So much to do, so little time

Trying to squeeze sense out of chemical data

Archive for the ‘base64’ tag

Update to the REST Descriptor Services

with 2 comments

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.

Written by Rajarshi Guha

January 11th, 2009 at 5:52 pm