Downloading Domoic Acid from PubChem

The identity of domoic acid has been under discussion (see here, here and here). (And I very much like the ChemSpider service to make it easy to copy data from ChemSpider into WikiPedia ChemBoxes; cheers!)

less than 1 minute read

CDK 1.2.1 Released

I just released CDK 1.2.1 (aka The CDK Workshop 2009 Release), which is now available for download from SourceForge. The source can be found in our Git repository. The changes since 1.2.0 are mostly bug fixing, new unit tests, and minor clean up here and there:

2 minute read

Bioclipse2 Scripting #3: XLogP calculatation using a XMPP CDK cloud service

In preparation of the CDK workshop next week, here is a small Bioclipse2 script to calculate the XLogP value for a given SMILES, using the a CDK-based XMPP service:

less than 1 minute read

Multiple inheritence for content types?

Bioclipse is an environment for handling and processing life sciences data. This data is present in files with a wide variety of formats, each of which can contain a particular data type. For example, a we can have a single molecule in MDL molfile and in CML.

less than 1 minute read

Rednael, CDK Git for Rajarshi's patches, PubChem SDF

Short blog item about some CDK Git updates. Could not get sleep, so might as well spend that time on CDK hacking, not? Reason why I actually could not catch sleep was the news that PubChem SD files are not regular MDL SD files, but use custom extensions, for example, for dative bonds (see this PDF). This surely explains the weird things I have seen, but, unfortunately, the big SDF button on PubChem does not warn about that. Anyway, thanx for Wolfgang for informing about that customization!

1 minute read

Groovy CDK and the Keyword List

Today I have been hacking a bit more on the CDK material for the CDK workshop (see CDK - The Documentation). Below are two previews, one with a LaTeX-ified keyword list (here as HTML):

less than 1 minute read

"Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source and Open Standards"

I have submitted today the abstract of my talk at the GDCh-Wissenschaftsforum Chemie 2009 in Frankfurt in August as part of the Open Notebook Science/Open Drug Discovery session:

1 minute read