Packaging and Progress

Development
1

Hi everyone,

First off, thanks very much to Donald for some great progress! I
apologize I haven’t been very active, but have been traveling for
various interviews. (Hopefully my travel schedule should be better
now that I have offers to consider.)

Donald and I are going to try some packaging for Windows and Mac for
demonstrating the potential of Avogadro and libavogadro.

I should remind everyone that we do have a wiki for communication, in
addition to the mailing list. I’m going to update the TODO list with
current progress (and problems) and hope others will too.

http://avogadro.sourceforge.net/wiki/To_Do

In particular, I think there are a few general pieces we should still
consider while we’re in the design phase and can make these changes
without re-implementing a huge amount of code again:

  • Multiple molecule files. Right now we only handle the first
    molecule in a file.

  • Animation (e.g., multiple coordinate sets). Right now, Open Babel
    has support in OBMol for multiple conformers/coordinates – this
    mainly requires a UI update (an animation tool?)

  • Undo/redo support. Basically, we’d need to address changes to the
    document with subclasses of QUndoCommand:
    http://doc.trolltech.com/4.2/qundocommand.html

I think we’re doing great, and hope I can help more in the near future!
-Geoff

2

Hi Geoff,

I haven’t done anything so far but I’ll contribute in the near future when
I’ll port kalzium to libavo:

  • i’ll fix a few issues with the way libavo reuses the kalzium code (esp.
    regarding display lists, a big optimization is missing)
  • if you like it, i’ll move to libavo some stuff i currently do in
    kalzium, like automatic orientation of the molecule and of double bonds.

Something I already discussed with Donald:

I’ve discussed with other KDE developers and on kde-devel the dependency
issues associated with having kalzium rely on libavo which itself relies
on eigen (which is in kde’s svn). From the point of view of KDE, the best
thing would be if libavogadro was developed in KDE’s SVN, in
/trunk/kdesupport. This is where Eigen already is, this directory is for
libraries who are also used by non-KDE projects.

As to the Avogadro app, it could stay in sourceforge, no need to have it
at the same place as libavogadro. But if you ever want to make it a KDE
application (KDE4 will support Windows and MacOSX natively without a X
server), it’s of course welcome in extragear or in playground depending on
its stability.

Cheers,
Benoit

On Fri, 2 Feb 2007, Geoffrey Hutchison wrote:

Hi everyone,

First off, thanks very much to Donald for some great progress! I
apologize I haven’t been very active, but have been traveling for
various interviews. (Hopefully my travel schedule should be better
now that I have offers to consider.)

Donald and I are going to try some packaging for Windows and Mac for
demonstrating the potential of Avogadro and libavogadro.

I should remind everyone that we do have a wiki for communication, in
addition to the mailing list. I’m going to update the TODO list with
current progress (and problems) and hope others will too.

http://avogadro.sourceforge.net/wiki/To_Do

In particular, I think there are a few general pieces we should still
consider while we’re in the design phase and can make these changes
without re-implementing a huge amount of code again:

  • Multiple molecule files. Right now we only handle the first
    molecule in a file.

  • Animation (e.g., multiple coordinate sets). Right now, Open Babel
    has support in OBMol for multiple conformers/coordinates – this
    mainly requires a UI update (an animation tool?)

  • Undo/redo support. Basically, we’d need to address changes to the
    document with subclasses of QUndoCommand:
    http://doc.trolltech.com/4.2/qundocommand.html

I think we’re doing great, and hope I can help more in the near future!
-Geoff

Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier.
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

3

Bonjour Benoit,

  • i’ll fix a few issues with the way libavo reuses the kalzium
    code (esp.
    regarding display lists, a big optimization is missing)
  • if you like it, i’ll move to libavo some stuff i currently do in
    kalzium, like automatic orientation of the molecule and of double
    bonds.

These both sound great. It’s always frustrating to open a file and
not find the molecule (because it’s off-screen).

I’ve discussed with other KDE developers and on kde-devel the
dependency
issues associated with having kalzium rely on libavo which itself
relies
on eigen (which is in kde’s svn). From the point of view of KDE,
the best
thing would be if libavogadro was developed in KDE’s SVN, in
/trunk/kdesupport.

I think this sounds like a good idea, since the recent mention on
dot.kde.org may gain some interest in libavogadro. Maybe other
projects will use the library. I know Carsten had once talked about a
KPart to allow for double-clicking molecule files.

Cheers,
-Geoff

4

Am Samstag, 3. Februar 2007 00:49 schrieb Geoffrey Hutchison:

I think this sounds like a good idea, since the recent mention on
dot.kde.org may gain some interest in libavogadro. Maybe other
projects will use the library. I know Carsten had once talked about a
KPart to allow for double-clicking molecule files.

In fact the 3D-widget thing in Kalzium is already a KPart. So in theory the
embedding in Konq (or KMail :wink: would already work. The other apps just don’t
know anything about the KPart, I need to add the Factory or whatever to
something somewhere.

I know nothing about all this but when I a) have more time and b) Kalzium is
using avo I will find out and do the work.

