Auto-orientation

Hi,

first of all, sorry that I broke compilation wednesday by removing a #include.

In Kalzium, at molecule loading, the molecule is automatically rotated to fit
as much as possible in the XY-plane. This means the user gets a nice top-down
view on the molecule, and then my cylinder code is designed so that the
double bonds get nicely oriented so that they don’t look like single bonds
from the default viewpoint.

As part of that is done in the cylinder drawing code that you already imported
(and that cylinder code could be made simpler if it weren’t for this feature)
I think it’d be good to have this whole feature in libavogadro. The problem
is that it seems that libavogadro doesn’t do the molecule loading itself. Is
that something that might change? If not, would you at least agree to let
libavogadro provide some utility function to rotate the molecule to fit it in
the XY-plane?

Cheers,
Benoit

On Mar 9, 2007, at 2:41 AM, Benoît Jacob wrote:

first of all, sorry that I broke compilation wednesday by removing
a #include.

Considering it’s ‘alpha’ or ‘beta’ software, I don’t think it’s a big
deal.

If not, would you at least agree to let libavogadro provide some
utility function to rotate the molecule to fit it in
the XY-plane?

I think that’s a much better approach. Remember that other programs
may have multiple sources for “reading” molecules. For example, let’s
say a user creates the molecule from scratch and then performs a
geometry optimization. Maybe they use some plugin which modifies the
coordinates.

There might also be some reason a user wants to turn it off. I can
imagine myself wanting to do some demonstration where the camera is
in a particular location – for example, an interesting region of a
protein. I don’t want the program to force me to see a different
orientation.

Just my $0.02,
-Geoff

(argh - I forgot to “reply-to-all”. Sorry Geoff, you receive this twice).

On Friday 09 March 2007 14:21:57 you wrote:

I think that’s a much better approach. Remember that other programs
may have multiple sources for “reading” molecules. For example, let’s
say a user creates the molecule from scratch and then performs a
geometry optimization. Maybe they use some plugin which modifies the
coordinates.

There might also be some reason a user wants to turn it off. I can
imagine myself wanting to do some demonstration where the camera is
in a particular location – for example, an interesting region of a
protein. I don’t want the program to force me to see a different
orientation.

Yes, I agree with you.

Cheers,
Benoit

Add this “recentering” functionality as a slot in the glwidget is what i
suggest. Maybe call it “rotateToFit” or rotateFit, better yet,
autoOrientation

man, sometimes i’m terrible with names.

(Fri, Mar 09, 2007 at 03:22:26PM +0100) Benoît Jacob jacob@math.jussieu.fr:

(argh - I forgot to “reply-to-all”. Sorry Geoff, you receive this twice).

On Friday 09 March 2007 14:21:57 you wrote:

I think that’s a much better approach. Remember that other programs
may have multiple sources for “reading” molecules. For example, let’s
say a user creates the molecule from scratch and then performs a
geometry optimization. Maybe they use some plugin which modifies the
coordinates.

There might also be some reason a user wants to turn it off. I can
imagine myself wanting to do some demonstration where the camera is
in a particular location – for example, an interesting region of a
protein. I don’t want the program to force me to see a different
orientation.

Yes, I agree with you.

Cheers,
Benoit


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OK, will do that. Maybe i’ll call it rotateMoleculeIntoXYPlane().
In the same vein, I’ll add centerMolecule() calling center() on the molecule,
OK?

Cheers,
Benoit

On Friday 09 March 2007 17:36:28 Donald Ephraim Curtis wrote:

Add this “recentering” functionality as a slot in the glwidget is what i
suggest. Maybe call it “rotateToFit” or rotateFit, better yet,
autoOrientation

man, sometimes i’m terrible with names.

(Fri, Mar 09, 2007 at 03:22:26PM +0100) Benoît Jacob
jacob@math.jussieu.fr:

(argh - I forgot to “reply-to-all”. Sorry Geoff, you receive this twice).

On Friday 09 March 2007 14:21:57 you wrote:

I think that’s a much better approach. Remember that other programs
may have multiple sources for “reading” molecules. For example, let’s
say a user creates the molecule from scratch and then performs a
geometry optimization. Maybe they use some plugin which modifies the
coordinates.

There might also be some reason a user wants to turn it off. I can
imagine myself wanting to do some demonstration where the camera is
in a particular location – for example, an interesting region of a
protein. I don’t want the program to force me to see a different
orientation.

Yes, I agree with you.

Cheers,
Benoit


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Hehe, whatever you want man.

(Fri, Mar 09, 2007 at 05:55:03PM +0100) Benoît Jacob jacob@math.jussieu.fr:

OK, will do that. Maybe i’ll call it rotateMoleculeIntoXYPlane().
In the same vein, I’ll add centerMolecule() calling center() on the molecule,
OK?

Cheers,
Benoit

On Friday 09 March 2007 17:36:28 Donald Ephraim Curtis wrote:

Add this “recentering” functionality as a slot in the glwidget is what i
suggest. Maybe call it “rotateToFit” or rotateFit, better yet,
autoOrientation

man, sometimes i’m terrible with names.

(Fri, Mar 09, 2007 at 03:22:26PM +0100) Benoît Jacob
jacob@math.jussieu.fr:

(argh - I forgot to “reply-to-all”. Sorry Geoff, you receive this twice).

On Friday 09 March 2007 14:21:57 you wrote:

I think that’s a much better approach. Remember that other programs
may have multiple sources for “reading” molecules. For example, let’s
say a user creates the molecule from scratch and then performs a
geometry optimization. Maybe they use some plugin which modifies the
coordinates.

There might also be some reason a user wants to turn it off. I can
imagine myself wanting to do some demonstration where the camera is
in a particular location – for example, an interesting region of a
protein. I don’t want the program to force me to see a different
orientation.

Yes, I agree with you.

Cheers,
Benoit


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Join SourceForge.net’s Techsay panel and you’ll get the chance to share
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