fix errors and add no_rdkit_log decorator

datamol/__init__.py

@@ -29,7 +29,7 @@
     "parallelized_with_batches": "datamol.utils",
     "JobRunner": "datamol.utils",
     "fs": "datamol.utils",
-    # log
+    # data
     "freesolv": "datamol.data",
     "cdk2": "datamol.data",
     "solubility": "datamol.data",
@@ -39,6 +39,7 @@
     "enable_rdkit_log": "datamol.log",
     "disable_rdkit_log": "datamol.log",
     "without_rdkit_log": "datamol.log",
+    "no_rdkit_log": "datamol.log",
     # mol
     "PERIODIC_TABLE": "datamol.mol",
     "TRIPLE_BOND": "datamol.mol",
@@ -233,6 +234,7 @@ def __dir__():
     from .log import enable_rdkit_log
     from .log import disable_rdkit_log
     from .log import without_rdkit_log
+    from .log import no_rdkit_log
 
     from .mol import PERIODIC_TABLE
     from .mol import TRIPLE_BOND

datamol/descriptors/descriptors.py

@@ -11,9 +11,11 @@
 
 from .. import Mol
 from ..convert import from_smarts
+from ..log import no_rdkit_log
 from .._version import is_lower_than_current_rdkit_version
 
 
+@no_rdkit_log
 def _sasscorer(mol: Mol):
     sys.path.append(os.path.join(RDConfig.RDContribDir, "SA_Score"))
     try:

datamol/fp.py

@@ -76,7 +76,7 @@
     "topological": {
         "includeChirality": False,
         "torsionAtomCount": 4,
-        "countSimulation": False,
+        "countSimulation": True,
         "countBounds": None,
         "fpSize": 2048,
         "atomInvariantsGenerator": None,
@@ -86,7 +86,7 @@
         "maxDistance": 30,
         "includeChirality": False,
         "use2D": True,
-        "countSimulation": False,
+        "countSimulation": True,
         "countBounds": None,
         "fpSize": 2048,
         "atomInvariantsGenerator": None,
@@ -159,7 +159,7 @@
     "topological-count": {
         "includeChirality": False,
         "torsionAtomCount": 4,
-        "countSimulation": False,
+        "countSimulation": True,
         "countBounds": None,
         "fpSize": 2048,
         "atomInvariantsGenerator": None,
@@ -169,7 +169,7 @@
         "maxDistance": 30,
         "includeChirality": False,
         "use2D": True,
-        "countSimulation": False,
+        "countSimulation": True,
         "countBounds": None,
         "fpSize": 2048,
         "atomInvariantsGenerator": None,

datamol/log.py

@@ -1,5 +1,6 @@
 from rdkit import RDLogger
 from rdkit import rdBase
+from functools import wraps
 
 
 class without_rdkit_log:
@@ -71,3 +72,53 @@ def enable_rdkit_log():
     """Enable all rdkit logs."""
     for log_level in RDLogger._levels:
         rdBase.EnableLog(log_level)
+
+
+def no_rdkit_log(
+    func=None,
+    *,
+    mute_errors: bool = True,
+    mute_warning: bool = True,
+    mute_info: bool = True,
+    mute_debug: bool = True,
+    enable: bool = True,
+):
+    """Decorator to disable RDKit logs.
+
+    This decorator can be used to suppress RDKit logs when executing a specific function.
+    By default, all log levels (error, warning, info, and debug) are muted.
+
+    Args:
+        mute_errors : Whether to mute error logs (default is True).
+        mute_warning : Whether to mute warning logs (default is True).
+        mute_info : Whether to mute info logs (default is True).
+        mute_debug : Whether to mute debug logs (default is True).
+        enable: Whether to enable the log muting (default is True). If set to False, no logs will be muted.
+
+    Example:
+    ```python
+    @no_rdkit_log()
+    def example_function():
+        # Your function code here
+        pass
+
+    example_function()  # RDKit logs won't show during this function's execution
+    ```
+    """
+
+    if func is None:
+        return lambda f: no_rdkit_log(
+            f,
+            mute_errors=mute_errors,
+            mute_warning=mute_warning,
+            mute_info=mute_info,
+            mute_debug=mute_debug,
+            enable=enable,
+        )
+
+    @wraps(func)
+    def wrapper(*args, **kwargs):
+        with without_rdkit_log(mute_errors, mute_warning, mute_info, mute_debug, enable):
+            return func(*args, **kwargs)
+
+    return wrapper

env.yml

@@ -24,7 +24,7 @@ dependencies:
   - scikit-learn
 
   # Chemistry
-  - rdkit >=2021.03
+  - rdkit >=2024.03.3
   - selfies
 
   # Optional deps

pyproject.toml

@@ -44,7 +44,7 @@ dependencies = [
     "packaging",
     "typing-extensions",
     "importlib-resources",
-    "rdkit",
+    "rdkit>=2024.03.3",
 ]
 
 [project.urls]

tests/test_fp.py

@@ -66,7 +66,7 @@ def test_all_fps():
         "erg": {"size": 315, "bits_sum": 23.4},
         "estate": {"size": 79, "bits_sum": 13},
         "avalon-count": {"size": 512, "bits_sum": 168},
-        "ecfp-count": {"size": 2048, "bits_sum": 35},
+        "ecfp-count": {"size": 2048, "bits_sum": 42},
         "fcfp-count": {"size": 2048, "bits_sum": 35},
         "topological-count": {"size": 2048, "bits_sum": 19},
         "atompair-count": {"size": 2048, "bits_sum": 78},

tests/test_log.py

@@ -3,6 +3,11 @@
 import datamol as dm
 
 
+@dm.no_rdkit_log
+def no_log_to_mol(smiles):
+    return dm.to_mol(smiles)
+
+
 def check_logs_are_shown(capfd):
     smiles = "fake_smiles"
     dm.to_mol(smiles)
@@ -17,10 +22,20 @@ def check_logs_are_not_shown(capfd):
     assert err == ""
 
 
+def check_logs_are_not_shown_deco(capfd):
+    smiles = "fake_smiles"
+    no_log_to_mol(smiles)
+    _, err = capfd.readouterr()
+    assert err == ""
+
+
 @pytest.mark.skip_platform("win")
 def test_rdkit_log(capfd):
     """Test multiple rdkit log scenarios."""
 
+    check_logs_are_shown(capfd)
+    check_logs_are_not_shown_deco(capfd)
+
     check_logs_are_shown(capfd)
     with dm.without_rdkit_log():
         check_logs_are_not_shown(capfd)