If my query table starts with Row0, what's the matching index for the column in the substructure match counter table? Is it number of matches 1?
Yes, the first column with Number of matches corresponds to the first row of your query table, and so on. It would be great if one could use the original query (SMARTS) as column header in the results table, or alternatively if one could add a descriptive column to the queries that could be used as column headers in the results table.
I added such functionality to the Substructure Match Counter node in to Indigo KNIME nodes 1.1.12 avialable from the nighlty builds.
Now you can specify a column in the query table that can be used a name for number of matches.