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Java problem when querying an Instant JChem database

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niel Joined: 13 Jun 2006 Posts: 6 Back to top	Post subject: Java problem when querying an Instant JChem database Posted: Wed Mar 12, 2008 4:47 pm  Hello The versions used are : Instant JChem Version: 2.2.1 (build: 080214) JChem Version: 3.2.12 Marvin Version: 4.1.14 (build date: 2007-12-11) Java: 1.6.0_02; Java HotSpot(TM) Client VM 1.6.0_02-b05. When I query an Instant JChemreaction database (6743 reactions), I do no retrieve any answer if I specify that a bond has the status "make/break". Then the java machine cannot be stopped and its used memory grows up to 150 Mo. This process must be killed within the Task Manager. If I don't specify any status for a given bond, the queries proceed well. Thank for your help
tdudgeon Joined: 05 Oct 2004 Posts: 559 IJC personnel Back to top	Post subject: Posted: Wed Mar 12, 2008 8:26 pm  I tried this with a simple example and it worked without problems. Are you able to provide more information (e.g the data file and the query)? Tim
niel Joined: 13 Jun 2006 Posts: 6 Back to top	Post subject: Java problem when querying an Instant JChem database Posted: Thu Mar 13, 2008 8:54 am  That's probably the data file that causes some crashes when I query by substructure with a cyclohexane having a "make/break" bond. I tested another rd file and the above query run well. I attached to you the problematic rd file and I would be pleased if you could detect any fault. Thank for your help Gilles  Filename: Aleadata.zip    Filesize: 4.21 MB    Downloaded: 105 Time(s)  Description:  6743 reactions
niel Joined: 13 Jun 2006 Posts: 6 Back to top	Post subject: Java problem when querying an Instant JChem database Posted: Thu Mar 13, 2008 3:16 pm  hello Tim, I worked again with the initial reaction data file (6743 reactions) and I noticed that I could query the InstantJchem database with a query containing a six-membered ring, a nitrogen atom and a "make:break" bond. On the opposite, the java machine crashes when I query a six-membered ring, all carbon atoms and a "make:break" bond. Where is the bug ? Thank you for your help  Filename: make-break-bond-2.mrv    Filesize: 1.65 KB    Downloaded: 87 Time(s)  Description:    Filename: make-break-bond-1.mrv    Filesize: 1.99 KB    Downloaded: 85 Time(s)  Description:
Szabolcs Joined: 03 Jun 2004 Posts: 771 ChemAxon personnel Back to top	Post subject: Posted: Thu Mar 13, 2008 4:14 pm  Hi, Thank you for the test data. We could reproduce the problem, and will investigate it. Szabolcs
rwagner Joined: 23 Nov 2007 Posts: 24 ChemAxon personnel Back to top	Post subject: Posted: Wed Apr 23, 2008 2:32 pm  Hi, We improved the performance, the search is executed, but we have yet to speed up some slow calculations. The improvements are available in version 5.0.3. Robert
niel Joined: 13 Jun 2006 Posts: 6 Back to top	Post subject: Problem solved Posted: Tue May 13, 2008 9:11 am  Thank you for tour help. I use now the new version 2.3 of InstantJChem and I've got no more problems when querying a substructure search including bond attributes such as Make/Break.
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