WebMolKit Sketcher

After much procrastination, there’s an updated demo of the WebMolKit sketcher on the main home page for Molecular Materials Informatics. The sketcher is open source, runs on any web platform, and has some fairly powerful functionality built into it.

The sketcher is part of the WebMolKit project, which has been open source for quite some time: it has a lot of molecular manipulation functionality as well as the ability to draw molecules, and is one of the most advanced cheminformatics projects that is 100% web based, being written in TypeScript and cross-compiled to work on any JavaScript-based runtime.

It’s the result of a very large number of liminal coding hours over many years. As time goes by it gradually accumulates features, as well as housekeeping and the robustness that comes from being used for various different kinds of projects

As well as having all of the usual toolbar icons and click’n’drag features that you would expect from an chemical structure drawing tool, there some features of the sketcher that are rather less common, such as:

  • two drawing paradigms: {tool + drag} vs. {select + command}, where the tool-based style is conventional, while the command-based style was worked out while designing for mobile platforms, and is really fast and efficient for power users who use it enough to start remembering keyboard shortcuts
  • helpful annotations for scientists (e.g. oxidation state, R/S and E/Z) as well as features for digging down into the underlying datastructure, like labelling by atom index, or editing precise geometry
  • inline abbreviation system that offers common (and custom) labels like Me, Et, Bu, Ph, etc., stored inside the molecular representation to guarantee that their meaning is never lost
  • handling of organometallics and coordination complexes, with prominent zero-bond functionality, and aesthetic options for rendering multicentre bonds in a scientist-friendly way without breaking the cheminformatics
  • specification of polymer unit cells in convenient ways (e.g. square-brackets tell the whole story) and optionally defining more complex multiple linkages between blocks
  • editing of query features which are displayed graphically on top of the sketch

Rather than going over each of these feature categories in detail, I’ll suggest that if any of this looks interesting, navigate to the Molecular Materials Informatics website and scroll down just a bit. You’ll see several molecule examples on the right hand side: try clicking on each of them in turn to get some idea of what it can do.

The sketcher and the underlying cheminformatics library is available to anyone as open source, but there’s a catch: you do need to abide by the GPL (Gnu Public License) which is the one where you can do anything you like with it internally, but distribution does require that all your own materials are also open source. But the copyright holder (that would be me) can grant any number of exemptions, if so inclined.

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