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Merge pull request #6 from Yoshanuikabundi/frame-semantics

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Frame semantics
This commit is contained in:
Daniel Bauer
2020-11-13 12:47:17 +01:00
committed by GitHub
parent d559f9e6df bbc0250af4
commit b0875b60a5
9 changed files with 61 additions and 80 deletions
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6
README.md
View File

@@ -21,13 +21,13 @@ fn main() -> Result<()> {
// 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]);
@@ -53,7 +53,7 @@ fn main() -> Result<()> {
for (idx, result) in trj.into_iter().enumerate() {
let frame = result?;
println!("{}", frame.time);
assert_eq!(idx+1, frame.step as usize);
assert_eq!(idx+1, frame.step);
}
Ok(())
}

1
benches/benchmarks.rs
View File

@@ -11,7 +11,6 @@ fn gen_test_traj(num_atoms: usize, num_frames: usize) -> Result<NamedTempFile> {
let mut f = XTCTrajectory::open_write(&tmp_path)?;
let mut frame = Frame {
num_atoms: num_atoms as u32,
step: 1,
time: 1.0,
box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],

4
src/c_abi/xdrfile_trr.rs
View File

@@ -52,7 +52,7 @@ mod tests {
let mut natoms = 0;
unsafe {
read_trr_natoms(path.as_ptr() as *const i8, &mut natoms);
read_trr_natoms(path.as_ptr(), &mut natoms);
}
assert!(natoms == 304);
Ok(())
@@ -64,7 +64,7 @@ mod tests {
let mut nframes: u64 = 0;
unsafe {
let code = read_trr_nframes(path.as_ptr() as *const i8, &mut nframes);
let code = read_trr_nframes(path.as_ptr(), &mut nframes);
assert!(code as u32 == exdrOK);
}
assert!(nframes == 38, "{:?}", nframes);

2
src/c_abi/xdrfile_xtc.rs
View File

@@ -60,7 +60,7 @@ mod tests {
let mut nframes: u64 = 0;
unsafe {
let code = read_xtc_nframes(path.as_ptr() as *const i8, &mut nframes);
let code = read_xtc_nframes(path.as_ptr(), &mut nframes);
assert!(code as u32 == exdrOK);
}
assert!(nframes == 38, "{:?}", nframes);

2
src/errors.rs
View File

@@ -304,7 +304,7 @@ mod tests {
let err = Error::from((path, mode));
assert_eq!(expected, err);
let frame = Frame::with_capacity(0);
let frame = Frame::with_len(0);
let expected = Error::WrongSizeFrame {
expected: 10,
found: 0,

46
src/frame.rs
View File

@@ -1,28 +1,22 @@
use std::fmt;
/// A frame represents a single step in a trajectory.
#[derive(Clone)]
#[derive(Clone, Debug)]
pub struct Frame {
/// Number of atoms in the frame
pub num_atoms: u32,
/// Trajectory step
pub step: u32,
pub step: usize,
/// Time step (usually in picoseconds)
pub time: f32,
/// 3x3 box vector
pub box_vector: [[f32; 3usize]; 3usize],
pub box_vector: [[f32; 3]; 3],
/// 3D coordinates for N atoms where N is num_atoms
pub coords: Vec<[f32; 3usize]>,
pub coords: Vec<[f32; 3]>,
}
impl Default for Frame {
fn default() -> Frame {
Frame {
num_atoms: 0,
step: 0,
time: 0.0,
box_vector: [[0.0; 3]; 3],
@@ -31,17 +25,6 @@ impl Default for Frame {
}
}
impl fmt::Debug for Frame {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
write!(
f,
"Frame {{ atoms: {}, step: {}, time: {}, \
box: {:?}, coords: {:?} }}",
self.num_atoms, self.step, self.time, self.box_vector, self.coords
)
}
}
impl Frame {
/// Creates an empty frame with a capacity of 0
pub fn new() -> Frame {
@@ -51,10 +34,9 @@ impl Frame {
}
/// Creates a frame with the given capacity
pub fn with_capacity(num_atoms: u32) -> Frame {
pub fn with_len(num_atoms: usize) -> Frame {
Frame {
num_atoms,
coords: vec![[0.0, 0.0, 0.0]; num_atoms as usize],
coords: vec![[0.0, 0.0, 0.0]; num_atoms],
..Default::default()
}
}
@@ -69,12 +51,16 @@ impl Frame {
.filter(|&(i, _)| indeces.contains(&i))
.map(|(_, elem)| elem)
.collect();
self.num_atoms = self.coords.len() as u32;
}
/// Length of the frame (number of atoms)
pub fn len(self: &Frame) -> usize {
self.num_atoms as usize
self.coords.len()
}
/// Resize the frame to have exactly `num_atoms` atoms, filling coords with zeros if necessary
pub fn resize(&mut self, num_atoms: usize) {
self.coords.resize(num_atoms, [0.0; 3])
}
}
@@ -84,28 +70,28 @@ mod tests {
#[test]
fn test_frame_with_capacity() {
let frame = Frame::with_capacity(10);
let frame = Frame::with_len(10);
println!("{:?}", frame.coords);
assert_eq!(frame.coords.len(), 10);
}
#[test]
fn test_frame_filter_atoms() {
let mut frame = Frame::with_capacity(3);
let mut frame = Frame::with_len(3);
frame.coords[0] = [1.0, 2.0, 3.0];
frame.coords[1] = [4.0, 5.0, 6.0];
frame.coords[2] = [7.0, 8.0, 9.0];
let filter: Vec<usize> = vec![1, 2];
let mut frame_new = frame.clone();
frame_new.filter_coords(&filter);
assert!(frame_new.num_atoms as usize == filter.len());
assert!(frame_new.len() == filter.len());
assert!(frame_new.coords[0] == frame.coords[1]);
assert!(frame_new.coords[1] == frame.coords[2]);
}
#[test]
fn test_frame_len() {
let frame = Frame::with_capacity(10);
let frame = Frame::with_len(10);
assert_eq!(frame.len(), 10);
}
}

