Crate xdrfile

xdrfile

Read and write xdr trajectory files in .xtc and .trr file format

This crate is mainly intended to be a wrapper around the GROMACS libxdrfile XTC library and provides basic functionality to read and write xtc and trr files with a safe api.

Basic usage example

use xdrfile::*;

fn main() -> Result<()> {
    // get a handle to the file
    let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;

    // find number of atoms in the file
    let num_atoms = trj.get_num_atoms()?;

    // a frame object is used to get to read or write from a trajectory
    // without instantiating data arrays for every step
    let mut frame = Frame::with_len(num_atoms);

    // read the first frame of the trajectory
    trj.read(&mut frame)?;

    assert_eq!(frame.step, 1);
    assert_eq!(frame.len(), num_atoms);

    let first_atom_coords = frame.coords[0];
    assert_eq!(first_atom_coords, [-0.8901, 0.4127, -0.055499997]);

    Ok(())
}

Frame iteration

For convenience, the trajectory implementations provide “into_iter” to be turned into an iterator that yields Rc. If a frame is not kept during iteration, the Iterator reuses it for better performance (and hence, Rc is required)

use xdrfile::*;

fn main() -> Result<()> {
    // get a handle to the file
    let trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;

    // iterate over all frames
    for (idx, result) in trj.into_iter().enumerate() {
        let frame = result?;
        println!("{}", frame.time);
        assert_eq!(idx+1, frame.step);
    }
    Ok(())
}

Modules

• c_abi
  Low level bindings to the c library from GROMACS

Structs

• Frame
  A frame represents a single step in a trajectory.
• TRRTrajectory
  Handle to Read/Write TRR Trajectories
• TrajectoryIterator
  Iterator for trajectories. This iterator yields a Result<Frame, Error> for each frame in the trajectory file and stops with yielding None once the trajectory is EOF. Also yields None after the first occurrence of an error
• XTCTrajectory
  Handle to Read/Write XTC Trajectories

Enums

• Error
  Error type for the xdrfile library
• ErrorCode
  Error codes returned from the C API
• ErrorTask
  The task being attempted when the C API returns an error
• FileMode
  File Mode for accessing trajectories.

Traits

• Trajectory
  The trajectory trait defines shared methods for xtc and trr trajectories

Type Aliases

• Result
  Result type for errors in the xdrfile crate