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:
Atom is a particle in the current
Frame. It stores the following
An analog to a mutable reference to an atom (
An analog to a reference to an atom (
Error type for Chemfiles.
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 is a set of atomic indexes matching a given selection. It can
mostly be used like a
An iterator over the properties in an atom/frame/residue
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,
An analog to a reference to a residue (
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 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 (
Trajectory type is the main entry point when using chemfiles. A
Trajectory behave a bit like a file, allowing to read and/or write
UnitCell represent the box containing the atoms, and its periodicity.
An analog to a mutable reference to an unit cell (
An analog to a reference to an unit cell (
Possible bond order associated with bonds
Available unit cell shapes.
Property is a piece of data that can be associated with an
Atom or a
Possible causes of error in chemfiles
Read configuration data from the file at
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.