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 ...
I have no free time anymore's user avatar
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 ...
Greg's user avatar
  • 1,807
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") ...
Geoff Hutchison's user avatar
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 ...
Geoff Hutchison's user avatar
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 ...
dwhswenson's user avatar
  • 2,047
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 ...
Tyberius's user avatar
  • 15.5k
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 ...
S R Maiti's user avatar
  • 6,841
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 ...
Geoff Hutchison's user avatar
7 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; ...
Tyberius's user avatar
  • 15.5k
5 votes

How to find topographic distance of molecule from mol format

First off, it's important to know that some (most?) mol files do not include 3D coordinates. So you'd need to generate them (e.g., from rdDistGeom or ETKDG). Your ...
Geoff Hutchison's user avatar
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 ...
stanton63's user avatar
  • 124
4 votes
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Most detailed molecule representation format

What you describe is unfortunately, not represented much by common interchange formats. As part of the Avogadro project, we've been developing an extensible, community standard schema for chemicaljson ...
Geoff Hutchison's user avatar
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. ...
rapelpy's user avatar
  • 546
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 ...
Geoff Hutchison's user avatar
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 ...
WaterMolecule's user avatar
3 votes

What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si

First, "best" is ill-defined. The best method would be full configuration interaction at the complete basis set limit including fully relativistic and quantum field theoretical corrections; ...
Susi Lehtola's user avatar
  • 19.1k
3 votes

How to do SMARTS reaction substructure mapping with RDKit

I changed the c_h_template to also use smiles and the substructMatch returns True. I am using rdkit version number: 2022.9.4 Here is the full reproducible code. <...
Vandan Revanur's user avatar
3 votes
Accepted

In the Chemistry Development Kit (CDK) IMolecule interface is missing

IMolecule has been removed because the only addition to the IAtomContainer API was the concept that the content of the ...
Egon Willighagen's user avatar
2 votes

Most detailed molecule representation format

Like mentioned in the comment, have a look at the Chemical Markup Language (CML). This Scholia page has relevant literature, but particularly check these two publications: Phadungsukanan, W., Kraft, ...
Egon Willighagen's user avatar
2 votes

Undefined stereochemistry in rdkit from mol2

Currently there is a bug with the Chem.MolFromMol2File, in latest rdkit version: 2023.3.1, which seems to remove Hydrogens from ...
Vandan Revanur's user avatar

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