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Published August 26, 2024 | Version 2.0.0
Software Open

qcscine/heron: Release 2.0.0

Description

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

Files

qcscine/heron-2.0.0.zip

Files (8.7 MB)

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md5:edb490dfe8f8aadc92e0a71f58d78e07
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Additional details

Related works

Is supplement to
Software: https://github.com/qcscine/heron/tree/2.0.0 (URL)