Technical Support Forum Index
Technical Support Forum
Access ChemAxon scientists and developers here. For registration and login issues contact website support.
R-group problem with JChem 5.3.2
To watch this topic for replies  Register (enables digests) or give email address:
Reply to topic
Display posts from previous:   
    View previous topic :: View next topic    
Author Message
JeffGao

Joined: 30 Aug 2006
Posts: 57

View user's profile

Back to top
Link to postPosted: Mon May 10, 2010 4:38 pmPost subject: R-group problem with JChem 5.3.2 Reply with quote

Dear Chemaxon,

We are using JChem 5.0 right now and we are considering to update to JChem 5.3.2. But we found one reaction file (.rxn) containing R-groups works well with JChem 5.0 but triggers an error message with JChem 5.3.2.

The .mrv file is attached in this thread, the SMILES string we are testing is, "c1ccc(cc1)-c1ccccc1" (biphenyl). Here are the output details,

JChem 5.0:

/react -a changing -v -r ../molecules/bt0353.mrv "c1ccc(cc1)-c1ccccc1"
Oc1cccc(-c2ccccc2)c1O
Total running time (ms) : 761
Reaction setting (ms)   : 219
Reactant setting (ms)   : 1
Reaction processing (ms): 541

JChem 5.3.2:

react -v -r ../molecules/bt0353.mrv "c1ccc(cc1)-c1ccccc1"
SEVERE: Array index out of range: 2147483647  [main|chemaxon.reaction.ConcurrentReactorProcessor.main|05/10/2010 10:32:52]
chemaxon.reaction.ReactionException: chemaxon.util.concurrent.processors.WorkUnitException: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 2147483647
Caused by:
java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 2147483647
Caused by:
Array index out of range: 2147483647
        at chemaxon.reaction.ConcurrentReactorProcessor.init(ConcurrentReactorProcessor.java:476)
        at chemaxon.reaction.ConcurrentReactorProcessor.react(ConcurrentReactorProcessor.java:495)
        at chemaxon.reaction.ConcurrentReactorProcessor.run(ConcurrentReactorProcessor.java:618)
        at chemaxon.reaction.ConcurrentReactorProcessor.main(ConcurrentReactorProcessor.java:1062)
Caused by: chemaxon.util.concurrent.processors.WorkUnitException: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 2147483647
        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(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at chemaxon.util.concurrent.worker.Worker.run(Unknown Source)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 2147483647
        at chemaxon.struc.MoleculeGraph.getAtom(Unknown Source)
        at chemaxon.reaction.ReactionPerformer.getSearchData(ReactionPerformer.java:1025)
        at chemaxon.reaction.ReactionPerformer.reactHit(ReactionPerformer.java:745)
        at chemaxon.reaction.ReactionPerformer.reactOne(ReactionPerformer.java:600)
        at chemaxon.reaction.ReactionPerformer.reactOneDuplicateFiltered(ReactionPerformer.java:565)
        at chemaxon.reaction.ReactionPerformer.reactBase(ReactionPerformer.java:552)
        at chemaxon.reaction.ReactionPerformer.react(ReactionPerformer.java:531)
        at chemaxon.reaction.Reactor.react(Reactor.java:1314)
        at chemaxon.reaction.ConcurrentReactorProcessor$ReactorWorkUnit.call(ConcurrentReactorProcessor.java:340)
        ... 14 more

ERROR: An error occured, check the log for details. Use --ignore-error option to ignore errors during reaction processing.

Would you please let us know how to fix this problem? Thanks a lot!

 

Best regards,

Jeff Gao




 Filename: bt0353.mrv    Filesize: 3.97 KB    Downloaded: 131 Time(s)
 Description:  
Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1039

View user's profile
Visit poster's website

Back to top
Link to postPosted: Tue May 11, 2010 12:09 pmPost subject: Reply with quote

Hi Jeff,

It's a bug, related to automatic mapping of R-atoms. We are working on the fix.

Until it's fixed please use the  "--skip-reaction-mapping-check" (or "-A") command line option to skip automapping of the reaction.

Example:

react -r bt0353.mrv --skip-reaction-mapping-check "c1ccc(cc1)-c1ccccc1"
Oc1cccc(-c2ccccc2)c1O

If the reaction is well-mapped, then it's safe to use this option.

Zsolt

JeffGao

Joined: 30 Aug 2006
Posts: 57

View user's profile

Back to top
Link to postPosted: Tue May 11, 2010 2:39 pmPost subject: Reply with quote

Zsolt wrote:

Hi Jeff,

It's a bug, related to automatic mapping of R-atoms. We are working on the fix.

