A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)

doi:10.3390/11040219

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Molecules 2006, 11(4), 219-231; doi:10.3390/11040219

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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
² Chemistry Department, Moscow State University, 117234, Moscow, Russia
³ Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831-6242, USA

^* Authors to whom correspondence should be addressed.

Received: 7 December 2005; in revised form: 24 March 2006 / Accepted: 24 March 2006 / Published: 29 March 2006

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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.

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MDPI and ACS Style

Trepalin, S.V.; Yarkov, A.V.; Pletnev, I.V.; Gakh, A.A. A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL). Molecules 2006, 11, 219-231.

AMA Style

Trepalin S.V., Yarkov A.V., Pletnev I.V., Gakh A.A. A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL). Molecules. 2006; 11(4):219-231.

Chicago/Turabian Style

Trepalin, Sergei V.; Yarkov, Alexander V.; Pletnev, Igor V.; Gakh, Andrei A. 2006. "A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)." Molecules 11, no. 4: 219-231.

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