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 ...
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  • 1,638
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 ...
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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 ...
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  • 1,877
9 votes
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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 ...
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  • 13.9k
8 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") ...
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4 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; ...
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