blueobelisk.github.io

Chemoinformatics Data Repositories

Blue Obelisk Data Repository (BODR)

Another core Blue Obelisk project is the development of a shared data repository. This repository lists many important chemoinformatics data such as elemental properties, atomic radii, etc. including references to original literature. Software developers can use this repository on online webpages or in chemistry software for free.

Download

The latest release can be downloaded from GitHub.

Ubuntu and Debian

Ubuntu package are available from the bodr package. Debian package are available from the bodr package.

Programs

These are the programs that use or will use the BODR data.

• Bioclipse
• CDK
• Gnome Chemistry Utils
• Jmol (maybe)
• Kalzium (as of KDE 4)
• OpenBabel 2.0.0 / JOELib2
  • Both systems use nearly the same expert system
  • But, there are slightly differences in the algorithms behind, namely:
    • expert system caller hierachy
    • atom hybridisation assignment
    • kekulization of bonds
    • and maybe other things, we have not thought about
  • more vendors are more than welcome

Chemical Structure Repository

A complementary project, called Chemical Structures, has been initiated in June 2006. It aims to provide a set of organic structures, which includes 3D coordinates, InChI code, molecular weight, melting point, etc. The last release (v2.2.0) contains over 570 structures. You can also browse the svn repository.

Download

The latest release can be downloaded from SourceForge.