Misc fixes to representation code.

leojklarner · Nov 2, 2023 · 86b09cd · 86b09cd
1 parent 2186a83
commit 86b09cd
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/gauche/representations/fingerprints.py b/gauche/representations/fingerprints.py
@@ -87,8 +87,8 @@ def ecfp_fingerprints(
     """
 
     rdkit_mols = [MolFromSmiles(s) for s in smiles]
-    fpgen = AllChem.GetMorganGenerator(radius=2)
-    fps = [fpgen.GetFingerprint(mol, bond_radius, nBits=nBits) for mol in rdkit_mols]
+    fpgen = AllChem.GetMorganGenerator(radius=bond_radius, fpSize=nBits)
+    fps = [fpgen.GetFingerprint(mol) for mol in rdkit_mols]
     return np.array(fps)
 
 

diff --git a/gauche/representations/graphs.py b/gauche/representations/graphs.py
@@ -4,11 +4,12 @@
 """
 
 from typing import List, Optional
+import networkx
 
 
 def molecular_graphs(
     smiles: List[str], graphein_config: Optional[bool] = None
-) -> List[networkx.MolecularGraph]:
+) -> List:
     """
     Convers a list of SMILES strings into molecular graphs
     using the feautrisation utilities of graphein.