# chematic
[日本語](README_ja.md) | [中文](README_zh.md)
A pure-Rust cheminformatics library targeting RDKit feature parity — **with zero C/C++ dependencies**.
> **Why does zero C/C++ matter?**
> RDKit.js, Indigo WASM, and OpenBabel all ship C++ code compiled via Emscripten.
> That means **30–50 MB WASM binaries**, complex build toolchains, and platform-specific build failures.
> chematic compiles to a **~550 KB WASM bundle** with a single `wasm-pack build` — no `cmake`, no `clang`,
> no `-sys` crates, no `build.rs` C compilation anywhere in the dependency tree.
---
## Live Demo
**[https://kent-tokyo.github.io/chematic/](https://kent-tokyo.github.io/chematic/)** — Interactive descriptor calculator, drug-likeness rules, fingerprint similarity, 3D viewer, and reaction schemes running entirely in your browser via WebAssembly.
---
## Design Goals
**Pure Rust, zero C/C++ FFI — guaranteed**
No `rdkit-sys`, no `openbabel-sys`, no `cc` build dependencies, no `bindgen`. Every
algorithm — from SSSR ring perception to ECFP fingerprints to force-field minimization —
is implemented in 100% safe Rust. The entire dependency tree is verified FFI-free.
**WASM-compatible and lightweight**
All crates compile to `wasm32-unknown-unknown` without modification. The npm package
`@kent-tokyo/chematic` is **~550 KB** versus 30–50 MB for C++ FFI alternatives.
No `cmake`, no `emcc`, no Emscripten toolchain required.
**80+ WebAssembly API endpoints**
The WASM layer exposes 80 functions covering descriptors, fingerprints, scaffold analysis,
stereoisomer enumeration, 3D geometry, diversity selection, and more — all callable from
JavaScript/TypeScript with full TypeScript type definitions.
**Domain-specific algorithms**
Rather than wrapping a generic graph library, chematic implements chemistry-specific
algorithms directly: Kekulization, Hückel aromaticity, CIP stereochemistry, SSSR ring
perception, Gasteiger charges, MaxMin/Butina diversity picking.
**Reproducible and deterministic**
Fingerprints use FNV-1a hashing with a fixed invariant ordering. Given the same SMILES
input, the same bits are always produced. No RNG, no platform-specific behavior.
---
## Current Status
All phases complete. **809 tests, all passing. Zero C/C++ dependencies.**
| `chematic-core` | Atom, Bond, Molecule, Element, kekulization (no deps) | 30 |
| `chematic-smiles` | OpenSMILES parser, writer, canonical SMILES | 52 |
| `chematic-perception` | SSSR (Balducci-Pearlman), Huckel aromaticity | 14 |
| `chematic-mol` | MOL/SDF V2000+V3000 parser and writer, SDF property read/write | 37 |
| `chematic-depict` | 2D SVG depiction with CPK coloring, atom/bond highlighting, SMARTS-highlighted grid | 30 |
| `chematic-chem` | 40+ descriptors, BRICS, QED, standardization, Murcko scaffold, CIP, IFG, Gasteiger, VSA, SA score, diversity, stereo enumeration | 285 |
| `chematic-fp` | ECFP2/4/6, FCFP4/6, MACCS 166-bit, TopoPF, AtomPair, Torsion — Tanimoto/Dice | 50 |
| `chematic-smarts` | SMARTS parser (recursive, valence, hybridization), VF2 subgraph isomorphism, MCS | 77 |
| `chematic-3d` | 3D coordinate generation, force-field minimization, shape descriptors, PDB/XYZ | 68 |
| `chematic-rxn` | Reaction SMILES parser and writer | 26 |
| `chematic-wasm` | **80 WASM exports** — npm: `@kent-tokyo/chematic` | 125 |
| `chematic` | Umbrella crate with feature flags (all sub-crates) | 1 |
```
cargo test --workspace # 809 tests, all passing
```
---
## Quick Start
### Using the umbrella crate
```toml
# Cargo.toml
[dependencies]
chematic = { git = "https://github.com/kent-tokyo/chematic", features = ["smiles", "fp"] }
```
```rust
use chematic::smiles::{parse, canonical_smiles};
use chematic::fp::ecfp4;
```
### Using individual crates
```toml
