Synthesizer Exhaustive Example Error

Hi,





I was trying to run synthesizer to get see if I could get results that might help what we are trying to do. I got an outofbounds error. I tried just reinstalling to no avail.





I have Java 1.6.0.3, XP a remote MySQL 5 database .


I was running the steps in the biodeg file and example


synthesize d -n biodegradation


synthesize c -n biodegradation -c Synthesizer.xml


synthesize i -n biodegradation -s S1 phenol.smiles


synthesize r -n biodegradation


I got the following error when running synthesize r -n biodegradation





Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 238


at chemaxon.marvin.modules.LonePairCounter.getMainGroupNumber(LonePairCo


unter.java:934)


at chemaxon.marvin.modules.LonePairCounter.calcLoneElectronCount(LonePai


rCounter.java:846)


at chemaxon.marvin.modules.LonePairCounter.calcLonePairCount(LonePairCou


nter.java:152)


at chemaxon.marvin.modules.LonePairCounter.callback(LonePairCounter.java


:126)


at chemaxon.struc.MoleculeGraph.callLonePairCounter(MoleculeGraph.java:2


986)


at chemaxon.struc.MoleculeGraph.getLonePairCount(MoleculeGraph.java:2974


)


at chemaxon.struc.MoleculeGraph.calcHybridization(MoleculeGraph.java:314


8)


at chemaxon.struc.StaticMolecule.init(StaticMolecule.java:494)


at chemaxon.struc.StaticMolecule.<init>(StaticMolecule.java:95)


at chemaxon.marvin.modules.MCS.setMolecules(MCS.java:319)


at chemaxon.marvin.modules.AutoMapper.initMCS(AutoMapper.java:1997)


at chemaxon.marvin.modules.AutoMapper.calculatePairWiseMCS(AutoMapper.ja


va:1979)


at chemaxon.marvin.modules.AutoMapper.perceiveMCSMaps(AutoMapper.java:19


18)


at chemaxon.marvin.modules.AutoMapper.init(AutoMapper.java:1722)


at chemaxon.marvin.modules.AutoMapper.map(AutoMapper.java:760)


at chemaxon.marvin.modules.AutoMapper.setReaction(AutoMapper.java:711)


at chemaxon.marvin.modules.AutoMapper.map(AutoMapper.java:1021)


at chemaxon.reaction.Reaction.setReaction(Reaction.java:875)


at chemaxon.reaction.Reaction.setReaction(Reaction.java:781)


at chemaxon.reaction.ReactorConfiguration.getReaction(ReactorConfigurati


on.java:756)


at chemaxon.reaction.ReactorConfiguration.getReaction(ReactorConfigurati


on.java:736)


at chemaxon.reaction.ReactorConfiguration.getReactionSequence(ReactorCon


figuration.java:673)


at chemaxon.reaction.SynthesisGraph.<init>(SynthesisGraph.java:245)


at chemaxon.reaction.SynthesisConfiguration.getAlgorithm(SynthesisConfig


uration.java:384)


at chemaxon.reaction.Synthesizer.<init>(Synthesizer.java:637)


at chemaxon.reaction.Synthesizer.<init>(Synthesizer.java:600)


at chemaxon.reaction.Synthesizer.<init>(Synthesizer.java:575)


at chemaxon.reaction.Synthesizer.dbmain(Synthesizer.java:1235)


at chemaxon.reaction.Synthesizer.main(Synthesizer.java:1422)








Thanks for your time.





Darcy

Hi,





this error is caused by some query atom types, like the not list atoms etc. It will be fixed in the next bug fix release which is due next week.





Apologies for any inconvenience this bug might cause.





Regards,


Miklos