4
src/iterator.rs
View File

@@ -4,7 +4,7 @@ use std::rc::Rc;
fn into_iter_inner<T: Trajectory>(mut traj: T) -> TrajectoryIterator<T> {
let num_atoms = traj.get_num_atoms();
let frame = match &num_atoms {
Ok(num_atoms) => Frame::with_capacity(*num_atoms),
Ok(num_atoms) => Frame::with_len(*num_atoms),
Err(_) => Frame::new(),
};
TrajectoryIterator {
@@ -58,7 +58,7 @@ impl<T: Trajectory> TrajectoryIterator<T> {
Some(item) => item,
None => {
// caller kept frame. Create new one
self.item = Rc::new(Frame::with_capacity(num_atoms));
self.item = Rc::new(Frame::with_len(num_atoms as usize));
Rc::get_mut(&mut self.item).expect("Could not get mutable access to new Rc")
}
};

74
src/lib.rs
View File

@@ -18,13 +18,13 @@
//!
//! // 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]);
@@ -50,7 +50,7 @@
//! for (idx, result) in trj.into_iter().enumerate() {
//! let frame = result?;
//! println!("{}", frame.time);
//! assert_eq!(idx+1, frame.step as usize);
//! assert_eq!(idx+1, frame.step);
//! }
//! Ok(())
//! }
@@ -205,14 +205,14 @@ pub trait Trajectory {
fn flush(&mut self) -> Result<()>;
/// Get the number of atoms from the give trajectory
fn get_num_atoms(&mut self) -> Result<u32>;
fn get_num_atoms(&mut self) -> Result<usize>;
}
/// Read/Write XTC Trajectories
pub struct XTCTrajectory {
handle: XDRFile,
precision: Cell<f32>, // internal mutability required for read method
num_atoms: Lazy<Result<u32>>,
num_atoms: Lazy<Result<usize>>,
}
impl XTCTrajectory {
@@ -245,9 +245,9 @@ impl Trajectory for XTCTrajectory {
fn read(&mut self, frame: &mut Frame) -> Result<()> {
let mut step: i32 = 0;
let num_atoms =
self.get_num_atoms()
.map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))? as usize;
let num_atoms = self
.get_num_atoms()
.map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))?;
if num_atoms != frame.coords.len() {
Err((&*frame, num_atoms))?;
}
@@ -265,7 +265,7 @@ impl Trajectory for XTCTrajectory {
frame.coords.as_mut_ptr(),
&mut self.precision.get(),
) as u32;
frame.step = step as u32;
frame.step = step as usize;
if let Some(err) = check_code(code, ErrorTask::Read) {
Err(err)
} else {
@@ -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],
@@ -304,7 +304,7 @@ impl Trajectory for XTCTrajectory {
}
}
fn get_num_atoms(&mut self) -> Result<u32> {
fn get_num_atoms(&mut self) -> Result<usize> {
self.num_atoms
.get_or_create(|| {
let mut num_atoms: i32 = 0;
@@ -320,7 +320,7 @@ impl Trajectory for XTCTrajectory {
if let Some(err) = check_code(code, ErrorTask::ReadNumAtoms) {
Err(err)
} else {
Ok(num_atoms as u32)
Ok(num_atoms as usize)
}
}
})
@@ -344,7 +344,7 @@ impl io::Seek for XTCTrajectory {
/// Read/Write TRR Trajectories
pub struct TRRTrajectory {
handle: XDRFile,
num_atoms: Lazy<Result<u32>>,
num_atoms: Lazy<Result<usize>>,
}
impl TRRTrajectory {
@@ -377,9 +377,9 @@ impl Trajectory for TRRTrajectory {
let mut step: i32 = 0;
let mut lambda: f32 = 0.0;
let num_atoms =
self.get_num_atoms()
.map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))? as usize;
let num_atoms = self
.get_num_atoms()
.map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))?;
if num_atoms != frame.coords.len() {
Err((&*frame, num_atoms))?;
}
@@ -400,7 +400,8 @@ impl Trajectory for TRRTrajectory {
std::ptr::null_mut(),
std::ptr::null_mut(),
) as u32;
frame.step = step as u32;
frame.step = step as usize;