# Cargo.toml
[dependencies]
chematic-smiles = { git = "https://github.com/kent-tokyo/chematic" }
chematic-perception = { git = "https://github.com/kent-tokyo/chematic" }
chematic-fp = { git = "https://github.com/kent-tokyo/chematic" }
```
```rust
use chematic_smiles::{parse, canonical_smiles};
use chematic_perception::{find_sssr, assign_aromaticity};
use chematic_fp::{ecfp4, tanimoto_ecfp4};
fn main() {
let benzene = parse("c1ccccc1").unwrap();
let toluene = parse("Cc1ccccc1").unwrap();
// Ring and aromaticity perception
let rings = find_sssr(&benzene);
println!("rings: {}", rings.ring_count()); // 1
// Fingerprint similarity
let sim = tanimoto_ecfp4(&benzene, &toluene);
println!("Tanimoto(benzene, toluene): {sim:.3}"); // ~0.5
// Canonical SMILES
println!("{}", canonical_smiles(&benzene)); // c1ccccc1
}
```
---
## SMARTS substructure search
```rust
use chematic_smiles::parse;
use chematic_smarts::{parse_smarts, find_matches};
let mol = parse("CC(=O)Oc1ccccc1C(=O)O").unwrap(); // aspirin
let query = parse_smarts("[$(C(=O)O)]").unwrap(); // carboxylic / ester C
let matches = find_matches(&query, &mol);
println!("C(=O)O groups: {}", matches.len()); // 2
```
---
## Molecular descriptors
```rust
use chematic_smiles::parse;
use chematic_chem::{molecular_weight, tpsa, logp_crippen, fsp3, qed, lipinski_passes};
let aspirin = parse("CC(=O)Oc1ccccc1C(=O)O").unwrap();
println!("MW: {:.2}", molecular_weight(&aspirin)); // ~180.16
println!("TPSA: {:.2}", tpsa(&aspirin)); // ~63.6
println!("LogP: {:.2}", logp_crippen(&aspirin)); // ~1.2
println!("Fsp3: {:.3}", fsp3(&aspirin)); // ~0.111
println!("QED: {:.3}", qed(&aspirin)); // drug-likeness score
println!("Lipinski: {}", lipinski_passes(&aspirin)); // true
```
---
## BRICS fragmentation
```rust
use chematic_smiles::parse;
use chematic_chem::brics_fragments;
let aspirin = parse("CC(=O)Oc1ccccc1C(=O)O").unwrap();
let frags = brics_fragments(&aspirin);
println!("fragments: {}", frags.len()); // ≥ 2
```
---
## Fingerprints
```rust
use chematic_smiles::parse;
use chematic_fp::{ecfp4, atom_pair_fp, torsion_fp};
let aspirin = parse("CC(=O)Oc1ccccc1C(=O)O").unwrap();
let caffeine = parse("Cn1cnc2c1c(=O)n(c(=O)n2C)C").unwrap();
let sim_ecfp4 = ecfp4(&aspirin).tanimoto(&ecfp4(&caffeine));
let sim_atompair = atom_pair_fp(&aspirin).tanimoto(&atom_pair_fp(&caffeine));
let sim_torsion = torsion_fp(&aspirin).tanimoto(&torsion_fp(&caffeine));
```
---
## 2D depiction
```rust
use chematic_smiles::parse;
use chematic_depict::depict_svg;
let caffeine = parse("Cn1cnc2c1c(=O)n(c(=O)n2C)C").unwrap();
let svg = depict_svg(&caffeine);
std::fs::write("caffeine.svg", svg).unwrap();
```
### Highlighted depiction
```rust
use std::collections::HashSet;
use chematic_smiles::parse;
use chematic_depict::depict_svg_highlighted;
let mol = parse("c1ccncc1").unwrap(); // pyridine
import init, {
parse_smiles, canonical_tautomer, murcko_scaffold,
largest_fragment, neutralize_charges,
tanimoto_ecfp4, tanimoto_ecfp6, tanimoto_maccs,
brics_fragments_json, mcs_smiles_json,
get_descriptors_json, sssr_rings_json,
enumerate_stereo_isomers_json,
sdf_to_records_json, sdf_from_records_json,
maxmin_picks_ecfp4_json, butina_cluster_ecfp4_json,
shape_descriptors_json, generate_3d_minimized_pdb,
} from '@kent-tokyo/chematic';
await init();
// ── Parsing & descriptors ─────────────────────────────────────────
const mol = parse_smiles('CC(=O)Oc1ccccc1C(=O)O'); // aspirin
console.log(mol.molecular_weight()); // ~180.16
console.log(mol.qed()); // drug-likeness [0,1]
console.log(mol.sa_score()); // synthetic accessibility [1,10]
console.log(mol.lipinski_passes()); // true
// All descriptors at once (JSON object)
const desc = JSON.parse(get_descriptors_json(mol));
