Chemfiles.jl

# Chemfiles.jl, a modern library for chemistry file reading and writing
# Copyright (C) Guillaume Fraux and contributors -- BSD license

module Chemfiles
    using DocStringExtensions

    @template METHODS =
    """
    $(TYPEDSIGNATURES)

    $(DOCSTRING)
    """

    module lib
        using Chemfiles_jll
        include("generated/types.jl")
        include("generated/cdef.jl")
    end

    include("misc.jl")
    include("utils.jl")

    export Trajectory, Topology, Atom, UnitCell, Frame, Selection, Residue

    function version()
        unsafe_string(lib.chfl_version())
    end

    # A `Property` is a generic container for additional data stored by some
    # formats
    struct Property
        __handle :: CxxPointer{lib.CHFL_PROPERTY}
    end

    """
    An `Atom` is a particle in the current [`Frame`](@ref).

    An atom stores the following atomic properties:
      - atom name
      - atom type
      - atom mass
      - atom charge

    The atom name is usually an unique identifier (`"H1"`, `"C_a"`) while the
    atom type will be shared among all particles of the same type: `"H"`,
    `"Ow"`, `"CH3"`.
    """
    struct Atom
        __handle :: CxxPointer{lib.CHFL_ATOM}
    end

    """
    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.*
    """
    struct Residue
        __handle :: CxxPointer{lib.CHFL_RESIDUE}
    end

    """
    A `Topology` describes the organisation of the particles in the system:
    what their names are, how they are bonded together, *etc.* A `Topology`
    is a list of [`Atom`](@ref)s in the system, together with the list of bonds
    between the atoms.
    """
    struct Topology
        __handle :: CxxPointer{lib.CHFL_TOPOLOGY}
    end

    """
    A `UnitCell` describes the bounding box of a system. It is represented by
    a 3x3 matrix containing the base vectors `a`, `b` and `c`.
    """
    struct UnitCell
        __handle :: CxxPointer{lib.CHFL_CELL}
    end

    """
    A `Frame` holds data for one step of a simulation. As not all formats
    provide all the types of information, some fields may be initialized to a
    default value. A `Frame` may contain the following data:

    - Positions for all the atoms in the system;
    - Velocities for all the atoms in the system;
    - The [`Topology`](@ref) of the system;
    - The [`UnitCell`](@ref) of the system.
    """
    struct Frame
        __handle :: CxxPointer{lib.CHFL_FRAME}
    end

    """
    A `Selection` is used to select a group of atoms. Examples of selections are
    "name H" and "(x < 45 and name O) or name C". See the `full documentation
    <http://chemfiles.org/chemfiles/latest/selections.html>`_ for more
    information about the selection language.
    """
    struct Selection
        __handle :: CxxPointer{lib.CHFL_SELECTION}
    end

    """
    Data (either binary or string) used for in-memory reading of trajectory

        DataBuffer = Union{AbstractString,Vector{UInt8},Nothing}
    """
    DataBuffer = Union{AbstractString,Vector{UInt8},Nothing}

    """
    A `Trajectory` represents a simulation file on the hard drive. It can read
    or write one or many [`Frame`](@ref)s to this file. The file format can be
    automatically determined from the extention, or manually specified.
    Writing to a `Trajectory` is buffered, which means that one needs to
    `close()` the trajectory and flush the buffer before being able to read the
    file again.
    """
    struct Trajectory
        __handle :: CxxPointer{lib.CHFL_TRAJECTORY}
        # hold a reference to the data to prevent garbage collection when using
        # a in-memory reader
        __data::DataBuffer
    end

    include("Property.jl")
    include("Atom.jl")
    include("Residue.jl")
    include("Topology.jl")
    include("UnitCell.jl")
    include("Frame.jl")
    include("Selection.jl")
    include("Trajectory.jl")

    include("atomsbase.jl")

    function __init__()
        if !startswith(version(), "0.10")
            error(
                """Chemfiles.jl requires the 0.10 version of libchemfiles,
                but $(version()) is installed."""
            )
        end
        set_warning_callback(__default_warning_callback)
    end
end