Archive for January, 2009
The folks at the EBI have been doing some great work on the CDK. A major effort is underway to revamp JChemPaint and part of this involves improving the rendering of 2D depictions. While not complete I rebuilt a version of the CDK 1.2.x branch with the latest rendering code from the jchempaint-primary branch and updated the CDK web service. The results are much nicer, though there’s scope for improvements. See for example
Thanks to Gilleain and Egon for pointing me in the right direction. Anybody using this service should see the new depictions automatically
The current version of the REST interface to the CDK descriptors allowed one to access descriptor values for a SMILES string by simply appending it to an URL, resulting in something like
This type of URL is pretty handy to construct by hand. However, as Pat Walters pointed out in the comments to that post, SMILES containing ‘#’ will cause problems since that character is a URL fragment identifier. Furthermore, the presence of a ‘/’ in a SMILES string necessitates some processing in the service to recognize it as part of the SMILES, rather than a URL path separator. While the service could handle these (at the expense of messy code) it turned out that there were subtle bugs.
Based on Pats’ suggestion I converted the service to use base64 encoded SMILES, which let me simplify the code and remove the bugs. As a result, one cannot append the SMILES directly to the URL’s. Instead the above URL would be rewritten in the form
All the example URL’s described in my previous post that involve SMILES strings, should be rewritten using base64 encoded SMILES. So to get a document listing all descriptors for “c1ccccc1COCC” one would write
and then follow the links therein.
While this makes it a little harder to directly write out these URL’s by hand, I expect that most uses of this service would be programmatic – in which case getting base64 encoded SMILES is trivial.
As part of my work at IU I have been implementing a number of cheminformatics web services. Initially these were SOAP, but I realized that REST interfaces make life much easier. (also see here) As a result, a number of these services have simple REST interfaces. One such service provides molecular descriptor calculations, using the CDK as the backend. Thus by visiting (i.e., making a HTTP GET request) a URL of the form
you get a simple XML document containing a list of URL’s. Each URL represents a specific “resource”. In this context, the resource is the descriptor values for the given molecule. Thus by visiting
one gets another simple XML document that lists the names and values of the AlogP descriptor. In this case, the CDK implementation evaluates AlogP, AlogP2 and molar refractivity – so there are actually three descriptor values. On the other hand something like the molecular weight descriptor gives a single value. To just see the list of available descriptors visit
which gives an XML document containing a series of links. Visiting one of these links gives the “descriptor specification” – information on the vendor, version, reference to a descriptor ontology and so on.
(I should point out that the descriptors available in this service are from a pretty old version of the CDK. I really should update the descriptors to the 1.2.x versions)
This type of interface makes it easy to whip up various applications. One example is the PCA analysis of compound collections. Another one I put together today based on a conversation with Jean-Claude was a simple application to plot pairs of descriptor values for a collection of SMILES.
The app is pretty simple (and quite slow, since it uses synchronous GET’s to the descriptor service for each SMILES and has to make two calls for each SMILES – hey, it was a quick hack!). Currently, it’s a bit restrictive – if a descriptor calculates multiple values, it will only use the first value. To see how many values a molecular descriptor calculates, see the list here.
With a little more effort one could easily have a pretty nice online descriptor calculation application rivaling a standalone application such as the the CDK descriptor GUI
With all the stuff I’ve been hearing about Git I’ve been looking to play around with it. While I have been hosting my own Subversion repo on my office machine, the use of GitHub seemed like a good way to play with Git and also have a stable external repo.
Which XRay ligands are closest to the Fontaine et al. structure-activity relationship data for allowing structure-based drug design?
Using Blue Obelisk tools and ChemSpider and where Fontaine et al. refers to the Fontaine Factor Xa dataset. You should read his post for a nice analysis of the problem. I just wanted to consider two points he had raised.