JChemPaint Basic Tutorial

General Usage

The general idea is that while using JChemPaint, the program always is in a "drawing mode". This means that clicks somewhere on the panel will draw a certain chemical entity. Examples for "drawing modes" are "single bond" or "Carbon atom". Drawing modes can be changed by the buttons or via menus. In addition to changing the mode, choosing a button or a menu item do also changes the currently selected items (if any). Context menus (which appear right clicking on the panel) change the element (atom, bond) on which you clicked for the menu. Apart from these "mode changes", there are also some buttons/menu items, which do a one-off action, but have no mode. Examples are "Cut" or "Generate Smiles". Keeping this in mind, we now show you how to create a molecule.

Another thing you should keep in mind is that JChemPaint is a "chemically aware editor". This means that many things are not drawn, but assigned as properties and then drawn by JChemPaint. The advantage is that import/exports to chemical formats can be much richer, but the usage is sometimes not as straightforward as with "direct" drawing. An example is if you want to have a title (like a name) rendered next to a molecule: You do not draw a string on the canvas, but assign the title to the menu and this is then rendered. Another example are reactions, you do not draw an arrow, but declare molecules as products or reactants and an arrow is then drawn between them.

Creating Molecules

When JChemPaint has been started, you automatically get an empty document. In order to paint a structure the typical steps would be the following:

Obviously the mentioned steps are only a suggestion. You can do them in any order. Have a look through the menus to see what is available or read the Reference Guide.

If you are interested in drawing reactions, see Drawing of Reactions.