BRICS node in knime?

Hello,

Is there a node which can apply BRICS to molecules? I notice that the RDKit Molecule Fragmenter does not use BRICS - in this post it mentions a BRICS node which will be released:

RDkit Molecule Fragmenter request - Community Extensions / RDKit - KNIME Community Forum

Has this been released? I am not able to find any information.

If not, how can I apply BRICS in knime?

Many thanks for your help!!

I don’t think there’s a node that can do this natively.

You can try using a Python node to call the BRICS module from RDKit. Here’s a quick example:

2 Likes

Hello,

Thank you so much! I’ve downloaded your workflow and tried it, however I’m getting a bad pickle format error:

This is what my preferences look like for knime-python integration:


I’m very new to Python, so if you have any help or suggestions that’d be really appreciated :smiley:

Thank you!

  1. Did you run my workflow as-is first? If so, what was the result?
  2. Can you upload both your workflow and/or the data you’re using so I can try running it?