chem-bla-ics: December 2012

CTR: resolving dependencies in Groovy with Grapes

+Mark Fortner commented on Google+ that my script was missing a @Grab statement. I had seen that mentioned before, but never looked at it. It turns out the be very useful, and it makes Groovy scripts standalone. That is, it will resolve the missing dependencies, using Maven repositories. Fortunately, CDK modules are available from repositories, e.g. the one at Plovdiv University, and I gave it a try.

Dec

CTR #3: Report the similarity between two structures

The next CTR I picked is not particularly hard either, given the functionality provided by the CDK. In fact, the fingerprinting functionality I will use for this CTR is actually one of the most used and oldest features of the CDK. CiteULike has a list of 26 papers using the CDK fingerprinting functionality.

Dec

CTR #2: Depict a compound as an image

This one was relatively easy, and roughly based on the first CDK-JChemPaint tutorial. Key aspects are the SMILES parsing, 2D coordinate generation with the StructureDiagramGenerator. The solution does not render the structure's title yet. I have do not have a solution for that right now (the CDK may; I am not sure).

Dec

CTR #1: Heavy atom counts from an SD file

The first Chemistry Toolkit Rosetta task is to count the number of heavy atoms in the structures given in a MDL SD file. This tasks starts with an SD file and counts for each structure in the file the number of heavy atoms (non-hydrogen atoms). Because we simply handle the structures one by one, the solution uses the IteratingMDLReader reader. The input file (benzodiazepine.sdf.gz) is a gziped file, which we handle by using a GZIPInputStream.

Dec

Chemistry Toolkit Rosetta: common cheminformatics tasks

The Chemistry Toolkit Rosetta wiki was set up some time ago by Andrew Dalke to demonstrate how certain basic cheminformatics tasks are done in the various cheminformatics toolkits around. I think it is a great idea, but never found enough time to do much with it, unfortunately. But it is holiday now, which is a time to take your mind of your work, and then some random hacking with the CDK is what I like to do.

Dec

Groovy Cheminformatics with the CDK: 7th edition

Already the 7th edition of my Groovy Cheminformatics with the Chemistry Development Kit book (and PDF eBook). It has been almost two years since the first release and has grown from an initial 72 pages to 212 pages today. There is still a lot I still want to write about, but only during the holidays I have time for it. New content includes: Chapter 6. Reactions Chapter 7. From IChemObject to IChemFile Section 17.1.2. Stereoisomerism (in InChIs) Rewrote Chapter 20. Documentation Appendix D.1.