#protein #modeling #pdb #atom #pose #atoms #proteins

bin+lib heme

PDB reader and other protein modeling tools

2 releases

Uses old Rust 2015

0.3.2 Mar 28, 2021
0.3.1 Jul 8, 2018

#170 in Biology

MIT license

61KB
235 lines

Heme: molecular modeling library written in Rust

Heme is an implementation of force-field based molecular modeling in the Rust language. It's a work in progress that's helping me learn Rust. I hope that it will eventually be useful, but right now it's not. (For good implementations of force-field based molecular modeling, see the OpenMM or Lumol projects.)

Features

Heme is centered around proteins, so right now

  • parse PDB structures
  • Pose object representing a protein structure
  • Atom object that represents a single atom
  • both Pose and Atom have methods that are useful for calculating structural features, such as the distance between two atoms, or the residues within some cutoff of a provided atom

Plans

  • I intend to keep Heme a simple library for reading PDBs and working with protein structures as I continue to learn Rust
  • Simple molecular modeling is possible, it would be interesting to learn about implementing a force field
  • I'd like to add some nice features like
    • get the sequence of a Pose object
    • a Residue object

No runtime deps