RGroupDecomposition w/ position variation bond

Hello

I would like to do an R-Group decomposition using jchembase in which my query contains a position variation bond which attaches to the R-group. I tried it with a relatively simple case, but got an ArrayIndexOutOfBoundsException within LigandHandler (see below for stack trace).  I'm not sure if this is even possible or what the results returned would be.  Thanks in advance.

query molecule cxsmiles:

Cc1ccccc1F.

• * |$;;;;;;;;_R1;$,m:9:4.3.2|
  
  

  target molecule smiles:

  
  

  Cc1c(N)cccc1F

  
  

  relevant code:

  
  

   

  
  

  RGroupDecomposition rGroupDecomp = new RGroupDecomposition();

  
  

  rGroupDecomp.setAttachmentType(RGroupDecomposition.ATTACHMENT_RLABEL);

  
  

  rGroupDecomp.setTarget(curWithoutStereoMol);

  
  

  rGroupDecomp.setQuery(coreMol);

  
  

  Decomposition rDecomp = rGroupDecomp.findFirstDecomposition();

  
  

   

  
  

   

  
  

  Stacktrace:

  
  

   

  
  

  Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 9

  
  

  at chemaxon.sss.search.ratom.LigandHandler.processAttachments(LigandHandler.java:349)

  
  

  at chemaxon.sss.search.ratom.LigandHandler.breakBonds(LigandHandler.java:307)

  
  

  at chemaxon.sss.search.ratom.LigandHandler.convertToLigands(LigandHandler.java:218)

  
  

  at chemaxon.sss.search.RGroupDecomposition.getDecomposition(RGroupDecomposition.java:785)

  
  

  at chemaxon.sss.search.RGroupDecomposition.findDecomposition(RGroupDecomposition.java:776)

  
  

  at chemaxon.sss.search.RGroupDecomposition.findFirstDecomposition(RGroupDecomposition.java:731)

  
  

  at main.rGroupDecomp.RGroupDecompThread.run(RGroupDecompThread.java:92)

  
  

  at main.Main.main(Main.java:50)

  
  

   

This is a bug in the 5.7 version but is not present in the upcoming 5.8 release.

I attach a test program with your code.

java RGDecompTest

The problem was also reproducible using rgdecomp:

rgdecomp -q 'Cc1ccccc1F.
* |$;;;;;;;;_R1;$,m:9:4.3.2|' 'Cc1c(N)cccc1F' 

Thanks for the report.

Thanks for the quick response, and for posting the code, that code is what I am trying to do.

I saw that version 5.7 was recently released, do you have an idea of when 5.8 will be out?  If that is going to be awhile, would it be possible for me to have access to a snapshot with the bug fix?  

Thank you again.

Dave

Hi Dave,

 

5.8 is expected within 1-2 weeks. Beta is already available:

https://www.chemaxon.com/forum/ftopic8544.html

 

Best regards,

Szabolcs