Until it's fixed please use the  "--skip-reaction-mapping-check" (or "-A") command line option to skip automapping of the reaction.

Example:

react -r bt0353.mrv --skip-reaction-mapping-check "c1ccc(cc1)-c1ccccc1"
Oc1cccc(-c2ccccc2)c1O

If the reaction is well-mapped, then it's safe to use this option.

Zsolt

Thank you for letting me know this Zsolt. Could you tell me how to implement the parameter "--skip-reaction-mapping-check" in java code?

Best,
- Jeff Gao

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1039

View user's profile
Visit poster's website

Back to top
Link to postPosted: Tue May 11, 2010 2:52 pmPost subject: Reply with quote

JeffGao wrote:

Thank you for letting me know this Zsolt. Could you tell me how to implement the parameter "--skip-reaction-mapping-check" in java code?

Best,
- Jeff Gao

Use the method Reactor.setSkipReactionMappingCheck(boolean).

Zsolt

JeffGao

Joined: 30 Aug 2006
Posts: 57

View user's profile

Back to top
Link to postPosted: Tue May 11, 2010 3:48 pmPost subject: Reply with quote

Zsolt wrote:
JeffGao wrote:

Thank you for letting me know this Zsolt. Could you tell me how to implement the parameter "--skip-reaction-mapping-check" in java code?

Best,
- Jeff Gao

Use the method Reactor.setSkipReactionMappingCheck(boolean).

Zsolt

Thank you!

- Jeff Gao

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1039

View user's profile
Visit poster's website

Back to top
Link to postPosted: Fri May 21, 2010 10:52 amPost subject: Reply with quote

This bug will be fixed in JChem 5.3.4.

Zsolt

JeffGao

Joined: 30 Aug 2006
Posts: 57

View user's profile

Back to top
Link to postPosted: Mon May 24, 2010 4:21 pmPost subject: Reply with quote

Zsolt wrote:

This bug will be fixed in JChem 5.3.4.

Zsolt

Thank you for lettimg me know this!

Jeff

JeffGao

Joined: 30 Aug 2006
Posts: 57

View user's profile

Back to top
Link to postPosted: Sat Jun 19, 2010 3:34 amPost subject: Reply with quote

JeffGao wrote:
Zsolt wrote:

This bug will be fixed in JChem 5.3.4.

Zsolt

Thank you for lettimg me know this!

Jeff

Zsolt,

I tried jchem 5.3.4.It will not output exceptions but the product looks still different from the version 5.0.

I used reactor (version 5.3.4 ) react -v -r /project/umbbd.msi.umn.edu/src/molecules/bt0353.mrv "c1ccc(cc1)-c1ccccc1"

And it gave me this product:
Oc1:cc:cc(-c2ccccc2):c1O

I used reactor (version 5.0) react -v -a changing -r /project/umbbd.msi.umn.edu/src/molecules/bt0353.mrv "c1ccc(cc1)-c1ccccc1"

And it gave me this product:
Oc1cccc(-c2ccccc2)c1O

Althought "Oc1:cc:cc(-c2ccccc2):c1O" can be standardized to "Oc1cccc(-c2ccccc2)c1O" by,

newMol = oldMol.toFormat("smiles");

the direct output from 5.3.4 still looks strange.

Thank you for any suggestions!

- Jeff

 

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1039

View user's profile
Visit poster's website

Back to top
Link to postPosted: Mon Jun 21, 2010 12:38 pmPost subject: Reply with quote

Jeff,

":" represents an aromatic bond, so  "Oc1:cc:cc(-c2ccccc2):c1O" and "Oc1cccc(-c2ccccc2)c1O" SMILES are equivalent.

We will check later why the SMILES representation of the output has changed.

Zsolt

JeffGao

Joined: 30 Aug 2006
Posts: 57

View user's profile

Back to top
Link to postPosted: Mon Jun 21, 2010 4:41 pmPost subject: Reply with quote

Zsolt wrote:

Jeff,

":" represents an aromatic bond, so  "Oc1:cc:cc(-c2ccccc2):c1O" and "Oc1cccc(-c2ccccc2)c1O" SMILES are equivalent.

We will check later why the SMILES representation of the output has changed.

Zsolt

Thanks.

Reply to topic
Page 1 of 1


To watch this topic for replies   Register (enables digests) or give email address  
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You can download files in this forum