Molconvert fallback option fails

Hi,


I have some smiles which were cleaned by molconvert,


however if I want to use the energy option and there are


some bad molecules the fallback option fails. Actually it


should report the error and go on. See the problematic smiles


as attachement. BTW also many other programs (cxcalc) fail.





Z:\>molconvert smiles -g -3:EP Z:\C8H10O1.smi -T Energy


#SMILES Energy


O[C@H]1[C@@H]2[C@H]3C[C@@H]4[C@H]3[C@H]1[C@H]24 160.03


O[C@H]1[C@@H]2[C@H]3C[C@H]4C2[C@@H]3[C@H]14 417.9


O[C@@H]1[C@H]2[C@H]3C[C@H]4[C@@H]1[C@@H]2[C@@H]34 214.65


O[C@H]1[C@H]2[C@@H]3[C@H]4C[C@H]4[C@H]2[C@H]13 305.84


O[C@H]1[C@H]2[C@@H]3[C@H]4C[C@@H]1[C@H]3[C@@H]24 425.3


O[C@H]1[C@H]2[C@@H]3[C@@H](C=C)[C@H]2[C@H]13 242.65


O[C@H]1C[C@H]2[C@H]3[C@H]4[C@@H]2[C@@H]3[C@@H]14 612.66


Invalid state in BuildCommand.


No regular build due to fallback.


Z:\C8H10O1.smi:8: error: 0


java.lang.ArrayIndexOutOfBoundsException: 0


at chemaxon.marvin.modelling.struc.MultiConformerImpl$1.isGreater(MultiConformerImpl.java:144)


at chemaxon.marvin.modules.Optimization.quickSort(Optimization.java:5039)


at chemaxon.marvin.modules.Optimization.quickSort(Optimization.java:5022)


at chemaxon.marvin.modelling.struc.MultiConformerImpl.sortByEnergy(MultiConformerImpl.java:141)


at chemaxon.marvin.modelling.build.FragClean$MultiFragBuildCommand.build(FragClean.java:676)


at chemaxon.marvin.modelling.build.FragClean.startClean(FragClean.java:98)


at chemaxon.marvin.modules.Clean3D.modfunc_0(Clean3D.java:1438)


at chemaxon.marvin.modules.Clean3D.modfunc(Clean3D.java:491)


at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3114)


at chemaxon.struc.Molecule.clean(Molecule.java:598)


at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3037)


at chemaxon.formats.MolConverter.convert0(MolConverter.java:679)


at chemaxon.formats.MolConverter.convert(MolConverter.java:514)


at chemaxon.formats.MolConverter.main(MolConverter.java:1245)





Tobias

Hi Tobias,





Thanks for the report, it seems to be OK in the development version which is under testing now, hopefully it will arrive to the next release.





Best wishes,





Ödön

TobiasKind wrote:

Hi, I have some smiles which were cleaned by molconvert, however if I want to use the energy option and there are some bad molecules the fallback option fails. Actually it should report the error and go on. See the problematic smiles as attachement. BTW also many other programs (cxcalc) fail. ... Tobias