Fwd: kalzium 3D

Moin Armando, hello Avogadro-list

I am forwarding an EMail by Armando Navarro Vázquez, the author of

http://desoft03.usc.es/armando/software/kryomol.html

Please read the attached EMail. It seems Avogadro has one more future
merge-candidate :wink:

---------- Weitergeleitete Nachricht ----------

Hi Armando! It’d be great if we could join effort.

We realized that we didn’t want to have a dependency on an external library
for the math stuff, and so we’re coding our own, named Eigen. It doesn’t have
any dependency, and is only a collection of headers containing class
templates. It will be used by several other KDE apps, including some in
KOffice. I think it’ll be another 2-3 weeks before it’s ready, and until then
I’m 100% focusing on it. But once it’s done I’d be very interested in working
together with you!

Benoit
PS: join us on #kalzium and #eigen on freenode!

Le mardi 12 septembre 2006 19:01, Carsten Niehaus a écrit :

Moin Armando, hello Avogadro-list

I am forwarding an EMail by Armando Navarro Vázquez, the author of

http://desoft03.usc.es/armando/software/kryomol.html

Please read the attached EMail. It seems Avogadro has one more future
merge-candidate :wink:

---------- Weitergeleitete Nachricht ----------

Subject: kalzium 3D
Date: Dienstag 12 September 2006 16:32
From: Armando Navarro Vázquez qoajnv@usc.es
To: cniehaus@kde.org

Dear Carsten:
I have read in the kde pages about the latest development in in kalzium,
which should include 3D molecular rendering capabilities.
I am the author of KryoMol an application intended mainly for analysis of
quantum chemical computations. I think that maybe we should think about
collaboration, since it seems that some of the features you want to
implement in kalzium are already implementing in kryomol (displaying of
pdb, xyz files). Note that KryoMol implements a basic molecular visor which
can be especialized for different purposes. Also, classes for management of
3D coordinates and quaternions are already written and also a C++ wrapper
on the ccmath library for linear algebra stuff.
Also, i think we should be careful about the handling of chemical mimetypes
in order to avoid contradiction of chemical applications.
I am confident that maybe we can join some efforts in order to do a good
handling of chemical documents in KDE.

My Best wishes
Armando

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


Dear All,
Thank you for your interest on this collaboration
I have been trying to compile svn Avogadro with the qt-4.2 version of KDE 3.8,
it compiles and seems to load the molecules but they are not displayed (it
claims something about not default rendering engine available).
Where is the qt-4 version of kalzium3D, in svn KDE 3.8 ?

First of all I would lke to analize what is already implemented in both
packages to think how things can be merged, study the API of openbabel and
setup my KDE4 development environment

My best wishes
Armando

Moin Armando, hello Avogadro-list

I am forwarding an EMail by Armando Navarro Vázquez, the author of

http://desoft03.usc.es/armando/software/kryomol.html

Please read the attached EMail. It seems Avogadro has one more future
merge-candidate :wink:

---------- Weitergeleitete Nachricht ----------

Subject: kalzium 3D
Date: Dienstag 12 September 2006 16:32
From: Armando Navarro Vázquez qoajnv@usc.es
To: cniehaus@kde.org

Dear Carsten:
I have read in the kde pages about the latest development in in kalzium,
which should include 3D molecular rendering capabilities.
I am the author of KryoMol an application intended mainly for analysis of
quantum chemical computations. I think that maybe we should think about
collaboration, since it seems that some of the features you want to
implement in kalzium are already implementing in kryomol (displaying of
pdb, xyz files). Note that KryoMol implements a basic molecular visor which
can be especialized for different purposes. Also, classes for management of
3D coordinates and quaternions are already written and also a C++ wrapper
on the ccmath library for linear algebra stuff.
Also, i think we should be careful about the handling of chemical mimetypes
in order to avoid contradiction of chemical applications.
I am confident that maybe we can join some efforts in order to do a good
handling of chemical documents in KDE.

