Avogadro 1.94: when deleting multiple selected atoms, other atoms become selected

MSoegtrop · July 10, 2021, 1:20pm

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 1.94 (nVidia transparent window patch)
Operating system and version: Windows 10 64 21H1

Expected Behavior

Atoms do not get randomly selected

Actual Behavior

When deleting a selection, other atoms become selected

Steps to Reproduce

Create a larger structure
Select half of the structure
press “DEL” to delete the selected structure
=> some atoms which have not been selected before become selected

ghutchis · July 10, 2021, 2:50pm

Yes, there’s already a GitHub issue for this:

github.com/OpenChemistry/avogadrolibs

Unselected atoms become selected (and vice versa) when other atoms are deleted

opened 02:44PM - 06 Jul 21 UTC

drew-parsons

**Avogadro version: 1.94.0-371-g7479d2e ** - Avogadrolibs: 1.9.4 - Qt: 5.15.…2 **Desktop version: ** - OS: Debian GNU/Linux] - Version linux 5.10.46 (debian unstable) - Compiler g++ 10.2.1 **Describe the bug** When some atoms in a molecule are selected, and other atoms are then deleted, some of the selected atoms become deselected. Conversely if some selected atoms are deleted, then some previously deselected atoms suddenly become selected. My guess is that the list of selected atoms is a list of indices to the atoms in the molecule, and is not refreshed when the lists of atoms in the molecule changes (e,g, by deletion). **To Reproduce** Steps to reproduce the behavior: 1. Create a simple ethane molecule 2. Click on Selection Tool and select the right-most methyl ![Screenshot from 2021-07-06 16-41-20](https://user-images.githubusercontent.com/26508288/124619551-09b1fa00-de79-11eb-9d79-31f64a5f2cce.png) 3. Select Build [pencil] tool 4. Delete (right-click) one of the unselected hydrogens on the left. That hydrogen disappears, but one of the hydrogens on the right becomes deselected. ![Screenshot from 2021-07-06 16-38-59](https://user-images.githubusercontent.com/26508288/124619237-c3f53180-de78-11eb-832c-2aa22ee57b0c.png) Conversely, 2'. Click on Selection Tool and select the left-most methyl ![Screenshot from 2021-07-06 16-31-23](https://user-images.githubusercontent.com/26508288/124618220-e63a7f80-de77-11eb-89f8-0bc7e29bc573.png) 4'. Delete (right-click) one of the selected hydrogens on the left. That hydrogen disappears, but one of the hydrogens on the right becomes selected. ![Screenshot from 2021-07-06 16-31-44](https://user-images.githubusercontent.com/26508288/124618471-1b46d200-de78-11eb-96a1-7797365dd5e6.png) **Expected behavior** Previously deselected atoms should not suddenly become selected when atoms are removed (or added). Previously selected atoms should not suddenly become deselected when atoms are removed (or added) (or alternatively the entire selection should get cleared).

ghutchis · July 12, 2021, 8:53pm

It’s fairly easy to fix - I’m waiting on a larger patch to merge (Wednesday?) and then will take care of this.

Put simply, the code that removes atoms wasn’t removing them from the list of selected atoms. Oops.

MSoegtrop · July 13, 2021, 6:54pm

Thanks, I am looking forward to it!

ghutchis · July 15, 2021, 1:01am

Okay, this should be fixed by this patch:
https://github.com/OpenChemistry/avogadrolibs/suites/3242013564/artifacts/75269997

From Fix #650 - deleting selected atoms by ghutchis · Pull Request #672 · OpenChemistry/avogadrolibs · GitHub

MSoegtrop · July 16, 2021, 5:23pm

Thanks! I can confirm that this does work now.

I will report further issues on GitHub.

system · July 19, 2021, 5:24pm

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