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Removed trivial casts and changed frame.step to usize

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This commit is contained in:
Josh Mitchell
2020-11-10 20:45:38 +11:00
committed by daniel
parent 734048d572
commit 3c36d3040e
6 changed files with 28 additions and 27 deletions
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4
README.md
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@@ -17,7 +17,7 @@ fn main() -> Result<()> {
let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?; let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
// find number of atoms in the file // find number of atoms in the file
let num_atoms = trj.get_num_atoms()? as usize; let num_atoms = trj.get_num_atoms()?;
// a frame object is used to get to read or write from a trajectory // a frame object is used to get to read or write from a trajectory
// without instantiating data arrays for every step // without instantiating data arrays for every step
@@ -53,7 +53,7 @@ fn main() -> Result<()> {
for (idx, result) in trj.into_iter().enumerate() { for (idx, result) in trj.into_iter().enumerate() {
let frame = result?; let frame = result?;
println!("{}", frame.time); println!("{}", frame.time);
assert_eq!(idx+1, frame.step as usize); assert_eq!(idx+1, frame.step);
} }
Ok(()) Ok(())
} }

4
src/c_abi/xdrfile_trr.rs
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@@ -52,7 +52,7 @@ mod tests {
let mut natoms = 0; let mut natoms = 0;
unsafe { unsafe {
read_trr_natoms(path.as_ptr() as *const i8, &mut natoms); read_trr_natoms(path.as_ptr(), &mut natoms);
} }
assert!(natoms == 304); assert!(natoms == 304);
Ok(()) Ok(())
@@ -64,7 +64,7 @@ mod tests {
let mut nframes: u64 = 0; let mut nframes: u64 = 0;
unsafe { 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!(code as u32 == exdrOK);
} }
assert!(nframes == 38, "{:?}", nframes); assert!(nframes == 38, "{:?}", nframes);

2
src/c_abi/xdrfile_xtc.rs
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@@ -60,7 +60,7 @@ mod tests {
let mut nframes: u64 = 0; let mut nframes: u64 = 0;
unsafe { 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!(code as u32 == exdrOK);
} }
assert!(nframes == 38, "{:?}", nframes); assert!(nframes == 38, "{:?}", nframes);

2
src/frame.rs
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@@ -2,7 +2,7 @@
#[derive(Clone, Debug)] #[derive(Clone, Debug)]
pub struct Frame { pub struct Frame {
/// Trajectory step /// Trajectory step
pub step: u32, pub step: usize,
/// Time step (usually in picoseconds) /// Time step (usually in picoseconds)
pub time: f32, pub time: f32,

2
src/iterator.rs
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@@ -2,7 +2,7 @@ use crate::*;
use std::rc::Rc; use std::rc::Rc;
fn into_iter_inner<T: Trajectory>(mut traj: T) -> TrajectoryIterator<T> { fn into_iter_inner<T: Trajectory>(mut traj: T) -> TrajectoryIterator<T> {
let num_atoms = traj.get_num_atoms().map(|n| n as usize); let num_atoms = traj.get_num_atoms();
let frame = match &num_atoms { let frame = match &num_atoms {
Ok(num_atoms) => Frame::with_len(*num_atoms), Ok(num_atoms) => Frame::with_len(*num_atoms),
Err(_) => Frame::new(), Err(_) => Frame::new(),

