ferritin_core/info/
constants.rs

1//! # Constants
2//!
3//! This module contains core data structures and functions for analyzing molecular structures.
4//!
5//! ## Residue Types
6//! The module provides functions to check residue types:
7//!
8//! - `is_amino_acid()` - Check if a residue is an amino acid
9//! - `is_carbohydrate()` - Check if a residue is a carbohydrate
10//! - `is_nucleotide()` - Check if a residue is a nucleotide
11//!
12//! ## Bond Information
13//! Bond data from CCD includes:
14//!
15//! - Bond lengths with standard deviations
16//! - Canonical amino acid connectivity
17//! - Bond order information
18//!
19
20use std::collections::{HashMap, HashSet};
21use std::sync::OnceLock;
22
23#[rustfmt::skip]
24#[allow(dead_code)]
25pub(crate) fn default_distance_range(a: &str, b: &str) -> Option<(f32, f32)> {
26    match (a, b) {
27        // https://github.com/biotite-dev/biotite/blob/main/src/biotite/structure/bonds.pyx#L1341C1-L1389C1
28        //               # Taken from Allen et al.
29        //                 min   - 2*std     max   + 2*std
30        ("B",  "C" ) => Some((1.556 - 2.0*0.015,  1.556 + 2.0*0.015)),
31        ("BR", "C" ) => Some((1.875 - 2.0*0.029,  1.966 + 2.0*0.029)),
32        ("BR", "O" ) => Some((1.581 - 2.0*0.007,  1.581 + 2.0*0.007)),
33        ("C",  "C" ) => Some((1.174 - 2.0*0.011,  1.588 + 2.0*0.025)),
34        ("C",  "CL") => Some((1.713 - 2.0*0.011,  1.849 + 2.0*0.011)),
35        ("C",  "F" ) => Some((1.320 - 2.0*0.009,  1.428 + 2.0*0.009)),
36        ("C",  "H" ) => Some((1.059 - 2.0*0.030,  1.099 + 2.0*0.007)),
37        ("C",  "I" ) => Some((2.095 - 2.0*0.015,  2.162 + 2.0*0.015)),
38        ("C",  "N" ) => Some((1.325 - 2.0*0.009,  1.552 + 2.0*0.023)),
39        ("C",  "O" ) => Some((1.187 - 2.0*0.011,  1.477 + 2.0*0.008)),
40        ("C",  "P" ) => Some((1.791 - 2.0*0.006,  1.855 + 2.0*0.019)),
41        ("C",  "S" ) => Some((1.630 - 2.0*0.014,  1.863 + 2.0*0.015)),
42        ("C",  "SE") => Some((1.893 - 2.0*0.013,  1.970 + 2.0*0.032)),
43        ("C",  "SI") => Some((1.837 - 2.0*0.012,  1.888 + 2.0*0.023)),
44        ("CL", "O" ) => Some((1.414 - 2.0*0.026,  1.414 + 2.0*0.026)),
45        ("CL", "P" ) => Some((1.997 - 2.0*0.035,  2.008 + 2.0*0.035)),
46        ("CL", "S" ) => Some((2.072 - 2.0*0.023,  2.072 + 2.0*0.023)),
47        ("CL", "SI") => Some((2.072 - 2.0*0.009,  2.072 + 2.0*0.009)),
48        ("F",  "N" ) => Some((1.406 - 2.0*0.016,  1.406 + 2.0*0.016)),
49        ("F",  "P" ) => Some((1.495 - 2.0*0.016,  1.579 + 2.0*0.025)),
50        ("F",  "S" ) => Some((1.640 - 2.0*0.011,  1.640 + 2.0*0.011)),
51        ("F",  "SI") => Some((1.588 - 2.0*0.014,  1.694 + 2.0*0.013)),
52        ("H",  "N" ) => Some((1.009 - 2.0*0.022,  1.033 + 2.0*0.022)),
53        ("H",  "O" ) => Some((0.967 - 2.0*0.010,  1.015 + 2.0*0.017)),
54        ("I",  "O" ) => Some((2.144 - 2.0*0.028,  2.144 + 2.0*0.028)),
55        ("N",  "N" ) => Some((1.124 - 2.0*0.015,  1.454 + 2.0*0.021)),
56        ("N",  "O" ) => Some((1.210 - 2.0*0.011,  1.463 + 2.0*0.012)),
57        ("N",  "P" ) => Some((1.571 - 2.0*0.013,  1.697 + 2.0*0.015)),
58        ("N",  "S" ) => Some((1.541 - 2.0*0.022,  1.710 + 2.0*0.019)),
59        ("N",  "SI") => Some((1.711 - 2.0*0.019,  1.748 + 2.0*0.022)),
60        ("O",  "P" ) => Some((1.449 - 2.0*0.007,  1.689 + 2.0*0.024)),
61        ("O",  "S" ) => Some((1.423 - 2.0*0.008,  1.580 + 2.0*0.015)),
62        ("O",  "SI") => Some((1.622 - 2.0*0.014,  1.680 + 2.0*0.008)),
63        ("P",  "P" ) => Some((2.214 - 2.0*0.022,  2.214 + 2.0*0.022)),
64        ("P",  "S" ) => Some((1.913 - 2.0*0.014,  1.954 + 2.0*0.005)),
65        ("P",  "SE") => Some((2.093 - 2.0*0.019,  2.093 + 2.0*0.019)),
66        ("P",  "SI") => Some((2.264 - 2.0*0.019,  2.264 + 2.0*0.019)),
67        ("S",  "S" ) => Some((1.897 - 2.0*0.012,  2.070 + 2.0*0.022)),
68        ("S",  "SE") => Some((2.193 - 2.0*0.015,  2.193 + 2.0*0.015)),
69        ("S",  "SI") => Some((2.145 - 2.0*0.020,  2.145 + 2.0*0.020)),
70        ("SE", "SE") => Some((2.340 - 2.0*0.024,  2.340 + 2.0*0.024)),
71        ("SI", "SE") => Some((2.359 - 2.0*0.012,  2.359 + 2.0*0.012)),
