Tuesday, 11 December 2012

Cinfony 1.2 released

Cinfony presents a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of Open Babel, the RDKit, the CDK, Indigo, OPSIN, JChem and cheminformatics webservices.

Cinfony 1.2 is now available for download.

The two major additions in this release are support for the JChem commercial cheminformatics toolkit, and the ability to specify options (via an 'opt' dictionary) for format conversion and some other operations. There were also some under-the-hood changes to consolidate source files for ease of maintenance.

These additions were principally contributed by AdriƠ Cereto MassaguƩ (of Universitat Rovira i Virgili and DecoyFinder) who joined the Cinfony team (i.e. me) earlier this year.

As usual, Cinfony has been updated to use the latest stable releases of each toolkit: Open Babel 2.3.2, CDK 1.4.15, RDKit 2012.09, Indigo 1.1, JChem 5.11 and OPSIN 1.3.

The Cinfony website has a somewhat condensed example showing the use of many of these resources in a dozen lines of Python. Here's a smaller example showing part of the new functionality:
>>> from cinfony import pybel, jchem
>>> mol = pybel.readstring("smi", "CC(=O)Cl")
>>> print mol.write("smi", opt={"f": 2, "l": 1}) # Make atom 2 the first and atom 1 the last
>>> fp = jchem.Molecule(mol).calcfp("ECFP")
>>> fp.bits
[39, 47, 55, 246, 397, 429, 700, 908]

To support Cinfony, please cite:
N.M. O'Boyle, G.R. Hutchison, Chem. Cent. J., 2008, 2, 24. [link]

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