Crate chemfiles

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:

• The overview of the classes organization;
• The list of supported formats;
• The documentation for the selection language;

Structs

• Atom
  An Atom is a particle in the current Frame. It stores the following atomic properties:
• AtomMut
  An analog to a mutable reference to an atom (&mut Atom)
• AtomRef
  An analog to a reference to an atom (&Atom)
• Error
  Error type for Chemfiles.
• FormatMetadata
  FormatMetadata contains metadata associated with one format.
• Frame
  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.
• Match
  A Match is a set of atomic indexes matching a given selection. It can mostly be used like a &[usize].
• MemoryTrajectoryReader
  MemoryTrajectoryReader is a handle for a Trajectory in memory.
• PropertiesIter
  An iterator over the properties in an atom/frame/residue
• 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.
• ResidueRef
  An analog to a reference to a residue (&Residue)
• Selection
  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 == != < <= > >=.
• Topology
  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.
• TopologyRef
  An analog to a reference to a topology (&Topology)
• Trajectory
  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.
• UnitCell
  An UnitCell represent the box containing the atoms, and its periodicity.
• UnitCellMut
  An analog to a mutable reference to an unit cell (&mut UnitCell)
• UnitCellRef
  An analog to a reference to an unit cell (&UnitCell)

Enums

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

Functions

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