Identify bad Structures

Dear Support,





I would like to know how I can identify bad structure (like on the file attached).


Actually the Molecular Graphe is Connex but there is a chemical error on the Oxygen atom with its number of bond.


How can I detect those chemical problems in a structure using JChem API.





I use this code to create a Molecule object from the MolFile... and actually there are no Exception.

Code:

private static Molecule streamMol(String s) throws MolFormatException, IOException{        return (new MolImporter(new MolInputStream(new ByteArrayInputStream(s.getBytes())))).read();     }

Is there a method in JChem API to seek for big chemical mistake? Or do I have to create myself a method with rules to identify connectivity, bond or charge problem?





Thank you so far for your help


Warmest Regards,





Jacques





ps: I saw too methods of MolecularGraph that might help:

Code:

m.valenceCheck();

but actually there are no output...


How can I use them?

Jacques,





Please check out the forum topic below.





http://www.chemaxon.com/forum/ftopic456.html





Best regards,





Szabolcs

thank you very much.


And I think qpropCheck() works like valenceCheck?





Can I do:


m.valenceChck();


m.qpropCheck(null);





and then loop on all the atoms?

Jacques,





There is no need to call qpropCheck(), because valenceCheck() already calls that.





Best regards,





Szabolcs

Dear Szabolcs,





Thank you very much.


It works perfectly.





Warm Regards


Jacques