molecule after importation

Dear Support,





I'm still using an old version of Jchem: 2.3.4.


While importing the molecule: it gives the following smiles:

Quote:

COc1ccc2[nH]cc(CCNCc3ccbrcc3)c2c1 |r|

If I use

Code:

MolHandler mh = new MolHandler(structure); mh.aromatize(); System.out.println(mh.toFormat("smiles");

I had the following smiles:

Quote:

COc1ccc2[nH]cc(CCNCc3ccbrcc3)c2c1

where does the |r| comes from?





When I make a substructure search with query the benzen molecule, I have the following error on the molecule imported above (molecule.mol)

Quote:

java.io.IOException: Unrecognized element type "r" at chemaxon.marvin.modules.SmilesImport.readSymbolAndAddAtom(SmilesImport.java:576) at chemaxon.marvin.modules.SmilesImport.readMol0(SmilesImport.java:390) at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:326) at chemaxon.jchem.db.DatabaseSearch.searchInCache(DatabaseSearch.java:1504) at chemaxon.jchem.db.DatabaseSearch.search1(DatabaseSearch.java:1611) at chemaxon.jchem.db.DatabaseSearch.search(DatabaseSearch.java:1861) at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:777) at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:796)

For now, I can't update the version of Jchem. Where does the problem comes from?





Thank you very much for your help





Kind Regards.


Jacques

Hi Jacques,





Please visit the following topic to read more about the |r| suffix:





http://www.chemaxon.hu/forum/ftopic144.html





(this suffix has nothing to do with the error)








The real cause of the error is the "br" string inside the SMILES string


(this is probably due to the non-standard valence count on the bromine).


My colleague Andras will give you a detailed answer about this issue.





Best regards,





Szilard

The first problem is that this molecule doesn't exist:


COc1ccc2[nH]cc(CCNCC3=CC=BrC=C3)c2c1


The second, that after aromatization and smiles export, the molecule contains aromatic Br, which doesn't exist either, moreover cannot be exported to smiles because of aromatic Br.


The third, that this aromatic Br is represented as 'br' in the string, which cannot be imported: COc1ccc2[nH]cc(CCNCc3ccbrcc3)c2c1

Please note that the above problem does not occur with the latest version.





I recommend to upgrade. (The latest version also contains many more fixes and performance enhancements, so I recommend it anyway.)





All the best,


Szabolcs

Thank you very much...


I beg your pardon for this mistake, I have not checked the chemical meaning of the molecule indeed.


in fact I am not able to upgrade JChem for now and for this case.


But I update all the database to the newest version of JChem as soon as is it possible.





Thank you again.





Best Regards.