#rdkit — Public Fediverse posts

#OpenBabel is dead, long live #RDKit!

https://github.com/RMeli/spyrmsd/issues/149

On a more serius note, it would be cool to have a cheminformatics library that actually works. Don't get me wrong, RDKit is very cool - but you can feel all the underlying problems it has when using it.

#Cheminformatics

Tonight I'm taking the train to Prague for the European edition of the 2025 #RDKit UGM.
I'm really looking forward to meeting a bunch of the community there!
We don't have space for any last-minute in-person registrations, but info on joining the live streams is here:
https://github.com/rdkit/UGM_2025/

New pre-proof in Journal of Molecular Liquids: ML predicts NMR chemical shifts for metal complexes (45Sc, 49Ti, 89Y, 91Zr, 139La). CatBoost+RDKit ≈7% RMSE for Sc/Y/La; 9% Ti; 13% Zr. SHAP highlights cyclic motifs & electrostatics. Read: https://doi.org/10.1016/j.molliq.2025.128417 #NMR #MachineLearning #MaterialsScience #TransitionMetals #RDKit #CatBoost #SHAP

I used chembl-downloader to create some nice charts on how the number of compounds, assays, activities, and other entities in ChEMBL have grown over time

📖 https://cthoyt.com/2025/08/26/chembl-history.html

#chembl #chemistry #chemometrics #chemoinformatics #cheminformatics #rdkit #cdk #proteochemometrics

I used chembl-downloader to create some nice charts on how the number of compounds, assays, activities, and other entities in ChEMBL have grown over time

📖 https://cthoyt.com/2025/08/26/chembl-history.html

#chembl #chemistry #chemometrics #chemoinformatics #cheminformatics #rdkit #cdk #proteochemometrics

I used chembl-downloader to create some nice charts on how the number of compounds, assays, activities, and other entities in ChEMBL have grown over time

📖 https://cthoyt.com/2025/08/26/chembl-history.html

#chembl #chemistry #chemometrics #chemoinformatics #cheminformatics #rdkit #cdk #proteochemometrics

I used chembl-downloader to create some nice charts on how the number of compounds, assays, activities, and other entities in ChEMBL have grown over time

📖 https://cthoyt.com/2025/08/26/chembl-history.html

#chembl #chemistry #chemometrics #chemoinformatics #cheminformatics #rdkit #cdk #proteochemometrics

Today's #RDKit blog post gets into the weeds of how inconsistent information in a common file format is handled by the RDKit.

https://greglandrum.github.io/rdkit-blog/posts/2025-08-22-interpreting-the-2d3d-flag.html

Today's #RDKit blog post shows a way to store partial charges in SD files. We really should stop using mol2 files.

https://greglandrum.github.io/rdkit-blog/posts/2025-07-24-writing-partial-charges-to-sd-files.html

Today's #RDKit blog post is a heartfelt plea for clearer communication.

https://greglandrum.github.io/rdkit-blog/posts/2025-07-17-naming-similarity-metrics.html

The new #RDKit blog post, inspired by a question from Kjell Jorner, looks at the impact of molecular size on similarity thresholds.
https://greglandrum.github.io/rdkit-blog/posts/2025-06-20-size-and-similarity-1.html

This week's #RDKit blog post shows how to use some of the information added to molecules that come from the chemical reactions code.

https://greglandrum.github.io/rdkit-blog/posts/2025-06-12-using-reaction-info.html

The new #RDKit blog post is a guest post from @jemonat with a tutorial on using Bemis-Murcko scaffolds.

https://greglandrum.github.io/rdkit-blog/posts/2025-06-06-murcko-scaffolds.html

This week I have updated and revised an old blog post showing how to perform extended Hueckel calculations with the #RDKit. This is a fun one for me because it involves work I did back in grad school. :-)
https://greglandrum.github.io/rdkit-blog/posts/2025-05-30-eHT-in-RDKit.html

This #RDKit blog post builds on the earlier one about chemical words; this time I'm using Morgan fingerprint bits as the "words".

https://greglandrum.github.io/rdkit-blog/posts/2025-05-22-common-chemical-words-2.html

The new #RDKit blog posts demonstrates how to work with your own fingerprints in the PostgreSQL cartridge.

https://greglandrum.github.io/rdkit-blog/posts/2025-05-17-custom-fingerprints-in-postgresql.html

This week's #RDKit blog post revisits and updates a really old post looking at the most common chemical "words".

https://greglandrum.github.io/rdkit-blog/posts/2025-05-09-common-chemical-words-1.html

Hi. I'm a scientist and programmer based in Basel, Switzerland. I'm a long-time advocate of #OpenSource and #OpenScience and am the primary developer of the #RDKit.

#introduction

There's a new #RDKit blog post introducing some new functionality that I'm really excited about: doing efficient substructure and similarity searches in very large chemical libraries:
https://greglandrum.github.io/rdkit-blog/posts/2024-12-03-introducing-synthon-search.html

Yes! #rdkit

A really interesting preprint caught my attention from Connor Coley’s group at MIT. ShEPhERD diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design https://macinchem.org/2024/11/23/shepherd-shape-electrostatics-and-pharmacophore-explicit-representation-diffusion/ #cheminformatics #RDKit

@dr_greg_landrum I'm sure I'm doing something either quite naive or unoriginal here (I'm a #RDKit newbie). @cthoyt says you have likely looked into this.

Dear #python community.

