Combinatorial Reaction Enumeration Node bug? and feature requests :-)

Community Extensions Indigo
#1

Hi,

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!!

Many thanks,

Simon.

#2

Hi Mikhail/Alexander,

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.

Thanks,

Simon.

#3

Hi,

 

I have also a problem with this node. With some combination I obtain two types of errors:

"pool: access to unused element 51"

and "array: invalid index -1 (size = 3)"

 

I obtained the two types of errors with the same compounds in entrance depending just on which nodes I put before the "combinatorial" node.

I cannot reproduce the first error but for the second I attached to this post a workflow as example of this error.

 

Otherwise I would like to thanks you for this node that is very very usefull.

Thanks,

Lionel

#4

Hi,

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.

Many thanks in advance,

Chris

#5

Hi,

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.

Best wishes,

Chris

#6

Hi,

I just downloaded the latest nightly build and this problem is fixed! Thank you very much indeed!

Best wishes,

Chris

#7

Hi Chris,

Many thanks for the bug finding. The fixed version is nightly available  (1.1.0.201202272004).

As for the other Reaction Enumerator issues, I have added them to the next version TODO list.

With best regards,

Alexander

#8

Hi Indigo team,

I noticed the bug was fixed also this morning, many thanks, my reactions now enumerate to give the correct number of products.

Thanks,

Simon.

#9

Hello,

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?

Best regards.