Molecule Type Cast // Smiles to SDF

KNIME Analytics Platform
1

Dear KNIME users,

given a table with SMILES coded in one column, I would like to output a SD file.

When using the "Molecule Type Cast" [Smiles as "Structure Column" and SDF as "Structure Type"], I end up in an empty column SDF Smiles...

What am I doing wrong?

 

Cheers & Thanks,

Paul

2

This node only changes the column type, it doesn't convert between formats. I'd recommend using the infocom/chemaxon nodes, the desired node called mol convert.

simon.

3

cool, thanks!

paul

4

The Chemaxon node is called Advanced MolConverter, you do need a license for it though.

Alternatively you could try the Openbabel node (Chemistry/Misc/Openbabel).
You need to install OpenBabel before using the node, http://openbabel.sourceforge.net/

 

5

Not any more, KNIME 2.7 comes with a bundled OpenBabel :-)

6

Good news, thank you.

Unfortunately not all node vendors have updated their nodes yet to work with 2.7, so if you depend on one (or more) of those, you will need to do it the old fashioned 'external tool' way.

7

The standard MolConverter is free, it's just the advanced version that comes in the paid for bundle of nodes.

 

Cheers

 

Sam

8

It seems that the OpenBabel node does not see the new Blob datatype.