https://github.com/dnlbauer/xdrfile
Rust Wrapper around the GROMACS libxdrfile library. A low level api to read and write molecular trajectories in .xtc and .trr format.
https://github.com/dnlbauer/xdrfile
gromacs molecular-dynamics trajectories trr xdrfile xtc
Last synced: about 1 year ago
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Rust Wrapper around the GROMACS libxdrfile library. A low level api to read and write molecular trajectories in .xtc and .trr format.
- Host: GitHub
- URL: https://github.com/dnlbauer/xdrfile
- Owner: dnlbauer
- Created: 2020-04-16T13:00:55.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2021-05-12T07:58:45.000Z (about 5 years ago)
- Last Synced: 2025-04-14T11:07:23.422Z (about 1 year ago)
- Topics: gromacs, molecular-dynamics, trajectories, trr, xdrfile, xtc
- Language: Rust
- Homepage:
- Size: 354 KB
- Stars: 7
- Watchers: 2
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
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README
[](https://travis-ci.org/danijoo/xdrfile) [](https://www.crates.io/crates/xdrfile) [](https://docs.rs/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.
## 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