Vernalis PMI node failure

So, I’ve found the source of the problem - not the stereochemistry, but the ‘Cl’ atom. For reasons I don’t remember, our Mol-block parsing code converts the whole line to uppercase each time, so the line:

M V30 16 Cl 2.18109 3.09803 -0.113906 0

becomes:

M V30 16 CL 2.18109 3.09803 -0.113906 0

The code to look up the atomic weight, which is required for the PMI calculations then fails to find anything for the element with the symbol ‘CL’. I will do a bit more checking to try to figure out if fixing this breaks anything else, add a ‘chloro’ example to the test cases and hopefully get a bug fix pushed out later today or tomorrow.

Thanks again for reporting this, and for your patience and help getting us to the bottom of the problem!

Steve

Hi Steve,

Interesting. I guess adding a CL to your MW lookup table would be the easiest way to fix it, as that will unlikely break anything else?

Glad to hear you figured it out though, as we are planning to use the PMI parameters as a diversity selection criterion.

Thanks,
Natasja

Hi, I’m getting a similar error running a similar workflow - I took the Cl -containing molecules out and still fails, so I removed all the -Br containing ones too and I don’t get the 'NullPointerException anymore, so presumably same issue (and with any other two-letter atom). I do however get another error message - will post on that separately if I can’t get it to run after some playing.
Nick

Dear Nick,

Yep, I’m afraid so - any 2-letter element symbol will break it at the moment. I’m hoping to get the fix out early next week - I have a few issues to resolve with the forthcoming release of KNIME 4.2 first.

Steve

Thanks Steve. I’m following the earlier steps you & Natasja went through and have added the Speedy SMILES Explicit Chirality filter as I have some structures that have the enhanced chiral flags. I’ve connected this to the output of an SDF Reader node (the KNIME Base chemistry one) and it has an output column SMILES containing the SMILES string, but on trying to configure the Speedy SMILES filter I get a ‘Dialogue cannot be opened for the following reason: No column in spec compatible to SmilesValue’? Do I need to use a Vernalis SDF reader?
Nick

You will need to use some sort of conversion node from sdf to SMILES format to do that - either the ‘RDKit from Molecule’ or ‘Canonical SMILES’ nodes from RDKit should be able to do that, or the freely available ‘Molconvertor’ node from the free Marvin/InfoChem nodes. If you go down that route, do make sure you keep the SDF column too though, as otherwise you will loose the 3D coordinates.

Steve

Aha, all sorted now, thanks! Will be interested to try your updated node once the -Cl/-Br problem is fixed.
Nick

Thanks Nick. I have the fix, we just have a strange problem with the community build server at the moment which is preventing us releasing it. The nice people at KNIME.com are working on figuring it out…

Steve

Hi Steve,

Do you have an update on this? I haven’t switched to 4.2 yet, but can obviously do that if that’s the only place the new node will be dropped.

Thanks,
Natasja

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

1 Like

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