Skip to content

Extend PlotConformer scan coordinate support#2840

Open
jcerezochem wants to merge 1 commit into
OpenChemistry:masterfrom
jcerezochem:scan_coord_pr
Open

Extend PlotConformer scan coordinate support#2840
jcerezochem wants to merge 1 commit into
OpenChemistry:masterfrom
jcerezochem:scan_coord_pr

Conversation

@jcerezochem

@jcerezochem jcerezochem commented May 6, 2026

Copy link
Copy Markdown
Contributor
  • Add support for plotting conformer data against scan coordinates (selected as constraints) instead of only frame index, so that relaxed scan plots can be visualized

  • Add active conformer marker, which is synchronized with the molecule's actual current coordinates so the plot updates when the conformer changes from other tools.

  • Use Avogadro angle/dihedral utilities for coordinate evaluation, and refresh available X-axis options when constraints change.

  • Add optional dihedral unwrapping with a dialog toggle

DISCLAIMER: AI tools were used to assist the development. The final code was fully human-revised

Signed-off-by: Javier Cerezo javier.cerezo@um.es

Developer Certificate of Origin
Version 1.1

Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
1 Letterman Drive
Suite D4700
San Francisco, CA, 94129

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.

Developer's Certificate of Origin 1.1

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I
have the right to submit it under the open source license
indicated in the file; or

(b) The contribution is based upon previous work that, to the best
of my knowledge, is covered under an appropriate open source
license and I have the right under that license to submit that
work with modifications, whether created in whole or in part
by me, under the same open source license (unless I am
permitted to submit under a different license), as indicated
in the file; or

(c) The contribution was provided directly to me by some other
person who certified (a), (b) or (c) and I have not modified
it.

(d) I understand and agree that this project and the contribution
are public and that a record of the contribution (including all
personal information I submit with it, including my sign-off) is
maintained indefinitely and may be redistributed consistent with
this project or the open source license(s) involved.

- Add support for plotting conformer data against scan coordinates
(selected as constraints) instead of only frame index, so that relaxed
scan plots can be visualized

- Add active conformer marker, which is synchronized with the molecule's
actual current coordinates so the plot updates when the conformer changes
from other tools.

- Use Avogadro angle/dihedral utilities for coordinate evaluation, and
refresh available X-axis options when constraints change.

- Add optional dihedral unwrapping with a dialog toggle

DISCLAIMER: AI tools were used to assist the development. The final
code was fully human-revised

Signed-off-by: Javier Cerezo <javier.cerezo@um.es>
@avo-bot

avo-bot commented May 22, 2026

Copy link
Copy Markdown

This pull request has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/may-2026-development-updates/7449/1

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants