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Pull request overview
This PR establishes the foundational data models for the dreid-forge molecular modeling library, implementing comprehensive type systems for chemical elements, molecular structures, topology potentials, and biological metadata. It also sets up a CI pipeline to maintain code quality through automated testing and linting.
Key Changes:
- Implemented complete periodic table support via
Elementenum (atomic numbers 1-118) with atomic mass and symbol lookup - Created molecular data structures (
Atom,Bond,System) with canonical bond ordering for efficient deduplication - Defined extensible topology potential types (harmonic, Morse, Lennard-Jones, etc.) with
ForgedSystemas the unified container - Added PDB-compatible biological metadata structures (
BioMetadata,AtomResidueInfo) - Configured GitHub Actions CI workflow for automated building, formatting, linting, and testing
Reviewed changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 10 comments.
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| File | Description |
|---|---|
src/model/types.rs |
Core types including Element enum (118 elements) with atomic masses, BondOrder enum with parsing support, and custom error types |
src/model/atom.rs |
Atom struct representing an element with 3D coordinates |
src/model/system.rs |
Bond struct with canonical ordering (i ≤ j) and System container for atoms, bonds, box vectors, and metadata |
src/model/metadata.rs |
PDB-style biological metadata structures (AtomResidueInfo, BioMetadata) for residue information |
src/model/topology.rs |
Comprehensive potential energy types (bond, angle, dihedral, improper, VdW, H-bond) and ForgedSystem aggregator |
src/model/mod.rs |
Module declarations for the model components |
src/lib.rs |
Library root exposing the model module |
.github/workflows/ci.yml |
CI pipeline configuration with format checking, clippy linting, testing, and documentation generation |
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…omParam struct and update related tests
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Summary:
Implemented the foundational architecture for the
dreid-forgeproject, establishing the core data models for molecular representation. This includes systems for atoms, bonds, topology potentials, and biological metadata, fulfilling the requirements for a unified system representation. Additionally, a Continuous Integration (CI) pipeline has been configured to ensure code quality and stability from the start.Changes:
Implemented Core Types and Elements:
Elementenum covering atomic numbers 1-118.BondOrderenum with value support and string parsing.Developed Molecular Data Structures:
Atomstruct to handle elemental identity and spatial coordinates.Bondstruct with canonical index ordering and deduplication logic.Systemclass as the central container for atoms, bonds, and periodic box vectors.Added Topology and Potentials:
BondPotential,AnglePotential,DihedralPotential,ImproperPotential).VdwPairPotential,HBondPotential).ForgedSystemto aggregate system data with atom types and forcefield parameters.Integrated Biological Metadata:
BioMetadataandAtomResidueInfoto support PDB-style data (residue names, chain IDs, insertion codes).Established CI Pipeline:
.github/workflows/ci.ymlto automate building, formatting checks (cargo fmt), linting (clippy), testing (cargo test), and documentation checks.Documentation and Testing: