The problem about Exact Fragment Search

Exact Fragment search will be void, when setStereoSearch is false.


I tested in Jchem3.2 and 3.2.3





Please find the attached query and target.


(1)When setStereoSearch is TRUE


either query1 or query2 could NOT be hit by ExactFragmentSearch.





(2)When setStereoSearch is FALSE


query1 could be hit, but query2 could NOT be hit by ExactFragmentSearch.





I would like to know the reason.





The following is my source:


----------------------------------------


:


if(searcher == null)


{


searcher = new JChemSearch();


ConnectionHandler conHandler = new ConnectionHandler();


conHandler.setConnection(conn);


searcher.setConnectionHandler(conHandler);


searcher.setSearchType(JChemSearch.EXACT_FRAGMENT);


searcher.setWaitingForResult(true);


searcher.setInfoToStdError(false);


searcher.setStereoSearch(false);


searcher.setReturnsNonHits(false);


}


searcher.setStructureTable(struTabName);


return searcher;


:


----------------------------------------

Hi,





I do not see any problems here.

Quote:

(1)When setStereoSearch is TRUE either query1 or query2 could NOT be hit by ExactFragmentSearch.

This is the intended behaviour: the query contains 3 chiral centers, while the chirality of these in the target is unspecified.


(setStereoSearch=TRUE prevents the match)





Please see the following section of our Query Guide:





http://www.chemaxon.com/jchem/doc/user/Query.html#stereobond

Quote:

(2)When setStereoSearch is FALSE query1 could be hit, but query2 could NOT be hit by ExactFragmentSearch.

This is because query2 contains a Cl as an additional fragment, which is not present in the target, therefore there are not hits.


The ExactFragmentSearch mode works the following way: additional fragments are allowed in the target, the whole query should fully match to a fragment of the target (no additional ligands are allowed).





Please see our Query Guide for further information:





http://www.chemaxon.com/jchem/doc/user/Query.html#otherSearchTypes





Best regards,





Szilard

Thank you for your answer.


I misunderstood the Exact Fragment search.