Reactor Crash

Hello.  Reactor (version 5.5.1.0) crashes while enumerating a library.  Reactor has always worked for me in the past so I'm not sure what I'm doing wrong this time.

This is the stack trace:

chemaxon.reaction.ReactionException: chemaxon.util.concurrent.processors.WorkUnitException: java.lang.NullPointerException

Caused by:

java.lang.NullPointerException

Caused by:

java.lang.NullPointerException

at chemaxon.reaction.ConcurrentReactorProcessor.reactNext(ConcurrentReactorProcessor.java:605)

at chemaxon.alchemist.reactor.ReactorAlchemistTask.calculate(ReactorAlchemistTask.java:168)

at chemaxon.alchemist.AlchemistTask$ActualTask.<init>(AlchemistTask.java:178)

at chemaxon.alchemist.AlchemistTask$1.construct(AlchemistTask.java:69)

at chemaxon.alchemist.utils.SwingWorker$2.run(SwingWorker.java:110)

at java.lang.Thread.run(Unknown Source)

Caused by: chemaxon.util.concurrent.processors.WorkUnitException: java.lang.NullPointerException

at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(Unknown Source)

at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(Unknown Source)

at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(Unknown Source)

at chemaxon.util.concurrent.processors.WorkUnitWorker.work(Unknown Source)

at chemaxon.util.concurrent.worker.Worker$1.call(Unknown Source)

at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)

at java.util.concurrent.FutureTask.run(Unknown Source)

at chemaxon.util.concurrent.worker.Worker.run(Unknown Source)

at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)

at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)

at java.util.concurrent.FutureTask.run(Unknown Source)

at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)

... 1 more

Caused by: java.lang.NullPointerException

at chemaxon.reaction.Reaction.getChangingAtomPropType(Reaction.java:1237)

at chemaxon.reaction.Reaction.storeAtomProperties(Reaction.java:1220)

at chemaxon.reaction.Reaction.getProductAtomProps(Reaction.java:573)

at chemaxon.reaction.ReactionPerformer.transformAtomProperties(ReactionPerformer.java:1171)

at chemaxon.reaction.ReactionPerformer.reactHit(ReactionPerformer.java:803)

at chemaxon.reaction.ReactionPerformer.reactOne(ReactionPerformer.java:606)

at chemaxon.reaction.ReactionPerformer.reactOneDuplicateFiltered(ReactionPerformer.java:571)

at chemaxon.reaction.ReactionPerformer.reactBase(ReactionPerformer.java:558)

at chemaxon.reaction.ReactionPerformer.react(ReactionPerformer.java:536)

at chemaxon.reaction.Reactor.react(Reactor.java:1259)

at chemaxon.reaction.ConcurrentReactorProcessor$ReactorWorkUnit.call(ConcurrentReactorProcessor.java:350)

... 14 more

 

 

-&

Hi,

Could you attach the reaction and the input reactants?

Zsolt

Hi guys,

I'm not the topic starter, but I saw the same error several times as well.
Here is an example of "reaction" that causes it.
I know it's not a real reaction scheme, but chemists who just started using Reactor tend to draw things like that.
It would be great if Reactor could die somewhat more gracious instead of just printing stack.

I checked 5.9.0 and 5.9.4, both behave the same way.

Cheers,
Val

We can reproduce the error with the attached reaction. It's a bug in Reactor, we will fix it. Fix can be expected in 5.10.x version.

Zsolt

Hi Zsolt,

I found a workaround as well. Apparently, the Reactor doesn't like contracted groups in the reaction scheme. If you just expand the group in the example above, it works just fine.
The groups in reactants do not cause the issue, so putting 'Expand Groups' in the reaction's Standardizer config doesn't help.

Cheers,
Val

Fix is available from the 5.10.1 version.

Zsolt