72        _ => None,
73    }
74}
75
76#[allow(clippy::type_complexity)] // (atom, atom, bond-order) bond table keyed by residue
77static AA_BONDS: OnceLock<HashMap<&'static str, Vec<(&'static str, &'static str, i32)>>> =
78    OnceLock::new();
79
80#[rustfmt::skip]
81/// get_bonds_canonical20
82///
83/// This is the bond information for the 10 canonical
84/// AAs.  Data were obtained from the [CCD](https://www.wwpdb.org/data/ccd).
85///
86pub(crate) fn get_bonds_canonical20() -> &'static HashMap<&'static str, Vec<(&'static str, &'static str, i32)>> {
87    AA_BONDS.get_or_init(|| {
88        let mut m = HashMap::new();
89        m.insert("ALA", vec![
90            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
91            ("CB","HB1",1), ("CB","HB2",1), ("CB","HB3",1), ("CA","N",1), ("H","N",1),
92            ("H2","N",1), ("HXT","OXT",1)
93        ]);
94        m.insert("ARG", vec![
95            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
96            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD","HD2",1), ("CD","HD3",1),
97            ("CD","NE",1), ("CD","CG",1), ("CG","HG2",1), ("CG","HG3",1), ("CZ","NH1",1),
98            ("CZ","NH2",2), ("CA","N",1), ("H","N",1), ("H2","N",1), ("CZ","NE",1),
99            ("HE","NE",1), ("HH11","NH1",1), ("HH12","NH1",1), ("HH21","NH2",1),
100            ("HH22","NH2",1), ("HXT","OXT",1)
101        ]);
102        m.insert("ASN", vec![
103            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
104            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CG","ND2",1), ("CG","OD1",2),
105            ("CA","N",1), ("H","N",1), ("H2","N",1), ("HD21","ND2",1), ("HD22","ND2",1),
106            ("HXT","OXT",1)
107        ]);
108        m.insert("ASP", vec![
109            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
110            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CG","OD1",2), ("CG","OD2",1),
111            ("CA","N",1), ("H","N",1), ("H2","N",1), ("HD2","OD2",1), ("HXT","OXT",1)
112        ]);
113        m.insert("CYS", vec![
114            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
115            ("CB","HB2",1), ("CB","HB3",1), ("CB","SG",1), ("CA","N",1), ("H","N",1),
116            ("H2","N",1), ("HXT","OXT",1), ("HG","SG",1)
117        ]);
118        m.insert("GLN", vec![
119            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
120            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD","NE2",1), ("CD","OE1",2),
121            ("CD","CG",1), ("CG","HG2",1), ("CG","HG3",1), ("CA","N",1), ("H","N",1),
122            ("H2","N",1), ("HE21","NE2",1), ("HE22","NE2",1), ("HXT","OXT",1)
123        ]);
124        m.insert("GLU", vec![
125            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
126            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD","OE1",2), ("CD","OE2",1),
127            ("CD","CG",1), ("CG","HG2",1), ("CG","HG3",1), ("CA","N",1), ("H","N",1),
128            ("H2","N",1), ("HE2","OE2",1), ("HXT","OXT",1)
129        ]);
130        m.insert("GLY", vec![
131            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","HA2",1), ("CA","HA3",1),
132            ("CA","N",1), ("H","N",1), ("H2","N",1), ("HXT","OXT",1)
133        ]);
134        m.insert("HIS", vec![
135            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
136            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD2","HD2",1), ("CD2","NE2",5),
137            ("CE1","HE1",1), ("CE1","NE2",5), ("CD2","CG",6), ("CG","ND1",5), ("CA","N",1),
138            ("H","N",1), ("H2","N",1), ("CE1","ND1",6), ("HD1","ND1",1), ("HE2","NE2",1),
139            ("HXT","OXT",1)
140        ]);
141        m.insert("ILE", vec![
142            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
143            ("CB","CG1",1), ("CB","CG2",1), ("CB","HB",1), ("CD1","HD11",1), ("CD1","HD12",1),
144            ("CD1","HD13",1), ("CD1","CG1",1), ("CG1","HG12",1), ("CG1","HG13",1),
145            ("CG2","HG21",1), ("CG2","HG22",1), ("CG2","HG23",1), ("CA","N",1), ("H","N",1),
