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Format with rustfmt

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This commit is contained in:
Josh Mitchell
2020-11-07 20:03:05 +11:00
parent 042f0f82c6
commit e30a175d0d
9 changed files with 204 additions and 139 deletions
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157
src/lib.rs
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@@ -8,7 +8,7 @@
//! # Basic usage example
//! ```rust
//! use xdrfile::*;
//! use std::path::Path;
//! use std::path::Path;
//!
//! let mut path = Path::new("tests/1l2y.xtc");
//! // get a handle to the file
@@ -16,18 +16,18 @@
//!
//! // find number of atoms in the file
//! let num_atoms = trj.get_num_atoms().unwrap();
//!
//!
//! // 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);
//!
//!
//! // read the first frame of the trajectory
//! let result = trj.read(&mut frame);
//! match result {
//! Ok(_) => {
//! assert_eq!(frame.step, 1);
//! assert_eq!(frame.num_atoms, num_atoms);
//!
//!
//! let first_atom_coords = frame.coords[0];
//! assert_eq!(first_atom_coords, [-0.8901, 0.4127, -0.055499997]);
//! }
@@ -45,12 +45,12 @@
//!
//! ```rust
//! use xdrfile::*;
//! use std::path::Path;
//! use std::path::Path;
//!
//! let mut path = Path::new("tests/1l2y.xtc");
//! // get a handle to the file
//! let trj = XTCTrajectory::open(path, FileMode::Read).unwrap();
//!
//!
//! // iterate over all frames
//! for (idx, frame) in trj.into_iter().filter_map(Result::ok).enumerate() {
//! println!("{}", frame.time);
@@ -58,33 +58,33 @@
//! }
//! ```
#[cfg(test)]
#[macro_use] extern crate assert_approx_eq;
#[macro_use]
extern crate assert_approx_eq;
extern crate lazy_init;
pub mod c_abi;
mod frame;
mod iterator;
pub mod c_abi;
pub use frame::Frame;
pub use iterator::*;
use c_abi::xdr_seek;
use c_abi::xdrfile;
use c_abi::xdrfile::XDRFILE;
use c_abi::xdr_seek;
use c_abi::xdrfile_xtc;
use c_abi::xdrfile_trr;
use c_abi::xdrfile_xtc;
use failure::{err_msg, Error};
use lazy_init::Lazy;
use std::cell::Cell;
use std::ffi::CString;
use std::path::Path;
use failure::{Error,err_msg};
use std::cell::Cell;
use lazy_init::Lazy;
pub enum FileMode {
Write,
Append,
Read
Read,
}
impl FileMode {
@@ -98,8 +98,8 @@ impl FileMode {
}
fn path_to_cstring(path: &Path) -> CString {
CString::new(path.to_str().unwrap()).unwrap()
}
CString::new(path.to_str().unwrap()).unwrap()
}
/// A safe wrapper around the c implementation of an XDRFile
struct XDRFile {
@@ -109,18 +109,22 @@ struct XDRFile {
}
impl XDRFile {
pub fn open(path: &Path, filemode: FileMode) -> Result<XDRFile, Error> {
let path_p = path_to_cstring(path).into_raw();
let mode_p = CString::new(filemode.value()).unwrap().into_raw();
unsafe {
let xdrfile = xdrfile::xdrfile_open(path_p, mode_p);
if ! xdrfile.is_null() {
if !xdrfile.is_null() {
let path = String::from(path.to_str().unwrap());
Ok(XDRFile { xdrfile, filemode, path })
} else { // Something went wrong. But the C api does not tell us what
Ok(XDRFile {
xdrfile,
filemode,
path,
})
} else {
// Something went wrong. But the C api does not tell us what
Err(err_msg("Failed to open trajectory file"))
}
}
@@ -133,75 +137,86 @@ impl Drop for XDRFile {
unsafe {
xdrfile::xdrfile_close(self.xdrfile);
}
}
}
}
/// The trajectory trait defines shared methods for xtc and trr trajectories
pub trait Trajectory {
/// Read the next step of the trajectory into the frame object
fn read(&mut self, frame: &mut Frame) -> Result<(), Error>;
/// Write the frame to the trajectory file
fn write(&mut self, frame: &Frame) -> Result<(), Error>;
/// Flush the trajectory file
fn flush(&mut self) -> Result<(), Error>;
/// Get the number of atoms from the give trajectory
fn get_num_atoms(&mut self) -> Result<u32, Error>;
fn get_num_atoms(&mut self) -> Result<u32, Error>;
}
