RDkit & databases

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1

I saw that there is a RDKit database cartridge, but there is no Knime integration? Does that mean you need to know SQL to use the db successfully? 

Are there any examples for Knime, one way or other?

 

2

Hi,

Yes, you need to know at least a little bit of SQL in order to take advantage of the database cartridge.

Documentation for installing and configuring the cartridge, as well as an example of loading the ChEMBL data set can be found here: http://rdkit.readthedocs.org/en/latest/Cartridge.html

The attached workflow demonstrates using KNIME nodes to do substructure and similarity queries using a local postgresql instance.

I hope this helps,

-greg

3

Thanks.

Would you say that once the database + cartridge is in place one can work with it solely from within Knime? Import of new compounds/data, deleting of data, etc?

4

I have used KNIME's database functionality only in a read-only mode, so I'm not a good one to answer this quesiton.

There are nodes for updating the database, but I'm not sure if that's going to be sufficient for what you need

-greg

 

5

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