WriteTrajectory

mutable struct WriteTrajectory

Represents a molecular dynamics trajectory being written to disk.

A trajectory consists of a set of states of a molecular simulation. This structure allows for writing frames into a trajectory sequentially.

Fields

• format: trajectory file format
• exported_particle_properties: particle properties written into trajectory
• filepath: path to trajectory (filename may contain mask '*')
• io: current output file stream
• isopen: trajectory is open flag

WriteTrajectory(
    filepath::String,
    format::MolecularDynamicsFiles.Format.T,
    exported_particle_properties::Vector{Symbol}
) -> WriteTrajectory

Create a WriteTrajectory with trajectory files specified by filepath, of format format, writing exported_particle_properties.

All the snapshots (MDFrame objects) may be written to a single file, in this case snapshot data will be written one after another in the file.

Alternatively, every frame may be written in a separate file: if the filename of filepath contains a single wildcard symbol "*", representing a mask. In this case, every frame is written in a separate file with the timestep of the frame in place of the mask.

If filename of filepath ends with ".gz", files are written in GZip format.

exported_particle_properties may contain properties defined in the frame, and also properties: :x, :y, :z, :xs, :ys, :zs, :xu, :yu, :zu, :xsu, :ysu, :zsu, :ix, :iy, :iz if they can be computed from the frame data. For example, if a frame has unwrapped positions, all of those properties can be computed.

Base.write(t::WriteTrajectory, frame::MDFrame)

Write a frame to a trajectory.

Base.close(t::WriteTrajectory)

Close the trajectory.

Must be called after finishing writing the trajectory to ensure that all data has been written.