Scine-chemoton

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New features
- Add SteeringWheel infrastructure for actively steering explorations.
- Add ThermoAggregateHousekeeping gear which allows sorting of structures with a frequency check.
- AtomPairFunctionalGroupFilter for specifying pairs of functional groups that are allowed to react.
- CentralSiteFilter to focus explorations on certain elements, suited well for homogeneous catalysis.
- New ElementaryStepGear to focus explorations on certain structures.
- New ReactiveSiteFilter based on substructures provided in .xyz or .mol files.
- The KineticModelingGear is now able to setup jobs for the puffin interface of the ReactionMechanismSimulator.

Changes
- Queries and utility functions related only to the database are moved to the `scine_database` package. The functionality here is deprecated and the unittests are removed.
- Update address in license

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New features
- Add improved handling of kill (SIGINT) and terminate (SIGTERM) signals to engines,
including new breakpoints in existing gears.
- Add a gear that allows the re-running of calculations that failed (e.g., failure to locate a transition state).
- Allow to either exclude or include reactive sites based on rules.
- New PathfinderKinetics gear to activate compounds based on the compound costs obtained with Pathfinder.
- New TrialGenerator for ElementaryStepGears based on reaction templates.

Improvements
- Many gears and also filters now use local caches for enhanced performance.
- All gears have an Options object holding at least a Model.
- All ElementaryStepGears and TrialGenerators expose a public method that allows access to the calculations
that would be set-up in the next run.
- Add option to ElementaryStepGear and TrialGenerator that allows to check all existing calculations for
an exact settings match, so that elementary step trials can be enhanced with more inclusive options.
- Allow to get all valid compounds for the BruteForceConformersGear
- Add caches to ElementaryStepGear and BasicBarrierHeightKinetics
- More gears can be limited with an AggregateFilter.
- Add type checking of reaction rules at runtime.
- More options to chose for building a graph with Pathfinder and more robust determination of compound costs.
- Allow restriction of compounds based on maximum reaction energy of reactions leading to them.

Changes
- Separate the reaction rule definitions from the reactive site filters and structure them.
- Redefine the FunctionalGroupRule.
- Rename CompoundFilter to AggregateFilter.
- Consider the explore status of each aggregate/reaction for the Thermo gear and add setting to allow to ignore
the status.
- Increase default number of optimization cycles for reactive complex optimization to find a potential
barrierless elementary step.

Bug Fixes:
- Add the calculation status to the safety query of the AggregateHousekeeping gear if the found structure is
the result of a minimization to avoid false positives due to race conditions with the results-adding puffin.
- Fix lastmodified query to correctly handle time zones.
- Fix bug in attack direction cache of the reactive complex generator.
- Fix bug in BasicBarrierHeightKinetics leading to too many activations in certain network arrangements.

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New features
- Introduce Pathfinder, a graph-based approach to analyze how compounds are connected via reactions while considering
kinetic and stoichiometric constraints.

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New features
- Introduce Flasks to the reaction networks (aggregates of stable non-bonded complexes)
- Elementary-step gear that uses the current minimum-energy conformer for reaction trial generation.
- Added a gear that sets up kinetic modeling jobs.
- Allow the refinement of a subset of elementary steps per reaction. The subset is given through an energy cut-off
above the lowest lying transition state.
- Introduce possibility to efficiently explore barrierless dissociations.

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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

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Closed source C++ prototype implementation.