Avogadro 2.0 Roadmap

Development
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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

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

Avogadro 1.95

Released August 2021

  • Protein ribbon / cartoon rendering
  • Atom / residue labels
  • New “layer” system
  • Apply color schemes to atoms and residues
  • Install and update translations
  • Many more features and bug-fixes…

Avogadro 1.96

Released June 2022

  • Property tables for atoms, bonds, angles, torsions, residues
  • Insert DNA/RNA
  • Close contact rendering
  • Create new layer from selection
  • Focus / unfocus on selected atoms
  • Label editor and custom labels for atoms
  • Many more features and bug fixes…

Avogadro 1.97

Released July 21, 2022

  • Translation / localization
  • Molecular, solvent accessible, and solvent-excluded surfaces
  • Mapped electrostatic potential (ESP) on molecular surfaces
  • Includes optional surface smoothing
  • Hydrogen bond, halogen bond, chalcogen bond rendering
  • Color atoms by partial charge
    • Includes models from Open Babel (Gasteiger, EEM, MMFF94)
    • Includes Python scripts for GFN2 and AM1-BCC / Antechamber
  • Help menu with links to forum, website, bug reporting
  • Now supports VTK 9
  • Many more features and bug fixes…

Avogadro 1.98

  • Improved rendering including ambient occlusion
  • New template tool for assembly of inorganic complexes and ligands / functional groups
  • Better perception of bond orders
  • New forcefield framework supporting external Python scripts (e.g., XTB, ASE, ANI-2x, etc.)
  • Align tool
  • Manual translate / rotate dialog
  • Integration with 3Dconnexion input devices on Mac and Windows
  • Fetch molecule names from PubChem
  • Commands to create centroid and center-of-mass points
  • Improved “fill unit cell”
  • Preview images of insert molecule fragments and import crystals
  • Build improvements, including initial support for Qt6
  • Add a generic compchem output reader
  • Initial scripting support

General needs:

  • Selection Tool & Menu
    • Needs a 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)
    Support for Python script interfaces
    • Frozen atoms
    • Adapt obmm Open Babel tool (IO with Cjson)
    • Constraints
    • Auto-optimize tool
  • Open Babel Conformer Search
  • Plugin downloader
    • 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
  • Align tool
  • 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
    • Plotting IR, UV/Vis, NMR, etc.
    • Orbital table
  • Build features
    • Insert SMILES
    • Insert fragment
    • Insert peptide
    • Insert DNA/RNA (via FASTA format)
  • Crystal structures
    • Crystallography
    • Perceive / Set space group
    • Fill unit cell
    • View Miller Plane
    • Generate slab

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
  • Enable ambient occlusion, depth-of-field on all rendering types
  • 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
    • Basic commands
    • Save Movie
  • Python terminal
    • “Shortcut” commands (e.g., select atom 5)
1 Like
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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.)
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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