MolImporter having problems on importing SMILES with "[

Hi I am testing JChem as academic license and I am facing a few problems with the standardizer and molimporter.


My first problem is that I get an MolFormatException for every SMILES I try to import which has a chiral S=O center. The MolFormatException.getMessage says:





java.io.IOException: Uncomplete asymmetric center ERROR (atom 5)





Example molecules:





CCN1C3=C((C2=C1C=CC(=C2)[N+]([O-])=O)=O)C=CC=C3





C(C(C)=O)Cl





Other software got no problems with it. I get this error every time a SMILES contains - replacing this string with an ordinary S solves the problem but is kind of a hash function.


Any suggestions for a solution ?





Cheers








Friedemann

Hi,





I have tested the folowing smiles on Daylight's depict page (http://www.daylight.com/daycgi/depict) : C(C(C)=O)Cl


It displays the following SMILES error message:

Quote:

WARNING: Chiral center has wrong connectivity -- ignored (dy_chianal) C(C(C)=O)Cl ^^^^

What do you think about droping a warning instead of exception.





Andras

Morning,


A warning would be perfect as long as one gets a "Molecule" and one can work with it. I got a whole bunch of those guys. Thanks for replying.





cheers


F.

Hi,


In the next release the Exception is replaced with Warning:

Code:

WARNING: Chiral center has wrong connectivity at atom 3 in smiles C(C[S@](C)=O)Cl. The chirality is ignored. CS(=O)CCCl

All the best


Andras

This will go. Thank you very much. Btw through which channel do you send the warning ? StdOut ? Or via a getWarning method.





cheers





Friedemann

We cannot write to stdout, because it would possibly corrupt other useful data written there.





The warning message will be written to the standard error (stderr).