A JChemPaint Hack-a-thon

Niels and I held a JChemPaint hack-a-thon today (the IRC log). We had a quite ambitious agenda:

1 minute read

NXClient on Ubuntu Gutsy

If you, like me, already upgrade to Ubuntu Gutsy, and use nxclient for remote login (highly recommended, though proprietary code), you might run into the problem that the login no longer works, returning the message “Cannot find KDE environment.”. Ubuntu’s Lauchpad (generally an excellent service) was rather uncooperative and disregarded a bug report about the problem, I found the solution with grep -ri kde /usr/NX:

less than 1 minute read

XCMS on Ubuntu Feisty

I just installed XCMS 1.9.2 on my Ubuntu system. XCMS is a GPL-ed R package for metabolomics data analysis. Just for the record, you need to install the Feisty packages for NetCDF:

less than 1 minute read

JChemPaint too: PNG embedded connectivity tables

Rich blogged about Firefly embedding MDL molfiles in PNG images, which I found really cool. Rich and Noel later showed how that metadata can be retrieved again, possibly with Python.

1 minute read

Automatic Classification of thousands of Crystal Structures

Clustering and classification of crystal structures is hot. Parkin hit the front cover of CrystEngComm with a story on Comparing entire crystal structures: structural genetic fingerprinting (DOI:10.1039/b704177b). Now, the story itself, while rather interesting and well written, has three major flaws:

2 minute read

Dapagliflozin: the molecular structure

An anonymous reader reported that the American Medical Association published the structure of dapagliflozin. Here are the details.

less than 1 minute read

Operator 0.8 released: a new Sechemtic user script

Mike released Operator 0.8, which picks up RDF (RDFa en eRDF) from HTML pages, and adds actions to it. I blogged earlier about the beta and wrote a script for it for chemical RDFa. At this moment, Chemical blogspace and RDF for Molecular Space (see this blog) are using chemical RDFa to semantically markup molecular information.

1 minute read