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Infocom Knime Nodes for 5.11
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Sander

Joined: 01 Sep 2011
Posts: 18

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Link to postPosted: Tue Oct 30, 2012 4:43 pmPost subject: Infocom Knime Nodes for 5.11 Reply with quote

Dear reader,

We recently updated from 5.10 to 5.11, which also required an update of our database to version 5.11. No problems so far.

Unfortunately, this update breaks the InfoCom JChem Search node in Knime, which cannot read structure tables from our database anymore.

We experienced a similar issue going from 5.9 to 5.10 (reported here: http://tech.knime.org/forum/jchem-extensions/instant-jchem-update-510-breaks-jchem-nodes-workaround). Is there any way for users to keep track of the InfoCom upgrade path in parallel to the ChemAxon updates?

In this way we could better time our updates (and avoid these issues).

Many thanks,

Sander Nabuurs.

Takahiro

Joined: 07 Mar 2005
Posts: 71

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Link to postPosted: Thu Nov 01, 2012 11:39 amPost subject: Reply with quote

Dear Sander Nabuurs,

We have just released JChem Extensions version 2.6.3.v0135 that uses JChem5.11.3.0.
I deeply apologize for my neglect.

Best regards,
Taka

Ellert

Joined: 26 Jul 2011
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Link to postPosted: Wed Nov 07, 2012 4:47 pmPost subject: Reply with quote

There seems to be a problem with the new node set, at least with the Standardizer.

If you select Clean2D and leave the options on the default 'Partial' the output will be maimed, all Molecules will show up as OH3, OH, BrH etc. instead of their original structures (those where +- 30 atom organic molecules)

If you switch to Full cleaning it works ok, but still this is quite unexpected.

Takahiro

Joined: 07 Mar 2005
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Link to postPosted: Fri Nov 09, 2012 6:37 amPost subject: Reply with quote

Hi,

What kind of format do you use for original structural file?
For instance, if you use smiles format, it seems not to work.
Currently partial and template based clean is available in 2D only.

Is it possible that you post sample data?

Thank you for your cooperation.

Best,
Taka

Ellert

Joined: 26 Jul 2011
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Link to postPosted: Mon Nov 12, 2012 4:55 pmPost subject: Reply with quote

It is a smiles file.
I guess that doing a partial coordinates calculation on compounds that do not have any coordinates is what couses this.

 

I can not attach files in this forum, can you tell me where to send the files by mail ?

Takahiro

Joined: 07 Mar 2005
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Link to postPosted: Thu Nov 15, 2012 4:45 amPost subject: Reply with quote

Hi,

Thank you for the information.
For now, I don't need the file.
Because I guess that you should not use smiles file with partial coordinates calculation.
Could you please use Full cleaning.

Best,
Taka

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