minor dehydrogenize exception

Tried molconvert smiles:un -Y on this file and got back:





Reading file 1: yo2.sdf (mol format) ...


yo2.sdf:73: error in molecule:


java.lang.ArrayIndexOutOfBoundsException: -1


at chemaxon.marvin.modules.Parity.putToTheTop(Parity.java:2383)


at chemaxon.marvin.modules.Parity.setupStereoBonds(Parity.java:802)


at chemaxon.marvin.modules.Parity.setParity(Parity.java:424)


at chemaxon.marvin.modules.Parity.modfunc(Parity.java:167)


at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1444)


at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1413)


at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.


java:267)


at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:51)


at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:547)


at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:


523)


at chemaxon.struc.RgMolecule.implicitizeHydrogens(RgMolecule.java:1720)


at chemaxon.formats.MolConverter.convert0(MolConverter.java:586)


at chemaxon.formats.MolConverter.convert(MolConverter.java:500)


at chemaxon.formats.MolConverter.main(MolConverter.java:1067)


java.lang.ArrayIndexOutOfBoundsException: -1


at chemaxon.marvin.modules.Parity.putToTheTop(Parity.java:2383)


at chemaxon.marvin.modules.Parity.setupStereoBonds(Parity.java:802)


at chemaxon.marvin.modules.Parity.setParity(Parity.java:424)


at chemaxon.marvin.modules.Parity.modfunc(Parity.java:167)


at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1444)


at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1413)


at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.


java:267)


at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:51)


at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:547)


at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:


523)


at chemaxon.struc.RgMolecule.implicitizeHydrogens(RgMolecule.java:1720)


at chemaxon.formats.MolConverter.convert0(MolConverter.java:586)


at chemaxon.formats.MolConverter.convert(MolConverter.java:500)


at chemaxon.formats.MolConverter.main(MolConverter.java:1067)











Workaround seems to be first converting the file to smiles:un, then doing another molconvert smiles:un -Y.





Molconvert version 4.0.5

The problem solved in 4.1.0.





Please update Marvin.