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.
https://github.com/rdkit/UGM_2014
You can get all presentations from github repo.
Like this…

iwatobipen$ git clone https://github.com/rdkit/UGM_2014.git

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

etc..

Then get source code from github.

iwatobipen$ git clone https://github.com/apahl/sdf_viewer.git

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

SDF_VIEWER_REPORTS=/Users/iwatobipen/Downloads/sdf_viewer-master
export SDF_VIEWER_REPORTS

Then move to /sdf-master and run sdf_viewer.py and load testset.sdf
Now…

It works. ;-)
To make histogram, it was easy only select property and click histogram.

To make scatter plot is easy too.