Comments on: Time for Attractive Structure Depictions on ChemSpider

By: Antony Williams

Antony Williams — Tue, 14 Oct 2008 15:55:24 +0000

Egon thanks for the feedback. We have some bigger issues to resolve right now about stereogenic protons and size of the images then we can consider tweaking issues like this. Keep the feedback coming..we welcome all input!

By: Egon Willighagen

Egon Willighagen — Tue, 14 Oct 2008 12:58:09 +0000

I’d like to see the NH in this example as HN, with the hydrogen away from the two bonds the nitrogen is involved in (left-aligned instead of right-aligned).

By: Antony Williams

Antony Williams — Mon, 13 Oct 2008 19:53:59 +0000

Generally we don’t have to generate the 2D coordinates because they are already supplied by our depositors. However, in those cases where we do not have the coordinates we are fortunate enough to have access to the OpenEye OEChem toolkit (thanks to the kindness of OpenEye in their support of ChemSpider) and we use OEChem for structure layout. Their structure CLEANing and layout tools are excellent.

By: Rajarshi

Rajarshi — Mon, 13 Oct 2008 19:24:44 +0000

Yes, they certainly look nice. What algo are you using generate the 2D coordinates?

By: Antony Williams

Antony Williams — Mon, 13 Oct 2008 16:35:30 +0000

Rajarshi, all of the structure depiction work was done in-house. It’s not quite perfect as yet and if you browse you’ll find a few issues but they should be knocked out by end of week. What do you think…like what you see?

By: Rajarshi

Rajarshi — Mon, 13 Oct 2008 16:14:37 +0000

Out of curiosity, are these depictions from ChemWriter?