Wednesday, 7 May 2008

ANN: cinfony 0.1 - the toolkit of cheminformatics toolkits

cinfony presents a common Python API to three open source cheminformatics toolkits: OpenBabel, RDKit and the CDK. cinfony makes it easy to carry common cheminformatics tasks, but allows you to access the underlying toolkit objects at any point.

(1) In the past, cheminformaticians have chosen a particular toolkit and have only used that toolkit. This is because of the impedance mismatch between APIs of different toolkits, and indeed, the language differences between different toolkits (CDK is Java, OpenBabel and RDKit are C++, for example). cinfony makes it easy to start using a new toolkit because the API for reading/writing files, calculating fingerprints, creating 2D depictions, etc. is the same no matter whether you are using OpenBabel, RDKit or the CDK.

(2) Different toolkits have different capabilities. cinfony allows you to access all of these capabilities in the same Python script. For example, you can read a molecule using OpenBabel, draw it using RDKit and calculate descriptors using the CDK.

cinfony 0.1 is now available for download from googlecode.

Early adopters. This is pretty much a test release.

Why are there so many dependencies?
Oops, look at the time. Gotta go. Have fun installing.

Image: DryIcons (modified)

1 comment:

Egon Willighagen said...

Noel, cheers! Integration of tools is indeed really important, and providing a common API is the key there. Bioclipse is doing the same thing, but in a different arena.