/// Read/Write XTC Trajectories
pub struct XTCTrajectory {
handle: XDRFile,
precision: Cell<f32>, // internal mutability required for read method
num_atoms: Lazy<Result<u32, Error>>
precision: Cell<f32>, // internal mutability required for read method
num_atoms: Lazy<Result<u32, Error>>,
}
impl XTCTrajectory {
pub fn open(path: &Path, filemode: FileMode) -> Result<XTCTrajectory, Error> {
let xdr = XDRFile::open(path, filemode)?;
Ok(XTCTrajectory { handle: xdr, precision: Cell::new(1000.0), num_atoms: Lazy::new() })
Ok(XTCTrajectory {
handle: xdr,
precision: Cell::new(1000.0),
num_atoms: Lazy::new(),
})
}
}
impl Trajectory for XTCTrajectory {
fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
unsafe {
// C lib requires an i32 to be passed, but step is exposed it as u32
// (A step cannot be negative, can it?). So we need to create a step
// variable to pass to read_xtc and cast it afterwards to u32
let mut step: i32 = 0;
let code = xdrfile_xtc::read_xtc(self.handle.xdrfile,
let code = xdrfile_xtc::read_xtc(
self.handle.xdrfile,
frame.num_atoms as i32,
&mut step,
&mut frame.time,
&mut frame.box_vector,
frame.coords.as_ptr() as *mut [f32; 3],
&mut self.precision.get(),
) as u32;
) as u32;
frame.step = step as u32;
match code {
xdrfile::exdrOK => Ok(()),
_ => Err(err_msg(format!("Failed to read trajectory. Error code: {}", code))),
_ => Err(err_msg(format!(
"Failed to read trajectory. Error code: {}",
code
))),
}
}
}
fn write(&mut self, frame: &Frame) -> Result<(), Error> {
unsafe {
let code = xdrfile_xtc::write_xtc(self.handle.xdrfile,
let code = xdrfile_xtc::write_xtc(
self.handle.xdrfile,
frame.num_atoms as i32,
frame.step as i32,
frame.time,
frame.box_vector.as_ptr() as *mut [[f32; 3]; 3],
frame.coords[..].as_ptr() as *mut [f32; 3],
1000.0) as u32;
1000.0,
) as u32;
match code {
xdrfile::exdrOK => Ok(()),
_ => Err(err_msg(format!("Failed to write trajectory. Error code: {}", code)))
_ => Err(err_msg(format!(
"Failed to write trajectory. Error code: {}",
code
))),
}
}
}
@@ -211,9 +226,12 @@ impl Trajectory for XTCTrajectory {
let code = xdr_seek::xdr_flush(self.handle.xdrfile) as u32;
match code {
xdrfile::exdrOK => Ok(()),
_ => Err(err_msg(format!("Failed to flush trajectory. Error code: {}", code)))
_ => Err(err_msg(format!(
"Failed to flush trajectory. Error code: {}",
code
))),
}
}
}
}
fn get_num_atoms(&mut self) -> Result<u32, Error> {
@@ -222,37 +240,42 @@ impl Trajectory for XTCTrajectory {
unsafe {
let path = CString::new(self.handle.path.as_str()).unwrap();
let path_p = path.into_raw();
let code = xdrfile_xtc::read_xtc_natoms(path_p, &mut num_atoms as *const i32) as u32;
let code =
xdrfile_xtc::read_xtc_natoms(path_p, &mut num_atoms as *const i32) as u32;
match code {
xdrfile::exdrOK => Ok(num_atoms as u32),
_ => Err(err_msg(format!("Failed to read atom number from trajectory. Error code: {}", code)))
_ => Err(err_msg(format!(
"Failed to read atom number from trajectory. Error code: {}",
code
))),
}
}
});
match result {
Ok(val) => Ok(*val),
// ugly hack because failure::Error is not "Clone"
Err(err) => Err(err_msg(format!("{}", err)))
Err(err) => Err(err_msg(format!("{}", err))),
}
}
}
/// Read/Write TRR Trajectories
pub struct TRRTrajectory {
handle: XDRFile,
num_atoms: Lazy<Result<u32, Error>>
num_atoms: Lazy<Result<u32, Error>>,
}
impl TRRTrajectory {
pub fn open(path: &Path, filemode: FileMode) -> Result<TRRTrajectory, Error> {
let xdr = XDRFile::open(path, filemode)?;
Ok(TRRTrajectory { handle: xdr, num_atoms: Lazy::new() })
Ok(TRRTrajectory {
handle: xdr,
num_atoms: Lazy::new(),
})
}
}
impl Trajectory for TRRTrajectory {
fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
unsafe {
// C lib requires an i32 to be passed, but step is exposed it as u32
@@ -261,7 +284,8 @@ impl Trajectory for TRRTrajectory {
// Similar for lambda.
