bauer/xdrfile
1
0
Fork 0
mirror of https://github.com/dnlbauer/xdrfile.git synced 2026-09-11 14:45:31 +00:00
Code Issues Packages Projects Releases Wiki Activity

Refactor frame to have desired semantics

Browse Source
This commit is contained in:
Josh Mitchell
2020-11-10 20:38:24 +11:00
committed by daniel
parent d559f9e6df
commit 734048d572
6 changed files with 36 additions and 53 deletions
Download Patch File Download Diff File Expand all files Collapse all files

29
src/lib.rs
View File

@@ -14,17 +14,17 @@
//! let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
//!
//! // find number of atoms in the file
//! let num_atoms = trj.get_num_atoms()?;
//! let num_atoms = trj.get_num_atoms()? as usize;
//!
//! // 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_capacity(num_atoms);
//! 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.num_atoms, num_atoms);
//! assert_eq!(frame.len(), num_atoms);
//!
//! let first_atom_coords = frame.coords[0];
//! assert_eq!(first_atom_coords, [-0.8901, 0.4127, -0.055499997]);
@@ -278,7 +278,7 @@ impl Trajectory for XTCTrajectory {
unsafe {
let code = xdrfile_xtc::write_xtc(
self.handle.xdrfile,
frame.num_atoms as i32,
frame.len() as i32,
frame.step as i32,
frame.time,
frame.box_vector.as_ptr() as *mut [[f32; 3]; 3],
@@ -413,7 +413,7 @@ impl Trajectory for TRRTrajectory {
unsafe {
let code = xdrfile_trr::write_trr(
self.handle.xdrfile,
frame.num_atoms as i32,
frame.len() as i32,
frame.step as i32,
frame.time,
0.0,
@@ -492,7 +492,6 @@ mod tests {
let natoms: u32 = 2;
let frame = Frame {
num_atoms: natoms,
step: 5,
time: 2.0,
box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
@@ -506,7 +505,7 @@ mod tests {
}
f.flush()?;
let mut new_frame = Frame::with_capacity(natoms);
let mut new_frame = Frame::with_len(natoms as usize);
let mut f = XTCTrajectory::open_read(tmp_path)?;
let num_atoms = f.get_num_atoms()?;
assert_eq!(num_atoms, natoms);
@@ -517,7 +516,7 @@ mod tests {
Ok(()) => {}
}
assert_eq!(new_frame.num_atoms, frame.num_atoms);
assert_eq!(new_frame.len(), frame.len());
assert_eq!(new_frame.step, frame.step);
assert_approx_eq!(new_frame.time, frame.time);
assert_eq!(new_frame.box_vector, frame.box_vector);
@@ -532,7 +531,6 @@ mod tests {
let natoms: u32 = 2;
let frame = Frame {
num_atoms: natoms,
step: 5,
time: 2.0,
box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
@@ -546,7 +544,7 @@ mod tests {
}
f.flush()?;
let mut new_frame = Frame::with_capacity(natoms);
let mut new_frame = Frame::with_len(natoms as usize);
let mut f = TRRTrajectory::open_read(tmp_path)?;
// let num_atoms = f.get_num_atoms()?;
// assert_eq!(num_atoms, natoms);
@@ -557,7 +555,7 @@ mod tests {
Ok(()) => {}
}
assert_eq!(new_frame.num_atoms, frame.num_atoms);
assert_eq!(new_frame.len(), frame.len());
assert_eq!(new_frame.step, frame.step);
assert_eq!(new_frame.time, frame.time);
assert_eq!(new_frame.box_vector, frame.box_vector);
@@ -569,7 +567,7 @@ mod tests {
pub fn test_manual_loop() -> Result<(), Box<dyn std::error::Error>> {
let mut xtc_frames = Vec::new();
let mut xtc_traj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
let mut frame = Frame::with_capacity(xtc_traj.get_num_atoms()?);
let mut frame = Frame::with_len(xtc_traj.get_num_atoms()? as usize);
while let Ok(()) = xtc_traj.read(&mut frame) {
xtc_frames.push(frame.clone());
@@ -583,7 +581,7 @@ mod tests {
}
for (xtc, trr) in xtc_frames.into_iter().zip(trr_frames) {
assert_eq!(xtc.num_atoms, trr.num_atoms);
assert_eq!(xtc.len(), trr.len());
assert_eq!(xtc.step, trr.step);
assert_eq!(xtc.time, trr.time);
assert_eq!(xtc.box_vector, trr.box_vector);
@@ -732,7 +730,7 @@ mod tests {
#[test]
fn test_err_could_not_read() -> Result<()> {
let file_name = "README.md"; // not a trajectory
let mut frame = Frame::with_capacity(1);
let mut frame = Frame::with_len(1);
let mut trr = TRRTrajectory::open_read(file_name)?;
if let Err(e) = trr.read(&mut frame) {
assert_eq!(Some(ErrorCode::ExdrMagic), e.code());
@@ -749,7 +747,6 @@ mod tests {
let natoms: u32 = 2;
let frame = Frame {
num_atoms: natoms,
step: 5,
time: 2.0,
box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
@@ -759,7 +756,7 @@ mod tests {
f.write(&frame)?;
f.flush()?;
let mut new_frame = Frame::with_capacity(natoms);
let mut new_frame = Frame::with_len(natoms as usize);
let mut f = XTCTrajectory::open_read(tmp_path)?;
f.read(&mut new_frame)?;