Fix potential features misalignment

chemprop/data/utils.py

@@ -173,22 +173,25 @@ def get_data(path: str,
             ignore_columns = set([smiles_column] + ([] if ignore_columns is None else ignore_columns))
             target_columns = [column for column in columns if column not in ignore_columns]
 
-        all_smiles, all_targets, all_rows = [], [], []
-        for row in tqdm(reader):
+        all_smiles, all_targets, all_rows, all_features = [], [], [], []
+        for i, row in tqdm(enumerate(reader)):
             smiles = row[smiles_column]
 
             if smiles in skip_smiles:
                 continue
 
             targets = [float(row[column]) if row[column] != '' else None for column in target_columns]
 
-            if skip_none_targets and all(x is None for x in targets):
             # Check whether all targets are None and skip if so
+            if skip_none_targets and all(x is None for x in targets):
                 continue
 
             all_smiles.append(smiles)
             all_targets.append(targets)
 
+            if features_data is not None:
+                all_features.append(features_data[i])
+
             if store_row:
                 all_rows.append(row)
 
@@ -201,7 +204,7 @@ def get_data(path: str,
                 targets=targets,
                 row=all_rows[i] if store_row else None,
                 features_generator=features_generator,
-                features=features_data[i] if features_data is not None else None
+                features=all_features[i] if features_data is not None else None
             ) for i, (smiles, targets) in tqdm(enumerate(zip(all_smiles, all_targets)),
                                                total=len(all_smiles))
         ])