Chemfiles classes overviewΒΆ

This figure represents how the basic classes of chemfiles are organised and how they interact together. The only classes a chemfiles user should worry about are the Trajectory, Frame, Topology, Residue, Atom, UnitCell and Selection. All of these are described in this section.

They are various way of interacting with these classes, all of them being described in the Classes and functions reference section for the C++ interface.


A Trajectory is the main entry point of chemfiles. It reads one or many Frame from a file on the disk using a specific format. The file type and the format are automatically determined from the extention.

A Frame holds data for one step of a simulation, consisting in the positions for all the atoms; optionally the velocities for all the atoms; the Topology and the UnitCell of the system.

The Topology describes the organisation of the particles in the system. It contains a list of Atom in the system, and informations about which atoms are bonded together. A Residue is a group of atoms bonded together, which may or may not corresponds to molecules. When working with bio-molecules and specifically proteins from the PDB data bank, the residues should correspond to amino-acids in the protein.

The Atom class contains basic information about the atoms in the system: the name (if it is available), mass, kind of atom and so on. Atoms are not limited to plain chemical elements.

The UnitCell class describes the boundary conditions of the system: where are the boundaries, and what is the periodicity of theses boundaries. An unit cell can be of three types: Infinite, Orthorombic or Triclinic. Infinite cells do not have any boundaries. Orthorombic cells are defined by three orthogonals vectors, and triclinic cells are defined by three vectors without any constrain.

Chemfiles also provides a selection language, implemented in the Selection class. This selection language allows the users to select a group of atoms from a Frame using a selection string. Examples of selections strings are "name H" and "(x < 45 and name O) or name C".