Trajectory
type
- type
Trajectory
- A
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.
- function
Trajectory
(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.
- function
Trajectory
(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...)
.
- function
path
(trajectory::Trajectory) - Get the path used to open a
trajectory
.
- function
read
(trajectory::Trajectory) - Read the next step of the
trajectory
, and return the corresponding Frame
.
- function
read_step
(trajectory::Trajectory, step::Integer) - Read the given
step
of the trajectory
, and return the corresponding
Frame
.
- function
write
(trajectory::Trajectory, frame::Frame) - Write the given
frame
to the trajectory
.
- function
set_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.
- function
set_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.
- function
set_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.
- function
length
(trajectory::Trajectory) - Get the number of steps (the number of frames) in a
trajectory
.
- function
close
(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.
- function
isopen
(trajectory::Trajectory) - Check if the
trajectory
is open.