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…ustom_rules_toml parameter
…erceptionSource enum
…and steric_number
…nitialization in tests
…c_number in condition matching
…y for hydrogen and carbon
…template matching
…e, Carboxylate, Nitro, and Phenol/Enol
…ulating electron counts in molecular graph
…the DreidTyper library
…rception phase in the dreid-typer pipeline
… and its iterative, priority-based algorithm
…ogy Builder phase in the dreid-typer pipeline
…ule System and its structure
… documentation links
…documentation checks
…d in PerceptionResult
… for clarity in aromaticity check
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Pull Request Overview
This pull request finalizes the dreid-typer library for its initial release by implementing a comprehensive public API, extensive documentation, and robust CI/CD infrastructure. The changes transform the project from an internal tool into a production-ready library suitable for chemical simulation and molecular modeling applications.
- Complete public API redesign with
assign_topologyandassign_topology_with_rulesas primary entry points - Comprehensive documentation including rustdoc comments, architectural guides, and integration examples
- Extensive integration test suite covering amino acids, nucleic acids, and complex chemical structures from the DREIDING paper
Reviewed Changes
Copilot reviewed 29 out of 31 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
src/lib.rs |
Implements the public API with comprehensive documentation and example usage |
src/core/mod.rs |
Adds detailed documentation to core types (Element, BondOrder, Hybridization) |
src/core/graph.rs |
Enhances graph structures with formal charge support and extensive documentation |
src/core/error.rs |
Documents all error types with examples and usage patterns |
src/processor/mod.rs |
Restructures processor module with new perception-templates-typer architecture |
src/processor/pipeline.rs |
New orchestration module for the three-phase perception process |
src/processor/perception.rs |
Comprehensive perception algorithms with electron counting and aromaticity detection |
src/processor/templates.rs |
Expert system for functional group recognition using template matching |
src/processor/typer.rs |
Enhanced typing engine with improved documentation and condition matching |
src/processor/graph.rs |
Updated processing graph with perception source tracking and formal charge |
src/rules/mod.rs |
Enhanced rule system with additional condition types and documentation |
src/builder/mod.rs |
Topology builder with comprehensive documentation for all generation algorithms |
tests/integration_tests.rs |
Extensive test harness with macro-generated tests for dozens of molecules |
tests/harness.rs |
Test infrastructure supporting atom type verification and error reporting |
tests/cases/nucleic_acids.rs |
Complete test cases for DNA/RNA bases and nucleotides |
resources/dreiding.rules.toml |
Refined DREIDING ruleset with improved priority hierarchy and steric number-based rules |
docs/ |
New architectural documentation explaining the pipeline, perception, typing, and rule system |
README.md |
Updated with quickstart guide and comprehensive usage examples |
.github/workflows/ci.yml |
Enhanced CI pipeline with formatting, linting, and documentation checks |
Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.
…implementation Co-authored-by: Copilot <[email protected]>
Co-authored-by: Copilot <[email protected]>
TKanX
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feature/7-finalize-library-api-implement-documentation-and-add-comprehensive-integration-tests
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Summary:
Finalizes the
dreid-typerlibrary for its initial release. It introduces a clean, user-friendly public API, comprehensiverustdocand architectural documentation, an extensive integration test suite, and a robust CI pipeline. The chemical perception engine has been significantly refactored for improved accuracy and clarity, and the default DREIDING ruleset has been refined to better handle complex chemical environments.Changes:
Finalized Public API and Added "Getting Started" Guide:
assign_topologyandassign_topology_with_rulesas the primary entry points.MolecularGraph,MolecularTopology,Element,BondOrder) to the crate root for ease of use.README.mdwith a complete, runnable example.Implemented Comprehensive Documentation:
rustdoccomments to all public functions, structs, and enums, explaining their purpose, arguments, and potential errors.docs/directory with detailed architectural documents explaining the core pipeline, chemical perception engine, and rule system.Refactored Chemical Perception Engine:
processormodule into a clearer, multi-phase pipeline (perception,templates,typer).ProcessingGraphwith rich chemical annotations before the typing engine runs.Developed an Extensive Integration Test Suite:
tests/directory with a robust test harness for running end-to-end molecule typing tests.tests/cases/) with dozens of molecules, including all 20 standard amino acids, nucleic acid bases, and complex structures from the original DREIDING paper, ensuring high accuracy and correctness.Established a Robust CI Pipeline:
ci.yml) that runs on every push and pull request.cargo fmt), linting (cargo clippy), documentation generation (cargo doc), and runs the full test suite (cargo test).