crn 0.1.2

Stochastic and deterministic simulation of chemical reaction networks.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134

//! # crn
//! A library for simulating chemical reaction networks.

#![warn(missing_docs)]

use std::collections::HashMap;
use std::fmt::Display;
use std::str::FromStr;

pub use det::DetCrn;
use itertools::Itertools;
pub use state::State;
pub use sto::Error;
pub use sto::StoCrn;

/// Deterministic CRNs.
pub mod det;
/// Parsing CRNs from strings.
pub mod parse;
/// Some fun CRNs to play with.
pub mod presets;
/// State of a CRN.
pub mod state;
/// Stochastic CRNs.
pub mod sto;

/// A chemical reaction, with a rate parameter.
#[derive(Clone, Debug, PartialEq)]
pub struct Reaction {
    reactants: HashMap<usize, i32>,
    products: HashMap<usize, i32>,
    delta: HashMap<usize, i32>,
    rate: f64,
}

impl Reaction {
    fn new(reactants: HashMap<usize, i32>, products: HashMap<usize, i32>, rate: f64) -> Self {
        Self {
            reactants: reactants.clone(),
            delta: {
                let mut hm = products.clone();

                for (species, count) in reactants {
                    if let Some(cur_count) = hm.get_mut(&species) {
                        *cur_count -= count;
                    } else {
                        hm.insert(species, -count);
                    }
                }
                hm
            },
            products,
            rate,
        }
    }
}

/// Shared behavior for stochastic and deterministic CRNs.
#[derive(Default, Clone)]
pub struct Crn<T> {
    /// The CRN's reactions.
    pub rxns: Vec<Reaction>,
    /// The CRN's current state.
    pub state: State<T>,
    /// The CRN's initial state, which it reverts to on a reset.
    pub init_state: State<T>,
    /// The name of each species.
    pub names: bimap::BiHashMap<usize, String>,
}

impl<T> Crn<T>
where
    T: Clone,
{
    /// Resets the CRN to its initial state.
    pub fn reset(&mut self) {
        self.state = self.init_state.clone();
    }
}

impl<T> Display for Crn<T>
where
    T: Display,
{
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
        let reactants_to_string = move |reactants: &HashMap<usize, i32>| -> String {
            if reactants.is_empty() {
                return String::new();
            }
            let mut result = reactants
                .iter()
                .sorted()
                .fold(String::new(), |acc, (i, count)| {
                    if *count == 1 {
                        acc + self.names.get_by_left(i).unwrap() + " + "
                    } else {
                        acc + &format!("{}{} + ", count, self.names.get_by_left(i).unwrap())
                    }
                });
            result.truncate(result.len() - 3);
            result
        };

        let mut result = String::new();

        for (i, ct) in self.state.species.iter().enumerate() {
            result.push_str(&format!(
                "{} = {};\n",
                self.names.get_by_left(&i).unwrap(),
                ct
            ));
        }

        for rxn in self.rxns.iter() {
            result.push_str(&format!(
                "{} -> {} : {};\n",
                reactants_to_string(&rxn.reactants),
                reactants_to_string(&rxn.products),
                rxn.rate
            ));
        }
        write!(f, "{}", result)
    }
}

impl<T> From<String> for Crn<T>
where
    T: Clone + Default + FromStr,
    <T as FromStr>::Err: std::fmt::Debug,
{
    fn from(s: String) -> Self {
        Self::parse(&s).unwrap()
    }
}