Indigo atom replacer node

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1

In the past I was using the Indigo atom replacer node to change attachment points/R groups from e.g. R group analyses into chromium (Cr) atoms for visualization with ChemDraw for Excel. It doesn't seem to be working anymore, no changes are made when using the node. Can you look into whether this is a bug due to recent upgrades?

Thanks,

Natasja

2

Personally, I use the At atom, which works well. And you can imagine "At" being an abbreviation for "Attachment". Its also in Group 7, and thus monovalent, so it works well for me.

Simon.

3

Hi Simon,

Is it still working for you though, as it's not for me anymore.

Thanks,

Natasja

 
4

Hello Natasja,

Are you using stable build or nightly build of Indigo nodes? In my testing enviroment Atom Replacer node works fine.

Could you also export your workflow with data and attach it to the message? This would help us to find the problem.

Best regards,
Mikhail

5

I've just tried it out using the nightly build. I tried to replace an R group for At and the node runs but the output doesn't change. Just like you mention.

simon.

6

Thanks for confirming Simon, I hadn't gotten a chance yet to test it on a small workflow to share with Indigo. I'm also on the latest build, so looks like it's a real bug.

Thanks,

Natasja

 
7

Hello Natasja and Simon,

I tried to reproduce the issue, but I didn't find an example. I have attached a workflow that works fine with stable and nightly builds (in nightly builds we changed internal format, so you might have to rerun Indigo nodes).

Simon, could you attach simple workflow where you have this issue? Just to reproduce exactly your enviroment could you also write what version of KNIME and Inidgo are you using, and is it 32 or 64 bit version?

Best,
Mikhail

8

I'm not at my pc right now to test the workflows attached, but can say that the "complex sar" workflow on the knime public workflow server demonstrates this At for R group problem.

simon.

9

Hi Simon,

Thank you! I found that it doesn't replace "R" atoms while "R1", "R2" are replaced. I will try to fix it soon.

Best regards,
Mikhail

10

Hi Natasja and Simon,

I fixed the issue in the latest nightly builds 1.1.10. Thank you again for the bug report!

Best regards,
Mikhail

11

Thanks Mikhail for fixing the bug. All back to working order in my workflows.

Best,

Natasja

 
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