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clean code

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This commit is contained in:
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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37
src/lib.rs
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@@ -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]