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Why a reaction could not be 'exact' search out
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Reply to topic    Home -> Forums -> Support -> Storage & search: JChem Base /Cartridge -> Why a reaction could not be 'exact' search out

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xuhong
Joined: 18 Jun 2008
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Post subject: Why a reaction could not be 'exact' search out
Link to postPosted: Mon Oct 13, 2008 9:59 am  Reply with quote
Hi,

A few reactions can be searched out using cd_id, but when I copied its structrue from MarvinView window and past it in the Marvin of query.jsp, use 'exact' search, I got 'no hit'. I also tried to copy it into Marvin of edit.jsp and 'insert' it into database, it really would be inserted again though the reaction has existed in the database table (before inserting, there's a 'perfect' searching to avoid such issue in the update.jsp, but the reaction seems also can not be 'perfect' search out, see the following error message:
java.lang.ArrayIndexOutOfBoundsException: 0
at chemaxon.jchem.db.JChemSearch.getResult(JChemSearch.java:2005)

The attached *.mrv is such a reaction.

Thanks,
Xu

 Filename: error_schemes.mrv    Filesize: 4.19 KB    Downloaded: 114 Time(s)
 Description:  
rwagner
Joined: 23 Nov 2007
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Link to postPosted: Mon Oct 13, 2008 7:11 pm  Reply with quote
Hi,

We will investigate the problem and return to you soon.
Thanks for the patience,
Robert
rwagner
Joined: 23 Nov 2007
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Link to postPosted: Fri Oct 17, 2008 5:25 pm  Reply with quote
Hi,

There is a small bug in the hash code calculation for reactions. We will fix it soon.
Bye,
Robert
rwagner
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Link to postPosted: Mon Nov 10, 2008 12:08 pm  Reply with quote
Hi Xu,

The new version 5.1.3 released last week contains the fix of this bug.
The correction will require the regeneration of reaction tables.
Thanks for reporting this bug.

Robert
xuhong
Joined: 18 Jun 2008
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Post subject: reaction can not be perfect search out after inserted
Link to postPosted: Fri Feb 13, 2009 9:51 am  Reply with quote
Quote:
Hi Robert,

I update the jchem to 5.1.4, and still found this bug. I found if the structure talbe created with ' --t:any', there's such a bug, and the searching speed is very slow(waiting.....checking.....). All reactions with contracted group in this table could not be perfect search out after inserted them. But if the structure table created with '--t:reactions', there'll be no such bug.
However I would like to use  structure talbe with 'any' property to store reactions, a few of which may be in markush format.  Thanks, Xu
Gyuri
Joined: 21 May 2004
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Link to postPosted: Fri Feb 13, 2009 9:27 pm  Reply with quote
We would like to understand the problem. Could you please attach some example image of those reactions?
xuhong
Joined: 18 Jun 2008
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Post subject: example reaction could not be perfect search after inserting
Link to postPosted: Wed Feb 18, 2009 2:15 am  Reply with quote
Hi,

One example is the attachment in my first post for this topic.

Thanks,

Xu
rwagner
Joined: 23 Nov 2007
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Post subject: Re: reaction can not be perfect search out after inserted
Link to postPosted: Fri Feb 20, 2009 6:14 pm  Reply with quote
Hi Xu,

We thought you were using reaction tables, and fixed the perfect/exact search problem for it.

Now I checked any tables and could reproduce problem. We will notify you when it is fixed.

Bye,

Robert
rwagner
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Link to postPosted: Thu Feb 26, 2009 4:48 pm  Reply with quote
Hi Xu,

We fixed the bug concerning searching of reactions with sgroups in any table.

Earlier we fixed a bug regarding bad hash code calculation. This time the problem was caused by inconsitent handling of sgroups.

We are sorry for the inconveniences and that this sgroup bug remained hidden the last time (for reaction tables).

The bugfix will appear with version 5.2 which is due to be released in the first half of march.

Bye,

Robert
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