exact search in the reaction

Hi

we have a reaction database in jchem base, we would like to search exact structure on the reactant or product side in one reaction. we wonder if there is any script instruction to realize this function? in addition, we might add ignore stereo to exact structure searching

Many thanks for your recommendation

Hi Juan,

See our reaction search related documentation: https://docs.chemaxon.com/display/docs/Reaction+search

You can see there that searching exclusively for the reactant or for the product side can be solved by drawing appropriate query structures which consist also the reaction arrow not only the chemical structure.

You should apply the proper search type. Duplicate search or full structure search is not applicable in this kind of search because they require to match the whole reaction, however, full fragment search can used.

Stereo information can be ignored, but charge, radical or valence information can be required to fully match.

If you run the command line jcsearch, we recommend the following:

jcsearch -q <here comes the path of the query file containing the reaction arrow> DB:<tablename> -t:ff --stereoSearchType:i --charge:e --radical:e --valence:d

Best regards,

Krisztina

Many thanks for prompt reply

we will try it

Hi, we changed the search type to Full fragment, and got some expected results. But for some reactions, we got the error message as "CIS bond cannot be set for bond 380 between atoms 354,355" or" Invalid string representation in DataSgroup" or "SMILES string contains no
atoms". we havn't find the possible cause for these three errors.

we wonder if you have met such error before? could you give us some clue to diagnose these three problem? the Jchem Version is 5.4.1. we save the reaction as "any structure"

Thanks

Hi Juan,

The console output doesn't give the cd_id of the target reactions generating these errors? Would you send us these reactions ?

Nevertheless, JChem 5.4.1 is a 5-year old product. Don't you plan to upgrade to the latest version? There were many improvements and bugfixes implemented in the meantime.

Best regards,

Krisztina