The Bond Menu

The Bond menu exist as a menu in the main menu and as a context menu, which is available when clicking on a bond. Both are identical except the select/cut/ copy/delete/properties items at the end of the context menu. Both menus set the drawing mode (see Tutorial for an explanation of modes). They both also change some atoms directly, the difference is the main menu does this on selection, the context menu on the item on which you clicked.

Single

Sets the selection or bond clicked on to a bond of bond order single. Puts JChemPaint in the single bond mode, which is the standard mode for building up chemical structures. If selected you can click on a point on the document and you'll create a single bond at this point. If you alreday have atoms in your drawing, there are several ways to draw bonds in this mode: Multiple clicking on an existing bond will cycle its bond order between the values 1, 2, 3 and 4.

Double,Triple,Quadruple

Sets the selection or bond clicked on to a bond of order double, triple or quadruple.

Stereo Up

Sets the selection or bond clicked on to stereo up (filled wedge) bond. Sets JChemPaint in a mode which enables you to either draw filled wedge bonds the same way as single bonds or change an existing bond into a filled wedge - the standard symbol to indicate that the atom at the thick end is above the 2D plane. Furthermore, multiple clicking on an existing bond will change it to a filled wedge and if it already has this shape it will toggle between the two possible orientations.

Stereo Down

Sets the selection or bond clicked on to stereo down (dashed wedge) bond. Sets JChemPaint in a mode which enables you to either draw dashed wedge bonds the same way as single bonds or change an existing bond into a dashed wedge - the standard symbol indicating that the atom at the thin end is below the 2D plane. While selected, a click on an existing bond will change it to a dashed wedge and if it already has this shape it will toggle between the two possible orientations.

Undefined Stereo

Sets the selection or bond clicked on to an undefined stereo bond (zigzag bond). Sets JChemPaint in a mode which enables you to either draw zigzag wedge bonds the same way as single bonds or change an existing bond into a zigzag wedge - this is sometimes used to indicating that the atom at the thick end is above or below the 2D plane. Note the latest IUPAC recommendation discourages using this, but recommends using the wiggly bond instead. While selected, a click on an existing bond will change it to a zigzag wedge and if it already has this shape it will toggle between the two possible orientations.

Undefined E/Z

Sets the selection or bond clicked on to an undefined E/Z bond (wiggly bond). Sets JChemPaint in a mode which enables you to either draw wiggly bonds the same way as single bonds or change an existing bond into a wiggly bond - this can indicate either up or down or undefined E/Z configuration. Note the latest IUPAC recommendation encourages using this for all undefined cases. While selected, a click on an existing bond will change it to a wiggly wedge.

Context Menu only items

The following menu items only exist in the context menu. They do not switch the mode.

Cut

Removes the bond clicked on from the drawing and puts it into the system clipboard. Paste can be used to use it again.

Copy

Copies the bond clicked on into the system clipboard. Paste can be used to use it again. JChemPaint uses several formats (SMILES, mol, CML, SVG) so you should also be able to paste it into other programs (depending on abilities of the program).

Delete

Removes the bond clicked on from the drawing. It is like cut without using the clipboard.

Select

Selects and marks the bond clicked on, so that it can be deleted, etc.

Select All

Selects and marks all atoms and bonds in the molecule, so that it can be rotated, moved, deleted, etc.

Reaction

Contains submenus for drawing reactions.

Properties

Here you can directly set teh order of the bond clicked on.

Molecule Properties

Here you can directly set properties (title which will be rendered below the molecule) of the molecule the bond is in.