Prepare release v.0.0.11

Changelog v0.0.11

Highlights

New Features & Enhancements

MolToGraph and GraphToMol

• Refactored source code for better modularity and maintainability.
• Introduced a lightweight version of MolToGraph and GraphToMol for efficiency.
• Added functionality to convert reaction SMILES into a graph representation.

Visualization

• Enabled 2D coordinate generation from RDKit molecules for improved user-friendly MolGraph and ITSGraph visualizations.
• Introduced a visualizer to process reaction SMILES with atom-atom mapping (AAM):
  • Outputs separate visualizations for reactants, ITS graphs, and products.
• Added the capability to save visualization outputs as PDFs for convenient sharing and documentation.

MØD Rule Application

• Introduced the Transformation subpackage to support MØD-based graph transformations.
• Enhanced compatibility with GitHub workflows by adding test cases for transformations.

PartialAAM Expansion (Preliminary Support)

• Added the SynAAM subpackage for expanding PartialAAM reaction SMILES (RSMI) into full AAM RSMI.
• Included a normalizer to reduce redundant hydrogen mappings and retain mappings only for hydrogens in the reaction center.
• Implemented ITS decomposer to split ITS graphs back into reactant and product graphs.

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Known Limitations

MØD and RDKit Compatibility Issues

• Problem: Conflicts between MØD (conda version) and RDKit lead to Boost.Python.ArgumentError when using RDKit.
• Workaround:
  • Add a workaround (using torch 2.0.1) before initializing MØD to mitigate compatibility issues.
  • For pytest, use a fixed test order to avoid conflicts during testing workflows.