Thanks for the quick response, Greg. I was able to use the method
described in your blog post
<https://greglandrum.github.io/rdkit-blog/tutorial/substructure/2021/12/20/substructlibrary-search-order.html>
to pickle the database.
Pat
On Sun, Mar 13, 2022 at 1:26 AM Greg Landrum <greg.land...@gmail.com> wrote:
> 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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>> Rdkit-discuss@lists.sourceforge.net
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>>
>
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