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Avogadro 2.0 Roadmap

I’ve placed various 2.0 roadmaps on different sites. It’s probably easiest to paste it here for discussion. :slight_smile:

Roadmap for Avogadro v2 Development

Avogadro2 0.9

Released March 2016

Avogadro 1.91

August 2018

  • Expanded support for import / export
  • Improved draw tool
    • Improved automatic adjustment of hydrogens
    • Automatic bond order - short bonds are double or triple
  • Improved crystal / materials support (GSoC project)
    • Integration with spglib to perceive space groups
    • Symmetrize unit cells
    • Reduce to primitive cells

Avogadro 1.92

Released Oct 2018

Avogadro 1.93

Released Feb 2020

Avogadro 1.94

Released June 2021

  • Insert fragment
  • Drag-and-drop files
  • Cp2k input
  • OpenMM input
  • Download from PDB
  • Rotate selected fragment
  • Many more features and bug-fixes…

Avogadro 1.95 (in progress)

To be released late July 2021

  • Protein ribbon / cartoon rendering
  • Many more features and bug-fixes…

General needs:

  • Selection Tool & Menu
    • Needs selection box
    • Selection needs to be undo/redo-able
    • Many features need to be “selection enhanced”
  • Residue / fragment support
  • Translation Setup (via Weblate)
  • Hydrogen geometry
  • Force field implementation (Lennard-Jones, UFF) - Geoff
    • Adapt obmm Open Babel tool (IO with Cjson)
    • Constraints
    • Updated geometries (i.e., drag an atom - force reoptimize w/ AutoOpt mode)
  • Global settings dialog
    • Download input generators
    • Download python IO layer
    • Search paths for fragments, etc.
    • Download / update translations

Tool needs:

  • Selection
  • Eye candy interaction rendering
  • Rotate around center-of-geometry
  • Auto-rotate tool

Extension needs:

  • View along axes
  • Re-center view
  • Improved force field support
    • Auto-optimize
    • Freeze / constraints
  • Selection
  • Properties Tables
    • Need bond, angle, torsion, non-bonded iterators
  • Spectra
    • Vibrations
    • Orbital table
  • Build features
    • Insert SMILES
    • Insert fragment
    • Insert peptide
    • Insert DNA/RNA (via FASTA format)
    • Invert chirality
  • Crystal structures
    • Crystallography (Patrick)
    • Perceive / Set space group
    • Fill unit cell

Rendering needs:

  • Labels
  • Dipole moment
  • Cartoon
    • Needs residue support
  • Hydrogen bonding
  • Forces
  • Settings Dialogs - couple of examples already there
    • Color plugins
    • Configure element colors
    • Valence check
    • Hybridization
    • Partial charge
  • Merge VdW rendering (Auto, AO off, AO on)
  • Volume density, contours (VTK integration)

Interface Polish

  • Settings / Preferences
    • Custom atomic colors
    • Custom radii
  • Menu reorganization
    • Help menu
      • Links to website, manual, bug reporting, etc.
  • Mac polish

Scripting

  • Python Bindings
    • Core classes
    • Jupyter integration
  • RPC calls
    • Open / Load File
    • Save File
    • Save Graphics
    • Save Movie
  • Python terminal
    • “Shortcut” commands (e.g., select atom 5)
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IMHO here are some of the biggest needs: (revised June 2021)

  • Interactive force field optimization
  • Finish Python plugin support including downloader
  • Residue / fragment / biomolecule support
  • Build features:
    • Insert fragment
    • Insert peptide
    • Insert DNA/RNA
  • Render:
    • Labels
    • Forces
    • VTK integration (volumetric rendering, etc.)

Here’s the Summer 2021 version:

Help, and feedback are most welcome!

Avogadro 2.0

  • Finish auto-optimize force field support
    • Add force field constraints
    • Force field plugins
  • Build features:
    • Insert peptide
    • Insert DNA/RNA
  • Render:
    • Labels
    • Cartoon / Ribbon (in progress now)
    • Molecular surfaces
    • Improved shaders / ambient occlusion, etc.
    • Hydrogen bonding
    • Apply color schemes (e.g. custom color, color-by-index, etc.)
  • Property Tables
    • Including copy / paste and multiple-select
  • Preferences dialog
    • Support for translation / localization