cdk-user

[John M. <joh...@gm...>]

Hi All,

I played around with the highlight the other day (see. attached). The current bond highlighting changes the colour of bond lines based on a ColorHash given to the render model. Atom highlight via a glow is only available in JChemPaint (or CDK-JChemPaint?).

I kind of think it might be nicer to have the ‘colour class’ on the container and then use the render options to change change colour palette (similar to how R handles plot colours)? This means you can create one renderer and pass it different molecules with different highlights and don’t need to touch the renderer parameters. Currently the colour class is simply and ‘int’ in a hashmap for atoms/bonds. Multiple colours  is also nice but it gets complicated for bonds when they are highlighted with a different ‘glow’ from their atoms - do you think how it’s handled below is okay?

Here’s an example for a use of multiple colours from CDK/JChemPaint/SMSD/EC-Blast atom mapping: http://www.ebi.ac.uk/thornton-srv/software/ecblast/rbl/images/reaction/bc/R00994.png

Oh I also spotted how to fix the skeletal/really thin bonds in large depictions and will add the atom symbol alignment fix.
Cheers,
J