3 unstable releases
0.2.1 | Apr 12, 2024 |
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0.2.0 | Apr 12, 2024 |
0.1.1 | Feb 11, 2024 |
0.1.0 |
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#97 in Biology
208 downloads per month
81KB
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RustSASA
RustSASA is a Rust library for computing the absolute solvent accessible surface area (ASA/SASA) of each atom in a given protein structure using the Shrake-Rupley algorithm[1].
Features:
- 🦀 Written in Pure Rust
- ⚡️ 3X Faster than Biopython and ~120% faster than Freesasa
- 🧪 Full test coverage
RustSASA Implementation vs Biopython Implementation
Benchmarks were performed on an M2 Apple Mac with 8GB of RAM and 8 Cores with the protein AF-A0A2K5XT84-F1 (AlphaFold).
-
Biopython: ~150ms
-
Freesasa: ~90ms
-
RustSASA: ~40ms
Example Usage with pdbtbx
:
use pdbtbx::StrictnessLevel;
use rust_sasa::{Atom, calculate_sasa, calculate_sasa_internal, SASALevel};
let (mut pdb, _errors) = pdbtbx::open(
"./example.cif",
StrictnessLevel::Medium
).unwrap();
let result = calculate_sasa(&pdb,None,None,SASALevel::Residue);
Documentation:
See https://docs.rs/rust-sasa/latest/rust_sasa/
Citations:
1: Shrake A, Rupley JA. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol. 1973 Sep 15;79(2):351-71. doi: 10.1016/0022-2836(73)90011-9. PMID: 4760134.
Dependencies
~8MB
~161K SLoC