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…ms, bonds, angles, and dihedrals
… in molecular graph validation
… iteration rounds
…oved error messaging
…r, and AssignmentError for better error handling
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Pull Request Overview
This PR establishes the foundational architecture for a molecular typing engine, introducing core data structures, error handling, and CI infrastructure for a Rust-based chemistry library.
- Implements molecular graph and topology data structures with chemical enums (Element, BondOrder, Hybridization)
- Creates a hierarchical error handling system for different failure modes
- Adds CI workflow for automated testing and building
Reviewed Changes
Copilot reviewed 5 out of 6 changed files in this pull request and generated 1 comment.
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| File | Description |
|---|---|
| src/lib.rs | Module declaration to expose the core module |
| src/core/mod.rs | Core chemical enumerations with FromStr/Display traits |
| src/core/graph.rs | Molecular graph and topology data structures with canonical ordering |
| src/core/error.rs | Comprehensive error handling system for validation and assignment failures |
| .github/workflows/ci.yml | GitHub Actions CI workflow for build and test automation |
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TKanX
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feature/1-architect-core-data-structures-for-topology-representation
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Summary:
Establishes the foundational architecture for the project's core logic. It introduces a comprehensive set of data structures for representing molecular graphs and their detailed topologies (atoms, bonds, angles, dihedrals). A robust, specific error-handling system and a basic CI workflow are also implemented to ensure code quality and stability from the outset.
Changes:
Implemented Core Molecular Data Structures:
MolecularGraphwithAtomNodeandBondEdgeto represent the initial molecular connectivity.MolecularTopologyand its components (Atom,Bond,Angle,ProperDihedral,ImproperDihedral) to hold the fully typed and analyzed molecular structure.Defined Fundamental Chemical Enumerations:
Elementenum covering the periodic table.BondOrder(Single, Double, etc.) andHybridization(SP, SP2, etc.) enums.FromStrandDisplaytraits for all enums to facilitate easy parsing and string representation.Established a Custom Error Handling System:
TyperErrorenum to categorize different failure modes (RuleParse,InvalidInputGraph,AssignmentFailed).GraphValidationErrorandAssignmentErrorto provide detailed diagnostic information.Added Project Infrastructure and CI:
ci.yml) to automatically build and run tests on every push and pull request..gitignorefile to properly exclude RustRover IDE-specific files (.idea/).