gchemol

gchemol is a graph-based chemical object library implemented in Rust programming language. This project is still in early development.

Features

• Fast and safe codes empowered by Rust.

• Static build without external dependencies: easy to deploy in HPC environment.

• Core graph data structure using petgraph

• Read/write molecules in common chemcial file formats.

• Linear algebra backed by nalgebra

• Render molecule in user defined formats by templating with handlebars and tera

How to use

Setup

follow the official guide:

• Installation · The Rust Programming Language

add gchemol dependency to your Cargo.toml:

[dependencies]
gchemol = "0.1"

Atom

use gchemol::Atom;

// construct from element and position
let a = Atom::new("C", [0.0, 0.0, 0.0]);
let b = Atom::new("C", [1.2, 1.2, 1.2]);

or simply convert from a string:

let a: Atom = "C 1.0 1.0 0.2"
    .parse()
    .expect("atom from string");

Molecule

1. Creating a molecule manually

   use gchemol::Molecule;
   
   let atoms = [
       Atom::new("C", [ 0.000000,   0.000000,  0.000000]),
       Atom::new("C", [ 0.000000,   0.000000,  1.089000]),
       Atom::new("C", [ 1.026719,   0.000000, -0.363000]),
       Atom::new("C", [-0.513360,  -0.889165, -0.363000]),
       Atom::new("C", [-0.513360,   0.889165, -0.363000])];
   
   // create a molecule from these atoms
   let mut mol = Molecule::from_atoms(atoms);
   

2. Reading and writing molecules

   use gchemol::io;
   use gchemol::prelude::*;
   use gchemol::Molecule;
   
   // Read an xyz file and write to a Gaussian Input file.
   let mol = Molecule::from_file("path/to/file.xyz")?;
   mol.to_file("methane.gjf")?;
   
   // get the total number of atoms
   let na = mol.natoms();
   // get the total number of bonds
   let nb = mol.nbonds();
   
   // read multiple molecules (trajectory) from a chemical file
   // the number of atoms in different frame could be different
   let mols = io::read("path/to/trajectory.xyz")?;
   

Related projects

• ase

• lumol

References

• Lessons from sixteen years of molecular simulation in Python | Konrad Hinsen's Blog