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