New Interactive Table in new RDKit Nodes

[manuelschwarze]

Dear All,

 

there is a new version of the RDKit Nodes available now as nightly build, which gets currently tested by the community. Beside a complete refactoring (that enables now multi-threading wherever possible and node setting and handling alignment between the different nodes) it comes also with some new goodies, e.g. an Atom Highlighting Node and an RDKit Interactive View.

 

The RDKit Interactive View is fully based on the common KNIME Interactive View and you will not notice a functional difference on first sight. Check out the RDKit Substructure Node, which offers the same view also as direct view, or put an RDKit Interactive View somewhere after the RDKit Substructure Counter node in your workflow. Then you will experience the new capatibility: In the columns that show the substructure count you will see structures being rendered in the table headers instead of just the SMILES headers as the normal table offers. These structures are rendered by using the Default Structure Renderer that is set in the KNIME Chemistry Preferences. The SMILES to be rendered are not picked up from the header name/title, but from properties that have been set for a column. This has the advantage that you may change the title without changing the structure. The current disadvantage is that you need nodes that can set these properties (like the RDKit Substructure Node does).

 

For developers: To make use of this feature the following sample code shows how to create a new column with the properties needed for rendering structures:

DataColumnSpecCreator creator = new DataColumnSpecCreator("My Column Name", IntCell.TYPE);
// The following single line adds the new capability to render SMILES
// The first parameter "Smiles" must be constant
// The second parameter is the structure to be rendered as SMILES string
// The third parameter defines the initial header height or -1 to use the default
new AdditionalHeaderInfo("Smiles", "<Put here your SMILES value>", -1).writeInColumnSpec(creator);
DataColumnSpec myNewColumnSpec = creator.createSpec();
// Add this spec to a new table

 

I hope this new view will be useful for some of you.

 

Kind regards,

Manuel Schwarze

[James_Davidson]

Hi Manuel,

The RDKit Interactive View is cool - good work!

I could imagine a nice additional use-case would be to add properties to the R group headers in the output of the R-Group Decomposition node(?)  This could allow R1, R2, R3, etc to be shown in context as attachement points on the query scaffold!

 

Kind regards

James

[richards99]

I agree with James that would be a nice feature.

ideally an additional node would be good to which you can set columns to use smiles structures as headers. This can be useful when doing a pivot node on an RGroup decomposition node.

thanks,

simon.

[richards99]

To take advantage of these structure headers, are there plans for an RDKit Pivot Table that you could do on the R-Group Decomposition node.

That would be very powerful for SAR analysis.

Simon.

[manuelschwarze]

There is a new RDKit SMILES Headers node available now in the nightly build that does the trick to set SMILES values for column headers, which can be shown then in the RDKit Interactive Table View.

-Manuel