https://github.com/dnlbauer/xdrfile

Rust Wrapper around the GROMACS libxdrfile library. A low level api to read and write .xtc and .trr files.
https://github.com/dnlbauer/xdrfile

gromacs molecular-dynamics trajectories trr xdrfile xtc

Last synced: 2 months ago
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Rust Wrapper around the GROMACS libxdrfile library. A low level api to read and write .xtc and .trr files.

• Host: GitHub
• URL: https://github.com/dnlbauer/xdrfile
• Owner: dnlbauer
• Created: 2020-04-16T13:00:55.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2021-05-12T07:58:45.000Z (over 3 years ago)
• Last Synced: 2023-03-11T19:03:51.045Z (almost 2 years ago)
• Topics: gromacs, molecular-dynamics, trajectories, trr, xdrfile, xtc
• Language: Rust
• Homepage:
• Size: 354 KB
• Stars: 3
• Watchers: 2
• Forks: 1
• Open Issues: 4
• Metadata Files:
  • Readme: README.md

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README

        
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# 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.

## Examples

### Basic usage

```rust

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[0];  // shorthand for 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)

```rust

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(())

}

```

## xdrfile

Uses the lowlevel xdrfile c library version 1.1.4 with some minor fixes and additions copied from [mdtraj](https://github.com/mdtraj/mdtraj).

## License

Licensed under LGPL because this is what the underlying c library (xdrfile) uses