Depth-First: A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype

A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype

Rich Apodaca — Wed, 02 May 2007 10:13:00 -0400

The previous article in this series discussed the requirements of Firefly, a new 2D chemical structure editor for the Web. Another article discussed Firefly's design constraints and the importance of embracing them. Why so much focus on a structure editor? Simply put, the structure editor is the key link between chemistry and cheminformatics. Without the structure editor, there would be no audience for cheminformatics software.

So far the discussion has been rather abstract. To make it less so, the following four screenshots illustrate the user interface and rendering capabilities of a Firefly prototype. All molecules were drawn with the Firefly interface running on Linux. Screenshots were directly captured from the running application.

Cholesterol

The image below illustrates fused rings and stereo atoms. Also notice that the atom label for oxygen has one implicit hydrogen atom that is properly placed to the left.

Doxorubicin

This image illustrates both atom labels and aromatic bonding. Notice the improperly-placed quinone double bond. Refining Firefly's aromaticity perception is currently a top priority.

Flunoxaprofen

Firefly comes complete with a developer-overridable atom coloring scheme. Also notice the correct length of the internal carbon-nitrogen double bond line.

Uric Acid

One of the more difficult aspects of rendering molecules with implicit hydrogens is placing them in the correct quandrant. In this screenshot of uric acid, notice how the hydrogens occupy three different quadrants relative to their hosting nitrogen atoms.

"A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype" by ambinter@wanadoo.fr

Sat, 05 May 2007 05:40:53 -0400

Could you ask Dr Rich Apodaca to add Ambinter into the thirty two free chemistry databases http://www.ambinter.com (5 millions chemicals) I have developed also ruby on rails chemical web site Is it possible to send some technical questions ?

Thanks Christian de Bouille

"A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype" by www.chemspider.com/Antony Williams

Wed, 02 May 2007 22:32:48 -0400

Looks great! The quality of the structures is very impressive. If and when you want to have it tested by the masses and are willing to share it with the ChemSpider crowd then we can offer Firefly as an alternative to the SDA we are using today (for functionality check http://www.chemspider.com/SDAManual.aspx regarding common functions etc). Keep up the good work. VERY attractive indeed.

"A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype" by Geoff

Wed, 02 May 2007 21:54:47 -0400

Looks great. As for the aromaticity issue -- I'm not sure it's a huge deal. For example, in ChemDraw, I could double-click on that double bond and it would change through three states: inside the benzene ring (the current case), in-line with half on each ring, and inside the quinone ring.

So if there are some rendering options for double bonds like that, I think the problem is minimal.

"A Chemical Structure Editor for the Web: Four Screenshots of a Firefly Prototype" by Joerg Kurt Wegner

Wed, 02 May 2007 14:48:56 -0400

User defined layout templates or a template library would be great as well, especially for larger SAR series.

Joerg