Publishers Note added on 29 June 2006 英文参考文献.docVIP

Molecules 2006, 11, 219-141 molecules ISSN 1420-3049 Full Paper A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL) Sergei V. Trepalin 1,*, Alexander V. Yarkov 1, Igor V. Pletnev 2 and Andrei A. Gakh 3,* 1 Institute of Physiologically Active Compounds RAS, 142432 Chernogolovka, Moscow Region, Russia Tel. +7 (095) 135-6369 2 Chemistry Department, Moscow State University, 117234, Moscow, Russia 3 Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831-6242, USA Tel. +1 (865) 574-1000 * Authors to whom correspondence should be addressed; e-mails: trep@ and gakhaa@ Received: 7 December 2005; in revised form: 24 March 2006 / Accepted: 24 March 2006 / Published: 29 March 2006 Abstract: A compact Modular Chemical Descriptor Language (MCDL) chemical structure editor (Java applet) is described. The small size (approximately 200 KB) of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI). Keywords: MCDL format, Java, open source, structure editor, structure diagram generation. Introduction Linear molecular descriptors are frequently used for storing, retrieval, and presentation of chemical information. Their role has increased significantly with the advent of the Internet. Although chemical structures on the Web can be presented as bitmap objects (in GIF, JPEG, or PNG formats), this method of representation is not optimal. An alternative method entails use of