117301307)
- * 160K+ molecules from various [MoleculeNet](http://moleculenet.ai/datasets-1) datasets
- * 36M+ molecules from the [eMolecules Database](https://www.emolecules.com/info/products-data-downloads.html).
-   Due to its large size, this dataset is not included on the repository. To run tests
-   on it, please download the dataset into the ``tests/test_sets`` directory
-   and run the ``tests/run_on_large_dataset.py`` script.
+ * 160K+ molecules from various [MoleculeNet](https://moleculenet.org/datasets-1) datasets
+
+In first releases, we also tested the 36M+ molecules from the [eMolecules Database](https://downloads.emolecules.com/free/2024-12-01/).
+
 
 ## Version History
 See [CHANGELOG](https://github.com/aspuru-guzik-group/selfies/blob/master/CHANGELOG.md).

selfies/bond_constraints.py

@@ -9,9 +9,9 @@
     "B": 3, "B+1": 2, "B-1": 4,
     "O": 2, "O+1": 3, "O-1": 1,
     "N": 3, "N+1": 4, "N-1": 2,
-    "C": 4, "C+1": 5, "C-1": 3,
-    "P": 5, "P+1": 6, "P-1": 4,
-    "S": 6, "S+1": 7, "S-1": 5,
+    "C": 4, "C+1": 3, "C-1": 3,
+    "P": 5, "P+1": 4, "P-1": 6,
+    "S": 6, "S+1": 5, "S-1": 5,
     "?": 8
 }
 
@@ -48,7 +48,7 @@ def get_preset_constraints(name: str) -> Dict[str, int]:
         +-----------------+-----------+---+---+-----+-----+---+-----+-----+
         |                 | Cl, Br, I | N | P | P+1 | P-1 | S | S+1 | S-1 |
         +-----------------+-----------+---+---+-----+-----+---+-----+-----+
-        | ``default``     |     1     | 3 | 5 |  6  |  4  | 6 |  7  |  5  |
+        | ``default``     |     1     | 3 | 5 |  4  |  6  | 6 |  5  |  5  |
         +-----------------+-----------+---+---+-----+-----+---+-----+-----+
         | ``octet_rule``  |     1     | 3 | 3 |  4  |  2  | 2 |  3  |  1  |
         +-----------------+-----------+---+---+-----+-----+---+-----+-----+

tests/test_specific_cases.py

@@ -359,4 +359,10 @@ def test_radical_kekulization():
     assert roundtrip_eq("c1ccs[n+]1c2ccccc2", "C=1C=CS[N+1]=1C2=CC=CC=C2")
     assert roundtrip_eq("c1ccs[nH+]1", "C=1C=CS[NH1+1]=1")
 
-
+
+def test_novel_charged_symbols():
+    """Test decoding of updated constraints for charged atoms (update in 2.2.0)."""
+    assert decode_eq("[N][#C+1][#NH1][#C@H1]", "N#[C+1]")
+    assert decode_eq("[O+1][=P+1][#P-1][#C@@]", "[O+1]=[P+1]=[P-1]#[C@@]")
+    assert decode_eq("[=C-1][#S+1][#B]", "[C-1]#[S+1]=B")
+