Custom Color/Radius on Selection?

Development
1

Hi Konstantin,

A question came up when I was showing off the new 1.1 features. Is it possible to set a custom color or atom radius on all atoms in a selection? It seems like this should be possible, but I could only bring up the menu for one atom or bond at a time.

Thanks,
-Geoff

2

26.05.2011, 00:12, “Geoffrey Hutchison” geoff.hutchison@gmail.com:

Hi Konstantin,

A question came up when I was showing off the new 1.1 features. Is it possible to set a custom color or atom radius on all atoms in a selection? It seems like this should be possible, but I could only bring up the menu for one atom or bond at a time.

It needs to be implemented but I don’t see any difficulties. Will look on it when I have some free time.

However there may be some troubles with supporting this feature for both atoms and bonds (what should be done for “mixed” selection?)

–
Regards,
Konstantin

3

It needs to be implemented but I don’t see any difficulties. Will look on it when I have some free time.

Great, thanks!

However there may be some troubles with supporting this feature for both atoms and bonds (what should be done for “mixed” selection?)

I think for most people, they care about the atoms rather than bonds in a “mixed” selection. I guess the best solution would be a dialog with tabs for atoms or bonds, but that’s probably better left as a ToDo for now.

-Geoff

4

26.05.2011, 21:02, “Geoffrey Hutchison” geoff.hutchison@gmail.com:

It needs to be implemented but I don’t see any difficulties. Will look on it when I have some free time.

Great, thanks!

However there may be some troubles with supporting this feature for both atoms and bonds (what should be done for “mixed” selection?)

I think for most people, they care about the atoms rather than bonds in a “mixed” selection. I guess the best solution would be a dialog with tabs for atoms or bonds, but that’s probably better left as a ToDo for now.

Probably it should be further polished to reduce code duplication

Also, maybe it’s a good time to fix custom property manipulations.

  • We discussed use of QProperties to reduce memory overhead
  • I don’t like how access to colors is implemented - first I need to check custom color, than color map, but it would be much more pleasant to have something like Atom::color() returning actual property value.

–
Regards,
Konstantin

5

On May 30, 2011, at 11:28 AM, Konstantin Tokarev wrote:

Support etting of custom properties for multi-atomic selections · annulen/avogadro@a69c045 · GitHub

Probably it should be further polished to reduce code duplication

So I assume when you’ve done the polish, you’ll submit to Gerrit?

Also, maybe it’s a good time to fix custom property manipulations.

  • We discussed use of QProperties to reduce memory overhead
  • I don’t like how access to colors is implemented - first I need to check custom color, than color map, but it would be much more pleasant to have something like Atom::color() returning actual property value.

I talked with Marcus a while ago about caching colors in the engines, which would also reduce the overhead from custom colors. The idea is that the engine class would get a signal when the molecule changed, check the colors (both custom and normal) and save them in a QList.

I’m not sure about your second point – Atom::color() only knows a color if it’s custom. Otherwise, I could set one color scheme for the Sticks engine (e.g., to reflect partial charge or somesuch) and another for Spheres.

BTW, I think it’s probably a good idea for v1.1 to revamp the standard ElementColor class to use its own text file for colors. I think there are a lot of savvy users who might want to use green for carbon or something like this.

What do you think?
-Geoff

6

30.05.2011, 19:54, “Geoffrey Hutchison” geoff.hutchison@gmail.com:

On May 30, 2011, at 11:28 AM, Konstantin Tokarev wrote:

Support etting of custom properties for multi-atomic selections · annulen/avogadro@a69c045 · GitHub

Probably it should be further polished to reduce code duplication

So I assume when you’ve done the polish, you’ll submit to Gerrit?

You can check right now if everything work as it should do.

Also, maybe it’s a good time to fix custom property manipulations.

  • We discussed use of QProperties to reduce memory overhead
  • I don’t like how access to colors is implemented - first I need to check custom color, than color map, but it would be much more pleasant to have something like Atom::color() returning actual property value.

I talked with Marcus a while ago about caching colors in the engines, which would also reduce the overhead from custom colors. The idea is that the engine class would get a signal when the molecule changed, check the colors (both custom and normal) and save them in a QList.

I’m not sure about your second point – Atom::color() only knows a color if it’s custom. Otherwise, I could set one color scheme for the Sticks engine (e.g., to reflect partial charge or somesuch) and another for Spheres.

I was thinking about some method which would incapsulate these actions:

  1. check if custom color is set;
  2. if not, figure out what engine paints this atom (if many - which of them is “main”, e.g. we should disregard force engine here)
  3. get color of atom from that engine

BTW, I think it’s probably a good idea for v1.1 to revamp the standard ElementColor class to use its own text file for colors. I think there are a lot of savvy users who might want to use green for carbon or something like this.

I.e. edit global color map - I think that would be useful (also it would be useful to have custom global map in each CML file)

–
Regards,
Konstantin