Creating a "MOL2" table

I am writing a node to use my application NEWLEAD in KNIME. The input, option parameter choice, and output generation are working.

    The output consists of a single MOL2 file containing several molecules. I can process it w/out problems with the MOL2 reader, CDK generator, and JMol node. However, I must explicitly enter it in the MOL2 reader, thereby breaking the workflow in two.
      What I would like to do is
        generate a table as OUTPUT for my node, and link it to the CDK generator, and so on.
            How to format this table?
          • Is it enough to have a molecule in each cell?
          • Do I have to format the cell as "MOL2"?
          • If so, how?
                Many thanks!
              • I didn’t completely understand how your workflow should look like, but maybe the following helps:

                • A Mol2 cell is essentially a string column, typed as Mol2 column (the Molecule Typecast node can “convert” string cells into various text-based molecules types)
                • Each molecule cell, regardless of the type, only carries a single molecule (there are exception with other vendors such as Schrödinger, but that needs to be enabled explicitly)
                • Creating a Mol2 cell from scratch (i.e. from a string) is done via the Mol2CellFactory

                Thank you for the prompt answer.
                Here’s some background. My program NEWLEAD generates 3D structures. I created a node wrapper for it that works well, namely, has the standard KNIME interface and can be registered as a standard node. It generated a single MOL2 file with many results (molecules). This file can be processed by the Mol2 reader, the molecule CDK converter, and the JMol node. So the workflow is like this:

                  Newlead(configure, run)
                  MOL2 Reader(read newlead output)->Molecule to CDK->JMol 3D display
                Thus, there are really two independent workflows. Going one further, this is what I would like to have
                  Newlead->Molecule to CDK->JMol 3D display
                If I undestand you correctly, I would have to split the output into strings -- one per molecule -- then create the MOL2 Cell Objects, and finally add them to the output table.
                  Is the Mol2 Cell Factory available in the stadard KNIME SDK? Do you have a link for an example of it?
                    Thanks again!

                    Yes, your plan is right. The Mol2CellFactory is part of the org.knime.chem.types plugin which comes with every chemistry related plugin. You just need to call Mol2CellFactory.create(mol2String).

                    Thanks! To be totally clear about this, is this

                        package available in the standard KNIME SDK that can be downloaded here, or do I need extra components?

                        It is not part of the SDK but you can install it via the Update Manager just as in KNIME Desktop.


                          It works. The Newlead node reads an input of two or more chemical fragments, connect them with spacers to create new molecules, and generates a table of MOL2 cells that can be converted into CDK entries and dispayed in 3D.

                            Thanks to everybody!