Tuesday, 28 October 2008

Cheminformatics toolkit face-off - Depiction Part 3

Part 1
Part 2

We've got two new additions to the face-off, both of which are still under development.

The first is a structure diagram generator which has been added to OpenBabel. This code comes from the MCDL Java applet, and has been translated from the original Java to C++ by one of its authors, Sergey Trepalin. There are a couple of rough edges so if you want anything sorted out before the next release, now's the time to test it out and get those bug reports in.

On the depiction front, Rich has just released the first beta of ChemPhoto, about which you can read more on his blog.

The same dataset was used as before, and the new additions are in the final columns: [depiction] and [structure diagram generation]. Feedback I'm sure is welcomed.

(1) Some OB generated images missing due to taking too long. Remember those rough edges I mentioned...?
(2) OB generated coordinates depicted using OASA


ChemSpiderMan said...

Noel...we've been doing our own depiction development work on ChemSpider...see http://www.chemspider.com/blog/time-for-attractive-structure-depictions-on-chemspider.html and, in terms of online structure layout here: http://www.chemspider.com/blog/cleaning-structures-on-chemspider.html

Anonymous said...

Noel, great stuff, thanks for posting this!

I notice one odd thing. For structure 3834779, the OASA depiction shows a chiral wedge bond where all the others show a double bond. Any idea why, or which is correct?

Craig James

baoilleach said...

@Craig: Good catch. The OASA depiction is definitely misleading as it does appear to be a double bond. However, I also note that Cactvs draws an unusual double double for that one. It might be worth looking at a 3D structure to see what's going on.