Extending Avogadro

Hello every one.
I’m student and I help biochemists in my university (Russia, Kazan city, KSU). It’s also will be my exhaust work.

So, at first time, I need to find solution for ‘bending’ crystallographic unit cells.
As I’ve looked internet for open source programs (molecular editors), I’ve found Avogadro most suitable
for it. Or you can advise another product? Or this feature already developing for you program?

To take a part in developing I must use Linux? Which one? As I understood on Windows I can only build a
copy of Avogadro, not take a part.

Aidar.

Dear Aidar,

I’m student and I help biochemists in my university (Russia, Kazan
city, KSU). It’s also will be my exhaust work.

Great.

So, at first time, I need to find solution for 'bending’
crystallographic unit cells.

Can you describe this a bit more. We have a variety of functions for
building up crystallographic unit cells. But I am not aware of the
term “bending.” Can you describe it?

To take a part in developing I must use Linux? Which one? As I
understood on Windows I can only build a
copy of Avogadro, not take a part.

No, you can definitely develop of Windows. The code is open and cross-
platform. However, you can’t use direct Win32 calls – we use the Qt
library to allow our program to work on Linux, Windows, and Mac.

Hope that helps,
-Geoff

Geoffrey Hutchison wrote:

Dear Aidar,

I’m student and I help biochemists in my university (Russia, Kazan
city, KSU). It’s also will be my exhaust work.

Great.

So, at first time, I need to find solution for 'bending’
crystallographic unit cells.

Can you describe this a bit more. We have a variety of functions for
building up crystallographic unit cells. But I am not aware of the
term “bending.” Can you describe it?

This is new to me too, I am sure it would be possible to do but I don’t
think we have any support for anything like this already. Good places to
look would be the unitcell and supercell extensions.

To take a part in developing I must use Linux? Which one? As I
understood on Windows I can only build a
copy of Avogadro, not take a part.

No, you can definitely develop of Windows. The code is open and cross-
platform. However, you can’t use direct Win32 calls – we use the Qt
library to allow our program to work on Linux, Windows, and Mac.

Tim and I both do packaging on Windows. I do not think that Windows is a
very good development environment, but it is certainly possible to
develop Avogadro on Windows and contribute to our project. As Geoff said
you have to be careful to use the Qt functions and not Windows system
calls. We of course have to do the same on Linux and the Mac too.

http://avogadro.openmolecules.net/wiki/Compiling_on_Windows

This page contains our notes on using MSVC 2008 to compile Avogadro and
its dependencies on Windows. Please ask here or on our IRC channel
(#avogadro on Freenode) if you have trouble getting this set up. I would
probably skip the Python deps initially at first and concentrate on
getting Qt, OpenBabel and Eigen working. I have tested Qt 4.5 on Windows
and it is working well with Avogadro.

Thanks,

Marcus

Hi all.

As a crystallographer, I never met this term. But I am anxious to
learn more abouut it!

Louis

Le 13 mars 09 à 21:37, Marcus D. Hanwell a écrit :

Geoffrey Hutchison wrote:

Dear Aidar,

I’m student and I help biochemists in my university (Russia, Kazan
city, KSU). It’s also will be my exhaust work.

Great.

So, at first time, I need to find solution for 'bending’
crystallographic unit cells.

Can you describe this a bit more. We have a variety of functions for
building up crystallographic unit cells. But I am not aware of the
term “bending.” Can you describe it?

This is new to me too, I am sure it would be possible to do but I
don’t
think we have any support for anything like this already. Good
places to
look would be the unitcell and supercell extensions.

Dear Aidar,

As to “bending,” that has not been used, although I think it could be
adjusted onto the new supercell builder extension. You would just add
a section to specify the bend angle and adjust the code which creates
new atoms accordingly.

Yes, we have discussed several builders, including a nanoparticle
builder. Your ideas for cube, ball, prism, etc. would be good. The
code itself would be fairly simple in Avogadro – but none of the
current active developers have had it on our "todo lists"
http://avogadro.openmolecules.net/wiki/To_Do_For_1.0

You can develop on any platform. The page you mention should probably
be revised – it doesn’t really help Mac developers either.

As to bugs… please submit bug reports or post to the list. We try to
fix bugs fairly fast, although obviously we cannot test anything. So
if you find problems, please let us know.

Cheers,
-Geoff

On Mar 13, 2009, at 4:40 PM, Aidar Mahmutov wrote:

Can you describe this a bit more. We have a variety of functions for
building up crystallographic unit cells. But I am not aware of the
term “bending.” Can you describe it?
Well, this feature is rare, otherwise we wouldn’t want to realise
it. Some known types of atoms in crystal lattice have possibility to
deflect from min to max angle.
In simple way it looks like this: http://en.wikipedia.org/wiki/File:Carbon_nanorim_zigzag_povray.PNG
But bend must be enable for any crystal lattice. For example,
ability to bend prism on some angle. This angle is known by
biochemists.

Also we need to make filling some form with any atoms of the same
type. For the first time, it can be simple forms: cube, ball, prism,
polyhedron. And must be possibility for further extending.

No, you can definitely develop of Windows.
On the page: http://avogadro.openmolecules.net/wiki/Building:Development_Version
Is written, that “The following instructions are intended for users
who wish to develop Avogadro. If you simply wish to build a copy of
Avogadro for yourself, please see separate instructions for: …”

PS: program have enough bugs :slight_smile:

Thanks for attention and reply,
Aidar.