O'woe is me - It's a capostrophe

"The username contains an illegal character." This is the final straw. I can take no more. I need to share the pain of living with an apostrophe.

Yesterday I read Pedro's post and decided to get on the crest of that Web 2.0 wave. So I requested a beta account on JournalFire, which sounds an interesting way to review the literature. Today, I received permission to create an account. It asked me to: "Enter your name as it would appear for publication. For example: John M. Delacruz". So I entered "Noel M. O'Boyle". And I received the infamous message, "The username contains an illegal character"!!

What's the story with this apostrophe anyway? Well, at some point in history, when my ancestor was called "Ó Baoighill", he had this great idea: "hey, what's the story with this accent on the O; I want to use this new thing called an apostrophe that's going to mess up web accounts for my descendants" (or more likely "Yó, cad é an scéal leis an fada seo; ba mhaith liom usaid a bhaint as an uaschamóg nua sin, a scriosfaidh saol mo pháistí ar an idirlíon"). I'd have appreciated a bit more foresight, forefather.

On the web, the Irish are outlaws. This isn't the first time this has happened. A lot of websites think I'm trying to hack into their systems with my carefully-crafted surname. SourceForge is one of the only sites that allows me to use the apostrophe. But even there, they spell my name "Noel O\'Boyle" just to say..."okay, you can use the apostrophe, but we're keeping an eye on you to make sure you don't try anything crazy with it". Actually, I've just noticed that it's gotten even worse. Now, my name is spelt "Noel O\\\'Boyle". That's like two pairs of handcuffs.

Certain organisations should be more familiar with author names than others; for example, a journal. A paper of mine was recently accepted by J. Comp. Chem. On the PDF proof, the names are all in capitals, i.e. "NOEL M. O'BOYLE" for mine. However, on the web abstract, in the Table of Contents, and in the XML they provided to PubMed, my name is "O'boyle". I feel diminished.

It's not only on the web, of course. When spelling your name over the phone you find yourself saying things like "it's a comma in the air" when trying to describe an apostrophe. Sometimes you just give up and spell your name "Oboyle" with the result that people think it's "O-boy-lay". I've even gotten letters in the post addressed to "Noel O?Boyle". Which, right now, is how I feel.

Bring PDB codes to life on web pages

Wouldn't it be nice if you could click on a PDB code on a web page and you could instantly see the actual structure in 3D? For example, you might be reading the HTML version of a paper which is discussing a particular protein structure.

Some time ago I wrote a Greasemonkey userscript to do just that. You can get it on the Blue Obelisk web site, as well as several other userscripts. Since I haven't previously mentioned it on this blog I thought I might do so now.

To avoid false positives, it only runs on web pages containing the words "protein", "pdb" or "enzyme". For any PDB codes found, it adds the appropriate link to Eric Martz's FirstGlance in Jmol site. For example, the PDB codes on this page are tranformed to:(The yellow Jmol links were added by the script)

RDKit: Not just yet another cheminformatics toolkit

I'm sitting here with a bandage covering my head, as RDKit has just blown my mind.

RDKit is an cheminformatics toolkit written in C++ and Python. It was developed in-house in a company called Rational Discovery (hence the RD) since 2001. In Feb 2006, it appeared on SourceForge under a liberal license (BSD, except for the GPL Qt code), an appearance which presumably coincided with the demise of Rational Discovery (the company, not the concept, that is :-) ). And there it stayed, actively developed by two developers, but unknown among the open source chemistry community until...

A month ago, I happened to be glancing through the SourceForge software map of chemistry software and I was intrigued by the description of RDKit as "A collection of cheminformatics and machine-learning software developed at Rational Discovery". The website was pretty minimal and there didn't even appear to be any documentation. I dashed off an email to Greg Landrum, the main developer (who it turns out is also the developer of YAeHMOP (Yet Another extended Huckel Molecular Orbital Package) ), and asked him what the story was. Two days ago, he returned from holidays and pointed me to the correct website and the documentation, and I couldn't believe what I was seeing...

Some features that I think are cool:
(1) Molecules based on the Boost Graph Library
(2) All the Python stuff works for me on Windows!
(3) 2D depiction!!!
(4) 2D depiction that mimics 3D conformations!!!
(5) 2D --> 3D conversion in a similar method to Rajarshi's smi23D! (doesn't use stochastic promixity embedding though)

Here's a summary of some of the rest: SMILES, substructure searching, sophisticated fingerprints, machine learning stuff, a GUI, clustering, MACCS keys, descriptors (84 or so), chemical reaction transformations, implementation of Recap (not sure what this is, but there's a ref in the docs), basic pharmacophore stuff, and two types of SSSR (there's some text about this in the docs).

