Publications

Open Source Programs

Using OpenEye Toolkits

Clearly, the OpenEye toolkits are not themselves open source. However, the programs below use them and are available for download under a BSD open-source license. To compile and run them, you will need to obtain from OpenEye licenses for the relevant toolkits.

Using RDKit

The RDKit is fully open-source, under a BSD license. As well as contributing to the core code itself, notably the 2D drawing functionality, David has published the following programs that use the toolkits:

In 2020, David overhauled the 2D drawing code, in particular to improve the positioning of atomic symbols and other text. This was presented at the RDKit 2020 Virtual UGM. As an example of the improvement, it went from to and if you want to irritate your colleagues you can use different fonts, such as the XKCD font

Miscellaneous

SDFs are a convenient format for passing structures and data around, for example between 2 organisations using different database systems for their cheminformatics. Most such systems can export and import in SDF format. They are less convenient if one wants to perform a quick inspection of the tabulated data with the associated structures. Normally this would require firing up a piece of commercial software which seems somewhat of overkill. The HTML/Javascript app HSV (https://github.com/DavidACosgrove/HTML-SDF-Viewer) addresses this. It is a simple completely self-contained web page that reads an SDF, tabulates the tagged data and displays the structures in either 2D or 3D form as appropriate.

Papers