My Best wishes
Armando

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



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

Am Mittwoch 13 September 2006 12:48 schrieb Armando Navarro Vázquez:

Thank you for your interest on this collaboration
I have been trying to compile svn Avogadro with the qt-4.2 version of KDE
3.8, it compiles and seems to load the molecules but they are not displayed
(it claims something about not default rendering engine available).

I cannot comment on this.

Where is the qt-4 version of kalzium3D, in svn KDE 3.8 ?

For Kalzium of KDE4 (which includes the 3D-Stuff) you need kdelibs of KDE4,
OpenBabel 2.1 (not yet released, you will need the version from svn) and of
course kdeedu from KDE4. You will find buildinstructions here:

http://developer.kde.org/build/trunk.html

First of all I would lke to analize what is already implemented in both
packages to think how things can be merged, study the API of openbabel and
setup my KDE4 development environment

That sounds good. Kalzium and Avogadro will try to share as much as possible,
it would be so great if you could join our affort so that we don’t waste
ressources by implementing the same stuff three times!


Gruß,
Carsten Niehaus

For now you need to run Avogadro from the src directory. All the
rendering engines are in src/engines

if you’re running it from /usr/bin/ it’s trying to look for the engines
in /usr/bin/engines which doesn’t exist. It’s just an initial thing.
There is also an environment variable you can set to point to those
engines; AVOGADRO_PLUGINS but i would guess this is going to change at
some point.

(Wed, Sep 13, 2006 at 12:48:48PM +0200) Armando Navarro Vázquez qoajnv@usc.es:

Dear All,
Thank you for your interest on this collaboration
I have been trying to compile svn Avogadro with the qt-4.2 version of KDE 3.8,
it compiles and seems to load the molecules but they are not displayed (it
claims something about not default rendering engine available).
Where is the qt-4 version of kalzium3D, in svn KDE 3.8 ?

First of all I would lke to analize what is already implemented in both
packages to think how things can be merged, study the API of openbabel and
setup my KDE4 development environment

My best wishes
Armando

Moin Armando, hello Avogadro-list

I am forwarding an EMail by Armando Navarro Vázquez, the author of

http://desoft03.usc.es/armando/software/kryomol.html

Please read the attached EMail. It seems Avogadro has one more future
merge-candidate :wink:

---------- Weitergeleitete Nachricht ----------

Subject: kalzium 3D
Date: Dienstag 12 September 2006 16:32
From: Armando Navarro Vázquez qoajnv@usc.es
To: cniehaus@kde.org

Dear Carsten:
I have read in the kde pages about the latest development in in kalzium,
which should include 3D molecular rendering capabilities.
I am the author of KryoMol an application intended mainly for analysis of
quantum chemical computations. I think that maybe we should think about
collaboration, since it seems that some of the features you want to
implement in kalzium are already implementing in kryomol (displaying of
pdb, xyz files). Note that KryoMol implements a basic molecular visor which
can be especialized for different purposes. Also, classes for management of
3D coordinates and quaternions are already written and also a C++ wrapper
on the ccmath library for linear algebra stuff.
Also, i think we should be careful about the handling of chemical mimetypes
in order to avoid contradiction of chemical applications.
I am confident that maybe we can join some efforts in order to do a good
handling of chemical documents in KDE.

My Best wishes
Armando

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



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
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

Hi everybody,
I managed finally to run successfully avogadro, the idea of having the
rendering engines implemented as plugins seems very good to me.
Now I am going to struggle a bit with KDE4.

My best wishes
Armando

For now you need to run Avogadro from the src directory. All the
rendering engines are in src/engines

if you’re running it from /usr/bin/ it’s trying to look for the engines
in /usr/bin/engines which doesn’t exist. It’s just an initial thing.
There is also an environment variable you can set to point to those
engines; AVOGADRO_PLUGINS but i would guess this is going to change at
some point.

