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:
- Directly click on an atom: A bond with default length will be drawn at a reasonable angle.
- Drag from an atom: A bond with default length will be drawn at the angle to drag to.
- Drag from an atom to another atom: A bond with default length will be drawn at the angle to drag to.
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.