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Category: Vortex Scripts

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Hints and Tutorials Vortex Scripts

Using MOE to dock ligands selected in Vortex

11 March 202329 June 2023 chris

One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web

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Hints and Tutorials Vortex Scripts

Vortex script using predictive models on OCHEM

11 March 202312 May 2023 chris

About OCHEM OCHEM is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from

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Hints and Tutorials Vortex Scripts

Vortex using MOE listener

11 March 20237 May 2023 chris

One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web

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Hints and Tutorials Vortex Scripts

Vortex Script Interacting with MOE using SOAP

11 March 202311 October 2023 chris

In a earlier script we looked at using the command line tool sddesc from Chemical Computing Group to calculate a number of molecular descriptors and then import them

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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 and Json import

11 March 202315 May 2023 chris

In a previous tutorial we made use of the Virtual Computational Chemistry Laboratory web service to calculate aLogP and LogS, both these results were returned in a

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Hints and Tutorials Vortex Scripts

Vortex script interacting with a web service

11 March 202325 April 2023 chris

In previous scripts we have generated data using a local Java program, C program, PERL script, and SVL program. In this tutorial rather than have

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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 to Calculate molecular properties using MayaChemTools

11 March 202318 May 2023 chris

In previous scripts I’ve shown how to use a couple of command line applications to calculate physicochemical properties. In this tutorial we will use 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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