Biology tools for Rust software
A coherent set of crates for MD, file operations, database integration, and numeric computations. These are the building blocks behind Daedalus and PlasCAD; you can embed them directly in your own software.
Python bindings are avaialble as well, installable with Pip or UV.
Core libraries
Bio Files
Load and save mmCIF, Mol2, SDF, PDBQT, map, Amber DAT/FRCMOD/lib, GRO, and more. Provides generic atom, bond, molecule, and residue structs so you can adapt them into your own model. Can load molecules remotely from databases (e.g. RCSB PDB, PubChem, DrugBank).
Bio APIs
Strongly-typed access to RCSB, PubChem, PDBe, DrugBank, NCBI BLAST, and Amber Geostd. Fetch structures, density, ligand files, or just open the corresponding browser pages.
Simulation tools
Molecular Dynamics
Runs classical forcefield-based MD with Amber force fields. For Rust and Python. Includes Velocity-Verlet and Langevin/CSVR integrators, thermostat and barostat, explicit OPC water, and the ability to load or compute force field parameters for arbitrary molecules. Run MD on any set of protein, nucleic acid, lipid, or small organic molecules.
Easy to use, and performance-oriented: Uses GPU via CUDA, our CPU SIMD and thread pools for parallelization. Ideal for embedding MD in custom tools and applications.
Numerics and visualization
Ewald
Calculate Smooth Particle Mesh Ewald (SPME) force. Fast coulomb forces with periodic boundary conditions. Uses CPU, or GPU via cuFFT or VkFFT (CUDA backend). Used by our MD tools to get order N log(N) scaling for long-range forces.
MCubes
Marching Cubes for Rust/Python. Generates meshes from amplitudes. For example, this can be used to visualize electron density, and solvent-accessible surfaces. Used to render Cryo-EM and crystallography maps in Daedalus. Outputs a simple mesh you can plug into your renderer. You can also compute the volume of the mesh.
