DB Nodes need more type handling (Chemistry)

KNIME Analytics Platform
1

The new DB nodes have all these type conversion options but what is not available is to map common chemical structure formats to string types and vice versa.

Loading smiles from DB still needs a molecule type cast node. OK, this doesn’t change anything.
The far bigger issue I’m no encountering when migrating workflows is that the DB Writer/Insert/Update doesn’t accept SMILES columns. I have to use a “dummy” node like String Manipulation with toNull() just so I can convert the smiles to a string type. Same applies for other text based chemical formats like molfile. This conversion to string was actually not needed with the old Database nodes!!! They did it automatically.

Or said in IT terms, this is clearly a feature regression. :grinning:

So ideally we get the old behavior back. Or at least add the chemistry types to the type mapping options of the new DB nodes so no dummy nodes are needed.

1 Like
2

I believe there is a ticket open for this at KNIME. @tobias.koetter can probably clarify.

Steve

3

Hello beginner,
as Steve mentioned we have a ticket open to implement the chemistry and biology type mapper. The plan is to release them with the summer release if no unexpected problems arise.
Bye
Tobias

3 Likes
4

This topic was automatically closed 182 days after the last reply. New replies are no longer allowed.