15 votes
Accepted

Artificial intelligence is a hot topic, but should I pursue it if I'm interested in Matter Modeling?

"I am a student now and should decide my major to research soon. AI/ML is a very hot research field and I am very interested in it, but I have some doubts before I study AI/ML." AI is ...
  • 29.2k
14 votes

How to start a Machine Learning project for chemical properties prediction?

Admittedly, there are tons of materials on the chemistry + machine learning topics. Let me give one: An introductory text I find useful is Machine Learning in Chemistry from Janet and Kulik in ACS in ...
  • 1,658
12 votes
Accepted

Getting interpretable chemical information from hashed molecular fingerprints

Using RDKit, it's fairly easy to depict bits on example molecules - it's even an example in the documentation "Generating Images of Fingerprint Bits") ...
9 votes
Accepted

How to create molecule image similar with molconvert using RDKit

You're not going to get something identical. Different toolkits use different code to do 2D molecule layout. Generally the current RDKit code (which uses the CoordGen library) tends to prefer ...
9 votes
Accepted

Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?

NetworkX This is a widely-used Python library for graph theory stuff. Open source (https://github.com/networkx/networkx) under a 3-clause BSD license. Caveat: since this is a tool that knows nothing ...
  • 1,887
9 votes
Accepted

Functional group detection for group contribution methods

ErtlFunctionalGroupsFinder A Java library for automated functional group implemented with the Chemical Development Kit (CDK) program. It should run on Windows/Mac/Linux operating systems. It relies on ...
  • 14.3k
8 votes

Artificial intelligence is a hot topic, but should I pursue it if I'm interested in Matter Modeling?

I did my master's research project in predicting absorption spectra using machine learning (with fingerprints). So, my research is somewhat in the field of material modelling you can say. I want to ...
  • 5,834
8 votes

What is the best way to measure similarity between molecules of the same formula?

tldr; The most common approach is to use fingerprints and compute the Tanimoto similarity There are a variety of ways to compute "molecular similarity" but the most common approach is to ...
5 votes

How to compute the synthetic accessibility score in Python?

Ertl and Schuffenhauer, who developed the synthetic accessibility score, provide an implementation packaged with RDKit called sascorer.py. This is provided in the Contrib folder of the RDKit repo; ...
  • 14.3k
4 votes

How to obtain fingerprint bits as SMARTS pattern in RDKit

Based on your code and the code found by Geoff. Additionally you have to find the neighbors and change their identity. ...
  • 411
4 votes

How to obtain fingerprint bits as SMARTS pattern in RDKit

I'm not entirely sure I understand your question. You want a SMARTS that matches DrawMorganBit but with an extra * added? If you ...
4 votes

Artificial intelligence is a hot topic, but should I pursue it if I'm interested in Matter Modeling?

While machine learning is becoming very important, I think physics-based models continue to be necessary in matter modeling. ML models are good for systems where there is a lot of data available. On ...
4 votes

Getting interpretable chemical information from hashed molecular fingerprints

I don't know of any simpler methods. Heuristic methods such as Neural Networks are likely your better option if you wish to actually reconstruct the original molecule. Keep in mind that an active bit ...

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