Hydrogen not removed

General Discussion Support
1

I believe this to be a bug with Avogadro

Avogadro version:1.97.0
Operating system and version:
Windows 10 Pro
Version 22H2
OS build 19045.2728

Expected Behavior

add atom adds hydrogens, erase same atom removes hydrogens

Actual Behavior

add atom adds hydrogens, erase atom leaves hydrogens, have to delete each hydrogen separately

Steps to Reproduce

open new file, add 1 carbon, hydrogens appear, erase the carbon, hydrogens remain

Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)

2

If one assumes Build → Hydrogens → Add / Adjust Hydrogens and Build → Hydrogens → Remove All Hydrogens / Remove Extrta Hydrogens does not work for you, did you try Extensions → OpenBabel → Add Hydrogens / Add Hydrogens for pH or Extensions → OpenBabel → Remove Hydrogens? Do you you have the optional “adjust Hydrogens” enabled?

hydrogen_option

Because the second approach depends on OpenBabel, ascertain the computer you use includes a functional installation of OpenBabel. Exectuables for either 32bit, or 64bit Windows are available on OpenBabel’s GitHub repository, section releases.

3

No, that’s definitely a bug… thanks for the report.

4

Okay, I have a patch in the works - When removing an atom, remove bonded hydrogens if needed by ghutchis · Pull Request #1230 · OpenChemistry/avogadrolibs · GitHub

You should be able to grab a Windows build from that link to see if it works for you.