About a year ago, SciTouch LLC announced the release of the open source cheminformatics library Indigo. At that time, the full API of the library was not exposed to the user. Instead, a set of simplified APIs were available along with a number of command-line applications.
Just a few weeks ago at Goslar, Dmitry and Mikhail of Indigo made a couple of announcements. First, the library, documentation, etc. is no longer at SciTouch, but at GGA software. Second, the full API is now being made available. It's actually a C library, but wrappers are available for C#, Java and Python. If you're interested in accessing it from Python, follow the Download link to the Python API.
The Indigo library is currently at the version 1.0 Beta 3 stage, but new API functions are being added on request over at the Indigo mailing list. So if there's something missing that you'd like to have, get over there now and ask about it.
Naturally, I'm interested in adding support for Indigo to Cinfony. I've already pretty much done the Python bindings. Just put indy.py into the same directory as indigo.py and away you go. As usual, let me know if you find any bugs.