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.
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.
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.
In some aspects JChemPaint is different from other 2D editors:
- JChemPaint is open source and free software. We believe that scientific software, especially when its development was publicly funded, should be free. As the GNU people put it: «`Free software´ is a matter of liberty, not price. To understand the concept, you should think of `free speech´, not `free beer´». Everyone can participate in the development of the program. Everyone can download and change the source code, provided that they make the changes publicly available again, according to the GNU Lesser General Public License, LGPL. This ensures that the community can take advantage of any bugfix or enhancement made to the system. It also ensures that a scientist, who needs a standard piece of software like a structure editor as a helper application in his/her new program, does not have to reinvent the wheel over and over again because all the structure editors that have been written before are now proprietary software. If there is a free structure editor, he/she can focus on the real science.
- JChemPaint is in constant development and you can help (see below).
- Since JChemPaint is written in Java, it runs on any computing platform and operating system for which a Java Virtual Machine (of version >= 1.3 up to JCP 2.4 and version >= 1.5 for JCP > 2.4) has been implemented (like Linux, Windows, Solaris, AIX and others).
- JChemPaint is available free of charge.
- JChemPaint is translated into several languages: Dutch, French, German, Polish, Portuguese and Spanish.
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