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Tag: openbabel

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Macinchem Blog Other Tips Science Apps Uncategorised

Mychem a chemoinformatics extension for MySQL

9 February 20259 February 2025 chris

Mychem is a chemoinformatics extension for MySQL that provides a set of functions that handles chemical data stored in a database. Mychem is based on

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Applescript Hints and Tutorials

Comparing Version Numbers

10 April 202310 April 2023 chris

I’m in the process of updating iBabel and one of the things I’m adding is the option to use some of the newer tools now

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Hints and Tutorials Vortex Scripts

Vortex script using Using OpenBabel fastsearch

11 March 202321 May 2024 chris

One thing I’ve needed to do a couple of times recently is give an idea of how many similar compounds are available to the set

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Hints and Tutorials Vortex Scripts

Vortex Script to add 2D depiction of 3D structures

11 March 20237 May 2023 chris

This script is no longer needed since you can now add SMILES from the “Calculate Properties” option from the Tools menu. However, it is a

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Hints and Tutorials Vortex Scripts

Vortex script using Openbabel for similarity searching

6 March 202315 May 2023 chris

An earlier script showed how to calculate molecular similarity between the first molecule in the file and all the other molecules using OpenBabel as shown

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Avatar Chris Swain @macinchem ·
6 Feb

Looking at TabPFN with Polaris datasets https://macinchem.org/2025/02/06/looking-at-tabpfn/ #cheminformatics

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Avatar RSC_CICAG @rsc_cicag ·
3 Feb

Don't forget to register for @RSC_BMCS Conformation Design in #DrugDiscovery conference on 3rd March! … #chemistry #medicinalchemistry #NMR #computationalchemistry #biologists

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Avatar Rowan @rowansci ·
31 Jan

RDKit is the standard software for cheminformatics, but RDKit doesn’t integrate naturally with high-accuracy chemistry simulation tools.

Starting from RDKit, it's non-trivial to simulate pKa, optimize conformers w/ ML, score tautomers, &c. There are many posts like this:

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Avatar Chris Swain @macinchem ·
31 Jan

Tabular Prior-data Fitted Network (TabPFN), a tabular foundation model on Apple Silicon. https://macinchem.org/2025/01/31/tabpfn-on-apple-silicon/

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