Aizynthfinder

Features

- Focussed bonds feature has been created to allow users to choose bonds to freeze and break.
- Functionality has been added to run the broken bonds scorer with MCTS.
- A disconnection-aware Chemformer expansion strategy has been introduced in the plugins.
- Weights for single expansion policies can now be provided as input through the config file.
- The priors returned from the multi-expansion strategy have been rescaled.
- Functionality to mask reaction templates is now supported in the `TemplateBasedExpansionStrategy`.
- The `TemplateBasedDirectExpansionStrategy` has been implemented to directly apply the template in the search process.
- Added support for the C++ version of RDChiral.
- The multi-objective MCTS core algorithm is now implemented within the MCTS search functionality.
- A separate GUI component has been introduced for doing MO tree analysis. Additional functionalities have been added to GUI widgets to set two rewards/objectives to MCTS search. Pareto front is automatically plotted if MO-MCTS is run. Route re-ordering is automatically disabled for MO-MCTS.
- Preprocessing of the tree search can now be done using `aizynthcli`.
- The `StockAvailablityScorer` has been updated such that it takes and additional `other_source_score` parameter.
- A `cutoff_number` parameter can be provided to the multi-expansion strategy to obtain only the top predictions.
- A `BrokenBondsScorer` has been created for scoring nodes and reaction trees based on the breaking of atom bonds.
- A `RouteSimilarityScorer` has been created for scoring based on an LSTM model for computing Tree Edit Distance to a set of reference routes.
- A `DeltaSyntheticComplexityScorer` has been created for scoring nodes based on the delta-synthetic-complexity of the node and its parent 'horizon' steps up in the tree.

Bug-fixes

- Fixed an issue of sending multiple fingerprints to the GPCR Tensorflow serving model.
- `aizynthcli` has been fixed after updating with multi-objective analysis such that the tool accurately informs the user if a target is solved or not.

Features

- `Configuration` now supports a `rescale_prior` property which rescales the priors in `TemplateBasedExpansionStrategy`.
- Functionality of `ScorerCollection` has been extended.
- Pricing is now supported in `InMemoryInchiKeyQuery`.
- Reward scorer has been added to Configuration scorers as `search_reward` item.
- `MaxTransformScorerer` and `FractionInStockScorer` have been created to separate scores in `StateScorer`.
- Reaction routes are scored with all reward scorers after the search is complete.
- `StockAvailabilityScorer` and `ReactionClassMembershipScorer` have been added to the scorers.
- Atom mapping existing in target molecule can be inherited.
- A caching feature has been add to the expansion strategies.
- Degenerate states can now be grouped in the MCTS algorithm.
- `ChemformerBasedExpansionStrategy` and `ModelZooExpansionStrategy` can be found under plugins and used as additional expansion strategies.
- Support for the stereocenter model has been added with to support chiral fingerprints for molecules and reactions.
- The `Configuration` format has been entirely revamped to a more easy-to-use format.
- A `MolbloomFilterQuery` has been created as a stock query class.

Trivial changes

- Python version requirements have been updated to versions 3.9 - 3.11.
- `MoleculeCost` has been moved from aizynthfinder.context.cost.collection to the Retro* package.

Deprecations

- Graphviz has been removed from aizynthfinder.utils.image.
- `Reaction` class has been removed from aizynthfinder.chem.reaction.
- aizynthfinder.context.cost package has been removed.

Bug-fixes

- Fixed an issue with `max_transforms` to ensure only the given number of maximum depth is considered.
- Pinned Jupyter notebook version to ^6.5.3 to avoid errors when displaying widgets.
- Rollout child has been removed from the MCTS search algorithm.

Features

- Environment variables can be loaded from YAML file.
- Restart feature in AiZynth CLI.
- Use ONNX models for expansion and filtering.
- Default filter is now loaded automatically in AiZynth CLI.

Trivial changes

- Using isort to sort the imports of packages.
- Tensorflow is now an optional dependency.
- more-itertools dependencies removed.

Breaking changes

- training modules has now been removed.

Bug-fixes

- Fixing an issue when concatenating JSON data files.

Features

- aizynthfinder can now be installed as a pure-python package
- ReactionTree now store at what iteration the route was created
- ReactionTree now supports a metadata property
- MCTS nodes populate a property that stores at what iteration the route was created
- aizynthcli now outputs stock information and route metadata and scores
- aizynthcli now has better error handling of invalid SMILES input
- Graphviz dependency for route drawing is removed, pure python implementation is used instead
- Dependencies reworked so that a minimal package can be installed
- Extra dependencies are related to route distances, clustering, training, MongoDB and external models
- Downloaded files are now the latest USPTO and Ringbreaker models

Trivial changes

- RDKit and route-distances package now installed from pypi
- Documentation updated and extended

Features

- Atom-mapping is tracked from product to reactant
- Support loading of template library from (gzipped) CSV file
- Support of saving aizynthcli output to (gzipped) JSON file
- AiZynthExpander now tracks non-applicable templates

Bug-fixes
- Fixed failing test case

Trival changes
- Silent progress bar when utilizing local Keras model

Features

- Gracefully fail predictions with aizynthcli if target is unsanitizable (Github issue 66)

Trivial changes
- Update version of Sphinx, scikit-learn and Black
- Remove usage of depracted Pandas function append (Github issue 63)
- Correct documentation of aizynthcli (Github issue 67)