Comments on: Structure Diagram Generation (SDG), 2D Layout, in the Chemistry Development Kit (Part 1)

By: Christoph Steinbeck

Christoph Steinbeck — Thu, 06 Sep 2007 12:04:03 +0000

Noel, the layout problem that you describe was due to a bug which is fixed in CVS.

By: baoilleach

baoilleach — Wed, 05 Sep 2007 16:43:00 +0000

Talking about difficult cases, if you try the following SMILES at RG’s webservice at:
http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkws/cdkws.html#sdg
the layout of the rings could be improved…

[smiles] Ic1ccc(Nc2[nH0]c(N)[nH0][nH0]c2c2ccccc2)cc1

By: Egon

Egon — Tue, 14 Aug 2007 12:26:00 +0000

Some time ago I blogged about the MCDL applet [1], which does SDG too. To solve difficult cases, they use, just like the CDK, a template library. Now seen from the size of their template set (105), I think a good deal of this last 10% can be covered by the template functionality. I would be nice to see a breakdown into difficult ring systems for that 10% to see if indeed a modest template library can bring CDK’s success rate up to some 98%.

1.http://chem-bla-ics.blogspot.com/2006/08/small-java-applet-for-2d-structure.html