Carsten

5

Moin all

I should remind everyone that we do have a wiki for communication, in
addition to the mailing list. I’m going to update the TODO list with
current progress (and problems) and hope others will too.

http://avogadro.sourceforge.net/wiki/To_Do

I just synced the To_Do-page with Kalziums TODO and removed the TODO in
Kalzium. I is much easier to handle it in the Wiki. Benoit: Please have a
look at http://avogadro.sourceforge.net/wiki/To_Do#From_Kalzium_TODO and
update it… I am especially interested in

“polish 3d navigation system, add cool visual feedback. ← That must be ready
for demoing at Solutions Linux 2007; i’m handling this (bjacob)”

:wink: Is that because of David Faure?

Carsten

6

On Sat, 3 Feb 2007, Carsten Niehaus wrote:

look at http://avogadro.sourceforge.net/wiki/To_Do#From_Kalzium_TODO and
update it… I am especially interested in

“polish 3d navigation system, add cool visual feedback. ← That must be ready
for demoing at Solutions Linux 2007; i’m handling this (bjacob)”

:wink: Is that because of David Faure?

Inititally it was only Anne-Marie Mahfouf whoo wanted to demo it…
ok I update the wiki.

Benoit

7

Ont thing that can be implemented in Kalzium is thumbnailing and KFilePlugin
stuff ( more or less the way KryoMol behaves). My idea is that Kalzium
should take care of getting basic info on files and implement a plugin
mechanism for other applications (KryoMol) to offer more technical
information to the users. I am now compiling last kde snapshot and i wiil
try to work a bit on this.

Am Samstag, 3. Februar 2007 00:49 schrieb Geoffrey Hutchison:

I think this sounds like a good idea, since the recent mention on
dot.kde.org may gain some interest in libavogadro. Maybe other
projects will use the library. I know Carsten had once talked about a
KPart to allow for double-clicking molecule files.

In fact the 3D-widget thing in Kalzium is already a KPart. So in theory the
embedding in Konq (or KMail :wink: would already work. The other apps just
don’t know anything about the KPart, I need to add the Factory or whatever
to something somewhere.

I know nothing about all this but when I a) have more time and b) Kalzium
is using avo I will find out and do the work.

Carsten

–
Dr. Armando Navarro-Vázquez
RIAIDT. Univdade de Resonancia Magnetica
Universidade de Santiago de Compostela
http://desoft03.usc.es/armando/index.html

8

Hi Armando,

I think that libavogadro is already a nice place for us to share code,
from which apps like Kalzium and KryoMol can derive. If KryoMol did use
the Kalzium KPart, it would

  1. add another layer to the cake, i.e.
    libavogadro->Kalzium KPart->KryoMol
  2. make us more dependant on one another, i.e. if I changed Kalzium in
    some way it would affect KryoMol.

So I think it’s better if we join efforts upstream, which is, in
libavogadro. Concretely, if at least two different apps (for example,
Kalzium and KryoMol) want the same feature, then that feature should be
moved to libavogadro.

Or do you see a reason why sharing a KPart is really better for us than
just sharing what libavogadro provides (a widget and helper functions) ?

Benoit

On Mon, 5 Feb 2007, Armando Navarro Vázquez wrote:

Ont thing that can be implemented in Kalzium is thumbnailing and KFilePlugin
stuff ( more or less the way KryoMol behaves). My idea is that Kalzium
should take care of getting basic info on files and implement a plugin
mechanism for other applications (KryoMol) to offer more technical
information to the users. I am now compiling last kde snapshot and i wiil
try to work a bit on this.

Am Samstag, 3. Februar 2007 00:49 schrieb Geoffrey Hutchison:

I think this sounds like a good idea, since the recent mention on
dot.kde.org may gain some interest in libavogadro. Maybe other
projects will use the library. I know Carsten had once talked about a
KPart to allow for double-clicking molecule files.

In fact the 3D-widget thing in Kalzium is already a KPart. So in theory the
embedding in Konq (or KMail :wink: would already work. The other apps just
don’t know anything about the KPart, I need to add the Factory or whatever
to something somewhere.

I know nothing about all this but when I a) have more time and b) Kalzium
is using avo I will find out and do the work.

Carsten

–
Dr. Armando Navarro-Vázquez
RIAIDT. Univdade de Resonancia Magnetica
Universidade de Santiago de Compostela
http://desoft03.usc.es/armando/index.html

Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier.
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

9

Am Montag, 5. Februar 2007 11:12 schrieb Armando Navarro Vázquez:

Ont thing that can be implemented in Kalzium is thumbnailing and
KFilePlugin stuff ( more or less the way KryoMol behaves). My idea is that
Kalzium should take care of getting basic info on files and implement a
plugin mechanism for other applications (KryoMol) to offer more technical
information to the users. I am now compiling last kde snapshot and i wiil
try to work a bit on this.

Moin all

Perhaps you could note these thoughts in this TODO:

http://avogadro.sourceforge.net/wiki/To_Do

That way we could all keep track on them… By the way, I like your idea! The
even is KFile-chemical:

http://websvn.kde.org/trunk/playground/utils/kfile-chemical/

Egon works on these plugins and I am also interested in them. Especially in
combination with Strigi.

Carsten