hang in addHydrogens

I am experiencing a hang in JChem 3.0.15 in MolHandler.addHydrogens(). The MolHandler instance is created with the following Mol string:








Marvin 11110513192D





8 7 0 0 0 0 999 V2000


1.0063 0.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.5896 1.5209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.4687 0.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-2.0521 0.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-0.6437 0.9375 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0


0.1813 0.9375 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0


-0.6437 1.7625 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


0.1813 1.7625 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


3 5 1 0 0 0 0


5 6 1 0 0 0 0


6 1 1 0 0 0 0


1 2 1 0 0 0 0


3 4 1 0 0 0 0


5 7 1 1 0 0 0


6 8 1 6 0 0 0


M ISO 2 7 2 8 2


M END





The next thing I do is call addHydrogens(). This call never returns.

Hi,





We have managed to reproduce the problem, it can also be invoked by


"Edit -> Add -> Explicit H atoms" in Marvin Sketch.


This bug has been fixed since Marvin 4.0 and JChem 3.1.


Please upgrade your JChem version.





Best regards,





Szilard





PS: We prefer to receive molecules as file attachments, or at least with "code" formatting. Otherwise the html formatting makes them invalid, and we must add the lost spaces painstakingly by hand.


Here is the same molecule attached both ways.

Code:

Marvin 11110513192D   8  7  0  0  0  0  999 V2000     1.0063    0.9375    0.0000 C  0  0  0  0  0  0  0  0  0  0  0  0     1.5896    1.5209    0.0000 C  0  0  0  0  0  0  0  0  0  0  0  0    -1.4687    0.9375    0.0000 C  0  0  0  0  0  0  0  0  0  0  0  0    -2.0521    0.3541    0.0000 C  0  0  0  0  0  0  0  0  0  0  0  0    -0.6437    0.9375    0.0000 C  0  0  1  0  0  0  0  0  0  0  0  0     0.1813    0.9375    0.0000 C  0  0  1  0  0  0  0  0  0  0  0  0    -0.6437    1.7625    0.0000 H  0  0  0  0  0  0  0  0  0  0  0  0     0.1813    1.7625    0.0000 H  0  0  0  0  0  0  0  0  0  0  0  0  3  5  1  0  0  0  0  5  6  1  0  0  0  0  6  1  1  0  0  0  0  1  2  1  0  0  0  0  3  4  1  0  0  0  0  5  7  1  1  0  0  0  6  8  1  6  0  0  0 M  ISO  2   7   2   8   2 M  END

Thanks, Szilard. I'll be more careful about formatting in the future. I upgraded to 3.1.3 and the problem has disappeared.