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Release announcements ?
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Ellert

Joined: 26 Jul 2011
Posts: 51

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Link to postPosted: Mon Dec 17, 2012 4:35 pmPost subject: Release announcements ? Reply with quote

It would be save a lot of time it there would be release announcements of the Infocom Knime nodes.

At this moment Knime 2.7 has been released, but we can not upgrade until the infocom nodes for Knime 2.7 have been released as well.

Takahiro

Joined: 07 Mar 2005
Posts: 71

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Link to postPosted: Tue Dec 18, 2012 3:32 amPost subject: Reply with quote

I'm sorry to have kept you waiting.
We will release new version at mid-Jan, 2013.
However, the latest version (2.6.3.v0135) can work in KNIME 2.7.

Best,
Taka

Ellert

Joined: 26 Jul 2011
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Link to postPosted: Wed Dec 19, 2012 10:17 amPost subject: Reply with quote

Unfortunately upgrading to knime 2.7 while using the 2.6 nodes breaks some functionality.

 

When reading an instantjchem table using the normal database reader node it now puts the cd_structure column in a blob column, for which knime 2.7 now has native support. But the Advanced Molconverter does not know about this new datatype yet, and thus fails to see it entirely.

Converting the column to a String column (using the Column Rename node) clips off the information of moderately large molecules, thus this is not an option either.

Only converting the column to a text column using a SQL Convert ( SELECT CONVERT(cd_structure USING utf8) FROM MOLECULES ) does the trick, but as this needs to be changed in all workflows that use the database reader, it is not a workaround that we will use just yet.

 

OpenBabel seems to have the same issue with blobs by the way.

Takahiro

Joined: 07 Mar 2005
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Link to postPosted: Wed Dec 19, 2012 1:01 pmPost subject: Reply with quote

Hi,

I will enhance the MolConverter node to support BLOB type.

Meanwhile, would it be possible that you use the "Binary objects to strings" node instead of the "Column Rename" node?

I'm sorry for the inconvenience I've caused you.

Best,
Taka

Ellert

Joined: 26 Jul 2011
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Link to postPosted: Wed Dec 19, 2012 1:12 pmPost subject: Reply with quote

This seems to work very well, thank you.

Ellert

Joined: 26 Jul 2011
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Link to postPosted: Tue Mar 19, 2013 5:34 pmPost subject: Reply with quote

The recent update to Instant JChem version 5.12 again breaks the JChem Search and other nodes that directly access the database.

Ofcourse this can be circumvented using the database reader and converting the structures (first from blob to string, then from string to marvin structure), but this again points out the problem of the nodes not being in-sync with the chemaxon releases.

 

It would be very helpfull if this organizational problem could be adressed.

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