fix: add lasso colors for atom_indices

datamol/__init__.py

@@ -4,7 +4,6 @@
 
 import importlib
 
-
 # The below lazy import logic is coming from openff-toolkit:
 # https://github.com/openforcefield/openff-toolkit/blob/b52879569a0344878c40248ceb3bd0f90348076a/openff/toolkit/__init__.py#L44
 

datamol/_sanifix4.py

@@ -5,7 +5,6 @@
 
 from rdkit import Chem, RDLogger
 
-
 logger = RDLogger.logger()
 
 

datamol/_version.py

@@ -10,7 +10,6 @@
 import rdkit
 import packaging.version
 
-
 try:
     __version__ = version("datamol")
 except PackageNotFoundError:

datamol/descriptors/descriptors.py

@@ -19,7 +19,7 @@
 def _sasscorer(mol: Mol):
     sys.path.append(os.path.join(RDConfig.RDContribDir, "SA_Score"))
     try:
-        import sascorer  # type:ignore
+        import sascorer  # type: ignore
     except ImportError:
         raise ImportError(
             "Could not import sascorer. If you installed rdkit-pypi with `pip`, please uninstall it and reinstall rdkit with `conda` or `mamba`."

datamol/fp.py

@@ -190,7 +190,7 @@
 
 
 def fp_to_array(
-    fp: Union[np.ndarray, SparseBitVect, ExplicitBitVect, UIntSparseIntVect]
+    fp: Union[np.ndarray, SparseBitVect, ExplicitBitVect, UIntSparseIntVect],
 ) -> np.ndarray:
     """Convert rdkit fingerprint to numpy array.
 

datamol/isomers/_structural.py

@@ -3,7 +3,6 @@
 from rdkit import Chem
 import datamol as dm
 
-
 IsomerReaction = collections.namedtuple(
     "IsomerReaction",
     ["name", "smarts", "reverse", "acyclic", "triplebond", "doublebond", "use"],

datamol/molar.py

@@ -1,12 +1,10 @@
-"""A set of utility functions to convert between various units and formats used in drug discovery.
-"""
+"""A set of utility functions to convert between various units and formats used in drug discovery."""
 
 from typing import Union
 from typing import Iterable
 
 import numpy as np
 
-
 _MOLAR_SCALES = {"M": 1, "mM": 1e-3, "uM": 1e-6, "nM": 1e-9, "pM": 1e-12, "fM": 1e-15}
 
 

datamol/predictors/esol.py

@@ -10,7 +10,6 @@
 from ..descriptors.descriptors import n_rotatable_bonds
 from ..descriptors.descriptors import n_aromatic_atoms_proportion
 
-
 _ESOL_INTERCEPT = 0.26121066137801696
 _ESOL_COEF = {
     "mw": -0.0066138847738667125,

datamol/reactions/_reactions.py

@@ -15,7 +15,6 @@
 
 import datamol as dm
 
-
 ATTACHING_RXN = rdChemReactions.ReactionFromSmarts("[*;h:1]>>[*:1][*]")
 
 

datamol/utils/fs.py

@@ -1,5 +1,4 @@
-"""The `fs` module makes it easier to work with all type of path (the ones supported by `fsspec`).
-"""
+"""The `fs` module makes it easier to work with all type of path (the ones supported by `fsspec`)."""
 
 from typing import Union
 from typing import Optional

datamol/utils/perf.py

@@ -2,7 +2,6 @@
 
 from loguru import logger
 
-
 duration_intervals = (
     ("weeks", 604800),  # 60 * 60 * 24 * 7
     ("days", 86400),  # 60 * 60 * 24