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.
When JChemPaint has been started, you automatically get an empty document. In order to paint a structure the typical steps would be the following:
,
etc.) you can build the
ring structures of the molecule. Click on a ring button (you switched to "Draw
x-membered ring mode") and then in the document. You can dock a ring to another ring by clicking
on an existing ring (the docking atom or bond will be highlighted while hovering over it). If the molecule
has no rings, go to the next step.
button (your are in "single bond mode" then), click on the atom where the chain
starts and then on the last atom of the chain to enlarge it. There are several
ways to draw bonds in this mode:
again and clicking on the bonds to make
double, triplei or quadruple. Alternatively you can use the bond context menu (right click on a bond)
to pick one of these bond orders by using the buttons
,
or
.
and
to make existing bonds wedge bonds or
you can draw wedge bonds directly by clicking on an existing atom. The "wedge bond
mode" works same as the "single bond mode" with respect to dragging etc., just
that the bonds created are wedges.
to choose an element. With
and
you can change the charge.If you are interested in drawing reactions, see Drawing of Reactions.