{"repo":"TKanX/bio-forge","free":true,"listed":false,"github":"https://github.com/TKanX/bio-forge","clone":"git clone https://github.com/TKanX/bio-forge.git","description":"A high-performance, pure Rust toolkit for standardizing and preparing biomolecular systems (proteins & nucleic acids). It heals missing atoms, resolves protonation states, adds solvation, and unifies topologies to forge simulation-ready structures.","language":"Rust","stars":141,"topics":["bioinformatics","biology","chemistry","dna","molecule","nucleic-acids","rna","rust","high-performance","javascript"],"license":"MIT","category":"cli-tools","readme_excerpt":"BioForge BioForge is a pure-Rust toolkit for automated preparation of biological macromolecules. It reads experimental structures (PDB/mmCIF), reconciles them with high-quality residue templates, repairs missing atoms, assigns hydrogens and termini, builds topologies, and optionally solvates the system with water and ions—all without leaving the Rust type system. Highlights - Template-driven accuracy – Curated TOML templates for standard amino acids, nucleotides, and water guarantee reproducible coordinates, charges, and bonding. - High performance – Multithreaded processing (via rayon) handles million-atom systems in milliseconds; single-pass parsing, in-place mutation, and zero-copy serialization minimize overhead. - Rich structure model – Lightweight Atom , Residue , Chain , and Structure types backed by nalgebra make geometric operations trivial. - Format interoperability – Buffered readers/writers for PDB, mmCIF, and MOL2 plus error types that surface precise parsing diagnostics. - Preparation pipeline – Cleaning, repairing, protonating, solvation, coordinate transforms, and topology reconstruction share a common ops::Error so workflows compose cleanly. - WebAssembly support – Full-featured WASM bindings for modern JavaScript bundlers (Vite, webpack, Rollup); ideal for browser-based molecular viewers and web applications. - Rust-first ergonomics – No FFI, no global mutable state beyond the lazily-loaded template store, and edition 2024 guarantees modern language features","default_branch":null,"files":null,"tree":[],"storefront":"/r/TKanX","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/TKanX/bio-forge/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}