Hi Pat,
I don't think you're doing anything wrong. This looks like a bug in the
RDKit.
It seems to be connected to the PatternHolder... I will look into it.
-greg
On Sat, Mar 12, 2022 at 10:26 PM Patrick Walters <wpwalt...@gmail.com>
wrote:
> Hi All,
>
> I'd appreciate any insight on what I'm doing wrong. I'm trying to save an
> rdSubstructLibrary. with library.toStream(). When library is empty I can
> save the library with library.toStream(), however when I've added molecule
> to the library, I get this error message.
>
> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe0 in position 121:
> invalid continuation byte
>
> Example code below. Any suggestions would be appreciated.
>
> Thanks,
>
> Pat
>
> #!/usr/bin/env python
>
> import sys
> from rdkit import Chem
> from rdkit.Chem import rdSubstructLibrary
>
> smiles_list = ["C","CC","CCC","CCCC","CCCCC"]
> mol_list = [Chem.MolFromSmiles(x) for x in smiles_list]
> library =
> rdSubstructLibrary.SubstructLibrary(rdSubstructLibrary.CachedSmilesMolHolder(),
>
> rdSubstructLibrary.PatternHolder())
> # Error when molecules are added
> # If the two lines below are commented, everything works
> for mol in mol_list:
> library.AddMol(mol)
> # -----------------------------
> with open("out.sslib","w") as f:
> library.ToStream(f)
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