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.
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.
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 :)
Glad you like the videos. I have made a playlist for machine learning where I'll include any RDKit videos I make ruclips.net/p/PLVxAq6ZYPp33b1n21cpeiY7Brollt13_6
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 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!
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.
@@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?
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!
Thank you very much you saved me! I tried to install unsuccessfully RDKit, but now with google colab, it became easy, thank you again
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.
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
why mine is error during installation? is it bcuz of i used windows?
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.
It's beeing much important for me these videos, thanks!
what is this for? can we perform QM calculations?
Hi sir,
How does one install this on windows?
Thanks
I just conda.I think you can visit Rdkit GuanWang.It write clearly
Hello sir
Please tell me what is the use , benefits for Rdkit.
I have to know sir .
Hello could you please introduce me One program to convert Fasta format to smiles cod ?
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 :)
Glad you like the videos. I have made a playlist for machine learning where I'll include any RDKit videos I make ruclips.net/p/PLVxAq6ZYPp33b1n21cpeiY7Brollt13_6
@@JanJensenCopenhagen Thanks :)
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?
This only works in Python notebooks AFAIK
@@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!
Hey Jan,
I was trying to install rdkit on my local machine.
Is there a way i can install it without using conda??
I suggest posting your question to the RDKit mailing list: sourceforge.net/p/rdkit/mailman/
@@JanJensenCopenhagen Okay Thanks!!
Basically , I have semi-large molecules and I would like to read off the functional groups of the indane ring within them. Any ideas?
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.
@@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?
@@nickcarp5732 have a look at www.rdkit.org/docs/GettingStartedInPython.html#other-fragmentation-approaches
@@JanJensenCopenhagen thank you
@@nickcarp5732 hi were you able to find out a solution to this? I am working on a similar project
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
I don't know what you mean by "molecule symbols"
@@JanJensenCopenhagen molecules name actually
@@faridehabdollahi1703 colab.research.google.com/drive/1HYC4Vb_6aT7uKyXWvGHfue6UE550Quqj?usp=sharing
05:30 I can recommend list comprehensions there :)
Thank you sir . really your explanations are next level !!
Thank you!
Thanks!
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) ?
Don't know, sorry
You could always look to convert your InChi(key) to a smiles format?
@@Jedders yes that will probably do it eventually. Thanks for the hint.
@@JanJensenCopenhagen Hey, a very good introduction. How exactly we transform SMILES into fingerprint composed of RDkit phys chem descriptors????
Installing RDKit with conda can take almost 2 minutes. Here's a faster way.(take 6 seconds)
!pip install kora
import kora.install.rdkit
Very nice! Thanks for sharing
Thank you!