Cool! There's obviously a lot of overlap between OpenBabel and RDKit, and hopefully we can use this to both projects' advantage in terms of testing against each other and developing interfaces. In the meanwhile, here's to diversity, and to discovering that someone else has implemented 2D depiction in C++ so I Don't Have To.

For more info, see www.rdkit.org, and in particular, the Python interface documentation which gives a good overview.

Image credit: Toolkit by Neil T (CC BY-SA 2.0)

Exclusive: PRISM's response to scientific community's outrage

In a world exclusive, I can reveal the considered response of PRISM to the detailed arguments raised by Peter Suber, Peter Murray-Rust, Steve Harnad, etc., etc.:



For more thoughtful lampoonery, see Trapped in the USA and PISD.

* Image credit: This is a derivative of the image in the Wikipedia article "All your base are belong to us". I plead fair use, and a sense of humour.

Wikifying chemistry

There has been some interest in using wikis to annotate molecules: e.g. the ChemSpider blog where Antony is interested in using a local wiki to annotate entries, chem-bla-ics where Egon is trying to ensure that molecular data on Wikipedia can be accessed like a database, and most recently where PMR has commented on DBPedia.

This idea is already being used in biology. The Rfam database at the Sanger Institute is directly using wikipedia to create annotations for the major RNA families, which each have a page on Wikipedia. The full list of Wikipedia pages seems to be available here. From what I've heard second-hand, interested academics are invited to contribute to the pages on their favourite families. Every day the pages are downloaded and backed up, and the information made available through the Rfam database. All edits are tracked using Wikipedia's own tracking facilities (i.e. watchlists) so that vandalism is easily detected, although apparently this hasn't been a problem.

I'm not sure how much this idea could be used in chemistry (perhaps a database of drugs...?), but it sure is some food for thought...

Scooby, D. D., where are you? - Searching for papers online

One of my pet annoyances is searching on a journal website for an article that I know exists, but not being able to find it. Let's take a real-life example...

I met Douglas Hawkins at the ACS and wanted to look up his papers in JCIM/JCICS. I've bookmarked the JCIM TOC page, so I go there. At the top is a handy little shortcut for finding papers by a particular author. So I type in "Hawkins" next to the Author drop-down box, and click "Search"...

10 documents. Of which half are Douglas Hawkins (the right guy), and the other half are Donald Hawkins (the wrong guy). In addition, both JCIM and JCICS were searched. Great. This is where I should have stopped. Instead I decided I only wanted to find those papers by Douglas Hawkins. The following are my attempts to find his papers:

Hawkins, D. M.: 7 article. All false positives.
Hawkins D M: ditto
"Hawkins, D. M.": 0 documents
D M Hawkins: It's my favourite 7 articles again.
D Hawkins: 24 articles. No articles by D. M. Hawkins included.

But how can I have found 24 articles for the last search? That's more than I found with just "Hawkins". Wait a second, I've been moved onto the "Advanced Article Search" page, which is searching all of the journals. So what did it find instead? It found "...Mass, J. D.; Hawkins, A. R.;". Pretty advanced searching, eh?

Thankfully, I happen to know that unlike most chemistry journals, the ACS has contributed data to PubMed. So off I go, and try:

Hawkins, D. M.: first hit contains "M. M. Hawkins"
DM Hawkins: first hit contains "Hawkins EC"
Hawkins DM: jackpot!

Now I just want those papers where Basak is a co-author:
Hawkings DM Basak: jackpot!

Incidentally, this is the first time that Pubmed has ever worked for me. This is because I always try "DM Hawkins Basak" which gives no hits (even after reading the instructions I was never able to find anything). As for how to limit the results to a particular journal? Why isn't there a drop-down box with a list of journals? Why do I have to read the instructions for the obscure syntax used by PubMed every time I want to find a paper?

What about Google scholar? "DM Hawkins" or "D. M. Hawkins" gives 1700 hits, of which the first page at least are true positives. Advanced Search allows me to specify the journal, and I get 1 hit with "J Chem Inf Comput Sci", a different hit for "J Chem Inf Comp Sci" (of which there are 5 versions, one of which has "Comput Sci" instead of "Comp Sci") and 1 for "J Chem Inf Model". In fact, Hawkins has 3 papers in JCICS and 2 in JCIM. You look good Google, but you're not trying very hard.

Searching by author should be easy. It's not quantum mechanics. It's not even rocket science. Can't they make it work better?

Python code for Huckel theory calculations

Over at Chemical Quantum Images, Felix has posted Python code that will read a file containing a molecular structure and calculate the molecular orbitals using Huckel theory. The code uses the OpenBabel Python module to read the structure, and NumPy, the Python extension for numerical computing, to do the heavy lifting (to diagonalise a matrix).

Now, if I only understood the theory...:-)