Prepare release v.0.0.4

Changelog v0.0.4

Highlights

New Features & Enhancements

Refactor Source Code Structure

• Merged the ITS and Graph subpackages for improved modularity.
• Separated its_decompose and get_rc into a dedicated Python file: its_decompose.py.
• Created a new Utils subpackage for future utility functions and support tools.

Performance Improvements

• Optimized the BatchCluster process for faster clustering of reaction centers.

Bug Fixes

• Fixed issues with Subgraph searching: networkx now handles both monomorphism and induced subgraph, whereas GML was limited to monomorphism only.

New Features

• Implemented CRN (Chemical Reaction Networks) in the Reactor module.
• Implemented PathFinder to find pathways from a starting compound to the target compound in CRN.
• Introduced RetroReactor in the Rule module, enabling the use of A* algorithm to search from target to starting compound without requiring a full system like CRN.

Known Limitations

Rule Composition

• Bug in the valence constraint of rule composition.
• Partial matching in rule composition may result in invalid compounds.

Retro

• Directed CRN can only find one solution, though it is 500 times faster than expanding CRN and using PathFinder.
• Retro framework using rule composition may result in invalid compounds.

Reactor

• ReactorEngine currently only supports balanced reactions.
• Performance issue: ReactorEngine is slow in certain cases.
• Memory leak in CoreEngine when scaled up.