I have now had several weeks experimenting with Taverna-CDK and with the
CDK in general, and finally seem to be getting what I need. I have a few
questions though:
1) I have two SMILES depth-1 lists being read from text files going into
the Substructure_Filter. One is the substructure list and the other is
list of molecules. The cross iteration works fine. But the result of
matched_structures is a 2-depth list (ie some substructures match more
than one compound). When I write the resultant SMILES list to a file
using a beanshell script, it gets flattened out. What I need to do is
write to a file the matched structure alongside the substructure that it
matches to. I've tried a number of different things too numerous to list
here and nothing works.
a) Basically, the question is how do I write a 2-depth list alongside a
1-depth list?
b) Do I need to write a new worker that gives the substructure as an
output? (If this is the case is there a way I can view the source code of
the original worker?
2) The current substructure list is 360 compounds long. The compound
list may be anywhere between 1 and 100,000 compounds long, Is there a
limit to the size of lists that can be passed?
3) I would like to eventually use the SMARTSQueryTool to perform the the
same search as above. Do any of the answers to the above questions
change?
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