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 and cheminformatics webservices.Cinfony 1.1 is now available for download.
The two major additions in this release are support for using the Indigo cheminformatics toolkit (the indy module) and support for OPSIN (IUPAC name to structure, the opsin module).
As usual, Cinfony has been updated to use the latest stable releases of each toolkit: Open Babel 2.3.1, CDK 1.4.5, RDKit 2011.09, Indigo 1.0 and OPSIN 1.1. Installation on Windows has also been simplified somewhat as Open Babel 2.3.1 now includes the necessary .jar file and .NET libraries (for use from Jython and IronPython).
The Cinfony website has a somewhat condensed (and only slightly contrived :-) example showing the use of all of these resources in just 12 lines of Python. Here's a small example showing that roundtripping of IUPAC names is now easy to play with:
>>> from cinfony import opsin, webel
>>> mol = opsin.readstring("iupac",
"1-chloro-2-bromopropane")
>>> print webel.Molecule(mol).write("iupac")
2-Bromo-1-chloropropaneTo support Cinfony, please cite:
N.M. O'Boyle, G.R. Hutchison, Chem. Cent. J., 2008, 2, 24. [link]
3 comments:
Hi Noel,
Learning how to use Python solely to use Cinfony!
Not sure if this is the right forum to ask, but how could I get Cinfony to search the nci with the chemspider resovlver?
i.e.
http://cactus.nci.nih.gov/chemical/structure/Rapamycin/smiles?resolver=name_by_chemspider
not
http://cactus.nci.nih.gov/chemical/structure/Rapamycin/smiles
Thanks
Iain
Hi Iain, See my answer to your (*cough*) cross-posted question. :-)
Hi Noel,
Thanks!
Not actually really a (*cough*) cross-posted question...
Really good feature request though, hope it is at the top of the list :)
Iain
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