Outputing name of compound that is found by jcsearch

Hi all,





I am trying to map names of from one database to another. I am using jcsearch to do it, but I at the moment I can not figure out how to output the names of the molecules that are matched. I only get the smiles string.


I am using two SMILES files both with names associated with the molecule


and my command line is "jcsearch -q test.smi 182msp.smi --or"





Any idea on how i can do this? Or if there is a more suitable tool available that would be great too.





cheers,





Iain

You can use the format option (-f) for this:

Quote:

-f :Tname

In general, this option is expecting a format string as <chemical format> [ :<format options> ]





In the above special case the chemical format is empty, so no structural info will be printed, only the fields specified by the T format option. (If no "name" property is found in the sdfile/molecule, then it will use the molecule name.)





In addition to jcsearch, you can run overlap analysis using Instant JChem.


See: http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/performing_overlap_analysis.html





However, in this case you need some custom programming to get out the molecule names into the database as we discussed in the other topic.





Best regards,


Szabolcs

Thanks, that is a great help :)