console.log(desc.mw, desc.tpsa, desc.logP, desc.fsp3);
// ── Molecule processing ───────────────────────────────────────────
const salt = parse_smiles('CC(=O)[O-].[Na+]');
const clean = largest_fragment(salt); // remove Na+
const neutral = neutralize_charges(clean); // neutralize [O-]
const tautomer = canonical_tautomer(parse_smiles('Oc1cccc2ccccc12'));
const scaffold = murcko_scaffold(parse_smiles('c1ccc(CC(=O)O)cc1'));
// ── Fingerprints & similarity ─────────────────────────────────────
const caffeine = parse_smiles('Cn1cnc2c1c(=O)n(c(=O)n2C)C');
console.log(tanimoto_ecfp4(mol, caffeine)); // ECFP4 Tanimoto
console.log(tanimoto_ecfp6(mol, caffeine)); // ECFP6 Tanimoto
console.log(tanimoto_maccs(mol, caffeine)); // MACCS Tanimoto
// ── Scaffold / fragmentation / MCS ───────────────────────────────
const frags = JSON.parse(brics_fragments_json(mol));
const mcs = mcs_smiles_json('["CC(=O)O","CC(=O)N"]');
// ── Stereochemistry ───────────────────────────────────────────────
const isomers = JSON.parse(enumerate_stereo_isomers_json(parse_smiles('C(F)(Cl)Br')));
// ["[C@@H](F)(Cl)Br","[C@H](F)(Cl)Br"]
// ── 3D geometry ───────────────────────────────────────────────────
const pdb = generate_3d_minimized_pdb(mol);
const shape = JSON.parse(shape_descriptors_json(mol));
console.log(shape.pmi1, shape.npr1, shape.asphericity);
// ── Diversity selection ───────────────────────────────────────────
const library = '["CC","c1ccccc1","CCO","CCCC","c1ccncc1"]';
const picks = JSON.parse(maxmin_picks_ecfp4_json(library, 3));
const clusters = JSON.parse(butina_cluster_ecfp4_json(library, 0.4));
// ── SDF round-trip with properties ───────────────────────────────
const records = JSON.parse(sdf_to_records_json(sdfString));
// records[0].smiles, records[0].name, records[0].properties.MW
const sdf = sdf_from_records_json(
'["CC(=O)O"]',
'["aspirin"]',
'["MW\t180.16\nSource\tChEMBL"]'
);
```
---
## Comparison with Other Cheminformatics Libraries
| **C/C++ dependencies** | **None — pure Rust** | Extensive C++ | Extensive C++ | C++ via Emscripten |
| **WASM binary size** | **~550 KB** | N/A (no WASM) | N/A (no WASM) | ~30 MB |
| **Build requirement** | `cargo build` only | cmake + clang | cmake + clang | Emscripten SDK |
| **WASM target support** | **Full (native)** | No | No | Yes (Emscripten) |
| Unsafe Rust | **None** | Extensive | Extensive | N/A |
| OpenSMILES parser | Full | Full | Full | Full |
| SMILES writer / canonical | Yes | Yes | Yes | Yes |
| Kekulization | Yes | Yes | Yes | Yes |
| Ring perception (SSSR) | Yes | Yes | Yes | Yes |
| SDF/MOL V2000+V3000 + SD fields | Yes | Yes | Yes | Yes |
| 2D depiction (SVG, CPK colors) | Yes | Yes | Yes | Yes |
| ECFP/FCFP fingerprints (2/4/6) | **All variants + bitvec**| Yes | Yes | Yes |
| AtomPair / Torsion / MACCS FP | Yes | Yes | Yes | Yes |
| Molecular descriptors | **40+ (MW/LogP/…/SA)** | ~30 | ~20 | ~30 |
| BRICS fragmentation | Yes (bonds + SMILES) | Yes | No | Yes |
| Murcko scaffold | Yes | Yes | No | Yes |
| Tautomer normalisation | Yes | Yes | No | Yes |
| MCS | Yes | Yes | No | Yes |
| Stereoisomer enumeration | **Yes** | Yes | No | Yes |
| CIP stereo (R/S, E/Z) detail | **Yes (per-atom JSON)** | Yes | Yes | Yes |
| 3D coordinate generation | Yes (DG + minimization) | Yes (ETKDG) | Yes | Yes |
| 3D shape descriptors (PMI/NPR/…) | **Yes** | Yes | No | Yes |
| PDB / XYZ file formats | Yes | Yes | Yes | Yes |
| MaxMin / Butina diversity picking | **Yes** | Yes | No | No |
| Reaction SMILES/SMIRKS | Yes | Yes | Yes | Yes |
| InChI / InChIKey | No (C lib required) | Yes | Yes | Yes |
| Maintenance (2026) | Active | Active | Minimal | Active |
Notes:
- chematic WASM binary size measured with `wasm-opt` optimization; RDKit.js is the official WASM build.
