I haven't used KNIME before but it was suggested as a good software for what I need. I have a fairly simple task, and hope somebody can suggest a good (and relatively simple) way of doing this.
So I have a list of PubChem CIDs, some 400,000 of them, and I would like to bulk download the PubChem SDF data for all of them and to calculate select 2D and 3D chemical descriptors using CDK, and export this data into a text/csv file in a table format.
I've been googling extensively for instructions/examples of how this is done, but can't find anything relevant. Would much appreciate any suggestions or step-by step instructions.