DreidTyper

DreidTyper is a high-performance, foundational software library for the automated assignment of DREIDING force field atom types and the perception of molecular topologies. It provides a modern, robust solution for translating simple chemical connectivity (a molecular graph) into a complete, engine-agnostic topological description essential for molecular simulations. This library is engineered from the ground up in Rust for exceptional performance, memory safety, and strict adherence to the principles of modular software design.

The core mission of DreidTyper is to provide a reliable, predictable, and easy-to-integrate tool for developers and researchers building the next generation of simulation tools for general chemistry, materials science, and drug discovery.

Features

• DREIDING Atom Typing: Assigns canonical DREIDING atom types from molecular connectivity.
• Full Topology Perception: Identifies bonds, angles, and proper/improper dihedrals.
• Memory Safe & Fast: Built in Rust for guaranteed memory safety and high performance.
• Rule-Based Engine: Uses a clear TOML-based rule system for atom typing logic.
• Engine-Agnostic: Produces a pure topological representation independent of any MD engine.

Getting Started

To get started with DreidTyper, add it as a dependency in your Cargo.toml:

[dependencies]
dreid-typer = "0.2.0"

Then, you can use it in your Rust code as follows:

use dreid_typer::{
    assign_topology, MolecularGraph, MolecularTopology,
    Element, BondOrder,
};

// 1. Define the molecule's connectivity using a `MolecularGraph`.
let mut graph = MolecularGraph::new();
let c1 = graph.add_atom(Element::C); // CH3
let c2 = graph.add_atom(Element::C); // CH2
let o = graph.add_atom(Element::O);
let h_c1_1 = graph.add_atom(Element::H);
let h_c1_2 = graph.add_atom(Element::H);
let h_c1_3 = graph.add_atom(Element::H);
let h_c2_1 = graph.add_atom(Element::H);
let h_c2_2 = graph.add_atom(Element::H);
let h_o = graph.add_atom(Element::H);

graph.add_bond(c1, c2, BondOrder::Single).unwrap();
graph.add_bond(c2, o, BondOrder::Single).unwrap();
graph.add_bond(c1, h_c1_1, BondOrder::Single).unwrap();
graph.add_bond(c1, h_c1_2, BondOrder::Single).unwrap();
graph.add_bond(c1, h_c1_3, BondOrder::Single).unwrap();
graph.add_bond(c2, h_c2_1, BondOrder::Single).unwrap();
graph.add_bond(c2, h_c2_2, BondOrder::Single).unwrap();
graph.add_bond(o, h_o, BondOrder::Single).unwrap();

// 2. Call the main function to perceive the topology.
let topology: MolecularTopology = assign_topology(&graph).unwrap();

// 3. Inspect the results.
assert_eq!(topology.atoms.len(), 9);
assert_eq!(topology.bonds.len(), 8);
assert_eq!(topology.angles.len(), 13);
assert_eq!(topology.proper_dihedrals.len(), 12);

// Check the assigned DREIDING atom types.
assert_eq!(topology.atoms[c1].atom_type, "C_3");   // sp3 Carbon
assert_eq!(topology.atoms[c2].atom_type, "C_3");   // sp3 Carbon
assert_eq!(topology.atoms[o].atom_type, "O_3");    // sp3 Oxygen
assert_eq!(topology.atoms[h_o].atom_type, "H_HB"); // Hydrogen-bonding Hydrogen
assert_eq!(topology.atoms[h_c1_1].atom_type, "H_"); // Standard Hydrogen

Note: This is a simplified example. For more complex molecules and edge cases, please refer to the API Documentation.

Documentation

• API Documentation - Comprehensive reference for all public types and functions.
• Architecture Documents - In-depth design and implementation details.

Tech Stack

• Core Language: Rust
• Build System: Cargo
• Rule Format: TOML

License

This project is licensed under the MIT License - see the LICENSE file for details.