diff --git a/datamol/__init__.py b/datamol/__init__.py index 769cf80c..d9e8de9f 100644 --- a/datamol/__init__.py +++ b/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 diff --git a/datamol/_sanifix4.py b/datamol/_sanifix4.py index 6b924d3c..7a6f35b3 100644 --- a/datamol/_sanifix4.py +++ b/datamol/_sanifix4.py @@ -5,7 +5,6 @@ from rdkit import Chem, RDLogger - logger = RDLogger.logger() diff --git a/datamol/_version.py b/datamol/_version.py index 19ec7efc..4239dc86 100644 --- a/datamol/_version.py +++ b/datamol/_version.py @@ -10,7 +10,6 @@ import rdkit import packaging.version - try: __version__ = version("datamol") except PackageNotFoundError: diff --git a/datamol/descriptors/descriptors.py b/datamol/descriptors/descriptors.py index ef6eb0e8..5bb7705a 100644 --- a/datamol/descriptors/descriptors.py +++ b/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`." diff --git a/datamol/fp.py b/datamol/fp.py index 3cb863c8..d5f27abb 100644 --- a/datamol/fp.py +++ b/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. diff --git a/datamol/isomers/_structural.py b/datamol/isomers/_structural.py index 61d2b52d..e71d3000 100644 --- a/datamol/isomers/_structural.py +++ b/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"], diff --git a/datamol/molar.py b/datamol/molar.py index 6eae37e4..3a037dab 100644 --- a/datamol/molar.py +++ b/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} diff --git a/datamol/predictors/esol.py b/datamol/predictors/esol.py index cc0a9fb1..fe4fd500 100644 --- a/datamol/predictors/esol.py +++ b/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, diff --git a/datamol/reactions/_reactions.py b/datamol/reactions/_reactions.py index 686feb96..28a8a4ba 100644 --- a/datamol/reactions/_reactions.py +++ b/datamol/reactions/_reactions.py @@ -15,7 +15,6 @@ import datamol as dm - ATTACHING_RXN = rdChemReactions.ReactionFromSmarts("[*;h:1]>>[*:1][*]") diff --git a/datamol/utils/fs.py b/datamol/utils/fs.py index 38b43c0a..ada4fc82 100644 --- a/datamol/utils/fs.py +++ b/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 diff --git a/datamol/utils/perf.py b/datamol/utils/perf.py index d2aef2af..24e4df85 100644 --- a/datamol/utils/perf.py +++ b/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