JChemPaint

January 2010: The JCP 3.0.1 release is available. This is a bugfix release for 3.0. Download here or have a look at the changelog. December 2009: We have finished the JCP 3.0 release. This is a totally reworked design, offering a more user friendly interface. We have done thorough testing and are confident this is a better and more stable release than ever. The applet is also signed so that it can do IO and is smaller and faster than ever. Downloads and a test page for the applet are available.

JChemPaint (or JCP for short here) is the editor and viewer for 2D chemical structures developed using CDK. It is implemented in several forms: a Java application and two varieties of Java applet.

JChemPaint Editor applet

• An applet is a Java program that runs only within a web page.
• The JCP Editor allows the user to draw chemical structures, and to import and export structure data in plain-text formats (SMILES, Molfile, CML)
• It also allows to programmatically load and display a chemical structure, which can then be edited by the user.

For demonstration, the Steinbeck group (EBI) hosts various releases of the applet. You can try the stable relase there, or preview the development version.
A snapshot of the 3.0 release applet is given below:

To learn how to insert and use the applet within a web page, see JChemPaint Inside Webpages.

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JChemPaint Viewer applet

• (An applet is a Java program that runs only within a web page.)
• The JCP Viewer only allows to programmatically display a chemical structure, which the user cannot modify.
• Demo page

To learn how to insert and use the applet within a web page, see JChemPaint Inside Webpages.

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JChemPaint application

• The application is a stand-alone program. It needs an installed Java Virtual Machine for operation. If your system does not have a JVM, get it from Sun's Java website.
• The JCP application has all the functionality of the JCP Editor applet (see below), plus file input and output.

Below a screenshot of the 3.0 release:

Features

These are the most prominent capabilities of the application; most of them are also available in the applets.

• Drawing and deletion of single, double, triple and stereo bonds.
• Ring templates (3-8 atoms) with one-click attachment.
• An extensive template library.
• Colouring of atom types, and other rendering settings.
• Editing of atomic charges, isotopes and hydrogen count.
• Loading and saving of structures in Chemical Markup Language (CML) and as MDL MOL files and SDF files (loading only).
• Automated Structure Layout, also known as Structure Diagram Generation.
• Loading structures from the Internet using CAS or NSC number.
• Normalization of structures, currently limited to aromaticity detection.
• Saving bitmap pictures of the structures.
• Saving structures as graphics (PNG, BMP, Scalable Vector Graphics (SVG)).
• Postscript printing. 

Source :  http://sourceforge.net/apps/mediawiki/cdk/index.php?title=JChemPaint