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
Category: Hints and Tutorials
Tutorials, Hints, Tips and Tricks
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
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
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
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
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
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
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,
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.
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