Many thanks for the implementation of a whole set of reaction nodes which is great to see, I am really happy about this.
Unfortunately I am having problems with the Enumerator node.
If I take a simple amide coupling reaction (Acid+Amine -> Amide) and use Reaction Automapper this bit works great. If I then take 2 acids (Pyridine Carboxylic Acid, Quinoline Acid), and 2 amines (Piperidine, 4-AminoCyclohexane) and add these to the enumerator node ports, the output is only 2 products (Rxn of the two acids with only one of the amines - the piperidine), why is the outcome not the 4 possible products ? Also why does the RowID in the KNIME table show "Reaction0, Reaction2", is this indicating a problem.
I see on the Indigo website there are also further options, for example when one of the reagents is a diacid for instance, where "All Reactions" allows the same amine to react multiple times, and "One Tube" where all of the amine combinations are possible. Also an "Intramolecular" option is shown where if an acid and amine exist in the same molecule, they can undergo an intramolecular reaction.
Is it possible for any of these features to be added, they look really cool!!
Did you manage to identify the issue with the combinatorial reaction enumeration node in the example I described above. I tried it again with the latest indigo build and am still encountering problems in terms of getting the correct number of output structures.
I am having exactly the same problem as Simon. I entered an RXN profile and SDF data for 3 alkenes and 3 amines into the combinatorial reaction enumerator, and I only get 6 products out, instead of the 9 that would be expected. The even-numbered reaction rows are there (Reaction0, Reaction2, Reaction4, Reaction6 and Reaction8) but the odd numbered reaction rows (Reaction1, Reaction3, Reaction5 and Reaction7) are missing! I would be really grateful if this bug could be fixed, please.
I've just had a look at the source code for the node (com.ggasoftware.indigo.knime.plugin.source_1.1.0.201202211836.jar -> IndigoReactionGeneratorNodeModel.java), and on line 153 the code rowNumber++; shouldn't be there; it is in a for loop that automatically increments rowNumber anyway. That would explain why the row numbers are incremented by 2 each time. I'm not too familiar with Java though, so I still can't quite work out why all of the reactions aren't being enumerated properly. I'll have a closer look later today.
I am trying to use this node to react three groups on a molecule with another molecule. However, I can only get individual products with a single reaction instead of one product having all groups reacted. How can I do the opposite?