[Kalzium] About Molecular Viewer

[Benoît Jacob]

Hi Leandro,

> And, when you said "You can
> then click on "optimize" to have the molecule automatically shape
> realistically", you meant, calculate how it should be or look in some kind
> of data base for fit it in some known pattern?

Much better: a simulation of the physical force fields is performed at 
runtime. This is a new feature of the OpenBabel library, developed jointly 
with libavogadro. And Kalzium makes use of all that goodness.

In the Avogadro application you can even enable auto-optimization: while you 
edit the molecule, the atoms progressively readjust. I can't describe how 
exhilarating that is to watch, you must try it out for yourself!

Why don't you just join the #avogadro channel on IRC, irc.freenode.net port 
6667. Hang around a bit if devs are currently asleep :)

Cheers,
Benoit

>
> And it was about the KDE 4.0 version. But, if you said so, then I think
> that I should look deeper at Avogadro.
>
> Thank you for your recommendation.
>
> bye
>
> On Sun, Jun 1, 2008 at 9:45 PM, Benoît Jacob <jacob at math.jussieu.fr> wrote:
> > Hi Leandro,
> >
> > Thanks for the kind words! Most of the credit goes to Marcus Hanwell and
> > the
> > rest of the Avogadro team.
> >
> > Are you talking of KDE 4.0 or 4.1 (current development version?)
> >
> > Kalzium in KDE 4.0 didn't allow to edit/create molecules. This is
> > changing in
> > KDE 4.1, of which you can already try the beta.
> >
> > In 4.1, on the left hand side of the Molecular Editor dialog, you have
> > three
> > tabs: Display, Edit, Measure. Just click on the Edit tab. Then the mouse
> > behavior changes so that when you click inside the OpenGL view, it
> > creates an
> > atom. By dragging the mouse you then create a bond. You can then click
> > on "optimize" to have the molecule automatically shape realistically.
> >
> > If you are serious about these things for your studies, I would recommend
> > that
> > you check out Avogadro. It is the project which develops the library that
> > Kalzium then uses for 3D stuff. The two teams intersect a lot.
> >
> > The standalone Avogadro application is like a much more powerful version
> > of the 3D Molecular editor of Kalzium 4.1.
> >
> > http://avogadro.openmolecules.net/
> >
> > Cheers,
> > Benoit
> >
> > On Sunday 01 June 2008 21:54:10 Leandro Boscariol wrote:
> > > Hi!
> > >
> > > I'm new at this list and I would like to ask a question, if you don't
> >
> > mind.
> >
> > > But before that, just want congratulate for the good job, its really
> >
> > nice!
> >
> > > Well, how do you draw the atoms of the molecule loaded by the Molecular
> > > Viewer? Its just using the pre known coordinates that are in the file
> > > loaded?
> > >
> > > I'm thinking about it and sound me a bit obvious that you don't
> > > calculate it.
> > >
> > > So, I'm asking this because I'm working on a project for conclude my
> > > graduation in Computer Science at University where I'll have to draw
> > > the molecule and calculate the energy's minimum for the bonds, angle
> > > bending, torsions and non-bonded interactions.
> > >
> > > My point is, what's the way that the rotation and translation are done
> > > if there is some using OpenGL and, also about the transformations, its
> > > used
> >
> > a
> >
> > > global or a local coordinate system?
> > >
> > > Well, thanks for your attention and keep doing the good work.
> >
> > _______________________________________________
> > Kalzium mailing list
> > Kalzium at kde.org
> > https://mail.kde.org/mailman/listinfo/kalzium


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