Learn to Smile

The Java Molecular Editor (JME) drawing applet is included below. The applet is used in the tutorial questions in this web site, as well as in the online testing package, Carmen. The applet will generate a "smiles" string (a text-based representation of the molecule) from your line-drawing, which will then be used to correct your answer. Remember, in a line drawing the ends of a line are assumed to be carbon atoms unless otherwise indicated by changing the atom type. Hydrogen atoms attached to carbons are NOT indicated in this type of drawing, only those attached to heteroatoms (i.e. O, N, S)

To use the editor, the second horizontal row of buttons is used for drawing the molecule. It is easiest to draw in the entire structure as carbon atoms first, and then change existing C atoms into other atom types (O, N, S...).

Drawing a Structure
Button	Function	Applet
	Draws in a single bond. note, you can generate a double or triple bond from a single bond by clicking on an existing single bond with the single bond button activated.	You have to enable Java and JavaScript on your machine ! smiles
	Draws in a double bond.
	Draws in a triple bond.
	Draws in a continuous chain of C atoms as long as the left mouse button is held down.
	Draws in a ring (i.e. a cyclopropane ring).
	The wedge button is used to indicate the 3-D location (or stereochemistry) of atoms, a solid wedge is above the plane of the page, a dashed wedge is behind the plane of the page. Clicking on an existing bond will change it to a wedge. Clicking on an existing wedge will change between to two wedge configurations.
	This will change an existing C atom into an O atom. Note: do NOT use the X button. This is used to add ANY atom or group in place of a C atom. If you use it, the smiles string will likely be incorrect!
	Note: multivalent nitrogen groups, such as nitro, azide, N-oxide, nitrile etc, should be drawn with a pentavalent nitrogen as shown below (if not the program will not recognize the correct answer, in most cases the software will convert to the approperiate structure automatically).

Fixing Errors
	The clear button will delete the entire structure.
	The delete button will remove atoms or bonds one at a time.
	The undo button will undo the last change to the structure.

Complete instructions for using the JME Molecular Editor

The following series of questions will help you learn to use the JME applet.