Introduction to RDKit Part 1

[@aaditagarwal24]

This introduction was what I was searching for the past week. It is such an amazing introduction to get started on the rdkit lib. Thank you so much!

[@rafikmenacer7007]

Thank you very much you saved me! I tried to install unsuccessfully RDKit, but now with google colab, it became easy, thank you again

[@ahmetsarigun]

I am very happy for your sharing. Please, could you create a playing list as "Introduction to RDKit" on your channel that we could follow your videos easily? Hope more videos will come. Thanks for your sharing :)

[@JanJensenCopenhagen]

Glad you like the videos. I have made a playlist for machine learning where I'll include any RDKit videos I make kzbin.info/aero/PLVxAq6ZYPp33b1n21cpeiY7Brollt13_6

[@ahmetsarigun]

@@JanJensenCopenhagen Thanks :)

[@WelingtonSilvaMusica]

It's beeing much important for me these videos, thanks!

[@ayuameliatulshahilah]

Hello Sir, I am trying to learn based on what you show in your video. I encountered a problem when I wanted to do smiles_list. The picture doesn't come out as output? Already copy one by one based on video. Your help is truly appreciated.

[@thefluffypanda2]

On most text editors simply typing in your variable name won’t print out the molecule. Even if you print it, it will just say “mol from this smile”xxxxx” “ and won’t actually show the compound. Anyway to get around this?

[@JanJensenCopenhagen]

This only works in Python notebooks AFAIK

[@thefluffypanda2]

@@JanJensenCopenhagen I’m using spyder which is an anaconda editor, so built for python, do you think it would be possible to use a gui for the representation or will it simply only work in python notebooks? Appreciate the help!

[@ewanfraser]

Is there a guide to how to get to where you start this video? I installed python and miniconda but I’m totally lost trying to follow the RDKit setup page.

[@yanzichen4528]

hello I use the code but it has a mistake just said there is no rdkit module.but sometimes before,it was true.how can I deal with it? thanks

[@ramachava1293]

Hello sir Please tell me what is the use , benefits for Rdkit. I have to know sir .

[@timithyboring5964]

Hi sir, How does one install this on windows? Thanks

[@yanzichen4528]

I just conda.I think you can visit Rdkit GuanWang.It write clearly

[@bariskurt007]

what is this for? can we perform QM calculations?

[@kora5]

Installing RDKit with conda can take almost 2 minutes. Here's a faster way.(take 6 seconds) !pip install kora import kora.install.rdkit

[@JanJensenCopenhagen]

Very nice! Thanks for sharing

[@ExploreMalaya]

Thank you sir . really your explanations are next level !!

[@rozgol2706]

Hello could you please introduce me One program to convert Fasta format to smiles cod ?

[@chevere3424]

Thanks!

[@florianro.9185]

05:30 I can recommend list comprehensions there :)

[@nickcarp5732]

Basically , I have semi-large molecules and I would like to read off the functional groups of the indane ring within them. Any ideas?

[@JanJensenCopenhagen]

I'm not sure what you mean. I suggest posting your question on the RDKit mailing list sourceforge.net/p/rdkit/mailman/. Give a specific example, i.e. here is my input molecules and here is what I would like as output.

[@nickcarp5732]

​@@JanJensenCopenhagen for example, if I input the molecule for phenol (ring structure) how do I parse through the SMILES string to output the OH group?

[@JanJensenCopenhagen]

@@nickcarp5732 have a look at www.rdkit.org/docs/GettingStartedInPython.html#other-fragmentation-approaches

[@nickcarp5732]

@@JanJensenCopenhagen thank you

[@sanjanadutta7145]

@@nickcarp5732 hi were you able to find out a solution to this? I am working on a similar project

[@prakashchandranr3274]

Thank you!

[@faridehabdollahi1703]

Hi, Thanks for your useful tutorial. Is it possible to convert a list of molecules symbols into there smiles with RDKit? And how? Thank you so much

[@JanJensenCopenhagen]

I don't know what you mean by "molecule symbols"

[@faridehabdollahi1703]

@@JanJensenCopenhagen molecules name actually

[@JanJensenCopenhagen]

@@faridehabdollahi1703 colab.research.google.com/drive/1HYC4Vb_6aT7uKyXWvGHfue6UE550Quqj?usp=sharing

[@jaskirat7809]

Hey Jan, I was trying to install rdkit on my local machine. Is there a way i can install it without using conda??

[@JanJensenCopenhagen]

I suggest posting your question to the RDKit mailing list: sourceforge.net/p/rdkit/mailman/

[@jaskirat7809]

@@JanJensenCopenhagen Okay Thanks!!

[@chikken007]

Hey Jan, thanks for the introdutction! Do you know if I can do hierarchical clustering on molecules and not only use smiles but the InChi(key) ?

[@JanJensenCopenhagen]

Don't know, sorry

[@Jedders]

You could always look to convert your InChi(key) to a smiles format?

[@chikken007]

@@Jedders yes that will probably do it eventually. Thanks for the hint.

[@raghavendratikare1659]

@@JanJensenCopenhagen Hey, a very good introduction. How exactly we transform SMILES into fingerprint composed of RDkit phys chem descriptors????

[@kingcheng2000]

Thank you!