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JChemPaint is a Java-based software designed for molecule editing. Please tell me how to install it so that I can make a desktop icon for it. I have the java file downloaded so where do I go from here to achieve this?

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I moved this from an answer to a comment since I realized it doesn't specifically answer your question about the .tar.gz file. At JChemPaint on GitHub, the most recent JChemPaint was available as a .jar file, which you can run with java -jar ./jchempaint-3.3-1210.jar. Do you need to compile it yourself rather than run the jar? – chaskes Feb 2 at 0:19
No I don't actually. I just thought the tarball was all there was available. But I would like the program to be installed instead of just able to be run via the executable file. I've modified my question accordingly so you can answer this in the form of a "answer" – Brenton Horne Feb 2 at 0:24

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Once you have jar file, you can run it:

1) From the command line with java -jar ./jchempaint-3.3-1210.jar.

2) Or through a jchempaint.desktop file, which you can place in /usr/share/applications so it will show up in Dash and be able to be locked to the Launcher.

The .desktop file would look like

[Desktop Entry]
Type=Application
Name=JChemPaint
Comment=Chemistry 2D Modeler
Exec=java -jar path/to/install/folder/jchempaint-3.3-1210.jar
Icon=/path/to/icon.png
Terminal=false
Categories=Science
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