Universal Database for both RMG-Py and RMG-Java

[rwest]

We just discussed (again) forming a universal database structure for both RMG-Py and RMG-Java. Here are my notes from the videoconference. Add discussion and development notes below...

Universal Database

• human editable and readable
  • look more like a spreadsheet - eg. one line per reaction.
  • minimize boilerplate
  • excel sheets? csv?
  • benefit of plan text
    • editable using emacs over ssh
    • works with git
• should store
  • dictionary in new 4-column adjacency list with explicit hydrogens
  • comments
  • uncertainties
  • confidences
  • libraries
  • rules
  • groups
  • depositories (actual reactions, with labeled atoms)
• exportable to Java
  • remove N and fourth column
  • or modify Java so it can parse the universal database
• exportable to Python
  • use "import to database" script,
  • or make it read the universal database
  • modify the .load() methods
• Instead of exporting, Make both read the universal database
  • Java could ignore the extra column in the adjacency list, and all N atom types
  • Benefit: people won't be tempted to edit the exported database!
  • Should be designed so new features are backwards compatible,
    • perhaps programs ignore stuff they don't understand
    • eg. temperature-dependent viscosity parameters in solvent database.
    • transition state estimate databases
    • new atom types
  • Possible drawback
    • risk slowing development of new features (barrier: have to implement in both)
    • or keep breaking RMG-Java

[connie]

Java is dead.