Is someone from #Madrid ( #spain ) here who is looking for a new #job opportunity in a global operating company (no agency or similar). I'm currently searching for a #python #fullstack developer who is familiar with #django. Ideally you should also have experience in development with chemistry software like #rdkit, #sbml (not a must). Job posting will be issued soon.
If you know someone please share

Ooh and you will have to work closely with me 😜

#jobs #FediHire

📝 "Decision tree"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/16_ML2-1_Decision_tree/2_data_prep_tran.html

#pyladies #python #machinelearningprojects #treemodels #datapreprocessing #chembldatabase #pandas #rdkit #datamol

📝 "Decision tree"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/16_ML2-1_Decision_tree/2_data_prep_tran.html

#pyladies #python #machinelearningprojects #treemodels #datapreprocessing #chembldatabase #pandas #rdkit #datamol

📝 "Decision tree"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/16_ML2-1_Decision_tree/2_data_prep_tran.html

#pyladies #python #machinelearningprojects #treemodels #datapreprocessing #chembldatabase #pandas #rdkit #datamol

📝 "Decision tree"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/16_ML2-1_Decision_tree/2_data_prep_tran.html

#pyladies #python #machinelearningprojects #treemodels #datapreprocessing #chembldatabase #pandas #rdkit #datamol

📝 "Decision tree"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/16_ML2-1_Decision_tree/2_data_prep_tran.html

#pyladies #python #machinelearningprojects #treemodels #datapreprocessing #chembldatabase #pandas #rdkit #datamol

Less than 24 hours until the #RDKitUGM2023 kicks off. I'm really psched to spend three days with the #RDKit community!

Good work is easy and fun to review - I just sent a golden recommendation to accept (with minor changes 😜) for "Cheminformatics Python Microservice (CPM): unifying access to open cheminformatics toolkits"

preprint: https://doi.org/10.26434/chemrxiv-2023-hk8zn)

code: https://github.com/Steinbeck-Lab/cheminformatics-python-microservice

service: https://api.naturalproducts.net/latest/docs

#cheminformatics #rdkit #openbabel #indigo #cdk #microservice #smiles #inchi #ocsr

@Kohulan @steinbeck good work, all

Good work is easy and fun to review - I just sent a golden recommendation to accept (with minor changes 😜) for "Cheminformatics Python Microservice (CPM): unifying access to open cheminformatics toolkits"

preprint: https://doi.org/10.26434/chemrxiv-2023-hk8zn)

code: https://github.com/Steinbeck-Lab/cheminformatics-python-microservice

service: https://api.naturalproducts.net/latest/docs

#cheminformatics #rdkit #openbabel #indigo #cdk #microservice #smiles #inchi #ocsr

@Kohulan @steinbeck good work, all

Good work is easy and fun to review - I just sent a golden recommendation to accept (with minor changes 😜) for "Cheminformatics Python Microservice (CPM): unifying access to open cheminformatics toolkits"

preprint: https://doi.org/10.26434/chemrxiv-2023-hk8zn)

code: https://github.com/Steinbeck-Lab/cheminformatics-python-microservice

service: https://api.naturalproducts.net/latest/docs

#cheminformatics #rdkit #openbabel #indigo #cdk #microservice #smiles #inchi #ocsr

@Kohulan @steinbeck good work, all

Good work is easy and fun to review - I just sent a golden recommendation to accept (with minor changes 😜) for "Cheminformatics Python Microservice (CPM): unifying access to open cheminformatics toolkits"

preprint: https://doi.org/10.26434/chemrxiv-2023-hk8zn)

code: https://github.com/Steinbeck-Lab/cheminformatics-python-microservice

service: https://api.naturalproducts.net/latest/docs

#cheminformatics #rdkit #openbabel #indigo #cdk #microservice #smiles #inchi #ocsr

@Kohulan @steinbeck good work, all

Good work is easy and fun to review - I just sent a golden recommendation to accept (with minor changes 😜) for "Cheminformatics Python Microservice (CPM): unifying access to open cheminformatics toolkits"

preprint: https://doi.org/10.26434/chemrxiv-2023-hk8zn)

code: https://github.com/Steinbeck-Lab/cheminformatics-python-microservice

service: https://api.naturalproducts.net/latest/docs

#cheminformatics #rdkit #openbabel #indigo #cdk #microservice #smiles #inchi #ocsr

@Kohulan @steinbeck good work, all

📝 "Working with scaffolds in small molecules"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/14_Scaffolds_in_small_molecules/chembl_anti-inf_data_prep_current.html

#pyladies #python #rdkit #datamol #pandas #polars #cheminformatics

📝 "Working with scaffolds in small molecules"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/14_Scaffolds_in_small_molecules/chembl_anti-inf_data_prep_current.html

#pyladies #python #rdkit #datamol #pandas #polars #cheminformatics

📝 "Working with scaffolds in small molecules"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/14_Scaffolds_in_small_molecules/chembl_anti-inf_data_prep_current.html

#pyladies #python #rdkit #datamol #pandas #polars #cheminformatics

📝 "Working with scaffolds in small molecules"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/14_Scaffolds_in_small_molecules/chembl_anti-inf_data_prep_current.html

#pyladies #python #rdkit #datamol #pandas #polars #cheminformatics

📝 "Working with scaffolds in small molecules"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/14_Scaffolds_in_small_molecules/chembl_anti-inf_data_prep_current.html

#pyladies #python #rdkit #datamol #pandas #polars #cheminformatics

Try to use recent version exmol #exmol #rdkit #chemoinformatics https://iwatobipen.wordpress.com/2023/05/04/try-to-use-recent-version-exmol-exmol-rdkit-chemoinformatics/ via @iwatobipen