Trajectory
Chemfiles.Trajectory
— TypeA Trajectory
represents a simulation file on the hard drive. It can read or write one or many Frame
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.
Chemfiles.Trajectory
— TypeTrajectory(path::AbstractString, mode::Char='r', format::AbstractString="")
The Trajectory
function opens a trajectory file, using the file at the given path
. The opening mode
can be 'r'
for read, 'w'
for write or 'a'
for append, and defaults to 'r'
. The optional format
parameter give a specific file format to use when opening the file.
Chemfiles.Trajectory
— MethodTrajectory(f::Function, args...)
Apply the function f
to the result of Trajectory(args...)
and close the resulting trajectory upon completion, similar to open(f, args...)
.
Base.close
— Methodclose(trajectory::Trajectory)
Close a trajectory
. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Base.isopen
— Methodisopen(trajectory::Trajectory)
Check if the trajectory
is open.
Base.length
— Methodlength(trajectory::Trajectory)
Get the number of steps (the number of frames) in a trajectory
.
Base.read!
— Methodread!(trajectory::Trajectory, frame::Frame)
Read the next step of the trajectory
data into the preexisting Frame
structure.
Base.read
— Methodread(trajectory::Trajectory)
Read the next step of the trajectory
, and return the corresponding Frame
.
Base.size
— Methodsize(trajectory::Trajectory)
Get the number of steps (the number of frames) in a trajectory
.
Base.write
— Methodwrite(trajectory::Trajectory, frame::Frame)
Write the given frame
to the trajectory
.
Chemfiles.path
— Methodpath(trajectory::Trajectory)
Get the path used to open a trajectory
.
Chemfiles.read_step!
— Methodread_step!(trajectory::Trajectory, step::Integer, frame:Frame)
Read the given step
of the trajectory
into an preexisting Frame
structure.
Chemfiles.read_step
— Methodread_step(trajectory::Trajectory, step::Integer)
Read the given step
of the trajectory
, and return the corresponding Frame
.
Chemfiles.set_cell!
— Methodset_cell!(trajectory::Trajectory, cell::UnitCell)
Set the cell
associated with a trajectory
. This cell will be used when reading and writing the file, replacing any unit cell in the file.
Chemfiles.set_topology!
— Functionset_topology!(trajectory::Trajectory, path::AbstractString, format::AbstractString = "")
Set the Topology
associated with a trajectory
by reading the first frame of the file at path
; and extracting the topology of this frame. The optional format
parameter can be used to specify the file format.
Chemfiles.set_topology!
— Methodset_topology!(trajectory::Trajectory, topology::Topology)
Set the Topology
associated with a trajectory
. This topology will be used when reading and writing the file, replacing any topology in the file.