Calculating Molecular Descriptors using RDKit and Mordred

[licidamarcristinadiazbamba]

Thaks for upload this! helps a loooot!

[kilua]

Thanks a lot for this amazing tutorial! It helps me a lot.

[АнтонГрадов-ъз]

Thank you very much. It is really helpful for my project in the university! And it would be really helpful if you prepare a video about application of descriptors in QSAR, machine learning….
Please!

[sumitkumar-elkc]

Thank you so much, sir. Can you teach me about protein descriptors too?

[jval]

Amazing video! About the FingerPrints, every time they are generated, does column 1 always correspond to the same chemical fragment?

[robertcormia]

A good demonstration, especially of coding proecedure, a little difficult to understand some pronunciation, for instance Morgan fingerprint, it was useful to have captioning available.

[awomutiadeboye]

Thanks for this tutorial Dr. Gashaw, could you give a line of code that could list the 1826 Mordred Descriptors just like you listed the RDkit descriptors during the video. I tried to do the same for Mordred, but it didn't work.

[satyarahul]

During the canonical smiles part. the number of compounds 2904 before and after running the function are the same. that means aren't any canonical smiles?

[DrHenryNguyen]

Dear Sir, I am new one. How can I run my data on your link? Thanks so much.

[boufissiou]

How do I get chemical compounds into colab server from a file in sdf format?

[abdallahabouhajal]

Thank you so much for this video, its really helpful. a quick question, can i choose which descriptors i want to calculate from Mordred instead of calculating the whole 1826. especially that after feature selection i know which ones i want to include in my model, and thus when testing new inputs. this shall help save so much time.

[juandavidrangel]

Thank you! Amazing tutorial. How can I download the mordred data frame to an excel file?. I have tried, but several errors are shown because mordred_descriptors' type is a MordredDataFrame not a "normal" DataFrame type. I mean, it has different methods and it is not possible to create the file.

[mrnicjic]

Great video Sir! I am a beginner in software but very interested and I just didn’t fully understand how I plug in my SMILES strings in the program. Could somebody explain it? Thanks in advance 🙏🏻

[attaullah]

Thank you Sir for your valuable knowledge. I followed the tutorial but i was not getting the molecular descriptors for mordred properly, for for descriptors it was showing 3D missing, what should i do? do i need to optimize the geometry? becuase i use the canonical smiles from pubchem for my molecules. Thanks

[fatemehf]

thank you so much for your grate video. could you please make a video about 4D descriptors? could you please name some software that I can calculate 4D descriptors?

[aisiazmi]

Prof, what is the code to save the results of rdkit and mordred?

[aisiazmi]

Sir, can you more explain about canonical smiles? What is the difference of SMILES and canonical SMILES? Thank you Sir

[milindrahatwal]

Thank you for sharing this video.
I keep getting this error on Rdkit features.:
XGBoostError: [01:58:25] ../src/data/data.cc:1104: Check failed: valid: Input data contains `inf` or `nan`.
I have used dropna() but I still can't get rid of the error. Also when I try to see if there are any nan or infinite values it shows 0.

[bomcimtube]

Thank you. In 2024, the function to calculate RDKit and Mordred descriptors give error.

[sriramvaidyanathan]

We find molecular descriptors after hydrogen explicit here is the finding descriptors with hydrogen can you confirm