chem-bla-ics: August 2007

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:/usr/NX/etc/node.cfg:CommandStartKDE="/usr/bin/dbus-launch --exit-with-session startkde"

The solution was to:sudo aptitude install dbus-x11which contains the dbus-launch executable, formerly found in the dbus package itself. I assume it works for "Cannot find GNOME environment" too.

Aug

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.

Aug

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.

But I did not like that Firefly could do this, and JChemPaint not. So, I started hacking. First I discovered I had to get rid of the use of JAI; then I had to adapt the JChemPaintPanel takeSnaphot() API to return a RendererImage; and finally, I had to figure out how to write the extra metadata.

Aug

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).

Aug

Dapagliflozin: the molecular structure

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

The full name is (2S,3R,4R,5S,6R)-2- [4-chloro-3-(4-ethoxybenzyl)phenyl]-6- (hydroxymethyl)tetrahydro-2H- pyran-3,4,5-triol and the PDF report the CAS number 461432-26-8, and InChI=1/C21H25ClO6/c1-2-27- 15-6-3-12(4-7-15)9- 14-10-13(5-8-16(14) 22)21-20(26)19(25)18 (24)17(11-23)28-21 /h3-8,10,17-21,23-26H, 2,9,11H2,1H3/t17?,18?,19?, 20?,21-/m0/s1.

Aug

Operator 0.8 released: a new Sechemtic user script

Mike release 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.

The new Operator release (download) has one notable API change: it now uses "RDF" as key for semantic information; the add-on now supports eRDF too.

Aug

Touchgraphing my blog

Via SciFoo Planet (from Partial immortalization)I learned about TouchGraph Google (Peter brought it into Chemical blogspace). It's cool, though not open source. Here's the touch graph for my blog:

As you can see, plenty of blogspot bloggers around me, among which, in purple, Useful Chemistry. Funny thing is, each time I repeat the Google search, the output is different.

Aug

Centralized or decentralized?

Peter wondered if data should be stored centralized or decentralized, when Deepak blogged about Freebase and Metaweb. Now, I haven't really looked into these two projects, but the question of centralized versus decentralized is interesting. It's MySQL versus the world wide web; it's the PubChem compound ID versus the InChI; it's http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4 versus info:inchi/InChI=1/CH4/h1H4 (see RDF-ing molecular space).

Aug

Molecular Connectivity Tables in Images

Rich blogged about to Never Draw the Same Molecule Twice: Viewing Image Metadata in which he shows his molecular editor outputting images of molecular structure where the connectivity table of structure is embedded in the image. His molecular editor can read the image again, and will automatically pick up the embedded connection table. Noel showed that such can not only be done in Java, but in Python too.

Aug

Molecules in Wikipedia without InChIs

I reported last week about the Molecules in Wikipedia and the plethora of templates used. Chemical blogspace has also been using Wikipedia URLs as molecular identifier and extracting InChIs from the wiki pages (see Using Wikipedia to recognize Molecules in Blogspace).