qcscine/chemoton: Release 2.0.0

Python rewrite, and open source release with the following initial features:

• Scriptable framework including a base set of features for the automated exploration of chemical reaction networks
• Initial chemical reaction networks consisting of
  • Structures aggregated into Compounds
  • Elementary Steps aggregated into Reactions
  • Properties tagged to Structures
  • Calculations that generated the network
• Definitions of Engines with perpetually running Gears to continuously perform tasks with chemical reaction networks (see list below)
• Storage and expansion of chemical reaction networks in a SCINE Database
• Automated job set up and execution via SCINE Puffin
• Definitions of basic filters to reduce number of Elementary Step trials (see list below)

Initial Engines/Gears:

• Basic bookkeeping jobs:
  • Sorting Structures into Compounds (BasicCompoundHousekeeping)
  • Sorting Elementary Steps into Reactions (BasicReactionHousekeeping)
  • Basic Scheduling and prioritization of Calculations (Scheduler)
• Data completion jobs:
  • Conformer generation per compound (BruteForceConformers)
  • Hessian generation per transition state and minimum energy Structure (BasicThermoDataCompletion)
• Elementary Step exploration based on existing Compounds:
  • For one Structure per Compound (MinimalElementarySteps):
    • Based on atoms/fragments (AFIR, NT1)
    • Based on bonds (NT2)
  • For all combinations of Structures per Compounds (BruteForceElementarySteps):
    • Based on atoms/fragments (AFIR, NT1)
    • Based on bonds (NT2)
• Steering of network growth via simple kinetic analyses:
  • Based on connectivity to user input (MinimalConnectivityKinetics)
  • Based on barrier heights of Elementary Steps (BasicBarrierHeightKinetics)

Initial set of filters:

• Compound filtering possible:
  • Base class, allows all compounds (CompoundFilter)
  • By element counts (ElementCountFilter, ElementSumCountFilter)
  • By atom counts or molecular weights (MolecularWeightFilter, AtomNumberFilter)
  • By database IDs (IDFilter, OneCompoundIDFilter, SelectedCompoundIDFilter)
  • By context (SelfReactionFilter)
  • By Hessian evaluation (TrueMinimumFilter)
  • By composition (CatalystFilter)
• Reactive site filtering possible:
  • Base class, allows all reactive sites (ReactiveSiteFilter)
  • By fixed, simple rankings (SimpleRankingFilter, MasmChemicalRankingFilter)
  • By custom user rules (AtomRuleBasedFilter, FunctionalGroupRule)
  • By atom types (ElementWiseReactionCoordinateFilter)
• All filters of the same type can be chained with logical operations to tailor the behaviour