gchemol-readwrite

A Rust library for reading and writing chemical file formats, built on top of the gchemol-core molecular manipulation library.

Features

• Support for multiple chemical file formats:
  • XYZ (.xyz)
  • CIF (.cif)
  • MOL2 (.mol2)
  • PDB (.pdb)
  • POSCAR/CONTCAR (VASP, *.vasp, POSCAR-xx)
  • Gaussian (.gjf)
  • And more...
• Powerful template engine for custom molecular file format generation using Jinja2-like syntax
• Integration with gchemol-core for molecular manipulation and analysis
• Extensible architecture for adding new file formats

Supported File Formats

Installation

Add this to your Cargo.toml:

[dependencies]
gchemol-readwrite = "0.1"

Usage

Reading Molecules

use gchemol_readwrite::prelude::*;
use gchemol_core::Molecule;

// Read a molecule from a file
let mol = Molecule::from_file("water.xyz")?;

// Or read from a string
let mol = Molecule::from_str("XYZ STRING HERE", "text/xyz")?;

Writing Molecules

use gchemol_readwrite::prelude::*;
use gchemol_core::Molecule;

// Assuming you have a Molecule object
let mol: Molecule = ...;

// Write to a file
mol.to_file("output.xyz")?;

// Or format as a string
let xyz_string = mol.format_as("text/xyz")?;

Using Templates

The library provides a powerful template engine for generating custom molecular file formats:

use gchemol_readwrite::prelude::*;
use gchemol_core::Molecule;

let mol = Molecule::from_file("structure.cif")?;

// Render using a Jinja2-like template
let rendered = mol.render_with("template.jinja".as_ref())?;

// Save the rendered output
std::fs::write("output.file", rendered)?;

See Template Usage Documentation for more details on the template system.

Template System

This library includes a flexible template engine based on MiniJinja that allows users to create custom molecular file formats. The template system provides access to molecular data structures and includes a built-in format filter for precise numeric formatting.

Templates can be used to generate input files for various computational chemistry programs like:

• Abacus (STRU)
• VASP (POSCAR)
• And many others

For detailed information about the template system, see Template Usage Documentation.

Documentation

• API Documentation
• Template Usage Guide

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.