mscore/chemistry/
amino_acid.rs

1use std::collections::HashMap;
2
3/// Amino Acids
4///
5/// # Arguments
6///
7/// None
8///
9/// # Returns
10///
11/// * `HashMap<&'static str, &'static str>` - a map of amino acid names to their one-letter codes
12///
13/// # Example
14///
15/// ```
16/// use mscore::chemistry::amino_acid::amino_acids;
17///
18/// let amino_acids = amino_acids();
19/// assert_eq!(amino_acids.get("Lysine"), Some(&"K"));
20/// ```
21pub fn amino_acids() -> HashMap<&'static str, &'static str> {
22    let mut map = HashMap::new();
23    map.insert("Lysine", "K");
24    map.insert("Alanine", "A");
25    map.insert("Glycine", "G");
26    map.insert("Valine", "V");
27    map.insert("Tyrosine", "Y");
28    map.insert("Arginine", "R");
29    map.insert("Glutamic Acid", "E");
30    map.insert("Phenylalanine", "F");
31    map.insert("Tryptophan", "W");
32    map.insert("Leucine", "L");
33    map.insert("Threonine", "T");
34    map.insert("Cysteine", "C");
35    map.insert("Serine", "S");
36    map.insert("Glutamine", "Q");
37    map.insert("Methionine", "M");
38    map.insert("Isoleucine", "I");
39    map.insert("Asparagine", "N");
40    map.insert("Proline", "P");
41    map.insert("Histidine", "H");
42    map.insert("Aspartic Acid", "D");
43    map.insert("Selenocysteine", "U");
44    map
45}
46
47
48/// Amino Acid Masses
49///
50/// # Arguments
51///
52/// None
53///
54/// # Returns
55///
56/// * `HashMap<&'static str, f64>` - a map of amino acid one-letter codes to their monoisotopic masses
57///
58/// # Example
59///
60/// ```
61/// use mscore::chemistry::amino_acid::amino_acid_masses;
62///
63/// let amino_acid_masses = amino_acid_masses();
64/// assert_eq!(amino_acid_masses.get("K"), Some(&128.094963));
65/// ```
66pub fn amino_acid_masses() -> HashMap<&'static str, f64> {
67    let mut map = HashMap::new();
68    map.insert("A", 71.037114);
69    map.insert("R", 156.101111);
70    map.insert("N", 114.042927);
71    map.insert("D", 115.026943);
72    map.insert("C", 103.009185);
73    map.insert("E", 129.042593);
74    map.insert("Q", 128.058578);
75    map.insert("G", 57.021464);
76    map.insert("H", 137.058912);
77    map.insert("I", 113.084064);
78    map.insert("L", 113.084064);
79    map.insert("K", 128.094963);
80    map.insert("M", 131.040485);
81    map.insert("F", 147.068414);
82    map.insert("P", 97.052764);
83    map.insert("S", 87.032028);
84    map.insert("T", 101.047679);
85    map.insert("W", 186.079313);
86    map.insert("Y", 163.063329);
87    map.insert("V", 99.068414);
88    map.insert("U", 168.053);
89    map
90}
91
92/// Amino Acid Composition
93///
94/// # Arguments
95///
96/// None
97///
98/// # Returns
99///
100/// * `HashMap<char, HashMap<&'static str, i32>>` - a map of amino acid one-letter codes to their atomic compositions
101///
102/// # Example
103///
104/// ```
105/// use mscore::chemistry::amino_acid::amino_acid_composition;
106/// use std::collections::HashMap;
107///
108/// let amino_acid_composition = amino_acid_composition();
109/// assert_eq!(amino_acid_composition.get(&'K'), Some(&HashMap::from([("C", 6), ("H", 12), ("N", 2), ("O", 1)])));
110/// ```
111pub fn amino_acid_composition() -> HashMap<char, HashMap<&'static str, i32>> {
112
113    let mut composition: HashMap<char, HashMap<&'static str, i32>> = HashMap::new();
114
115    composition.insert('G', HashMap::from([("C", 2), ("H", 3), ("N", 1), ("O", 1)])); // Glycine
116    composition.insert('A', HashMap::from([("C", 3), ("H", 5), ("N", 1), ("O", 1)])); // Alanine
117    composition.insert('S', HashMap::from([("C", 3), ("H", 5), ("N", 1), ("O", 2)])); // Serine
118    composition.insert('P', HashMap::from([("C", 5), ("H", 7), ("N", 1), ("O", 1)])); // Proline
119    composition.insert('V', HashMap::from([("C", 5), ("H", 9), ("N", 1), ("O", 1)])); // Valine
120    composition.insert('T', HashMap::from([("C", 4), ("H", 7), ("N", 1), ("O", 2)])); // Threonine
121    composition.insert('C', HashMap::from([("C", 3), ("H", 5), ("N", 1), ("O", 1), ("S", 1)])); // Cysteine
122    composition.insert('I', HashMap::from([("C", 6), ("H", 11), ("N", 1), ("O", 1)])); // Isoleucine
123    composition.insert('L', HashMap::from([("C", 6), ("H", 11), ("N", 1), ("O", 1)])); // Leucine
124    composition.insert('N', HashMap::from([("C", 4), ("H", 6), ("N", 2), ("O", 2)])); // Asparagine
125    composition.insert('D', HashMap::from([("C", 4), ("H", 5), ("N", 1), ("O", 3)])); // Aspartic Acid
126    composition.insert('Q', HashMap::from([("C", 5), ("H", 8), ("N", 2), ("O", 2)])); // Glutamine
127    composition.insert('K', HashMap::from([("C", 6), ("H", 12), ("N", 2), ("O", 1)])); // Lysine
128    composition.insert('E', HashMap::from([("C", 5), ("H", 7), ("N", 1), ("O", 3)])); // Glutamic Acid
129    composition.insert('M', HashMap::from([("C", 5), ("H", 9), ("N", 1), ("O", 1), ("S", 1)])); // Methionine
130    composition.insert('H', HashMap::from([("C", 6), ("H", 7), ("N", 3), ("O", 1)])); // Histidine
131    composition.insert('F', HashMap::from([("C", 9), ("H", 9), ("N", 1), ("O", 1)])); // Phenylalanine
132    composition.insert('R', HashMap::from([("C", 6), ("H", 12), ("N", 4), ("O", 1)])); // Arginine
133    composition.insert('Y', HashMap::from([("C", 9), ("H", 9), ("N", 1), ("O", 2)])); // Tyrosine
134    composition.insert('W', HashMap::from([("C", 11), ("H", 10), ("N", 2), ("O", 1)])); // Tryptophan
135    composition.insert('U', HashMap::from([("C", 3), ("H", 5), ("N", 1), ("O", 1), ("Se", 1)])); // Selenocysteine
136
137    composition
138}
mscore/chemistry/amino_acid.rs

mscore/chemistry/
amino_acid.rs
