fix: apply black

src/gt4sd/algorithms/conditional_generation/regression_transformer/implementation.py

@@ -1086,9 +1086,11 @@ def filter_substructures(
  f"{keep} is not a valid SMILES/SELFIES. Instead substructure filtering "
  f"based on sequence alone can be done and is set to: {self.text_filtering}"
  )
- if keep not in self.substructures_to_keep and not Chem.MolFromSmiles( # type: ignore
+ if keep not in self.substructures_to_keep and not Chem.MolFromSmiles(  # type: ignore
  self.target
- ).HasSubstructMatch(subs_mol):
+ ).HasSubstructMatch(
+ subs_mol
+ ):
  logger.info(
  f"{keep} could not be identified in SMILES/SELFIES on text level AND no "
  "substructure match occurred, hence it will be ignored"
@@ -1120,7 +1122,7 @@ def filter_substructures(
  sane = False
  break
  else:
- if not mol.HasSubstructMatch(subs_mol): # type: ignore
+ if not mol.HasSubstructMatch(subs_mol):  # type: ignore
  # Desired substructure not found
  sane = False
  break

src/gt4sd/algorithms/conditional_generation/regression_transformer/utils.py

@@ -65,18 +65,18 @@ def filter_stubbed(
  Tuple of tuples of length 2 with filtered, generated molecule and its properties.
  """
 
- seed = Chem.MolFromSmiles(target) # type: ignore
+ seed = Chem.MolFromSmiles(target)  # type: ignore
 
  seed_atoms = len(list(seed.GetAtoms()))
- seed_bonds = seed.GetNumBonds() # type: ignore
+ seed_bonds = seed.GetNumBonds()  # type: ignore
 
  smis: List[str] = []
  props: List[str] = []
  for smi, prop in property_sequences:
  if smi == "":
  continue
  try:
- mol = Chem.MolFromSmiles(smi) # type: ignore
+ mol = Chem.MolFromSmiles(smi)  # type: ignore
  num_atoms = len(list(mol.GetAtoms()))
  num_bonds = mol.GetNumBonds()
 

src/gt4sd/algorithms/generation/diffusion/geodiff/core.py

@@ -253,8 +253,8 @@ def visualize_2d_input(self, data: Data) -> None:
  molSize = (450, 300)
  drawer = MD2.MolDraw2DSVG(molSize[0], molSize[1])
  drawer.DrawMolecule(mc)
- drawer.FinishDrawing() # type: ignore
- svg = drawer.GetDrawingText() #type: ignore
+ drawer.FinishDrawing()  # type: ignore
+ svg = drawer.GetDrawingText()  # type: ignore
  display(SVG(svg.replace("svg:", "")))
 
  def visualize_3d(self, mols_gen: List[Chem.Mol]) -> None:

src/gt4sd/domains/materials/__init__.py

@@ -71,7 +71,7 @@ def validate_smiles(
  for index, molecule in enumerate(molecules)
  if molecule is not None and molecule != ""
  ]
- return molecules, valid_ids # type: ignore
+ return molecules, valid_ids  # type: ignore
 
 
 def validate_selfies(

src/gt4sd/properties/molecules/functions.py

@@ -195,7 +195,7 @@ def number_of_rotatable_bonds(mol: SmallMolecule) -> int:
 def number_of_large_rings(mol: SmallMolecule) -> int:
  """Calculate the amount of large rings (> 6 atoms) of a molecule."""
  mol = to_mol(mol)
- ringinfo = mol.GetRingInfo() # type: ignore
+ ringinfo = mol.GetRingInfo()  # type: ignore
  return len([x for x in ringinfo.AtomRings() if len(x) > 6])
 
 

src/gt4sd/properties/scores/core.py

@@ -235,7 +235,7 @@ def score(self, smiles: str) -> float:
  descriptor=self.descriptor,
  score_modifier=self.modifier,
  )
- return scoring_function.score_mol(Chem.MolFromSmiles(smiles)) # type: ignore
+ return scoring_function.score_mol(Chem.MolFromSmiles(smiles))  # type: ignore
 
 
 class TanimotoScorer(TargetValueScorer):
@@ -274,7 +274,7 @@ def score(self, smiles: str) -> float:
  fp_type=self.fp_type,
  score_modifier=self.modifier,
  )
- return scoring_function.score_mol(Chem.MolFromSmiles(smiles)) # type: ignore
+ return scoring_function.score_mol(Chem.MolFromSmiles(smiles))  # type: ignore
 
 
 class IsomerScorer(TargetValueScorer):

src/gt4sd/properties/utils.py

@@ -49,14 +49,14 @@ def to_mol(mol: SmallMolecule) -> Chem.Mol:
  a rdkit.Chem.Mol object.
  """
  if isinstance(mol, str):
- mol = Chem.MolFromSmiles(mol) # type: ignore
+ mol = Chem.MolFromSmiles(mol)  # type: ignore
  elif isinstance(mol, Chem.Mol):
  pass
  else:
  raise TypeError(
  f"Please provide SMILES string or rdkit.Chem.Mol object not {type(mol)}"
  )
- return mol # type: ignore
+ return mol  # type: ignore
 
 
 def to_smiles(mol: SmallMolecule) -> str:
@@ -70,7 +70,7 @@ def to_smiles(mol: SmallMolecule) -> str:
  """
  if isinstance(mol, str):
  try:
- mol = Chem.MolFromSmiles(mol) # type: ignore
+ mol = Chem.MolFromSmiles(mol)  # type: ignore
  except Exception:
  raise ValueError(
  f"Could not convert SMILES string to rdkit.Chem.Mol: {mol}"
@@ -82,7 +82,7 @@ def to_smiles(mol: SmallMolecule) -> str:
  f"Pass a SMILES string or rdkit.Chem.Mol object not {type(mol)}"
  )
 
- return Chem.MolToSmiles(mol, canonical=True) # type: ignore
+ return Chem.MolToSmiles(mol, canonical=True)  # type: ignore
 
 
 def get_similarity_fn(