KNIMEtech | Indigo to Molecule with SDF

Sat, 05/21/2011 - 10:37

dpavlov

Offline

Joined: 03/31/2011

Simon,

Hmm, is not that what the KNIME's SDF Writer node does?

Best regards,

Dmitry

Sat, 05/21/2011 - 10:46

richards99

Joined: 12/06/2010

Hi Dmitry,

I do not mean writing out to an SDF format file, I mean to make the structures in the KNIME cell as SDF Cell format, as the nodes by MOE require structures to be as SDF. It would be nice to easily go from using the Indigo nodes to the MOE nodes, otherwise a series of translator nodes would be needed (Indigo to Molecules as MOL, and then Mol to SDF node from MOE)

Thanks

Simon.

Sat, 05/21/2011 - 22:43

(Reply to #3) #4

James Davidson

Joined: 05/12/2010

Hi Simon,

I believe you can use the Molecule Type Cast node to convert a MOL column to SDF column (maybe not strictly the 'cleanest' way of doing it, as an error message is raised... but it works). Also, the SDF inserter node works - but I have found this a bit variable in behaviour - eg hanging unless a new column name is set - but again, I think it gets you to the point where the MOE nodes are happy to work on the output column.

Kind regards

James

Fri, 05/27/2011 - 12:26

(Reply to #3) #5

The new version of Indigo nodes ( 1.0.0.0000948) is able to export to SDF cell.

Sat, 05/21/2011 - 22:49

gkirsten

Joined: 05/13/2011

The next version of the MOE nodes will accept molecules in SdfCell, MolCell, CtabCell, Mol2Cell and PDBCell format. I hope to release them late June or early July. In the meantime you need the Molecule Type Casts.

Best regards

Guido

Sat, 05/28/2011 - 18:17

Thanks very much for the SDF addition.

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Indigo to Molecule with SDF