MongoChemWeb: Bringing Together Tangelo, VTKweb and the Clean Energy Project

May 30, 2014

We have been working on making chemical data more accessible as part of the Open Chemistry project. We have also been very lucky to have the opportunity to collaborate with the Harvard Clean Energy Project, which recently won a Data+ award, on making large computational chemistry data sets more accessible. This was an opportunity to put MongoChem through its paces, and also to prototype a web application based on technologies developed as part of the Open Chemistry project, Tangelo, VTKweb, and several other open source projects that went into building these frameworks.

The live demo is available at, and it features similarity search/substructure search using the excellent JSME for structure input, and it makes use of Helium, developed by Tim Vandermeersch, for fast in-memory fingerprint searches of the millions of structures that are part of the data set. There is inline documentation of the search syntax, and clicking on any card will bring up a detailed view of the molecule. Please take a look, and let us know what you think.

This is an early prototype of what is possible, the 2D depictions were generated using Open Babel, and the interactive 3D views offered are using image delivery from VTKweb. The 3D structure can be downloaded in a few different formats. The same MongoDB instance can be accessed and edited using the MongoChem desktop application too. The source for the web components is available here.

We acknowledge that the development of MongoChem and MongoChemWeb has been funded by a US Army SBIR with the Engineering Research Development Center under contract (W912HZ-12-C-0005) at Kitware, Inc., along with contributions from the community.

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