On Jun 8, 2010, at 2:43 AM, Noel O'Boyle wrote: >> OB also supports using a molecule as the query rather than a SMARTS. > > Hmm...not sure about this. Does it?
I thought it did, but you and others disagree. I'll look again. > MACCS key is in there. There is also support for user-defined fingerprints. Huh. That was added last year with 2.2.1 and I missed it. Thanks! On the topic of documentation quality (which Geoff asked about), how does one find this out? Go to http://openbabel.org/wiki/Develop and there's mention of FP2, FP3 and FP4 but not MACCS fingerprints. Go to http://openbabel.org/wiki/Developer:API and search 2.2.0 documentation for MACCS and it isn't there. There's no link to the 2.2.1 documentation and for some reason there's a link to the 2.1.x beta API docs, which would be very out of date now, and pointless, yes? (BTW, what's the reason that OB prefers these point releases, like - 2009-07-31 Open Babel 2.2.3 Released - 2009-07-10 Open Babel 2.2.2 Released - 2009-02-03 Open Babel 2.2.1 Released - 2008-07-04 Open Babel 2.2.0 Released ? There's been some major changes during those releases, so would seem to warrant 2.3, 2.4, and higher.) >> OB does not do depiction. For that case people should turn to other >> libraries, such as OASA. > > OB can do depiction, at least in the development version. One of the difficulties I have in making my report is that all of the libraries have things in development, available for the next release. Is there a roadmap/timeline for that? The one at http://openbabel.org/wiki/Roadmap seems out of date since the last edit was Dec 2006. At the last Python conference, Mark Shuttleworth's keynote address was on "Cadence, Quality, and Design" http://us.pycon.org/2010/conference/schedule/event/122/ and one lesson I learned was the usefulness of having predictable schedules. It's still something I'm thinking about, and I thought might be interesting in this context. Again regarding documentation, how does one learn how to do this? http://www.google.com/search?client=safari&rls=en&q=depiction+site:openbabel.org&ie=UTF-8&oe=UTF-8 finds all of two pages, both for pybel saying it uses OASA. Will pybel in 2.2.4 (or 2.3?) use the internal depicter instead of OASA? I see it will support SVG, but will it also support a bitmap format of some sort? > Also MacOSX and Ruby. Also Cygwin, ... Indeed, but my client doesn't use those. ;) > Don't forget Pybel is part of OpenBabel. *smacks* *head* D'oh! I was thinking about the C++ interface here, comparing it to Python. Brain reset. > One other feature you haven't mentioned is that it has a plugin > architecture for fingerprints, formats, operations, charge models and > so forth (it's the same architecture in each case). Despite my subject line, this thread is more "OB features my client is interested in, based on talking with them." While I know that it's possible, I can't find the documentation about it. How does one develop a new fingerprint? During testing can the new .so be in the user's directory space, or must extensions be in the OpenBabel installation? Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
