RDKit

Just poking my head up here to remind people that registration is open for #RDKitUGM2024, to be held in Zurich Switzerland from 11-13 September. The (free) registration link is here: eventbrite.com/e/13th-rdkit-u…

We're done here. Future "social" activity and announcements will be on mastodon or bsky (check the profile for the handles), the linkedin group, and github discussions.

Here's a reminder that registration for the 2023 RDKit UGM in Mainz is still open. We also still have some slots open for speakers (there's a link from the registration page to submit a talk idea). eventbrite.com/e/12th-rdkit-u…

@skepteis @pythonsummit @betatim That is, unfortunately, the same time as our UGM in Mainz

@pythonsummit @betatim I mean... @RDKit_org belongs there 😊

The Call for Proposals for the next Swiss #Python Summit (September 21, 2023 in Rapperswil) is now open! Any topic is welcome as long as it has something to do with Python. For more information: python-summit.ch/cfp/

The next major RDKit release, v2023.03.1 is finally here: github.com/rdkit/rdkit/re… Builds of the new version are up on conda-forge and NPM and I believe the pypi version will also be updated soon.

The beta of the 2023.03 #RDKit release is now available. Release notes and instructions for how to "conda install" the beta are available here: github.com/rdkit/rdkit/di… Please give the beta a try and let us know if you find any problems.

@rishabh16_ Unfortunately, that's not currently possible.

Hey, @ @RDKit_org power users: Is it possible to "register" new amino acids? I have a few AAs not in the usual 20. RDKit can't seem to read the atoms from those artificial residues from my PDB file. What's a good strategy to overcome this issue? Any help appreciated!

Registration for #RDKitUGM2023, to be held in Mainz Germany from 20-22 September, is now open: eventbrite.com/e/12th-rdkit-u… This will, once again, be an in-person UGM with live streaming of the presentations.

@TheAbhijitDN please post rdkit questions to either the mailing list or github discussions: github.com/rdkit/rdkit/di…

@RDKit_org Great, but module 'rdkit.Chem.Descriptors' has no attribute for the followings : Descriptors.NumCarbons(mol) Chem.rdchem.GetNumHeavyAtoms(mol) Descriptors.NumRings(mol) Descriptors.NumRigidBonds(mol) Descriptors.NumNitrogenAtoms(mol) please suggest what to do...

We're happy to announce that the next feature release of the #RDKit, v2022.09.1, is now available. Python binaries are available in pypi and conda-forge and the JS wrappers in NPM have been updated. The release notes are here: github.com/rdkit/rdkit/re…

There's a new #RDKit blog post with a short tutorial on descriptor calculation. greglandrum.github.io/rdkit-blog/pos…

If you are using (or interested in using) the RDKit Javascript wrappers, @michelml6 is looking for feedback on them: github.com/rdkit/rdkit-js…

Delighted to introduce FEgrow: An Open-Source Molecular Builder and Free Energy Preparation Workflow! By @bieniekmat @ChemCree @rachaelpirie203 @joshhorton93 @drnataliej Now out on @ChemRxiv #compchem: doi.org/10.26434/chemr… 🧵tweetorial...

@BioInorgChem_UW @jwmay @dalkescientific @andrewwhite01 @kmjablonka Depends on the atoms involved and that is pretty straightforward to turn off if you know you're going to be working with molecules where standard organic valence constraints don't apply

Bijective string representation. Now just needs to be modified to be robust? TUCAN SELFIES? 🦜🤳?

@jwmay @BioInorgChem_UW @dalkescientific @andrewwhite01 @kmjablonka Yeah, the RDKit has molhash implemented

@BioInorgChem_UW @dalkescientific @andrewwhite01 @kmjablonka @RDKit_org Yes they are canonicalised before, it should build for multiple back ends (RDKit/OpenBabel/OEChem) but the idea is easy to port easily to CDK/JChem and reuses existing infrastructure. I think @RDKit_org may have integrated it directly in the end.

If you'd like to present or do a poster, please submit your ideas here: forms.gle/J2eHVkNjh4ngg1…

The 2022 RDKit UGM will take place in Berlin Germany from 12-14 October. It's being organized by the Machine Learning Research group at Bayer Pharma. We'll live-stream the sessions for those who can't attend in person. Registration is open here: eventbrite.com/e/11th-rdkit-u…

@dalkescientific @baoilleach @intconfchemstr Hopefully I'll manage to finish putting everything together for the announcement about this year's RDKit UGM early next week. :-)

@baoilleach @intconfchemstr On 2nd thought, I don't think ICCS is the right venue. There was a lot of engineering work, but the only algo dev. was Mahendra's solution to task partitioning. And I can't present scientific applicability/usefulness. While at an @RDKit_org UGM I can also discuss FOSS funding.

A question for @intconfchemstr: do the abstracts submitted need to fit one page?

@RDKit_org's ability to highlight substructure matches is great, though limited to 2D. For some molecules, it's easier to look at those matches in 3D. I made a little code snippet that does exactly that, perhaps someone finds it useful. gist.github.com/cisert/d05664d…

You can also watch the recording of @h_heberle and Christina Humer's talk about CIME at this year's RDKit UGM here: youtube.com/watch?v=s9d31A…