primer3-rs

Safe, idiomatic Rust bindings to the primer3 C library for PCR primer design and oligonucleotide thermodynamic calculations.

[!WARNING] primer3-rs is licensed under GPL-2.0-or-later.

This is unusual for our crates, and it is non-negotiable: the upstream primer3 C library is GPL-2.0-or-later, and primer3-rs statically compiles and links it. Any application, library, or pipeline that depends on primer3, primer3-sys, or primer3-tool — whether via static or dynamic linking — forms a combined work subject to the terms of the GNU General Public License. In practice this means:

Distributing a binary that links primer3-rs requires releasing the complete corresponding source of that binary under a GPL-compatible license.

You cannot combine primer3-rs with proprietary, closed-source, or permissively-licensed-but-non-GPL-compatible code in a distributed product.

Internal/in-house use is unrestricted; the GPL's obligations trigger on distribution, not on use.

If these constraints are a problem for your use case, consider invoking the upstream primer3_core binary as a subprocess instead — the GPL does not reach across process boundaries in the same way. See the License section below for details.

Not legal advice. The above is our good-faith reading of the GPL and how it applies to primer3-rs. We are not lawyers, this is an opinion rather than a legal determination, and the line between "mere aggregation" and a "combined work" can be fact-specific. If the licensing implications matter to your project, please seek qualified legal counsel.

Overview

primer3-rs provides three crates:

primer3-sys -- Raw FFI bindings generated via bindgen against the primer3 C headers
primer3 -- Safe, idiomatic Rust API with builders, strong types, and proper error handling
primer3-tool -- CLI binary exposing tm, hairpin, homodimer, heterodimer, and design subcommands

Features

Melting temperature (Tm) calculation with multiple methods (Breslauer, SantaLucia, SantaLucia 2004)
Thermodynamic analysis: hairpin, homodimer, heterodimer, and 3' end stability
Full primer design via design_primers() with typed settings and results
Builder patterns for all complex configuration
Thread-safe: thermodynamic functions are safe to call concurrently; design_primers() and align() are mutex-guarded
Vendored C source compiled automatically -- no system dependencies required

Installation

Supported platforms: Linux and macOS. Windows is not supported.

Add to your Cargo.toml:

[dependencies]
primer3 = "0.1"

The primer3 C library source is vendored and compiled automatically during build. You will need a C/C++ compiler and libclang (for bindgen).

Command-line tool

To install the primer3-tool CLI (which exposes tm, hairpin, homodimer, heterodimer, and design subcommands):

cargo install primer3-tool

System library (advanced)

To link against a system-installed libprimer3 instead of compiling from source:

[dependencies]
primer3 = { version = "0.1", default-features = false, features = ["system"] }

Quick Start

Melting Temperature

use primer3::calc_tm;

let tm = calc_tm("GTAAAACGACGGCCAGT").unwrap();
println!("Tm = {tm:.1} C");

Thermodynamic Analysis

use primer3::{calc_hairpin, calc_heterodimer};

let hairpin = calc_hairpin("CCCCCATCCGATCAGGGGG").unwrap();
println!("Hairpin Tm = {:.1} C, dG = {:.0} cal/mol", hairpin.tm(), hairpin.dg());

let dimer = calc_heterodimer("AAAAAAAAAA", "TTTTTTTTTT").unwrap();
println!("Heterodimer Tm = {:.1} C", dimer.tm());

Primer Design

use primer3::{design_primers, SequenceArgs, PrimerSettings};

let seq_args = SequenceArgs::builder()
    .sequence("ATCGATCGATCGATCGATCG...")
    .target(100, 200)
    .build()
    .unwrap();

let settings = PrimerSettings::builder()
    .primer_opt_tm(60.0)
    .primer_min_tm(57.0)
    .primer_max_tm(63.0)
    .product_size_range(75, 150)
    .build()
    .unwrap();

let result = design_primers(&seq_args, &settings, None, None).unwrap();
for pair in result.pairs() {
    let left = pair.left();
    let right = pair.right();
    println!(
        "Left: {} (Tm={:.1}), Right: {} (Tm={:.1}), Penalty={:.2}",
        left.sequence(), left.tm(),
        right.sequence(), right.tm(),
        pair.penalty(),
    );
}

Development

Prerequisites

Rust (see rust-toolchain.toml for the pinned version)
C/C++ compiler (for compiling the vendored primer3 C library)
libclang (for bindgen to generate FFI bindings)

Getting Started

git clone --recurse-submodules https://github.com/fg-labs/primer3-rs.git
cd primer3-rs
cargo build
cargo test

Git Hooks

Install pre-commit hooks to run formatting and linting checks before each commit:

./scripts/install-hooks.sh

CI Commands

cargo ci-fmt    # Check formatting
cargo ci-lint   # Run clippy with strict settings
cargo ci-test   # Run all tests

License

primer3-rs is licensed under GPL-2.0-or-later. All three crates in this workspace (primer3-sys, primer3, primer3-tool) carry the same license. See the warning at the top of this README for the practical implications.

Why GPL?

The upstream primer3 C library is licensed under GPL-2.0-or-later and its copyright holders have declined requests to relicense it under a more permissive license. Because primer3-rs statically compiles and links primer3's C source into the resulting artifacts, the entire workspace is a derivative work and must be distributed under a GPL-compatible license. We chose GPL-2.0-or-later (rather than GPL-2.0 only) to give downstream users the option of combining primer3-rs with GPL-3.0-compatible code, including Apache-2.0–licensed code, at their discretion.

Escape hatches

If the GPL's copyleft obligations are incompatible with your project, the only clean path is to not link against primer3-rs at all. Instead, invoke the upstream primer3_core binary as a subprocess and communicate via the Boulder I/O format on stdin/stdout. Running a GPL program as a separate process does not impose GPL terms on the calling program, provided there is no intimate linking (shared address space, shared data structures, etc.).

Acknowledgments

primer3 -- the underlying C library for primer design
primer3-py -- Python bindings that inspired this project's API surface

primer3 0.1.0