Crate chemfiles [−] [src]

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 informations about atomic or residues names and positions. Some format also have additional informations, such as velocities, forces, energy, …

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

The overview of the classes organisation;
The lisf of supported formats;
The documentation for the selection language;

As all the function call the underlying C library, they all can fail and thus all return a Result<_, Error> value.

Structs

Atom	An `Atom` is a particle in the current `Frame`. It stores the following atomic properties:
Error	Error type for Chemfiles.
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 should be used like a `&[u64]`.
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.
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.
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.

Enums

CellShape	Available unit cell shapes.
Status	Possible causes of error in chemfiles

Functions

set_warning_callback	Use `callback` for every chemfiles warning. The callback will be passed the warning message.
version	Get the version of the chemfiles library.

Type Definitions

Result

Custom result type for working with errors in chemfiles