Struct chemfiles::Trajectory

pub struct Trajectory { /* fields omitted */ }

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.

Implementations

impl Trajectory

pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error> where
    P: AsRef<Path>, 

Open the file at the given path in the given mode.

Valid modes are 'r' for read, 'w' for write and 'a' for append.

Errors

This function fails if the file is not accessible for the given mode, if it is incorrectly formatted for the corresponding format, or in case of I/O errors from the OS.

Example

let trajectory = Trajectory::open("water.xyz", 'r').unwrap();

pub fn open_with_format<'a, P, S>(
    filename: P,
    mode: char,
    format: S
) -> Result<Trajectory, Error> where
    P: AsRef<Path>,
    S: Into<&'a str>, 

Open the file at the given path using a specific file format and the given mode.

Valid modes are 'r' for read, 'w' for write and 'a' for append.

Specifying a format is needed when the file format does not match the extension, or when there is not standard extension for this format. If format is an empty string, the format will be guessed from the extension.

Errors

This function fails if the file is not accessible for the given mode, if it is incorrectly formatted for the corresponding format, or in case of I/O errors from the OS.

Example

let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();

pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
    S: Into<&'a str>, 

Read a memory buffer as though it was a formatted file.

The memory buffer used to store the file is given using the data argument. The format parameter is required and should follow the same rules as in the main Trajectory constructor.

Errors

This function fails if the data is incorrectly formatted for the corresponding format, or if the format do not support in-memory readers.

Example

let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap();
let mut frame = Frame::new();
trajectory.read(&mut frame).unwrap();
assert_eq!(frame.size(), 6);

pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error> where
    S: Into<&'a str>, 

Write to a memory buffer as though it was a formatted file.

The format parameter should follow the same rules as in the main Trajectory constructor, except that compression specification is not supported.

The memory_buffer function can be used to retrieve the data written to memory of the Trajectory.

Errors

This function fails if the format do not support in-memory writers.

Example

let trajectory_memory = Trajectory::memory_writer("SMI");

// Binary formats typically do not support this feature
assert!(Trajectory::memory_writer("XTC").is_err());

pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>

Read the next step of this trajectory into a frame.

If the number of atoms in frame does not correspond to the number of atom in the next step, the frame is resized.

Errors

This function fails if the data is incorrectly formatted for the corresponding format, or in case of I/O errors from the OS.

Example

let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
let mut frame = Frame::new();

trajectory.read(&mut frame).unwrap();

pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>

Read a specific step of this trajectory into a frame.

If the number of atoms in frame does not correspond to the number of atom at this step, the frame is resized.

Errors

This function fails if the data is incorrectly formatted for the corresponding format.

Example

let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
let mut frame = Frame::new();

trajectory.read_step(10, &mut frame).unwrap();

pub fn write(&mut self, frame: &Frame) -> Result<(), Error>

Write a frame to this trajectory.

Errors

This function fails if the data is incorrectly formatted for the corresponding format.

Example

let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap();
let mut frame = Frame::new();

trajectory.write(&mut frame).unwrap();

pub fn set_topology(&mut self, topology: &Topology)

Set the topology associated with this trajectory. This topology will be used when reading and writing the files, replacing any topology in the frames or files.

Example

let mut topology = Topology::new();
topology.add_atom(&Atom::new("H"));
topology.add_atom(&Atom::new("O"));
topology.add_atom(&Atom::new("H"));
topology.add_bond(0, 1);
topology.add_bond(1, 2);

let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
trajectory.set_topology(&topology);

pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error> where
    P: AsRef<Path>, 

Set the topology associated with this trajectory by reading the first frame of the file at the given path using the file format in format; and extracting the topology of this frame.

Errors

This function fails if the topology file is incorrectly formatted for the corresponding format, or in case of I/O errors from the OS.

Example

let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
trajectory.set_topology_file("topology.pdb").unwrap();

pub fn set_topology_with_format<'a, P, S>(
    &mut self,
    path: P,
    format: S
) -> Result<(), Error> where
    P: AsRef<Path>,
    S: Into<&'a str>, 

Set the topology associated with this trajectory by reading the first frame of the file at the given path using the file format in format; and extracting the topology of this frame.

If format is an empty string, the format will be guessed from the path extension.

Errors

This function fails if the topology file is incorrectly formatted for the corresponding format, or in case of I/O errors from the OS.

Example

let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();

pub fn set_cell(&mut self, cell: &UnitCell)

Set the unit cell associated with a trajectory. This cell will be used when reading and writing the files, replacing any unit cell in the frames or files.

Example

let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));

pub fn nsteps(&mut self) -> usize

Get the number of steps (the number of frames) in a trajectory.

Example

let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();

println!("This trajectory contains {} steps", trajectory.nsteps());

pub fn memory_buffer(&self) -> Result<&str, Error>

Obtain the memory buffer written to by the trajectory.

Errors

This fails if the trajectory was not opened with Trajectory::memory_writer.

Example

let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();

let mut frame = Frame::new();
frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
frame.add_bond_with_order(0, 1, BondOrder::Single);

trajectory_memory.write(&frame).unwrap();

let result = trajectory_memory.memory_buffer();
assert_eq!(result.unwrap(), "CC\n");

pub fn path(&self) -> String

Get file path for this trajectory.

Example

let trajectory = Trajectory::open("water.xyz", 'r').unwrap();

assert_eq!(trajectory.path(), "water.xyz");

Trait Implementations

impl Drop for Trajectory

fn drop(&mut self)

Executes the destructor for this type.