let mut step: i32 = 0;
let mut lambda: f32 = 0.0;
let code = xdrfile_trr::read_trr(self.handle.xdrfile,
let code = xdrfile_trr::read_trr(
self.handle.xdrfile,
frame.num_atoms as i32,
&mut step,
&mut frame.time,
@@ -269,19 +293,23 @@ impl Trajectory for TRRTrajectory {
&mut frame.box_vector,
frame.coords.as_ptr() as *mut [f32; 3],
std::ptr::null_mut(),
std::ptr::null_mut()
) as u32;
std::ptr::null_mut(),
) as u32;
frame.step = step as u32;
match code {
xdrfile::exdrOK => Ok(()),
_ => Err(err_msg(format!("Failed to read trajectory. Error code: {}", code)))
_ => Err(err_msg(format!(
"Failed to read trajectory. Error code: {}",
code
))),
}
}
}
fn write(&mut self, frame: &Frame) -> Result<(), Error> {
unsafe {
let code = xdrfile_trr::write_trr(self.handle.xdrfile,
let code = xdrfile_trr::write_trr(
self.handle.xdrfile,
frame.num_atoms as i32,
frame.step as i32,
frame.time,
@@ -289,10 +317,14 @@ impl Trajectory for TRRTrajectory {
frame.box_vector.as_ptr() as *mut [[f32; 3]; 3],
frame.coords[..].as_ptr() as *mut [f32; 3],
std::ptr::null_mut(),
std::ptr::null_mut()) as u32;
std::ptr::null_mut(),
) as u32;
match code {
xdrfile::exdrOK => Ok(()),
_ => Err(err_msg(format!("Failed to write trajectory. Error code: {}", code)))
_ => Err(err_msg(format!(
"Failed to write trajectory. Error code: {}",
code
))),
}
}
}
@@ -302,9 +334,12 @@ impl Trajectory for TRRTrajectory {
let code = xdr_seek::xdr_flush(self.handle.xdrfile) as u32;
match code {
xdrfile::exdrOK => Ok(()),
_ => Err(err_msg(format!("Failed to flush trajectory. Error code: {}", code)))
_ => Err(err_msg(format!(
"Failed to flush trajectory. Error code: {}",
code
))),
}
}
}
}
fn get_num_atoms(&mut self) -> Result<u32, Error> {
@@ -313,27 +348,30 @@ impl Trajectory for TRRTrajectory {
unsafe {
let path = CString::new(self.handle.path.as_str()).unwrap();
let path_p = path.into_raw();
let code = xdrfile_trr::read_trr_natoms(path_p, &mut num_atoms as *const i32) as u32;
let code =
xdrfile_trr::read_trr_natoms(path_p, &mut num_atoms as *const i32) as u32;
match code {
xdrfile::exdrOK => Ok(num_atoms as u32),
_ => Err(err_msg(format!("Failed to read atom number from trajectory. Error code: {}", code)))
_ => Err(err_msg(format!(
"Failed to read atom number from trajectory. Error code: {}",
code
))),
}
}
});
match result {
Ok(val) => Ok(*val),
// ugly hack because failure::Error is not "Clone"
Err(err) => Err(err_msg(format!("{}", err)))
Err(err) => Err(err_msg(format!("{}", err))),
}
}
}
#[cfg(test)]
mod tests {
use super::*;
use tempfile::NamedTempFile;
use tempfile::NamedTempFile;
#[test]
fn test_read_write_xtc() {
@@ -413,4 +451,3 @@ mod tests {
assert_eq!(new_frame.coords, frame.coords);
}
}