- "None" for C/C++ means verified: no `*-sys` crates, no `cc` build dependencies, no `build.rs` C compilation in the entire dependency tree.
---
## Roadmap
### Phase 1 — Foundation (complete)
Core types, OpenSMILES parse/write, Kekulization, canonical SMILES.
### Phase 2 — Molecular Perception (complete)
SSSR, Huckel aromaticity, SDF/MOL V2000+V3000, 2D SVG depiction.
### Phase 3 — Chemical Intelligence (complete)
Descriptors (MW, LogP, TPSA, Fsp3, Lipinski), QED, BRICS fragmentation,
ECFP4/6 fingerprints, SMARTS+VF2 (recursive SMARTS, valence, hybridization),
molecular standardization, Murcko scaffold, CIP R/S and E/Z.
### Phase 4 — Similarity and Search (complete)
MACCS 166-bit keys, topological path FP, AtomPair FP, Topological Torsion FP,
MCS, tautomer normalization.
### Phase 5 — 3D Chemistry (complete)
Rule-based 3D coordinate generation, PDB/XYZ formats, UFF-like minimization.
### Phase 6 — RDKit Parity (complete)
Reaction SMILES/SMIRKS ✓, umbrella crate with feature flags ✓,
WASM npm package `@kent-tokyo/chematic` ✓, CPK coloring + highlighted depiction ✓,
ChEMBL 37 full-set validation (2,897,819 molecules, 100.000%) ✓.
### Phase 7 — Extended Descriptors and Diversity (v0.1.14–v0.1.15, complete)
EState indices (Hall & Kier 1991), path fingerprint (DFS path FP, 2048-bit),
SDF/MOL WASM bindings,
functional group identification (Ertl 2017 IFG), Gasteiger-Marsili PEOE partial charges,
VSA descriptors (SlogP_VSA × 12, SMR_VSA × 10, PEOE_VSA × 14),
SA score (complexity-based), MaxMin diversity picking, Butina clustering.
See `tasks/todo.md` for the detailed per-task breakdown.
---
## Repository Structure
```
chematic/
├── Cargo.toml workspace root
├── CHANGELOG.md version history
├── crates/
│ ├── chematic-core/ Atom, Bond, Molecule, Element, kekulization
│ ├── chematic-smiles/ OpenSMILES parser, writer, canonical SMILES
│ ├── chematic-perception/ SSSR ring perception, Huckel aromaticity
│ ├── chematic-mol/ MOL/SDF V2000+V3000 parser and writer
│ ├── chematic-depict/ 2D SVG depiction engine (CPK colors, highlighting)
│ ├── chematic-chem/ Descriptors, BRICS, QED, standardization, scaffold
│ ├── chematic-fp/ ECFP4/6, MACCS, path, AtomPair, Torsion FP
│ ├── chematic-smarts/ SMARTS parser + VF2 subgraph isomorphism, MCS
│ ├── chematic-3d/ 3D coordinate generation, PDB/XYZ formats
│ ├── chematic-rxn/ Reaction SMILES parser and writer
│ └── chematic/ Umbrella crate with feature flags
└── tasks/
├── todo.md full roadmap checklist (Japanese)
└── lessons.md development lessons learned
```
---
## Development Commands
```bash
cargo build --workspace # build all crates
cargo test --workspace # run all tests (736)
cargo check --workspace # type-check without building
cargo clippy --workspace # lints
```
---
## License
Licensed under either of Apache License 2.0 or MIT License, at your option.