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clean code

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Daniel Bauer
2020-03-10 09:44:32 +01:00
parent 5390b089ac
commit b9f6b24b20
5 changed files with 46 additions and 36 deletions
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7
Cargo.lock generated
View File

@@ -20,6 +20,12 @@ dependencies = [
"winapi",
]
[[package]]
name = "assert_approx_eq"
version = "1.1.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3c07dab4369547dbe5114677b33fbbf724971019f3818172d59a97a61c774ffd"
[[package]]
name = "atty"
version = "0.2.14"
@@ -355,6 +361,7 @@ name = "wham"
version = "0.9.6"
dependencies = [
"GSL",
"assert_approx_eq",
"clap",
"error-chain",
"rand",

3
Cargo.toml
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@@ -13,6 +13,9 @@ rand = "0.5.5"
GSL = "1.0.0"
rayon = "1.0.3"
[dev-dependencies]
assert_approx_eq = "1.1.0"
[profile.release]
opt-level = 2

8
src/histogram.rs
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@@ -239,10 +239,10 @@ mod tests {
fn get_x_for_bin() {
let ds = build_hist_set();
let expected: Vec<f64> = vec![0,1,2,3,4,5,6,7,8].iter()
.map(|x| *x as f64 + 0.5).collect();
for i in 0..9 {
assert_eq!(expected[i], ds.get_coords_for_bin(i)[0]);
}
.map(|x| *x as f64 + 0.5).collect();
expected.iter().enumerate().for_each(|(i, exp)| {
assert_approx_eq!(exp, &ds.get_coords_for_bin(i)[0]);
})
}
#[test]

27
src/io.rs
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@@ -35,7 +35,7 @@ pub fn read_data(cfg: &Config) -> Result<Dataset> {
let bin_width: Vec<f64> = (0..cfg.dimens).map(|idx| {
(cfg.hist_max[idx] - cfg.hist_min[idx])/(cfg.num_bins[idx] as f64)
}).collect();
let num_bins = cfg.num_bins.iter().fold(1, |state, &bins| state*bins);
let num_bins = cfg.num_bins.iter().product();
let dimens_length = cfg.num_bins.clone();
let f = File::open(&cfg.metadata_file).chain_err(|| "Failed to open metadata file")?;
@@ -118,7 +118,7 @@ fn is_in_time_boundaries(time: f64, cfg: &Config) -> bool {
false
}
// parse a timeseries file into a histogram
// parse a time series file into a histogram
fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
let f = File::open(window_file)
.chain_err(|| format!("Failed to open sample data file {}.", window_file))?;
@@ -139,7 +139,7 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
while buf.read_line(&mut line).chain_err(|| "Failed to read line")? > 0 {
linecount += 1;
// skip comments and empty lines
if line.starts_with("#") || line.starts_with("@") || line.len() == 0 {
if line.starts_with('#') || line.starts_with('@') || line.is_empty() {
line.clear();
continue;
}
@@ -182,14 +182,14 @@ pub fn write_results(out_file: &str, ds: &Dataset, free: &[f64],
let header: String = (0..ds.dimens_lengths.len()).map(|d| format!("coord{}", d+1))
.collect::<Vec<String>>().join(" ");
writeln!(buf, "#{} {} {} {} {}",
header, "Free Energy", "+/-", "Probability", "+/-").unwrap();
writeln!(buf, "#{} Free Energy +/- Probability +/-", header).unwrap();
for bin in 0..free.len() {
let coords = ds.get_coords_for_bin(bin);
let coords_str: String = coords.iter().map(|c| {format!("{:8.6} ", c)})
.collect::<Vec<String>>().join("\t");
writeln!(buf, "{}{:8.6} {:8.6} {:8.6} {:8.6}", coords_str, free[bin], free_std[bin], prob[bin], prob_std[bin])
writeln!(buf, "{}{:8.6} {:8.6} {:8.6} {:8.6}", coords_str,
free[bin], free_std[bin], prob[bin], prob_std[bin])
.chain_err(|| "Failed to write to file.")?;
}
Ok(())
@@ -198,6 +198,7 @@ pub fn write_results(out_file: &str, ds: &Dataset, free: &[f64],
#[cfg(test)]
mod tests {
use super::*;
use assert_approx_eq::assert_approx_eq;
fn cfg() -> Config {
Config {
@@ -227,12 +228,12 @@ mod tests {
let h = super::read_window_file(&f, &cfg).unwrap();
println!("{:?}", h);
assert_eq!(5000, h.num_points);
assert_eq!(0.0, h.bins[2]);
assert_eq!(11.0, h.bins[3]);
assert_eq!(2236.0, h.bins[4]);
assert_eq!(2714.0, h.bins[5]);
assert_eq!(39.0, h.bins[6]);
assert_eq!(0.0, h.bins[7]);
assert_approx_eq!(0.0, h.bins[2]);
assert_approx_eq!(11.0, h.bins[3]);
assert_approx_eq!(2236.0, h.bins[4]);
assert_approx_eq!(2714.0, h.bins[5]);
assert_approx_eq!(39.0, h.bins[6]);
assert_approx_eq!(0.0, h.bins[7]);
}
@@ -244,7 +245,7 @@ mod tests {
assert_eq!(25, ds.num_windows);
assert_eq!(cfg.num_bins.len(), ds.dimens_lengths.len());
assert_eq!(cfg.num_bins[0], ds.dimens_lengths[0]);
assert_eq!(cfg.temperature * k_B, ds.kT);
assert_approx_eq!(cfg.temperature * k_B, ds.kT);
assert_eq!(25, ds.histograms.len())
}

