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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

[0.0.6] - 2024-12-09

Added

  • New feature: Added ITSArbitrary to generate all possible ITS Graphs from AAM (Atom-Atom Mapping).

    • Note: This feature is still under development and may experience slow performance and potential memory issues when the number of combinations exceeds 8! (i.e., 40,320).

  • Dependencies split: Separate lightweight installation options:

    • pip install syntemp: Installs the basic version (without Atom-Atom Mapping tools).
    • pip install syntemp[all]: Installs the full set of dependencies, including tools for Atom-Atom Mapping (rxnmapper, localmapper, and graphormermapper).

Changed

  • Enhanced rule clustering: Improved rule clustering functionality to handle batch processing and mitigate the combinatorial explosion problem.

    • Note: This change does not yet integrate with Hierarchical Clustering.

  • Improved Isomorphic Filter: Integrated a new graph signature filter, reducing the ITS clustering time from 78 minutes to just 2 minutes.

  • Hydrogen Inference Refactor:

    • Refactored the hydrogen inference function for better readability and efficiency.
    • Integrated graph signature to reduce isomorphism checks, improving processing time by 50%.
    • Removed the timeout option (planned for removal in version 0.0.10 due to redundancy).
    • Issue: The process remains slow, and there may be potential memory explosion if the number of combinations exceeds 8! (i.e., 40,320).

  • ITSExtraction refactor: Removed redundant deepcopy calls, resulting in a 50% reduction in processing time.

  • Code Cleanup:

    • Removed redundant Python functions, which have now been moved to the synutility repository.
    • Removed unused variables in the syntemp command-line interface (CLI).

Deprecated

  • Deprecation Warning: The following features will be removed in version 0.0.10:
    • SynUtils and SynChemistry modules have been moved to the synutility repository.
    • ITSConstruction will also be removed as it has been moved to synutility.

Fixed

  • Memory Usage & Performance: Improved memory management and processing performance in several functions, especially in hydrogen inference and ITS extraction.

Security

  • No security updates in this release.