Dataframe supplier can use columns containing Mol objects instead of SMILES strings

Author: Oliver Scott

scaffoldgraph/core/graph.py

@@ -952,7 +952,8 @@ def from_dataframe(cls, df, smiles_column='Smiles', name_column='Name', data_col
         df : pd.DataFrame
             A pandas DataFrame containing SMILES strings and a molecule identifier.
         smiles_column : value, optional
-            Label of column containing SMILES strings. The default is 'Smiles'.
+            Label of column containing SMILES strings. The default is 'Smiles'. The
+            column may instead contain precomputed rdkit Mol objects.
         name_column : str
             Label of column containing SMILES strings. The default is 'Name'.
         data_columns : list

scaffoldgraph/io/dataframe.py

@@ -4,7 +4,7 @@
 Contains functions for reading molecules from pandas dataframes.
 """
 
-from rdkit.Chem import MolFromSmiles
+from rdkit.Chem import MolFromSmiles, Mol
 from loguru import logger
 
 
@@ -48,7 +48,10 @@ def __iter__(self):
     def __next__(self):
         values = next(self.supplier)
         try:
-            mol = MolFromSmiles(values[0])
+            if isinstance(values[0], Mol):
+                mol = values[0]
+            else:
+                mol = MolFromSmiles(values[0])
             mol.SetProp('_Name', str(values[1]))
             if self.data_cols is not None:
                 for key, value in zip(self.data_cols, values[2]):
@@ -75,7 +78,7 @@ def read_dataframe(df, smiles_column, name_column, data_columns=None):
     df : pandas.DataFrame
         Dataframe to read molecules from.
     smiles_column : str
-        Key of column containing SMILES strings.
+        Key of column containing SMILES strings or rdkit Mol objects.
     name_column : str
         Key of column containing molecule name strings.
     data_columns : list, optional