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Synthesizer Exhaustive Example Error

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Home -> Forums -> Support -> Library enumeration, virtual synthesis and metabolite generation -> Synthesizer Exhaustive Example Error

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darcy Joined: 24 Jun 2006 Posts: 23 Back to top	Post subject: Synthesizer Exhaustive Example Error Posted: Sun Mar 09, 2008 2:33 am  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
mvargyas Joined: 21 May 2004 Posts: 579 ChemAxon personnel Back to top	Post subject: Posted: Mon Mar 10, 2008 11:04 pm  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
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