chemfiles / Chemfiles

Chemfiles: a library for reading and writing chemistry files

Chemfiles is a high-quality library for reading and writing trajectory files created by computational chemistry simulations programs. To help you access information (atomic positions, velocities, names, topology, etc.) about these files, Chemfiles provides a simple and unified interface to a variety of file formats.

• unified: the same code will work with all supported formats;
• simple: the interface is easy to use and extensively documented.

You can use Chemfiles to conduct post-processing analysis and extract physical information about the systems you're simulating, to convert files from one format to another, to write trajectories with your own simulation software, and anything that requires reading or writing the file formats used in computational chemistry.

Chemfiles is used in multiple scientific software

• cfiles provides ready-to-use analysis algorithms simulations trajectories as a command line tool;
• lemon is a framework for rapidly mining structural information from the Protein Data Bank;
• lumol is a prototype of universal extensible molecular simulation engine, supporting both molecular dynamics and Metropolis Monte Carlo simulations;
• ANA detects cavities, calculates their volume and their flexibility in macromolecular structures and molecular dynamics trajectories;

This repository contains the core of the chemfiles library — written in C++11, with a C99 interface. You can also use chemfiles from other languages: Python 2&3, Fortran, Rust, and Julia.

Quick Links

• Is chemfiles for you?
• Main features of chemfiles
• Contact / Contribute / Cite
• Getting Started
• Supported File Formats
• Full documentation
• Documentation for using Chemfiles from various languages:
  • Python 2 and 3
  • Fortran
  • C and C++
  • Julia
  • Rust

Is chemfiles for you?

You might want to use chemfiles if any of these points appeals to you:

• you don't want to spend time writing and debugging a file parser;
• you use binary formats because they are faster and take up less disk space;
• you write analysis algorithms and want to read more than one trajectory format;
• you write simulation software and want to use more than one format for input or output.

There are other libraries doing the roughly the same job as chemfiles, have a look at them if chemfiles is not for you. Here we also say why we could not use them instead of creating a new library.

• OpenBabel is a C++ library providing convertions between more than 110 formats. It is more complex than chemfiles, and distributed under the GPL license.
• VMD molfile plugins are a collection of plugins witten in C and C++ used by VMD to read/write trajectory files. They do not support a variable number of atoms in a trajectory.
• MDTraj, MDAnalyis, cclib are Python libraries providing analysis and read capacities for trajectories. Unfortunely, they are only usable from Python.

Chemfiles Features

• Reads both text (XYZ, PDB, ...) and binary (NetCDF, TNG, ...) file formats;
• Transparently read and write compressed files (.gz, .xz and .bz2);
• Filters atoms with a rich selection language, including constrains on multiple atoms;
• Supports non-constant numbers of atoms in trajectories;
• Easy-to-use programming interface in Python, C++, C, Fortran 95, Julia and Rust;
• Cross-platform and usable from Linux, OS X and Windows;
• Open source and freely available (3-clauses BSD license);

Contact / Contribute / Cite

Chemfiles is free and open source. Your contributions are always welcome!

If you have questions or suggestions, or need help, please open an issue or join us on our Gitter chat room.

If you are using Chemfiles in a published scientific study, please cite us using the following DOI: https://doi.org/10.5281/zenodo.3653157.

Getting Started

Here, we'll help you get started with the C++ and C interface. If you want to use Chemfiles with another language, please refer to the corresponding documentation.

Installing Compiled Packages

We provide compiled packages of the latest Chemfiles release for Linux distributions. You can use your package manager to download them here.

We also provide conda packages in the conda-forge community channel for Linux and OS X. This package provides the C++, C and Python interfaces. Install the conda package by running:

conda install -c conda-forge chemfiles

Find more information about pre-compiled packages in the documentation.

Building from Source

You will need cmake and a C++11 compiler.

git clone https://github.com/chemfiles/chemfiles
cd chemfiles
mkdir build
cd build
cmake ..
make
make install

Usage Examples

This is what the interface looks like in C++:

#include <iostream>
#include "chemfiles.hpp"

int main() {
    chemfiles::Trajectory trajectory("filename.xyz");

    auto frame = trajectory.read();
    std::cout << "There are " << frame.size() << " atoms in the frame" << std::endl;

    auto positions = frame.positions();
    // Do awesome science with the positions here !
}

License

Guillaume Fraux created and maintains Chemfiles, which is distributed under the 3 clauses BSD license. By contributing to Chemfiles, you agree to distribute your contributions under the same license.

Chemfiles depends on multiple external libraries, which are distributed under their respective licenses. All external libraries licenses should be compatible with chemfiles's 3 clauses BSD. One notable execption depending on your use case is Gemmi which is distributed under the Mozilla Public License version 2. You can use CHFL_DISABLE_GEMMI=ON CMake flag to remove this dependency.

The AUTHORS file lists all contributors to Chemfiles. Many thanks to all of them!