chematic-core 0.3.2

Core types (Atom, Bond, Molecule) for chematic — pure-Rust RDKit alternative, WASM-compatible
Documentation

chematic-core

Core types for chematic: Atom, Bond, Molecule, and Element. Low-level graph representation for all chematic crates. Pure Rust, WASM-compatible.

Features

  • Molecule graph: adjacency-list representation with atoms and bonds
  • Atom types: element, hybridization, formal charge, aromatic flag, isotope
  • Bond types: single, double, triple, aromatic bonds with configurable order
  • Element table: periodic table with atomic number, mass, electronegativity, van der Waals radius
  • Molecular properties: atom count, bond count, molecular weight, formula
  • WASM-compatible: zero C/C++ dependencies

Quick Start

use chematic_core::{Molecule, AtomIdx, Element, BondOrder};

// Create a molecule manually (or use a parser)
let mut mol = Molecule::new();

// Add atoms (returns their indices)
let c0 = mol.add_atom(Element::C.properties(), false);  // methane C
let h0 = mol.add_atom(Element::H.properties(), false);
let h1 = mol.add_atom(Element::H.properties(), false);
let h2 = mol.add_atom(Element::H.properties(), false);
let h3 = mol.add_atom(Element::H.properties(), false);

// Add bonds
mol.add_bond(c0, h0, BondOrder::Single);
mol.add_bond(c0, h1, BondOrder::Single);
mol.add_bond(c0, h2, BondOrder::Single);
mol.add_bond(c0, h3, BondOrder::Single);

// Query the graph
println!("Atoms: {}", mol.atom_count());      // 5
println!("Bonds: {}", mol.bond_count());      // 4
println!("Mass: {:.2}", mol.molecular_weight());  // 16.04

// Iterate neighbors
for (neighbor_idx, bond_idx) in mol.neighbors(c0) {
    println!("Neighbor: {}", neighbor_idx.0);
}

API Overview

Types

  • Molecule — molecular graph: atoms, bonds, adjacency
  • Atom — atomic data: element, charge, hybridization, aromaticity, isotope
  • Bond — bond data: atoms, order, stereochemistry (Up/Down, E/Z)
  • Element — element info: atomic number, mass, vdW radius, electronegativity
  • AtomIdx, BondIdx — newtype wrappers for type safety

Molecular Properties

let mw = mol.molecular_weight();
let formula = mol.formula();
let neighbors = mol.neighbors(atom_idx);
let atom = mol.atom(atom_idx);
let bond = mol.bond(bond_idx);

Element Constants

use chematic_core::Element;

Element::C,     // carbon
Element::H,     // hydrogen
Element::N,     // nitrogen
Element::O,     // oxygen
Element::P,     // phosphorus
Element::S,     // sulfur
Element::Cl,    // chlorine
// ...and all others

Dependencies

None (no external dependencies).

See Also