Changelog

Documentation
• Comprehensive SynTemp user guide covering installation, configuration and code examples
• API reference with detailed parameter descriptions and usage scenarios

Dependency
• Downgraded scikit-learn from 1.7.0 to 1.6.1 for improved compatibility with legacy pipelines

Testing
• PyPI test suite now runs automatically every Monday at 03:00 UTC via GitHub Actions

- Python
Published by TieuLongPhan 8 months ago

RDKit dependency bumped to 2025.3.1
Ensures compatibility with the latest chemoinformatics APIs and performance improvements.
SynKit dependency bumped to 0.0.9
Aligns with upstream fixes and new features in the SynKit toolkit.
Transformers dependency foreced to 4.51.1
Solve conflict in RXNMapper with Transformers.

- Python
Published by TieuLongPhan 9 months ago

Release 1.0.0 - 2025-04-09

Introduced a preprocessing step to standardize reaction SMILES prior to input into SynRBL for improved consistency and accuracy.
Optimized memory usage in the save_file function by converting networkX graphs to GML format for templates and replacing .pkl.gz files with .list.json.
Resolved redundant output issues in AutoTemp. Now, metadata will be saved in save_dir/meta, and templates data will be stored in save_dir/templates.
Added additional test cases to enhance the robustness and reliability of the pipeline.
Enhanced citation details in documentation to improve reference clarity and compliance.
Updated and clarified usage instructions in the README to assist new users in navigating the software more effectively.

- Python
Published by TieuLongPhan 11 months ago

Resolved Pytorch version conflict: Kept version 2.2.0 for consistency across the codebase.
Updated the mapper version: Note that the reproducibility of the paper cannot be guaranteed with the latest version. For reproducibility, please refer to version 0.0.6 and below.
Removed MØD from this version for improved functionality.
Replaced synutility with synkit: This update ensures consistency and better integration across the modules.

Deprecation Warning: The following features will be removed in version 1.0.1:
- The SynUtils, SynComp, and SynChemistry modules have been moved to the synutility repository.
- ITSConstruction will be removed, as it has been moved to synutility.

Users are encouraged to transition to the updated modules and take note of upcoming removals to ensure smooth upgrades in future versions.

- Python
Published by TieuLongPhan 11 months ago

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).

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).

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.

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

- Python
Published by TieuLongPhan about 1 year ago

ITSGraph Enhancements
- ITSGraph now robustly handles Unsanitized RDKit Molecules. This update resolves previous issues with hydrogen mapping, allowing for the direct use of hydrogen annotations within SMILES/SMARTS when transforming to ITSGraph. This enhancement improves the accuracy and utility of molecule transformations in computational chemistry workflows.