View SDF using open source toolkit.

There are lots of commercial tools to visualize structures from SDF files.
Also I often use Spotfire, etc in my lab, but not use in my house.

In 2014RDKit-UGM open source SDF viewing tool was presented.
Today I installed it and used. If reader who interested this tool, there is nice presentation in following link.
You can get all presentations from github repo.
Like this…

iwatobipen$ git clone

So, Let’s enjoy sdf_viewer.
At first, this product written in Python (2.7), RDKit (2014_03_1), PyQt (4.11.2), Matplotlib.
If you use OsX, RDKit, PyQt Matplotlib can install easily using homebrew.

iwatobipen$ brew install rdkit
iwatobipen$ brew install pyqt


Then get source code from github.

iwatobipen$ git clone

Now, I got all files.
Next set up my env.
Follow the install manual, I set SDF_VIEWER_REPORTS.
In .bashrc…


Then move to /sdf-master and run and load testset.sdf
Screen Shot 2015-01-11 at 9.25.26 PM
It works. ;-)
To make histogram, it was easy only select property and click histogram.
Screen Shot 2015-01-11 at 9.46.47 PM
To make scatter plot is easy too.
Screen Shot 2015-01-11 at 9.49.58 PM

This tool is easy to handle visualization settings via GUI.
If more details need, I recommend to check author’s PDF.


Published by iwatobipen

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

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