I have been trying to make a workflow that analyses a given library for similarity distance distributuion. The workflow I came up with works like a charm for smaller libraries, but my actual use case for it is to analyse sets of 10k+ compounds, and here is where it struggles.
For example, I left it running overnight on a library of 40k compounds, and my loop count only got to a thousand. I have noticed that the Transpose node is likely the rate-limiting step in my loop, when working with these bigger libraries. Is thete a way to avoid using it in this case?
I have attached a workflow to this post, and would be really grateful if someone took a look at it and pointed me at what exactly am I doing wrong. Similarity distance.knwf (454.6 KB)