jcsearch output query

Hi guys!

I enjoy using jcsearch, but I have a real trouble with it. I want it to output my query as well as search results but I didn'f find out how to do that.

My query is a list of smiles, and my target library is also a list of smiles:

jcsearch -q test_100.smi --or -t:f ../../tmp/6_p0_MW_sorted_000.smi

The output smiles file returns all possible matches, BUT without any reference to the query molecule. 

Is it possible to output the corresponding query in the search results? Or just print out those query molecules that have matches in target library?

Example: if test_100.smi contains Mol1, Mol2, Mol3, and 6_p0_MW_sorted_000.smi contains Mol101, Mol102, Mol103..., I want my output to look like:

Mol1 - Mol 102 (if they match)

Mol2 - Mol 103

etc.. Or (good enough too):

Mol1 - matched

Mol2 - matched

Mol3 - not matched

Instead, I have only Mol102, Mol103 etc. in my output, so I can't track the correspondence between query and target libraries.

Could you please help?

Thanks!

Hi Alexey,

As you certainly checked, jcsearch, unfortunately, has not any output option to write out the queries with/without the matching targets.

We recommend embedding the jcsearch command into a script which handles your queries one-by-one: writes out the first query, runs jcsearch with the first query and writes out the matching targets of the first query,  ....

Best regards,

Krisztina