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Structure Format is ignored when importing SD file
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CATHERINE

Joined: 26 Apr 2006
Posts: 145

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Link to postPosted: Tue Oct 30, 2012 12:11 pmPost subject: Structure Format is ignored when importing SD file Reply with quote

Hello

I may have found a bug with IJC 5.9.3

I have a structure table in an Oracle database with a JChem index, the structure column is VARCHAR2 (2000) as I prefex to store the structures as Smiles

The table has been promoted into IJC, and in the Entity extra attributes for the Column I have chosen the Format to Save Structure to be Smiles.

When I use the 'Add' row from the Form, this works fine and Smiles are inserted into the database.

However, when I import an SD file, the structures are saved as MolFiles, which means that I exceed the 2000 limit for my column.

Can you let me know if you can reproduce the issue, is there another option which could be used as a work-around ?

At the moment, we will have to convert the structures to Smiles and then import a Text file.

Thanks

Catherine

 

fzimandl

Joined: 23 Jun 2011
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Link to postPosted: Tue Oct 30, 2012 12:33 pmPost subject: Reply with quote

Hi Catherine

Yes I can reproduce your issue. I don't have a workaround yet. Please give me some time to investigate this deeper.

Thanks for your report.

Filip 

fzimandl

Joined: 23 Jun 2011
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Link to postPosted: Tue Oct 30, 2012 5:31 pmPost subject: Reply with quote

Here is the promised workaround.

1. Create a new structure table according your preferences.
2. Set the Format for saving structures to a required value.
3. Add a new molecule from IJC manually to the empty structure table.
4. Proceed with the import.

It should import all molecules in the prefered format. But note that you must first add a new row molecule by sketcher in IJC to the empty table.

Cheers,
Filip 

CATHERINE

Joined: 26 Apr 2006
Posts: 145

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Link to postPosted: Mon Nov 05, 2012 9:52 amPost subject: Reply with quote

Thanks

Catherine

fzimandl

Joined: 23 Jun 2011
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Link to postPosted: Tue Dec 04, 2012 12:55 pmPost subject: Reply with quote

We have fixed this. It will work in IJC 5.12 which is going to be released next year in January.

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