Vernalis PMI node failure

There should be no need to upgrade unless you want to. The problem is applying across all our builds at the moment, so that will not make a difference. I will ask the people over at KNIME if they are any nearer understanding the source of the issue.

Steve

Any closer to being able to update the nodes?

Thanks,
Natasja

Sorry @natasja - still stuck with this at the moment. I’ve been away for most of the last 3 weeks, and the guys at KNIME have not managed to track anything down at their end yet. At my end, my work PC is currently refusing to reboot after 3 weeks off. It is high up my priority list to sort this though - I need it working too!

Steve

Thanks for the update. Fingers crossed they’ll figure it out soon.

Best wishes,
Natasja

Hi Natasja,

Thanks for your patience. This is now fixed in our nightly build and 4.2 stable builds. The other release (4.1, 4.0, 3.7) will follow hopefully tomorrow. Details at Update to v1.27.0 - New Nodes and Bug Fixes

Steve

This should now also be available in the stable builds (3.7, 4.0, 4.1 and 4.2) - Update to v1.27.0 - New Nodes and Bug Fixes

Steve

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Hi Steve,

Thanks for sharing the updates. I’m on 4.2 now and the updated node is working fine. I did notice that I had to convert my SDF file to canonical smiles with RDKIT --> RDKIT conf gen --> PMI. If I just used the SDF file to generate the conformers it fails. Not quite sure why, but perhaps another atom typing issue or something like that. Anyway, glad I can use it again.

Best wishes,
Natasja

Thanks @natasja. If you were able to identify which molecule it is in your incoming sd-file that causes the failure and were able to share it that would be really helpful to see if we can fix that issue for you, but understand if that’s not possible.

Steve

Hi there, I am trying to generate the PMI of a collection of 100K members. 3D coordinates generation node works but the PMI seems to fail. I think the workflow is correct but the PMI fails maybe because of the size of the library. Is there a maximum of members? I can read above that there is a limitation on chiral molecules, so what is the max number of chiral molecules tolerated and what is the general number of molecules accepted?
Thank you
Best regards
Iolanda

Hi @Iolanda,

Firstly, the answer to the questions:

  1. There shouldnt be any limit to the maximum library size
  2. here is no limit on chiral molecules. The bug above was to do with the handling of Cl and Br atoms - it happened that those molecules were also chiral.

So there is something else wrong - to figure out what I’m going to need some more information:

  1. What version of our plugins do you have installed? (Help -> About KNIME Analytics Platform, then click on ‘Installation Details’ - you should be able to find us somewhere on the Features or Plugins tabs - you need at least v1.27.0 for the above fixes.
  2. What type of input column are you using? (Mol, PDB etc)
  3. What is the error message when the node fails? Is there any additional information in the KNIME console?
  4. Does it run OK for a subset of the molecules in your table? If so, can you use a chunk loop to identify the first molecule that fails (assuming that the answer to 3. above doesnt already tell you the Row ID or input molecule!) If you are able to share the input molecule, please could you do so, as that might also help to pin down the problem. (The answer at Vernalis PMI node failure above - the link is to a specific comment in this thread - can show you how to get to the first broken molecule)

Thanks

Steve

Hi Steve, thank you for the quick reply. I have checked and the plugin version is actually v1.26.0 so perhaps that’s the reason?
The workflow works fine for a small subset of molecules (7 taken from a paper as a ref), so that’s how I started to doubt on the limit and not on other aspects. But ok then I will try to update the plugin and see if the problem gets solved.
Thank you
Best regards
Iolanda

Btw these are the two workflows where you can also see the error on the node:

Thanks Iolanda - the NullPointerException was I think the problem which hopefully is now fixed in v1.27.0 upwards. Let me know how you get on with the updated version.

Steve

Hi Steve, unfortunately it keeps doing the same. I have now installed the version 27 and restarted KNIME. I kept 3D coordinates output only re-ran PMI node but it fails immediately, doesn’t show anything in the output table.
No sure exactly what I am doing wrong actually… the workflow is the same used for the small set with only the insertion of a col filter…

Are you able to attach a copy of the failed workflow and I will see if I can reproduce the error?

Thanks

Steve

Hi Steve, thanks! I now made a change in the configuration of the initial file which I found to be the only difference with the testset that worked. I am now calculating it again and calculating also another subset of 10000 non-confidential molecules that I can eventually share with you. I am waiting for it to finish (3D coordinates generation takes a while) and I will get back to you.
Thanks and get back to you soon,
Best
Iolanda

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Hi Steve (@Vernalis),

sorry I completely forgot to write you back. In the end I managed to solve. So the problem was due to a single structure which in the initial milion subset was written in the wrong way:
image
The nitrogen of the pyrazole ring was missing its hydrogen and thus 3D coordinates were not generated for one molecule and this was responsible for the error in the PMI node.
So all good and the workflow works just fine.
Thanks for your support
Best regards
Iolanda

Hi,

Thanks for getting back to me. Could I ask you, what was in the input cell for this molecule? Was it a missing/empty cell or something else - it would be good to know to see what broke it and see if we can make it more resistant!

Steve

Hi Steve,

Yes I was actually getting back to you on this. The cell on the 3D coordinates was empty. I just made a trial for you to show you what is visible:
image
You can also try to reproduce yourself, try for example C1(C2=CC=CC=C2)=N[N]C(C3CCC3)=C1
The thing is that the 3D coordinate will proceed as normal, so it will simply leave the empty cell for those molecules which do not work, but the node itself will make its work. It is the PMI that will fail. I think a way to go around it is to add an option in the PMI node to “ignore empty cells” or something like that. I tried to put a node in between the 3D coordinates node and the PMI code to split the table and remove the rows with empty cell from the 3D coordinates but somehow it didn’t work… no sure if I was doing something wrong though.
Hope it helps, let me know if you need any other info,
Best
Iolanda

Ah, OK - thank you. That’s definitely a bug in the node. Hopefully not too difficult to fix and I can get it out in our next update.

Steve

Sounds good, thanks for your responsiveness all the way through :slight_smile: .
Best
Iolanda

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