(Wed, Sep 13, 2006 at 12:48:48PM +0200) Armando Navarro Vázquez
qoajnv@usc.es:

Dear All,
Thank you for your interest on this collaboration
I have been trying to compile svn Avogadro with the qt-4.2 version of KDE
3.8, it compiles and seems to load the molecules but they are not
displayed (it claims something about not default rendering engine
available).
Where is the qt-4 version of kalzium3D, in svn KDE 3.8 ?

First of all I would lke to analize what is already implemented in both
packages to think how things can be merged, study the API of openbabel
and setup my KDE4 development environment

My best wishes
Armando

Moin Armando, hello Avogadro-list

I am forwarding an EMail by Armando Navarro Vázquez, the author of

http://desoft03.usc.es/armando/software/kryomol.html

Please read the attached EMail. It seems Avogadro has one more future
merge-candidate :wink:

---------- Weitergeleitete Nachricht ----------

Subject: kalzium 3D
Date: Dienstag 12 September 2006 16:32
From: Armando Navarro Vázquez qoajnv@usc.es
To: cniehaus@kde.org

Dear Carsten:
I have read in the kde pages about the latest development in in
kalzium, which should include 3D molecular rendering capabilities.
I am the author of KryoMol an application intended mainly for analysis
of quantum chemical computations. I think that maybe we should think
about collaboration, since it seems that some of the features you want
to implement in kalzium are already implementing in kryomol (displaying
of pdb, xyz files). Note that KryoMol implements a basic molecular
visor which can be especialized for different purposes. Also, classes
for management of 3D coordinates and quaternions are already written
and also a C++ wrapper on the ccmath library for linear algebra stuff.
Also, i think we should be careful about the handling of chemical
mimetypes in order to avoid contradiction of chemical applications.
I am confident that maybe we can join some efforts in order to do a
good handling of chemical documents in KDE.

My Best wishes
Armando

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



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
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


Dr. Armando Navarro Vázquez
RIAIDT. Universidade de Santiago de Compostela

Well, basically Kryomol is a KParts based aplication, so things work more or
less this way

The base visor is called GLVisor and it does basic operations, rendering, atom
picking, trallback rotation etc (trackball rotation and atom picking is a bit
tricky if you have not implemented you may take a look at my code).
In GLVisor there are several virtual rendering function which are called
inside paintGL(), mainly

virtual void RenderMolecule(GLenum mode=GL_RENDER);
virtual void RenderScreenText() {};

GLVisorBase has a Molecule object (similar to the OpenBabel class ) and a
vector of Molecules, this is quite ineficcient (in fact I changed these
classes in another specialized application I am writing).

So there are several subclasses of GLVisorBase, mainly

KryoVisor : public GlVisorBase
KryoVisorOpt: public Kryovisor //optimizaion jobs
KryoVisorDens : public KryoVisor //density jobs
KryoVisorFreq : public KryoVisor //frequency jobs

each of these classes reimplements RenderMolecule

KryoVisorDens::RenderMolecule()
{
GLVisorBase::RenderMolecule();
… own stuff…
}

There is a class for automatically detected the type of file, called
QuantumFile. Once, the file type is determined a parser object is built in
the heap and a also the apropiate subclass of GLVisorBase is built, so data
are put onto molecular containers memeber of the GLVisorBase object.

So, maybe a possible scenario should be

Implement a simple class maybe not very different to GLVisorBase but,
should have a molecular container similar to std::vector<OBMolecule*>, and
maybe a single OBMolecule* object, all allocated on the heap to allow the use
of subclasses of OBMol* , ( for instance I have noted that the API of
openbabel only allows retrieval of a class of energy, but in molecular
dynamics frequently you want to store kinetic and potential energy. and
implement the avogadro plugin rendering mechanism inside this base class.

