problem generating molecule from blob data

[nicokant]

I'm following the tutorial, but when I try to add a new compound using
Compound.objects.create(name='benzene', molecule='c1ccccc1') I got the following error:

django.db.utils.DataError
django.db.utils.DataError: problem generating molecule from blob data

my requirements.txt file has:

# RDKIT
rdkit-pypi==2021.9.4
-e git+https://github.com/rdkit/django-rdkit.git@v0.3.1#egg=django_rdkit

while my models.py file is:

from django_rdkit import models

class Compound(models.Model):
    name = models.CharField(max_length=500)
    structure = models.MolField(verbose_name="Structure")

[rvianello]

@nicokant I think this error is probably originating from a postgres server running with a version of the rdkit cartridge which is too old to support the binary format submitted by the rdkit code on the client side (see also #21). You could try either upgrading the postgres server to the current rdkit release, or downgrading the rdkit toolkit on the client side.

[nicokant]

@rvianello I'm using a docker container for running the postgres database with the cartridge, in particular https://github.com/mcs07/docker-postgres-rdkit. I think it uses the 2020.03.2 version, to which version should I port it? to the same as my requirements? (2021.9.4)

Thanks for your help!

[rvianello]

@nicokant yes, ideally the same version (or at least the same major release, currently 2021.09) should be available on the database server and client sides. Please note that rebuilding the last RDKit release may currently run into a configuration-time error (rdkit/rdkit#4892). You can try adding the workaround documented at the linked RDKit issue into your Dockerfile.

[nicokant]

Thank you for your support, I ended up using a custom docker image using the conda distribution to avoid rebuilding rdkit from source and now everything works