When using certain renderers for SDF molecule types (Indigo render, CCG MOE renderer), the renderer to image node produces black background pngs, obscuring most of the information contained in the cell. Other renderers (e.g. Marvin) provide white backgrounds.
Is it possible to control this behaviour?
I remember that we had problems with the MOE renderer having black boxes on the right end of the cell. This was a knime problem and has been fixed. Your bug report reminds me of this issue. I have never tested this knime node but will do now. If we can reproduce the issue, we will fix it asap.
Well the Marvin renderer very nicely has options in the knime preferences/ chemistry settings which you can change all sorts of settings and options over how molecules are displayed.
ideally we could do with similar facilities for the other rendering types.
That would be excellent. I eventually got the effect I wanted using the Marvin renderer, but it was annoying because I had to change the preferences to make it look 'right', whereas Indigo and MOE already did (until the renderer node got hold of them, at least!)
I guess this is because these renderers do not clear the background (paint it white) before painting the molecule. In a table the background is cleared by other means, but when renderer into a PNG the default background seems to be black. Maybe it's also a transparency issues and black is supposed to be transparent. I will have a look at it next week.
Fixed for 2.8.2. The default background for PNGs will then be transparent instead of black.