On Jun 8, 2010, at 10:43 AM, Andrew Dalke wrote: > 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.
Point taken. > (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.) Our version number policy is that plugins (e.g., new fingerprints, formats, etc.) can be added along with "point releases" since they only affect one minor section of the code. In other words, adding MACCS fingerprints doesn't make any other part of the code more or less stable. The major release (1.x., 2.x, 3.x) reflect breaking backwards compatibility with other code. There will be a v3.0, and classes and methods will be removed and reorganized. The minor release (2.0.x, 2.1.x, 2.2.x, 2.3.x) reflect adding additional major features (force fields, 3D coordinate generation, 2D depiction, re-written stereo engine, etc.) and API calls. Nothing is removed, although binaries may need to be recompiled. New plugin types can be added as API enhancements. (For example, v2.3 will bring point charge models, so we can calculate charges beyond Gasteiger, now including MMFF94, QEq and the new QTPIE method). The point release reflects improved bug-fixing and added plugins. The "plugin" nature is critical, since we (or others) can add code modules without affecting anyone. We could add a dozen fingerprints, descriptors, formats, and they're all accessed the same way. Users and code can test for the presence of different plugins and fail gracefully. If I used another version numbering scheme, we could easily be on Babel 5.0 or Babel 2010 SP2.3. I understand adding 3D generation and 2D generation are big features, but our version numbering also emphasizes stability. We don't break other people's programs lightly, and in turn, we're used by over 30 open source projects and uncounted others. > 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 http://openbabel.org/wiki/Roadmap seems out of date since the last edit was 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. Version 2.3 should be released this summer. The code is already production-quality, but we obviously like to clean up bug reports and ensure our API enhancements are enough to support users for another year. > 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? Since the wiki covers released versions (to prevent confusion), there are no pages on the 2.3 release. The OB code will not support a bitmap format, as that would require an additional dependency. I suspect Pybel will integrate the internal depiction routines for v2.3. > 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? The easiest way to develop a new fingerprint is to copy an existing one as model. You raise a good point that there is not yet an example fingerprint code. For testing, the new .so can be in a user-specified location using the environment variable BABEL_LIBDIR. This is how I do *my* development. Hope that helps, -Geoff ------------------------------------------------------------------------------ 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
