Use Lilly MedChem rules for scoring of REINVENT4 #cheminformatics #reinvent4 #rdkit

Now I’m reading code of new version of REINVENT4. The pacakge supports not only json but also toml format config file. It make easy to set config for users. And I found that this version seems easy add new scoring function which defined by users. Long time ago, I wrote blog post about Lilly MedChemRules.

Update Scikitlearn and visualize chemical space with rdkit #RDKit #Chemoinformatics #Scikitlearn

As most of readers know that new version of scikitlearn is released ;) There are lots of improvements are implemented. And you can see the details in original documenation.https://scikit-learn.org/stable/whats_new/v1.3.html One of interesting news is that scikit-learn v13 has implemented HDBSCAN. The origainal article is following link. And it implemented indpendend package of python.Article: https://link.springer.com/chapter/10.1007/978-3-642-37456-2_14Package: https://github.com/scikit-learn-contrib/hdbscan

Run Knime workflow without GUI #chemoinfo #knime #RDKit

I enjoyed knime summit last week. I could learn lots of useful features of new version of Knime (ver5). Knime is useful tool for chemoinformatics but I mainly write code with python so I’m not heavy user of knime but recently I’m interested in Knime and learning to apply it in my projects. As reader

Extract macro cyclic compounds from ChEMBLDB with rdkit_cartridge #chemoinformatics #RDKit

As you know, RDKit has really useful postgreSQL cartridge. So it’s easy to do substructure or similarity search of query structure from postgresql ChEMBLDB. But I don’t know how to retrieve only macrocyclic compound from ChEMBLDB with the cartridge. I searched RDKit mailing list and got good answer! Thanks for the community. This is the

Update announcement of shape-it #chemoinformatics #RDKit #shape-it

The end of the last year, I tried to update shape-it and shared my code on github. My new version of shape-it could supports openbabel3.xhttps://github.com/iwatobipen/shape-it-ob3 After that, I got really wonderful offer from @dr_greg_landrum. He modified the code which uses RDKit instead of Openbabel and be used as library instead of command line tool. It’s

Lilly’s Chemoinformatics Tool Kit #memo #chemoinformatics

Almost 7 years ago, I posted a topics about Lilly’s MedChem filter which is disclosed on github. https://iwatobipen.wordpress.com/2013/08/06/lilly%E3%81%AE%E3%83%95%E3%82%A3%E3%83%AB%E3%82%BF/ It’s interesting for me because most of languages of code on Lilly’s repository are not python and C++, R etc. And one of interesting code is LillyMol. The licence of the code is Apache 2.0. I felt

Visualize atom weight of AttentiveFP #DGL #RDKit #Chemoinformatics

Yesterday, I posted an example of DGL (almost same as original example code). And I could make regression model with my own dataset. Fortunately DGL developer provides a code for visualize atom weights of trained model. It means that, after building the model with AttentiveFP, you can visualize atom weight of the give molecule which