Make interactive plot with Knime #RDKit #Chemoinformatics #Knime

Dalia Goldman provided very cool presentation in RDKit UGM 2018 about Knime.

Click to access Goldmann_KNIMEandRDKit.pdf

She demonstrated interactive analysis with RDKit knime node and Javascript node. I was really interested but it was difficult to build the workflow by myself at that time.

BTW, I need to learn knime for data preparation in this week. So I learned about knime and how to make interactive plot with knime.

Following sample is very simple but shows power of knime.
The example is making interactive chemical space plot with knime. All work flow is below. Version of knime is 3.7.

At frist load SDF and calculate descriptors and fingerprint with RDKit node and the split fingerprint with FingerprintExnpander. Then conduct PCA with calculated FP.
Then convert molecule to SVG with openbabel node for visualization.

Key point of this flow is wrapped metanode!
This node is constructed from two JS node ‘Scatter plot’ and ‘Card view’.

After the making metanode, I defined visual layout. The setting can call from right botton of menue bar

And I set card view option as show selected only and several scatter plot option.

Now ready. Then run the work flow! I can view selected compounds from chemical space.
Image is below.

New version of Knime is powerful tool for not only data analysis but also data visualization. ;-)


Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

3 thoughts on “Make interactive plot with Knime #RDKit #Chemoinformatics #Knime

  1. Hi, I tried to reproduce your code in KNime. Unfortunately, I am not able to generate the image as you show in the video.

    1. Thanks for your comment but I don’t provide any information because I can’t know details of your env such as version of knime , packaege etc..

  2. Hi, I have been following your blog for some time and am also a big fan of KNIME, I have used it from very early on and do so still almost every day. It would be great if you could upload and link your workflows to the KNIMe Hub:


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: