On 8 June 2010 15:43, Andrew Dalke <da...@dalkescientific.com> wrote: > 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 very out of date now, and pointless, yes?
We do appreciate feedback on this, as we receive very little. I usually google "openbabel fingerprints" which points you to http://openbabel.org/wiki/Tutorial:Fingerprints. I'll fix the other pages. > (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.) The numbering is based on API changes, not features (or marketing!). The next version is 2.3.0 for example. >>> 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 http://openbabel.org/wiki/Roadmap seems out of date since the last edit was 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. There isn't. > 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. I don't think this is feasible, unless we have more developers who will fix bugs. > 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? Our documentation focuses on the released version. I'm not sure right now what Pybel will do; I think I may support both OASA and the internal depictor but it depends on the time constraints. >> 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? I'm not sure. > > 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 > ------------------------------------------------------------------------------ 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
