On Fri, Apr 12, 2013 at 9:29 AM, David Lonie <david.lo...@kitware.com> wrote: > Hi Jens, > > On Fri, Apr 12, 2013 at 5:00 AM, Jens <linuck...@gmail.com> wrote: >> Really great to hear that avogadro2 is now on the scene and I'm excited to >> see how it develops in the future. >> >> It's already looking very impressive - I read in some pretty big molecules >> and the performance and responsiveness was incredibly snappy. > > Great to hear the positive feedback! Out of curiousity, just how big > were your molecules? > >> Where's the place to log bug reports while it's still in the initial testing >> phase? I found one (see below) but it wasn't immediately obvious on the >> openchemistry website where the tracker was. > > We have a bug tracker up here: > > http://projects.openchemistry.org/ > > I'll add a link on the openchemistry wiki and see about adding one to > www.openchemistry.org.
The main site already has a link (Resources, Bug Tracker), we can certainly get links on the wiki too. The Doxygen links there too, but let's work on making it as obvious as possible. > > As for the bug: > >> draw C atom, click Extensions -> Open Babel -> Add Hydrogens: >> >> Command-line output: >> >> OBProcess::executeObabel: Running >> "/Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel" "-icml >> -ocml -h" >> "/Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel" >> stderr: >> "============================== >> *** Open Babel Error in RegisterOptionParam >> The number of parameters needed by option "t" in The LPMD file format. >> differs from an earlier registration. >> 0 molecules converted >> " >> Bad CML: "" > > I noticed this odd behavior in obabel and brought it up on > openbabel-devel a little while ago, see > http://forums.openbabel.org/obabel-h-bug-while-adding-hydrogens-td4655976.html. > This is a feature, not a bug from their perspective. > > We plan to implement our own add-hydrogens routine (and maybe even our > own "remove-hydrogens", if I can figure that out ;-) ). I've filed a > bug for this here: > > http://projects.openchemistry.org/issues/169 > There seem to be a few bugs on the Mac with obabel and CML too, so I am afraid geometry optimization looks a little dicey. I think there are some simple workarounds we can implement there to improve things in the next release. Thanks for the feedback Jens. I think ensuring anyone can have Avogadro 1 and 2 installed should make it easier to try out the new stuff without having to give up Avogadro 1. Marcus ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
