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…formal charge parameter
…r atom charge inference
…hate/phosphine oxide groups
… anions involving single-bonded oxygen
…ition for clarity
…dition for clarity
…removing formal charge checks
…reation for clarity
…ddition for clarity
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Pull Request Overview
This PR implements automatic charge and lone pair perception in the chemical perception engine, simplifying the public API by removing the formal_charge parameter from MolecularGraph::add_atom. The new perception logic uses VSEPR theory and functional group templates to accurately model common chemical structures including zwitterionic amino acids and oxyacid anions.
- Removed
formal_chargeparameter fromMolecularGraph::add_atomAPI - Implemented advanced chemical perception algorithm for automatic charge/lone pair inference
- Updated all test cases and documentation to use the simplified API
Reviewed Changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| tests/harness.rs | Removed charge field from AtomBlueprint and updated test atom creation calls |
| tests/cases/nucleic_acids.rs | Updated all nucleic acid test cases to use new API without charge parameters |
| tests/cases/dreiding_paper.rs | Updated Dreiding paper test cases, including expected atom type changes for dimethyl sulfoxide |
| tests/cases/amino_acids.rs | Updated all amino acid zwitterion test cases to use new API |
| src/processor/typer.rs | Updated all test method calls to remove charge parameters |
| src/processor/templates.rs | Updated template predicates to use lone pairs instead of formal charge for pattern matching |
| src/processor/pipeline.rs | Updated test cases to use new atom creation API |
| src/processor/perception.rs | Added comprehensive charge and lone pair perception logic with helper functions |
| src/processor/graph.rs | Removed formal_charge field initialization in ProcessingGraph constructor |
| src/lib.rs | Updated documentation examples to use new API |
| src/core/graph.rs | Removed formal_charge field from AtomNode and updated add_atom method signature |
| src/builder/mod.rs | Updated test code to remove formal_charge field reference |
| docs/01_pipeline.md | Updated documentation to reflect removal of formal_charge field |
| README.md | Updated example code to use new simplified API |
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Summary:
Significantly refactors the chemical perception engine to automatically infer formal charges and lone pair counts directly from the molecular graph. This enhancement simplifies the public API by removing the
formal_chargeparameter fromMolecularGraph::add_atom, making the library more user-friendly and robust. The new perception logic uses a combination of VSEPR theory and an expert system of functional group templates to accurately model common chemical structures, including zwitterionic amino acids, oxyacid anions (e.g., carboxylates, phosphates), and hypervalent species.Changes:
Simplified Public API:
formal_chargeargument fromMolecularGraph::add_atom. Users are no longer required to specify formal charges, as they are now automatically perceived.README.md, doc comments) to reflect the new, simpler API.Implemented Advanced Chemical Perception Logic:
perceive_charge_and_lone_pairs) that runs during the initial processing stage.processor::templates) to correctly handle resonance-stabilized charged groups like carboxylates, phosphates, and nitro groups, ensuring accurate charge and hybridization assignment.Updated Integration Test Suite:
chargeparameter from test case definitions (AtomBlueprint).