It is easy to implement a external plugin mechanism for OpenGL rendering so
for instance you will have

MyVisor::RenderMolecule()
{
GLVisorBase::RenderMolecule();
std::list<Plugin*>::iterator it;
for (it=…)
{
it->Render();
}
}

and OpenGL calls can be done inside the Render method of each plugin, however
I will write this not on the very base class since cause a degradation of
performance.

Waiting for your comments and ideas
Armando

Yes, it’s still in the works. We’re going to reimplement the engines
when we get a chance and all the specs (ideas) we have are documented in
the avogadro-devel mailing list (i think).

At this point we have no intention of implementing KDE4 extensions into
Avogadro; however at some point we’d like to make the viewer a library
type so that it can be shared across applications.

Just trying to stay as platform independant as possible.

I did run Kryomol but couldn’t get some of the labels to work correctly
(maybe a QT issue) and i started to dig through some of the code but
didn’t seem to understand where to start.

It looks like you have implemented the viewer as a “MolPart” or
something like that so that it is a KDE component. Very interesting if
that is the case.

We’re open to any advice or suggestions that your experience has taught
you.

-Donald

(Thu, Sep 14, 2006 at 12:26:22PM +0200) Armando Navarro Vazquez
qoajnv@usc.es:

Hi everybody,
I managed finally to run successfully avogadro, the idea of having the
rendering engines implemented as plugins seems very good to me.
Now I am going to struggle a bit with KDE4.

My best wishes
Armando

For now you need to run Avogadro from the src directory. All the
rendering engines are in src/engines

if you’re running it from /usr/bin/ it’s trying to look for the engines
in /usr/bin/engines which doesn’t exist. It’s just an initial thing.
There is also an environment variable you can set to point to those
engines; AVOGADRO_PLUGINS but i would guess this is going to change at
some point.

(Wed, Sep 13, 2006 at 12:48:48PM +0200) Armando Navarro Vázquez

qoajnv@usc.es:

Dear All,
Thank you for your interest on this collaboration
I have been trying to compile svn Avogadro with the qt-4.2 version of
KDE 3.8, it compiles and seems to load the molecules but they are not
displayed (it claims something about not default rendering engine
available).
Where is the qt-4 version of kalzium3D, in svn KDE 3.8 ?

First of all I would lke to analize what is already implemented in
both packages to think how things can be merged, study the API of
openbabel and setup my KDE4 development environment

My best wishes
Armando

Moin Armando, hello Avogadro-list

I am forwarding an EMail by Armando Navarro Vázquez, the author of

http://desoft03.usc.es/armando/software/kryomol.html

Please read the attached EMail. It seems Avogadro has one more
future merge-candidate :wink:

---------- Weitergeleitete Nachricht ----------

Subject: kalzium 3D
Date: Dienstag 12 September 2006 16:32
From: Armando Navarro Vázquez qoajnv@usc.es
To: cniehaus@kde.org

Dear Carsten:
I have read in the kde pages about the latest development in in
kalzium, which should include 3D molecular rendering capabilities.
I am the author of KryoMol an application intended mainly for
analysis of quantum chemical computations. I think that maybe we
should think about collaboration, since it seems that some of the
features you want to implement in kalzium are already implementing
in kryomol (displaying of pdb, xyz files). Note that KryoMol
implements a basic molecular visor which can be especialized for
different purposes. Also, classes for management of 3D coordinates
and quaternions are already written and also a C++ wrapper on the
ccmath library for linear algebra stuff. Also, i think we should be
careful about the handling of chemical mimetypes in order to avoid
contradiction of chemical applications. I am confident that maybe
we can join some efforts in order to do a good handling of chemical
documents in KDE.

My Best wishes
Armando

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



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=121
642 _______________________________________________
Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


Dr. Armando Navarro Vázquez
RIAIDT. Universidade de Santiago de Compostela


Dr. Armando Navarro Vázquez
RIAIDT. Universidade de Santiago de Compostela