July 2022 Development Update

It’s July! For those of us in the Northern Hemisphere, it’s been :fire: … (I know, some of you are used to > 38-40°C weather. The rest of us … are ready for temps to cool down.)

If you’re curious to follow, the GitHub page shows the details I use to pull in these updates.

New 1.97 Release :tada: - the latest release was on 21 July and is highly recommended.

As a reminder, suggestions, bug reports, and the like are always welcome! and we greatly appreciate help with language translation, coding, and Python plugin development.

If you’d like to try developments beyond the 1.97.0 release, there are nightly builds for:

Recent Work

Lots of bug and performance fixes!

  • If you have some time - even only a little, you can contribute to our translations. Kudos to Ovari for a 100% complete Hungarian translation. We also have Serbian, Esperanto, Portuguese, Turkish, German, Georgian, French, and Japanese translations with at least 45% coverage. There’s been considerable improvement over the last few weeks, so thanks! :tada:

Feedback is always welcome - we’ve been squashing lots of i18n bugs:

Translation status
  • Aritz merged dramatically improved surface code, including mapped charges / electrostatics, solvent-excluded, and solvent-accessible surface areas.

    • If you’re interested in configurable solvent radii, please make some suggestions.
  • I merged a new electrostatics framework, allowing atomic partial charges and electrostatics maps. Defaults include models from Open Babel (Gasteiger, MMFF94, EEM, EQEq)

    • There’s also support for Python scripts to assign charges or electrostatic potentials. If you have xtb or antechamber in your environment, you can now assign GFN2 and AM1-BCC charges, respectively. If you would like to use other tools, please let me know - these scripts are easy.
  • You can now edit bond lengths, angles, and torsions using the property tables (e.g., to set an bond to exactly 1.45 Å, or a torsion to 134.5°).

  • I added new selection commands to select peptide backbone atoms, side-chains, and water fragments.

  • There are also new commands to expand a selection or shrink a selection in 2Å increments.

  • New and improved rendering types are available for:

    • hydrogen-bonds
    • halogen bonds
    • chalcogen bonds
    • close contacts
    • salt bridges
    • “bad” contacts (eg., +/+ or -/- nearby residues)
  • We fixed a bug in which the bond-centric manipulate tool wouldn’t adjust bonds between rings. (The bug ignored any atom in a ring … but of course inter-ring bonds are fine.)

  • You can now navigate in the periodic table windows using arrow keys, typing out an element symbol (e.g. “Br” => jump to bromine) or an atomic number.

  • Aritz fixed a bug with weird hydrogen geometries (e.g., C=C added two hydrogens, but as if the carbon atoms were sp3).

  • We upgraded the Windows and Mac builds to use Qt 5.15, which include a number of bug fixes and minor improvements, including support for Markdown rendering.

  • Aritz also has added support for PDB “alternate locations” (i.e., multiple geometries in one PDB entry).

Work In Progress

Feedback Welcome

Many people have provided feedback, particularly to the new 1.97 release. Please continue to post - this is a community, open source project and suggestions, complaints, critiques are very welcome. We try to squash :bug: :beetle: and tweak features …

Thoughts? Questions? Ideas?

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I’ve also been working on improvements to the https://two.avogadro.cc website.

  • Automation: the repository will now automatically update at least once per day, including checking for a new Avogadro release (to update the download links) and generating the HTML from the source files.

  • Improved notes on script plugins. Want to write a short Python script to add an input generator, or add a menu command? It’s easy.

I’m open to ideas on the website, particularly for translation!