Prepare release v.0.0.6

Release v.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.

v0.0.5: Prepare release v.0.0.5

Changelog for syntemp

New Release Highlights

Improvements

• 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.

Deprecations

• Consolidation of Similar Subpackages
  • As part of our ongoing efforts to streamline our software and improve maintainability, we have begun consolidating similar subpackages across projects into the synutility package. This shift means that functionalities previously found in SynChemistry, SynUtils, and SynVis are now deprecated and will be phased out. These subpackages are scheduled for removal in version 0.0.10. Users are encouraged to transition to synutility to continue receiving updates and support.

Codebase Cleanup

• Function Consolidation
  • We have reduced redundancy in our codebase by eliminating overlapping functions. Key functionalities have been refined and integrated into synutility, enhancing coherence and reducing bloat in the syntemp package. This cleanup supports a leaner, more efficient suite of tools for our users.

v0.0.4

v0.0.4

v0.0.3

v0.0.3

v0.0.2

v0.0.2

v0.0.1

v0.0.1