Expand description
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
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]
.
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
)
Enums
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
Functions
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.