Release 2.0.0

Changes:

• Add SCINE Chemoton tab to run explorations from within Heron
• Add tab to run the Chemoton Steering Wheel
• Add SCINE ReaDuct tab to carry out any ReaDuct task (e.g., structure optimizations)
• Modify Interactive to run with any SCINE backend calculator
• Add QM/MM capabilities, SFAM parametrization, and automated QM region selection to Interactive including database support
• Add option to construct Chemoton aggregate and reactive site filters
• Add option to store and generate reaction templates for SCINE Art
• Add possibility to slice trajectories
• Select and move multiple atoms in Interactive
• Add activate/deactive buttons to compounds in network view for rudimentary exploration control
• Allow direct connection to a database at start-up from the command line
• Introduce binary and human readable save formats for some tabs
• Added package variants for easier installation of optional requirements
• Generate graph of the entire CRN or import graph of the CRN for efficient processing purposes
• Introduced cache for every local CRN around a centroid; once built, it can be easily accessed again
• Enable fast filtering on barriers, flux, or date created (can be easily expanded to other filters)
• Reactions trajectory consistently extends from the center to the outer node
• Highlighting connected nodes when clicking on them
• Add new color style, legacy, based on Chemoton 1.0 colors
• Carry out steering wheel preview in background with progress bar with time estimate. The preview query can be aborted should it take too long
• Format reaction equation in path energy level widget
• Add timeout option for shortest path search, allowing users to easily interrupt lengthy searches if needed
• Add support for StructureFilter
• Add support for changed GearOptions
• Add AggregateFilter to database viewer tab
• Extend graph building capabilities
• Improve visualization of (shortest) path searches
• Improve error messaging
• Moved database queries to the SCINE Database module
• Rename 'Molecular Viewer' to 'Interactive'
• Node positions are now efficiently determined by algorithms implemented in Networkx
• Status bar in graph traversal is now identical to the main status bar
• Implement new caching logic for shortest paths, storing paths with and without two reactions in a path
• Add support for ElementaryStepFilter and ReactionFilter required by Chemoton 4.0.0.
• Handle the case of loading a completely empty database
• Prevent overlapping nodes in reactions
• Implement plateaus in spline representation to enhance visualization
• Being capable of representing local CRNs with more than 100 nodes
• Removed complicated code for positioning compound and reaction nodes, improving code readability and maintainability
• Functionalized individual parts to render and position nodes
• Functionalized reaction profile and cleaned up redundant code
• Employed energy diagram class for plateaus in reaction profile
• Removed substep_callback in Worker
• Update address in license

Release 1.0.0

Initial Features:

• Main Molecular Viewer
  • Real-time calculations of energies and forces (using SCINE Sparrow)
  • Haptic device support
  • Real-time energy plot
  • Basic molecular building/editing
  • Isosurface plots of orbitals and densities
• Reaction Network Viewer
  • Excerpt view of Aggregates and Reactions
  • Basic filtering options based on reaction energies
  • Navigation around a single centered Aggregate
  • (Shortest) path searches based on Aggregate IDs
  • Expansion tab for Aggregates (showing contained Structures)
  • Expansion tab for Reactions (showing contained Elementary Steps)
  • SVG export of all graph views
• SCINE Database Statistics
  • Database content statistics
  • Calculation status statistics
  • Runtime histogram
• SCINE Database Browser
  • Listing, searching and displaying of individual database entries
    • Reaction and Elementary Steps
    • Compounds and single-molecule Structures
    • Flasks and multi-molecule complexes (also Structures)