37
src/lib.rs
View File

@@ -5,6 +5,10 @@ extern crate error_chain;
extern crate rand;
extern crate rgsl;
extern crate rayon;
#[cfg(test)]
#[macro_use]
extern crate assert_approx_eq;
pub mod io;
pub mod histogram;
@@ -21,7 +25,7 @@ pub mod errors { error_chain!{} }
use errors::*;
#[allow(non_upper_case_globals)]
static k_B: f64 = 0.0083144621; // kJ/mol*K
static k_B: f64 = 0.008_314_462_1; // kJ/mol*K
// Application config
#[derive(Debug)]
@@ -180,16 +184,11 @@ pub fn run(cfg: &Config) -> Result<()>{
let (P, F, F_prev) = perform_wham(&cfg, &dataset)?;
let P_std: Vec<f64>;
let free_energy_std: Vec<f64>;
if cfg.bootstrap > 0 {
let error_est = error_analysis::run_bootstrap(&cfg, dataset.clone(), &P, cfg.bootstrap);
P_std = error_est.0;
free_energy_std = error_est.1;
let (P_std, free_energy_std) = if cfg.bootstrap > 0 {
error_analysis::run_bootstrap(&cfg, dataset.clone(), &P, cfg.bootstrap)
} else {
P_std = vec![0.0; P.len()];
free_energy_std = vec![0.0; P.len()];
}
(vec![0.0; P.len()], vec![0.0; P.len()])
};
// calculate free energy and dump state
println!("Finished. Dumping final PMF");
@@ -292,21 +291,21 @@ mod tests {
let F = vec![1.0; dataset.num_bins] ;
let expected = vec!(0.0, 0.082_529_668_703_131_6, 40.923_558_470_974_93,
124_226.700_033_77, 2_308_526_035.528_374_7);
for b in 0..dataset.num_bins {
let p = super::calc_bin_probability(b, &dataset, &F);
assert_delta!(expected[b], p, 0.000_000_1);
}
}
expected.iter().enumerate().for_each(|(i, exp)| {
let p = super::calc_bin_probability(i, &dataset, &F);
assert_delta!(exp, p, 0.000_000_1);
})
}
#[test]
fn calc_bias_offset() {
let dataset = create_test_dataset();
let probability = vec!(0.0, 0.1, 0.2, 0.3, 0.4);
let expected = vec!(15.927_477_169_990_633, 15.927_477_169_990_633);
for window in 0..dataset.num_windows {
let F = super::calc_window_F(window, &dataset, &probability);
assert_delta!(expected[window], F, 0.000_000_1);
}
expected.iter().enumerate().for_each(|(i, exp)| {
let F = super::calc_window_F(i, &dataset, &probability);
assert_delta!(exp, F, 0.000_000_1);
})
}
#[test]