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:

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