I'm trying to make our project working with adapter cells to get rid of our converter nodes. In the last KNIME version I see adapter cells for Sdf, Mol, Mol2 and Smiles formats only. Are adapters supposed to be implemented for other types (like Rxn, Smarts, CML, Inchi etc.) in the future? Or, if needed, user should create it himself?
We only added adapter cells for the standard molecule types that every KNIME chemistry node is supposed to support. We can add more if there is another common format that is recognized by several toolkits.
Thor, thank you for your reply.
So, may I ask to add adapters for some types which are part of KNIME in according to
? I'm talking at least about CML, Rxn, Smarts and Inchi types? They're quite common as far as I can judge. We need them as well as need already existing adapters because the formats can be converted into our representation for further processing. We would greatly appritiate it!
Besides this I am a bit confused regarding a case of adapter cells using. If a molecule is supposed to be modified in our representation, new adapter cells should be created using our representation. Do I understand it correct that the adapter must contain all the adapters which it included before with updated (modified) molecule/reaction value? I see it as follows: for instance, we have SmilesAdapterCell as input --> convert it into our representation --> then apply all the required modifications in our representation --> then create OurAdapterCell taking the modified value --> then add SmilesAdapterCell created with the modified value --> as a result we have adapter cell with our and smiles adapters inside and every of the cells has actual state. Probably this is obvious, but I got confused.
Thans in advance,
KNIME 3.1 will contain more adapter cell implementations.
If you modify a molecule or create a new one, you must drop all other representations. There is no need to re-create them all from the modified molecule. However, you should add at least one standard representation (SDF or Smiles) to the new adapter cell so that other toolkits can (re)create their representation from it.
Now it's completely clear, thank you!
Is there a rough or an exact RTM date for 3.1 version? And the last question: may I know if KNIME 3.1 will contain RxnAdapterCell or not? My further actions depend on it.
Thanks in advance,
The release is planned for December, 6th. It will include additional adapter cells for Smarts, Inchi, Rxn, and CML. We will send around a preview to all community contributors today or tomorrow.