Structure Search With Option and R-group

Dear Support,





I have to other question.


I'm using in that case: jchem 3.0.12





First, I'd like to know if using R-group in a mol query is used only for substructure search? Because I'm using R-group as a query and substructure and exact search give the same results.


Is it normal?

Quote:

Mon Sep 05 12:02:20 CEST 2005 Search mode: SUBSTRUCTURE Structure table: USER.TAB_CSMOL Query: [$(CO),$(COC),$(CC(O)CC)]-c1cccn1 Screened: 607 Hits: 11 Cache loading: 3297 ms Cache size (this table / total): 1.36 / 1.36 MBytes Total time: 1391 ms Screening: 16 ms Processing threads: 2 Current / peak / maximum searches per minute: 1 / 1 / 20

Quote:

Mon Sep 05 12:03:52 CEST 2005 Search mode: EXACT Structure table: USER.TAB_CSMOL Query: [$(CO),$(COC),$(CC(O)CC)]-c1cccn1 Screened: 607 Hits: 11 Cache loading: 3266 ms Cache size (this table / total): 1.36 / 1.36 MBytes Total time: 1296 ms Screening: 0 ms Processing threads: 2 Current / peak / maximum searches per minute: 1 / 1 / 20

actually, the exact search give the same result as the substructure search. All the molecule are not exact.





My second question is that atoms option are not working


If I make a search with isi1.mol I get:

Quote:

Mon Sep 05 11:50:56 CEST 2005 Search mode: SUBSTRUCTURE Structure table: USER.TAB_CSMOL Query: c1nncc2cncc12 Screened: 432 Hits: 411 Cache loading: 10953 ms Cache size (this table / total): 6.28 / 6.28 MBytes Total time: 640 ms Screening: 0 ms Processing threads: 2 Current / peak / maximum searches per minute: 1 / 1 / 20

and with isi2.mol that contain an atom option "any"

Quote:

Mon Sep 05 11:53:35 CEST 2005 Search mode: SUBSTRUCTURE Structure table: USER.TAB_CSMOL Query: A1C=C2C=NN=CC2=C1 Screened: 0 Hits: 0 Cache loading: 12922 ms Cache size (this table / total): 6.28 / 6.28 MBytes Total time: 219 ms Screening: 16 ms Processing threads: 2 Current / peak / maximum searches per minute: 1 / 1 / 20

is it a common behaviour?





Thank you so far for your help.


Kind regards,





Jacques

Hi,





Regarding your first question:





This is a bug in our R-group search code.


We have fixed the bug, future JChem versions will work fine.





If you need a workaround for existing versions, it's good to know, that the affected part of the code is only executed, if the R-logic options are on the default setting.





The default occurrence is ">0". If you substitute it with ">0, 1" (which means the same), the exact search will work fine (although the search will probably be slower this way).





Code for the workaround:

Code:

Molecule queryMol=new MolHandler(queryString).getMolecule();                 if (searchType==SearchConstants.EXACT                 && queryMol instanceof RgMolecule) {             RgMolecule rgMol=(RgMolecule) queryMol;             if (rgMol.getRgroupCount()>0                     && rgMol.getRlogicRange(0).equals(">0")) {                 rgMol.setRlogicRange(0, ">0,1");             }         }         //then use the queryMol for the search...

Thank you for the bug report.





Regarding your second question:





Prior to graph search or fingerprint generation, the structures have to be standardized. For the query structures this is automatically performed by JChemSearch, the targets are stored in the table in a standardized form.


The most important standardization step is aromatization.


Please see:





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





In your case, the smaller ring is not aromatized because of the "Any" atom.


(if a ring contains an Any atom we cannot be sure it's aromatic)


So the search looks for structures with single and double bonds in this ring instead of aromatic bonds, and there are no hits.





If you know in advance that the ring is aromatic (e.g. you change an atom to "Any" in an aromatic ring), you should change the bond types in the ring to aromatic to achieve the desired search result.





See the attached "aromany.mol".





The menu Edit -> Bonds -> Aromatize can help you to determine which rings are aromatic.





Best regards,





Szilard

thank you so far, it works perfectly.


Best regards


Jacques