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RGroupDecomposition w/ position variation bond
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dllahr

Joined: 15 Nov 2011
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Link to postPosted: Wed Jan 04, 2012 12:58 amPost subject: RGroupDecomposition w/ position variation bond Reply with quote

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)

 

Nora
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Link to postPosted: Wed Jan 04, 2012 1:45 pmPost subject: Re: RGroupDecomposition w/ position variation bond Reply with quote

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.




 Filename: RGDecompTest.java    Filesize: 752 Bytes    Downloaded: 23 Time(s)
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dllahr

Joined: 15 Nov 2011
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Link to postPosted: Wed Jan 04, 2012 4:21 pmPost subject: Reply with quote

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

Szabolcs
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Joined: 03 Jun 2004
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Link to postPosted: Wed Jan 04, 2012 5:10 pmPost subject: Reply with quote

Hi Dave,

 

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

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

 

Best regards,

Szabolcs

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