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Category: Hints and Tutorials

Tutorials, Hints, Tips and Tricks

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Hints and Tutorials Vortex Scripts

Vortex script using MOE to calculate properties

6 March 202321 June 2023 chris

MOE from Chemical Computing Group is probably best known as a graphical user interface to a suite of computational chemistry tools, whilst this is indubitably the means

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Hints and Tutorials Vortex Scripts

Vortex script to analyze categories

5 March 202312 April 2023 chris

I often need to tag individual molecules within a dataset with a specific property, perhaps the results of clustering algorithms, the results of PAINS filtering, or Liver

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Hints and Tutorials Other Tips Vortex Scripts

Options for Clustering large datasets of Molecules

5 March 202310 April 2025 chris

Clustering is an invaluable cheminformatics technique for subdividing a typically large compound collection into small groups of similar compounds. One of the advantages is that

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Data Analysis Tools Hints and Tutorials Vortex Scripts

Calculating molecular properties using the ChemAxon cxcalc

4 March 202325 April 2023 chris

ChemAxon’s Calculator (cxcalc) is a really useful command line program in Marvin Beans and JChem that performs chemical calculations using calculator plugins. There are a

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Hints and Tutorials Vortex Scripts

Scripting Vortex and OpenBabel

4 March 202312 April 2023 chris

I’m finding that I using Vortex more and more in my day job, it is an excellent application for displaying and exploring large or complex

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Data Analysis Tools Hints and Tutorials

Knime Tutorial

4 March 202315 April 2023 chris

This tutorial was kindly provided by Greg a Macinchem reader. OVERVIEW AND APPLICATION OF KNIME AND CDKDescUI.jar KNIME1, the Konstanz Information Miner, is a visual platform

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Hints and Tutorials Macinchem Blog Reviews Software Reviews

ChemDoodle Web Components

4 March 202312 April 2023 chris

Introduction and Background ChemDoodle Web Components are pure javascript objects derived from ChemDoodle™ to solve common chemistry related tasks on the web. These components are powerful,

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Hints and Tutorials Vortex Scripts

Vortex script to flag duplicates

18 February 202312 April 2023 chris

When working with multiple data sets of molecules, particularly if combining them from multiple sources, one of the most common tasks is removal of duplicates.

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Hints and Tutorials Other Tips

Useful Unix commands

18 February 202321 April 2023 chris

I’m regularly handling very large files containing millions for chemical structures and whilst BBEdit is my usual tool for editing text files in practice it

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Hints and Tutorials Jupyter Notebook

Jupyter Notebook for docking either locally or using Colab

17 February 202317 February 2023 chris

Here are two variations of a Jupyter Notebook to help with docking experiments. The first version runs locally and requires the user to install RDKit,

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