Crate chemfiles

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Chemfiles is a multi-language library written in modern C++ for reading and writing from and to molecular trajectory files. These files are created by your favorite theoretical chemistry program, and contains information about atomic or residues names and positions. Some format also have additional information, such as velocities, forces, energy, …

This crate expose the C API of chemfiles to Rust, and make all the functionalities accessible. For more information on the C++ library, please see its documentation. Specifically, the following pages are worth reading:


  • An Atom is a particle in the current Frame. It stores the following atomic properties:
  • An analog to a mutable reference to an atom (&mut Atom)
  • An analog to a reference to an atom (&Atom)
  • Error type for Chemfiles.
  • FormatMetadata contains metadata associated with one format.
  • A Frame contains data from one simulation step: the current unit cell, the topology, the positions, and the velocities of the particles in the system. If some information is missing (topology or velocity or unit cell), the corresponding data is filled with a default value.
  • A Match is a set of atomic indexes matching a given selection. It can mostly be used like a &[usize].
  • MemoryTrajectoryReader is a handle for a Trajectory in memory.
  • An iterator over the properties in an atom/frame/residue
  • A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.
  • An analog to a reference to a residue (&Residue)
  • A Selection allow to select atoms in a Frame, from a selection language. The selection language is built by combining basic operations. Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in == != < <= > >=.
  • A Topology contains the definition of all the atoms in the system, and the liaisons between the atoms (bonds, angles, dihedrals, …). It will also contain all the residues information if it is available.
  • An analog to a reference to a topology (&Topology)
  • The Trajectory type is the main entry point when using chemfiles. A Trajectory behave a bit like a file, allowing to read and/or write Frame.
  • An UnitCell represent the box containing the atoms, and its periodicity.
  • An analog to a mutable reference to an unit cell (&mut UnitCell)
  • An analog to a reference to an unit cell (&UnitCell)


  • Possible bond order associated with bonds
  • Available unit cell shapes.
  • A Property is a piece of data that can be associated with an Atom or a Frame.
  • Possible causes of error in chemfiles


  • Read configuration data from the file at path.
  • Get the list of formats known by chemfiles, as well as all associated metadata.
  • Get the format that chemfiles would use to read a file at the given path.
  • Use callback for every chemfiles warning. The callback will be passed the warning message. This will drop any previous warning callback.
  • Get the version of the chemfiles library.