Tuesday, 12 August 2008

ANN: cinfony 0.8 - "the one with documentation"

I've just released a new version of cinfony. This one comes with full documentation of the API as well as a description of how the API is used. It should be ready for use on both Windows and Linux.

The website is at http://cinfony.googlecode.com and here's the front page:


Cinfony presents a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of OpenBabel, RDKit and the CDK.



Rajarshi said...

I'm traveling right now, so it's not a very in depth comment. I took a quick look at the Fingerprint class in the cdkjype module - is there no way to select which fingerprint to generate?

Also making | the symbol for tanimoto similarity is a bit misleading - given binary fingerprints, it should mean logical OR

Rajarshi said...

Also, out of curiosity, is it possible to load a molecule using OB but then manipulate it with CDK? Or is one meant to stick to one underlying implementation?

Noel O'Boyle said...

Regarding fingerprints, the API docs say:
calcfp(self, fp='daylight')

Optional parameters:
fp -- the fingerprint type (default is "daylight"). See the fps variable for a list of available fingerprint types.

The fps variable is ['daylight', 'graph']. These appeared (to me) to be the only working fingerprints in CDK 1.0.3.

Regarding the | symbol, Greg also complained about this. I don't feel so bad about it. The alternative is to have fp_a.tanimoto(fp_b) and dump the |.

Regarding loading with OB and manipulating with CDK. Yes!! That's a key aspect of the project and that's why it's in the example on my cinfony front page. For example, this makes it easy to calculate descriptor values for the same molecule with both the CDK and RDKit.