Package for ML task management #chemoinformatics #memo #machine_learning #RDKit

Now we can build lots of predictive models rapidly with useful ML tools such as keras, pytorch, scikit-learn, lightGBM etc… The problem for me is that how to manage these experimental results. I posted about the topics previously and I used MLflow, optuna as examples. These tools are has different features but both are very

Rendering tool of cube file on jupyter-notebook #psikit #psi4 #memo

Visualize molecular orbital is one of the good way for understating molecular reactivity. Opensource quantum chemistry package ‘Psi4’ can generate cube file for MO rendering and psikit has function for rendering MO with pymol. Here is an example notebook.https://github.com/Mishima-syk/psikit/tree/master/examples/Rendering_Orbital_in_PyMol And recently I found new tool for cube file rendering named fortecubeview package. The license of

Read SDF with Multi thread #RDKit #memo #chemoinformatics

In the chemoinformatics task, I often use SDFiles and call SDMolSuppier to read them. BTW, from rdkit version 2020.09.1, Multithreaded file reader for SMILES and SDF is implemented but I’ve never used it. So I used it and compared its speed against default SDMolSupplier. Here is an example. At first I got compound data from