41
src/lib.rs
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@@ -14,7 +14,7 @@
//! let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?; //! let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
//! //!
//! // find number of atoms in the file //! // find number of atoms in the file
//! let num_atoms = trj.get_num_atoms()? as usize; //! let num_atoms = trj.get_num_atoms()?;
//! //!
//! // a frame object is used to get to read or write from a trajectory //! // a frame object is used to get to read or write from a trajectory
//! // without instantiating data arrays for every step //! // without instantiating data arrays for every step
@@ -50,7 +50,7 @@
//! for (idx, result) in trj.into_iter().enumerate() { //! for (idx, result) in trj.into_iter().enumerate() {
//! let frame = result?; //! let frame = result?;
//! println!("{}", frame.time); //! println!("{}", frame.time);
//! assert_eq!(idx+1, frame.step as usize); //! assert_eq!(idx+1, frame.step);
//! } //! }
//! Ok(()) //! Ok(())
//! } //! }
@@ -205,14 +205,14 @@ pub trait Trajectory {
fn flush(&mut self) -> Result<()>; fn flush(&mut self) -> Result<()>;
/// Get the number of atoms from the give trajectory /// 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 /// Read/Write XTC Trajectories
pub struct XTCTrajectory { pub struct XTCTrajectory {
handle: XDRFile, handle: XDRFile,
precision: Cell<f32>, // internal mutability required for read method precision: Cell<f32>, // internal mutability required for read method
num_atoms: Lazy<Result<u32>>, num_atoms: Lazy<Result<usize>>,
} }
impl XTCTrajectory { impl XTCTrajectory {
@@ -245,9 +245,9 @@ impl Trajectory for XTCTrajectory {
fn read(&mut self, frame: &mut Frame) -> Result<()> { fn read(&mut self, frame: &mut Frame) -> Result<()> {
let mut step: i32 = 0; let mut step: i32 = 0;
let num_atoms = let num_atoms = self
self.get_num_atoms() .get_num_atoms()
.map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))? as usize; .map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))?;
if num_atoms != frame.coords.len() { if num_atoms != frame.coords.len() {
Err((&*frame, num_atoms))?; Err((&*frame, num_atoms))?;
} }
@@ -265,7 +265,7 @@ impl Trajectory for XTCTrajectory {
frame.coords.as_mut_ptr(), frame.coords.as_mut_ptr(),
&mut self.precision.get(), &mut self.precision.get(),
) as u32; ) as u32;
frame.step = step as u32; frame.step = step as usize;
if let Some(err) = check_code(code, ErrorTask::Read) { if let Some(err) = check_code(code, ErrorTask::Read) {
Err(err) Err(err)
} else { } else {
@@ -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 self.num_atoms
.get_or_create(|| { .get_or_create(|| {
let mut num_atoms: i32 = 0; let mut num_atoms: i32 = 0;
@@ -320,7 +320,7 @@ impl Trajectory for XTCTrajectory {
if let Some(err) = check_code(code, ErrorTask::ReadNumAtoms) { if let Some(err) = check_code(code, ErrorTask::ReadNumAtoms) {
Err(err) Err(err)
} else { } else {
Ok(num_atoms as u32) Ok(num_atoms as usize)
} }
} }
}) })
@@ -344,7 +344,7 @@ impl io::Seek for XTCTrajectory {
/// Read/Write TRR Trajectories /// Read/Write TRR Trajectories
pub struct TRRTrajectory { pub struct TRRTrajectory {
handle: XDRFile, handle: XDRFile,
num_atoms: Lazy<Result<u32>>, num_atoms: Lazy<Result<usize>>,
} }
impl TRRTrajectory { impl TRRTrajectory {
@@ -377,9 +377,9 @@ impl Trajectory for TRRTrajectory {
let mut step: i32 = 0; let mut step: i32 = 0;
let mut lambda: f32 = 0.0; let mut lambda: f32 = 0.0;
let num_atoms = let num_atoms = self
self.get_num_atoms() .get_num_atoms()
.map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))? as usize; .map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))?;
if num_atoms != frame.coords.len() { if num_atoms != frame.coords.len() {
Err((&*frame, num_atoms))?; Err((&*frame, num_atoms))?;
} }
@@ -400,7 +400,8 @@ impl Trajectory for TRRTrajectory {
std::ptr::null_mut(), std::ptr::null_mut(),
std::ptr::null_mut(), std::ptr::null_mut(),
) as u32; ) as u32;
frame.step = step as u32;
frame.step = step as usize;
if let Some(err) = check_code(code, ErrorTask::Read) { if let Some(err) = check_code(code, ErrorTask::Read) {
Err(err) Err(err)
} else { } else {
@@ -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 self.num_atoms
.get_or_create(|| { .get_or_create(|| {
let mut num_atoms: i32 = 0; let mut num_atoms: i32 = 0;
@@ -456,7 +457,7 @@ impl Trajectory for TRRTrajectory {
if let Some(err) = check_code(code, ErrorTask::ReadNumAtoms) { if let Some(err) = check_code(code, ErrorTask::ReadNumAtoms) {
Err(err) Err(err)
} else { } else {
Ok(num_atoms as u32) Ok(num_atoms as usize)
} }
} }
}) })
@@ -490,7 +491,7 @@ mod tests {
let tempfile = NamedTempFile::new().expect("Could not create temporary file"); let tempfile = NamedTempFile::new().expect("Could not create temporary file");
let tmp_path = tempfile.path(); let tmp_path = tempfile.path();
let natoms: u32 = 2; let natoms = 2;
let frame = Frame { let frame = Frame {
step: 5, step: 5,
time: 2.0, time: 2.0,
@@ -505,7 +506,7 @@ mod tests {
} }
f.flush()?; f.flush()?;
let mut new_frame = Frame::with_len(natoms as usize); let mut new_frame = Frame::with_len(natoms);
let mut f = XTCTrajectory::open_read(tmp_path)?; let mut f = XTCTrajectory::open_read(tmp_path)?;
let num_atoms = f.get_num_atoms()?; let num_atoms = f.get_num_atoms()?;
assert_eq!(num_atoms, natoms); assert_eq!(num_atoms, natoms);
@@ -567,7 +568,7 @@ mod tests {
pub fn test_manual_loop() -> Result<(), Box<dyn std::error::Error>> { pub fn test_manual_loop() -> Result<(), Box<dyn std::error::Error>> {
let mut xtc_frames = Vec::new(); let mut xtc_frames = Vec::new();
let mut xtc_traj = XTCTrajectory::open_read("tests/1l2y.xtc")?; let mut xtc_traj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
let mut frame = Frame::with_len(xtc_traj.get_num_atoms()? as usize); let mut frame = Frame::with_len(xtc_traj.get_num_atoms()?);
while let Ok(()) = xtc_traj.read(&mut frame) { while let Ok(()) = xtc_traj.read(&mut frame) {
xtc_frames.push(frame.clone()); xtc_frames.push(frame.clone());