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@TieuLongPhan TieuLongPhan released this 22 Jul 12:53
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v1.6.0
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Version 1.6.0

🧠 Lewis-aware chemistry. Executable electron flow. Fully native graph rewriting.

Version 1.6.0 introduces a resource-aware framework for representing, executing, and validating chemical mechanisms. Lewis-labelled graphs now form the core molecular state model, electron-flow annotations can be replayed as executable graph transformations, and all supported workflows run on the native NetworkX backend.

⚛️ Lewis-Labelled Graphs

  • Added Lewis-labelled graph states with explicit electronic resources:

    • lone pairs,
    • radical electrons,
    • σ-bond resources,
    • π-bond resources.

  • Added derived formal-charge and bond-order fields that remain synchronized with the underlying electronic-resource representation.

  • Added resource-aware graph matching and rewriting with explicit checks for:

    • resource availability,
    • transition admissibility,
    • policy validity,
    • Lewis-state consistency.

  • Prevented transformations that consume unavailable electrons, violate local valence policies, or generate internally inconsistent molecular states.

➰ Executable Arrow-Pushing Grammar

  • Added locus-sorted two-electron curved-arrow moves for deterministic execution, comparison, and serialization.

  • Added atomically coupled one-electron fishhook groups for radical transformations that must execute as a single coordinated event.

  • Added executable polar transition classes and reusable radical macros.

  • Added mechanistic validity checks covering:

    • electron-count integrality,
    • locality,
    • resource availability,
    • endpoint validity,
    • transition replay,
    • product-state consistency.

  • Added deterministic verification of supplied electron-flow annotations.

  • Added structured diagnostics for:

    • malformed arrows,
    • invalid source or destination loci,
    • unavailable electronic resources,
    • inconsistent move ordering,
    • incomplete radical groups,
    • disagreement between the proposed mechanism and the resulting graph state.

🕸️ Native Graph Backend

  • Completed the migration from the external MØD-backed infrastructure to the native NetworkX graph stack.

  • Removed the legacy MØD-backed:

    • reactor adapters,
    • rule-composition adapters,
    • chemical-reaction-network adapters,
    • visualization adapters,
    • persistence adapters.

  • Standardized supported graph construction, matching, rewriting, and mechanism-execution workflows on the native backend.

  • Retained GML as a supported interchange and serialization format through the native graph readers and writers.

🧹 Removed

  • Removed deprecated MØD integration paths.
  • Removed backend-specific rule-composition and reactor interfaces.
  • Removed persistence and visualization components that depended on the external MØD runtime.

💾 Serialization

  • Preserved native GML import and export.
  • Standardized graph serialization around the NetworkX-compatible molecular-state representation.
  • Improved portability of Lewis-labelled graphs, executable rules, and mechanism-verification outputs.

⚠️ Breaking Changes

This release contains breaking backend changes for projects that depend directly on the removed MØD adapters.

Custom integrations should migrate to the native NetworkX interfaces for:

  • molecular graph construction,
  • rule matching,
  • graph rewriting,
  • mechanism execution,
  • graph serialization.

✨ Highlights

  • Explicit Lewis-electron accounting
  • Executable polar and radical mechanisms
  • Deterministic arrow replay
  • Structured mechanism diagnostics
  • Native NetworkX execution
  • No external MØD runtime dependency
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