if let Some(err) = check_code(code, ErrorTask::Read) {
Err(err)
} else {
@@ -413,7 +414,7 @@ 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,
@@ -441,7 +442,7 @@ impl Trajectory for TRRTrajectory {
}
}
fn get_num_atoms(&mut self) -> Result<u32> {
fn get_num_atoms(&mut self) -> Result<usize> {
self.num_atoms
.get_or_create(|| {
let mut num_atoms: i32 = 0;
@@ -456,7 +457,7 @@ impl Trajectory for TRRTrajectory {
if let Some(err) = check_code(code, ErrorTask::ReadNumAtoms) {
Err(err)
} else {
Ok(num_atoms as u32)
Ok(num_atoms as usize)
}
}
})
@@ -490,9 +491,8 @@ mod tests {
let tempfile = NamedTempFile::new().expect("Could not create temporary file");
let tmp_path = tempfile.path();
let natoms: u32 = 2;
let natoms = 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 +506,7 @@ mod tests {
}
f.flush()?;
let mut new_frame = Frame::with_capacity(natoms);
let mut new_frame = Frame::with_len(natoms);
let mut f = XTCTrajectory::open_read(tmp_path)?;
let num_atoms = f.get_num_atoms()?;
assert_eq!(num_atoms, natoms);
@@ -517,7 +517,7 @@ 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 +532,6 @@ 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 +545,7 @@ 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 +556,7 @@ 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 +568,7 @@ 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()?);
while let Ok(()) = xtc_traj.read(&mut frame) {
xtc_frames.push(frame.clone());
@@ -583,7 +582,7 @@ 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);
@@ -635,9 +634,8 @@ mod tests {
let tempfile = NamedTempFile::new()?;
let tmp_path = tempfile.path();
let natoms: u32 = 2;
let natoms: usize = 2;
let frame = Frame {
num_atoms: natoms,
step: 5,
time: 2.0,
box_vector: [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]],
@@ -649,7 +647,7 @@ mod tests {
assert_eq!(f.tell(), 144);
f.flush()?;
let mut new_frame = Frame::with_capacity(natoms);
let mut new_frame = Frame::with_len(natoms);
let mut f = TRRTrajectory::open_read(tmp_path)?;
assert_eq!(f.tell(), 0);
@@ -664,9 +662,8 @@ mod tests {
let tempfile = NamedTempFile::new()?;
let tmp_path = tempfile.path();
let natoms: u32 = 2;
let natoms: usize = 2;
let mut frame = Frame {
num_atoms: natoms,
step: 0,
time: 0.0,
box_vector: [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]],
@@ -681,7 +678,7 @@ mod tests {
let after_second_frame = f.tell();
f.flush()?;
let mut new_frame = Frame::with_capacity(natoms);
let mut new_frame = Frame::with_len(natoms);
let mut f = TRRTrajectory::open_read(tmp_path)?;
let pos = f.seek(std::io::SeekFrom::Current(144))?;
assert_eq!(pos, after_first_frame);
@@ -689,7 +686,7 @@ mod tests {
f.read(&mut new_frame)?;
assert_eq!(f.tell(), after_second_frame);
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);
@@ -732,7 +729,7 @@ 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 +746,6 @@ 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 +755,7 @@ 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)?;

2
tests/integration.rs
View File

@@ -8,7 +8,7 @@ mod integration {
fn test_use_library() -> Result<()> {
let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
let num_atoms = trj.get_num_atoms()?;
let mut frame = Frame::with_capacity(num_atoms);
let mut frame = Frame::with_len(num_atoms as usize);
trj.read(&mut frame)?;
trj.read(&mut frame)?;