R-Group Decomposer

Community Extensions Indigo
#1

Hi Mikhail,

Many many thanks for all these new nodes recently, I have still not had chance to play with them all yet.

However, I do have a request around an existing node, the R-Group Decomposer.

Is it possible to make it so that when a core is specified and the R-Groups are decomposed into separate columns, that the R-Groups are separated out consistently into the same columns.

For instance, if you have a pyridine core with groups around it, can it be achieved in such a way that the R-Groups are positioned into the same R column for each row. I have numerous examples, where the R-Group splitting seems to randomly change, therefore meaning a common R group in each of the molecules attached to the same position on a pyridine suddenly ends up going from the R-Group #1 column to the R-Group #5 column. I assume this is because the numbering around the Pyridine can be counted from either way round.

One way this might be achieved is by comparing results from the last 5 rows to look for the same or similar group, to help determine which way around the Pyridine to count and therefore to help the R-Group columns be moved into consistently the same column.

Thanks

Simon.

#2

Dear Simon,

We are working with RGroup decomposer at the moment. There are several requests (you can find it in the google groups) for the indigo decomposer, so, I think, the KNIME node version will be uploaded soon. I have reproduced the issue with Pyridine. The issue can be expanded on all highly-simmetric scaffold molecules. I will try to resolve it as well.

With best regards,

Alexander

#3

Hello all,

The bug with RGroup decomposer highly-simmetric scaffold molecules was fixed. The new version will be available in the upcoming release

PS. After an absence we have returned to the KNIME development! I will try to resolve all the issues collected from the forum topics

With best regards,

Alexander

GGA Software Services LLC.