Calculate ligand RMSD with rdkit contrib package #RDKit #memo

Today is the last day of my summer vacation…. Due to COVID-19 pandemic, I and my family didn’t go travel during the vacation however, we’ll go to national championship of dodgeball game in next sturday. It will be exciting day!

BTW as you know, rdkit has lots of contrib packages. And I would like to introduce a package named CalcLigRMSD which is calculator of two molecules RMSD.

It is easy to use it. And good example code is disclosed in original repo.
https://github.com/rdkit/rdkit/tree/master/Contrib/CalcLigRMSD

I would like to use the package so I tried to run the code on my PC.

Here is an my code. (Most of code is borrowed from original repository)

https://nbviewer.org/gist/iwatobipen/7456f75e7d5f23607cd9c9885c7f5ff0

It is easy to two ligands RMSD with the package. In the original repositry, more useful examples are introduced. If reader has interest the code, pls check original repo ;)

Thanks for reading.

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Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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