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Markush Detection
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lbullard

Joined: 08 Jun 2009
Posts: 5

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Link to postPosted: Thu Jun 18, 2009 11:29 amPost subject: Markush Detection Reply with quote

Hi,

I'm using PLP to extract structures from some Word documents using the Scitegic Embedded Molecules Reader then inserting into a JChem Base table (structures).  However, some of the extracted items are markush so I need a way of detecting this and re-directing the insert into a different (markush) table.

Can you help ?

 

Thanks

Luke

Zsolt
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Joined: 11 Jan 2006
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Link to postPosted: Fri Jun 19, 2009 12:46 pmPost subject: Reply with quote

Hi Luke,

We will add an isMarkush() Chemical Terms fuction to JChem, that will help identifying Markush structures. My colleague will explain in details how this function can be used in Pipeline Pilot.

Zsolt

Szilard
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Joined: 21 May 2004
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Link to postPosted: Sat Jun 20, 2009 2:39 amPost subject: Reply with quote

Hi,

You will be able to use this function via the "ChemAxon Chemical Terms Filter" component once you have upgraded your PP configureation to the JChem version which contains this new feature.


By the way regular structures can also be stored and searched fine in Markush tables.

The only problem is that (depending on the number of structures) this might be a waste of resources due to the bigger fingerprint size (hard disk, structure cache size in RAM).


Best regards,


Szilard

 

 

Szilard
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Link to postPosted: Wed Jul 15, 2009 10:12 pmPost subject: Reply with quote

Hi,

JChem 5.2.3 has been released, and it supports the "isMarkush() Chemical Terms function.

However inside Pipeline Pilot (may depend on version) some markush features may not be properly converted in the ChemAxon Chemical Terms Component using the standard PP Java API.

So we have created a more dedicated ChemAxon Markush Filter component, which can be found under the Prototypes directory for now in the latest early access release:

http://www.chemaxon.com/download.php?dl=&d=/data/download/pp/devel/ChemAxon_for_Pipeline_Pilot_TEST_2009_07_15.zip

 

Best regards,

Szilard

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