Chemistry with Python - an Introduction to RDKit

Learn how to perform basic chemistry operations with Python and RDKit.
0:00​​​​​ Intro
0:25 Project setup
0:45 The SMILES format
2:04 Importing molecules
5:59 Operations on molecules
10:25 Molecular descriptors
14:15 Lipinski's rule of five
16:13 Summary
WHO AM I:
I'm Bernhard, a software engineer working in Vienna, Austria. I make videos about technology, productivity and engineering.
LINKS:
RDKit documentation: www.rdkit.org/docs/
Drugbank: go.drugbank.com/
SMILES format: en.wikipedia.org/wiki/Simplif...
Lipinski's rule of five: en.wikipedia.org/wiki/Lipinsk...

[@askhataubakirov9370]

Thank you for the very descriptive and useful introduction! Please keep it going - I would be happy to see more

[@Stelo555]

Thank you for this nice little tutorial. I'm a chemist and just started to get more into cheminformatics ... watching your video was a great start. I would love to see more like that. :-)

[@Bunnybobscodes]

I was not aware of the RDKit tooling this is really helpful!

[@scienceaddicted3431]

Great video! It's a topic I also intend to tackle on my channel. Thank you for your work! 👍

[@70shahin]

I totally needed that. thanks

[@khinchang7628]

Hi. I am learning Conputational chemistry. I hope you will post more videos related to chemistry. Thank you so much for your tutorial.

[@jackq2331]

Great course.

[@taosun8549]

Thanks, great video. I have learned a bit Rdkit as well, but I am not sure if we could use it to analyze the reaction mechanism, like how cool it would be if we could generate an electron pushing arrow image automatically.

[@alice920124]

HI! I appreciate your great effort in introducing a tutorial of RDKit. Would it be possible to perform quantum computational studies such as calculation of Fermi energy?

[@maihoa9032]

I hope you will upload a lot of videos realted to Chemistry in the future. I am studying computation chemistry. I am using python

[@piergiorgiocianciullo6784]

Super! 👏🏻

[@user-dn9wm5ei2j]

I m from Brasil, well done machine learning

[@jestinpjiji260]

Hey is there any function in Rdkit which can convert the smiles text into the corresponding IUPAC Name or compound name for eg: we know that 'C' is the smiles format of methane so is there any function to which we provide smiles as an input and provide u Methane as an output

[@hyejihwang1490]

thank you!!!

[@ayaalaa6261]

thank you!

[@debanjansen1282]

Haloo, I have 1milion compounds retrieved from chembl dB. I want to build 3D mol2 structures from each smales and calculate as much as descriptors calculation for ML model. How to do that with RDkit?

[@DrWillWood]

Great tutorial, thank you!

[@kirk0831]

Great. Can you do how rk do chemical enumeration?

[@satyarahul8007]

Hello , i an excel sheet of compounds and i need to find the aromatic rings in the compound by iterating through compunds. But what is condition to find aromatic rings.

[@faridehabdollahi1703]

Hi, Thanks for your useful tutorial. Can you please tell me are there any methods for converting a list of molecules to their smiles code with RDKit package and how? Thanks

[@aminaghamohamadi1165]

I believe you can use a pandas library and the function Chem.MolToCXSmiles from RDKit to achieve that.

[@petelok9969]

Hi Bernard, nice tutorial. I'm getting an import error when I run 'from rdkit import chem' jupyter can see the path but just can't do it.

[@piyushpaliwal6823]

kzbin.info/www/bejne/e4PZhpmVobOiptE

[@ramachava1293]

Hello sir I'm a PG (organic chemistry) student. Could you please. Tell me some chemistry related IT courses. Thank you And thank you for video

[@balajeeramachandran2141]

great intro tutorial learning how to import from online databank but the background music is horrible. Easily getting diverted.

[@crimson4066]

No music necessary