I am fairly new to knime, but I have been working on it for a few weeks now. This topic may need to be in the chemi informatics section, I'm not sure. Onwards!
I am trying to figure out how to take a picture of a molecule, specifically a SMILE, and put it into excel. I can put the text in easily, but the person I'm doing this for would prefer to see the molecules, not the text.
I have tried to find similar issues to this on these forums, but I either cannot understand how they are doing it or the data seems out of date. I currently have the information being written through Data to Report node, however that does not get the images to excel and I don't know where to procceed from here.
This is a tricky topic. There are two ways that I know of to get images of chemical structures from KNIME into Excell.
First is to use a JChem for Excell writer, as provided by Infocom/Chemaxon.
The second option is to use BIRT along with a 3rd part XLS emitter from a company named Arctorus. I have used it a bit before, and it seems very nice.
It does feel disappointing that a weakness in KNIME has recently emerged over the last year or so where its now no longer possible to get chemical structures out as images into Excel or Powerpoint without resorting to commercial plugins.
Has anybody tried LICCS (Win only)?
I've played with it, but not used it for any serious work.
(the other) Simon
This topic came up at our Learnathon in Cambridge this week and I learned that there were some unanswered questions on the Forum about how to get molecule images into Excel.
Getting an Excel spreadsheet with a column containing PNGs with molecule images is actually pretty straightforward using the “Renderer to Image” node which is part of KNIME’s SVG support.
The attached workflow shows how to do this using the Marvin renderer for an SDF column (can also be used for SMILES columns) and the RDKit renderer for an RDKit molecule column. Notice that the RDKit molecule itself ends up in the Excel file as a SMILES.
Mols to Excel.knwf (72.8 KB)