Chem4Word and Blue Obelisk software




Egon Willighagen has been a pillar of ODOSOS chemistry and comments yesterday in Chem4Word goes Apache 2.0


Early March I reported about Konstantin‘s JChemPaint-based chemistry plugin for OpenOffice, but there is competition: Chem4Word. Being for Microsoft Word, the plugin only works on top of proprietary software, unfortunately; therefore, I cannot tell you if Chem4Word release is any good, but what Jim has showed me about a year ago, it is pretty cool. Another big difference is that Microsoft gave the Chem4Word a big grant, and Konstantin does not have such funding, AFAIK, and relies on community support.
Now, Chem4Word was released earlier this month, as announced by Joe, and I just heard from Jim about it now being opensourced (and Peter blogged it too). Congratulations to all involved in the development! The Chem4Word project page indicates the actual license: Apache 2.0. Good choice!
Now, I said that a limitation of the plugin is that it requires proprietary software to run. This is why you will not quickly see my use it. Well, this is even why you do not see any screenshot! However, this should not spoil the news. This is for two reasons:

1.    The plug-in is Open Source: this means that the community can learn from their project, and how the make molecular structures in Word documents semantic.

2.    The plug-in saves the chemistry in the Chemical Markup Language in the XML-based Word document: this means that anyone will be able to extract the molecular structures in a semantic meaningful way.

And that’s, to me, the biggest news: if the organic chemists start using this plug-in, this will be a big win for Open Data. I am sure this is the hidden agenda of an unorthodox move of our fellow Blue Obelisk community members.


Many thanks Egon – carefully argued. I wouldn’t describe C4W as competition for OpenOffice – even if the community wishes to port it. In the Blue Obelisk community we have a useful amount of “duplication” or different ways of doing things, but we don’t compete. We are, in fact, glad when others come up with solutions that mean we don’t have to write code ourselves. Typical examples are CDK and JUMBO and Joelib, JChempaint and Chem4Word, etc. These give people an environment in which to try out new ideas, check consistency of data, etc. But we avoid having having 2 different versions of the Periodic table, bonding radii etc. We try to agree on the explicit and implicit semantics and interpretation of chemistry. We use CDK for substructure search and 2D diagram generation, for example; openbabel for substructure search and JUMBO for crystallography and geometry.

In the current case Konstantin is welcome to borrow material from C4W as long as credit is given. In practice .NUMBO is sufficiently different from existing approaches that there probably aren’t major bits that can be borrowed.  But maybe it offers a chance for a fork – I don’t know enough about the details of the code. But the more Open offerings that there are, the more we convince the chemistry community that it’s worth using and worth developing.



This entry was posted in Uncategorized. Bookmark the permalink.

One Response to Chem4Word and Blue Obelisk software

  1. Ah, well, I did not want to imply a hostile competition; nothing like ManUnited versus Arsenal, or Feyenoord versus Ajax. They are just in for the same market share, so they compete for single CPUs, so to say. And, I fully agree, duplication is not bad, and the Blue Obelisk has plenty of duplication. Different programming languages, different licenses is what makes this duplication worthwhile.

Leave a Reply

Your email address will not be published. Required fields are marked *