146            ("H2","N",1), ("HXT","OXT",1)
147        ]);
148        m.insert("LEU", vec![
149            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
150            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD1","HD11",1), ("CD1","HD12",1),
151            ("CD1","HD13",1), ("CD2","HD21",1), ("CD2","HD22",1), ("CD2","HD23",1),
152            ("CD1","CG",1), ("CD2","CG",1), ("CG","HG",1), ("CA","N",1), ("H","N",1),
153            ("H2","N",1), ("HXT","OXT",1)
154        ]);
155        m.insert("LYS", vec![
156            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
157            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD","CE",1), ("CD","HD2",1),
158            ("CD","HD3",1), ("CE","HE2",1), ("CE","HE3",1), ("CE","NZ",1), ("CD","CG",1),
159            ("CG","HG2",1), ("CG","HG3",1), ("CA","N",1), ("H","N",1), ("H2","N",1),
160            ("HZ1","NZ",1), ("HZ2","NZ",1), ("HZ3","NZ",1), ("HXT","OXT",1)
161        ]);
162        m.insert("MET", vec![
163            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
164            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CE","HE1",1), ("CE","HE2",1),
165            ("CE","HE3",1), ("CG","HG2",1), ("CG","HG3",1), ("CG","SD",1), ("CA","N",1),
166            ("H","N",1), ("H2","N",1), ("HXT","OXT",1), ("CE","SD",1)
167        ]);
168        m.insert("PHE", vec![
169            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
170            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD1","CE1",5), ("CD1","HD1",1),
171            ("CD2","CE2",6), ("CD2","HD2",1), ("CE1","CZ",6), ("CE1","HE1",1), ("CE2","CZ",5),
172            ("CE2","HE2",1), ("CD1","CG",6), ("CD2","CG",5), ("CZ","HZ",1), ("CA","N",1),
173            ("H","N",1), ("H2","N",1), ("HXT","OXT",1)
174        ]);
175        m.insert("PRO", vec![
176            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
177            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD","HD2",1), ("CD","HD3",1),
178            ("CD","CG",1), ("CG","HG2",1), ("CG","HG3",1), ("CA","N",1), ("CD","N",1),
179            ("H","N",1), ("HXT","OXT",1)
180        ]);
181        m.insert("SER", vec![
182            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
183            ("CB","HB2",1), ("CB","HB3",1), ("CB","OG",1), ("CA","N",1), ("H","N",1),
184            ("H2","N",1), ("HG","OG",1), ("HXT","OXT",1)
185        ]);
186        m.insert("THR", vec![
187            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
188            ("CB","CG2",1), ("CB","HB",1), ("CB","OG1",1), ("CG2","HG21",1), ("CG2","HG22",1),
189            ("CG2","HG23",1), ("CA","N",1), ("H","N",1), ("H2","N",1), ("HG1","OG1",1),
190            ("HXT","OXT",1)
191        ]);
192        m.insert("TRP", vec![
193            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
194            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD1","HD1",1), ("CD1","NE1",5),
195            ("CD2","CE2",6), ("CD2","CE3",5), ("CE2","CZ2",5), ("CE3","CZ3",6), ("CE3","HE3",1),
196            ("CD1","CG",6), ("CD2","CG",5), ("CH2","HH2",1), ("CH2","CZ2",6), ("CZ2","HZ2",1),
197            ("CH2","CZ3",5), ("CZ3","HZ3",1), ("CA","N",1), ("H","N",1), ("H2","N",1),
198            ("CE2","NE1",5), ("HE1","NE1",1), ("HXT","OXT",1)
199        ]);
200        m.insert("TYR", vec![
201            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
202            ("CB","CG",1), ("CB","HB2",1), ("CB","HB3",1), ("CD1","CE1",5), ("CD1","HD1",1),
203            ("CD2","CE2",6), ("CD2","HD2",1), ("CE1","CZ",6), ("CE1","HE1",1), ("CE2","CZ",5),
204            ("CE2","HE2",1), ("CD1","CG",6), ("CD2","CG",5), ("CZ","OH",1), ("CA","N",1),
205            ("H","N",1), ("H2","N",1), ("HH","OH",1), ("HXT","OXT",1)
206        ]);
207        m.insert("VAL", vec![
208            ("C","O",2), ("C","OXT",1), ("C","CA",1), ("CA","CB",1), ("CA","HA",1),
209            ("CB","CG1",1), ("CB","CG2",1), ("CB","HB",1), ("CG1","HG11",1), ("CG1","HG12",1),
210            ("CG1","HG13",1), ("CG2","HG21",1), ("CG2","HG22",1), ("CG2","HG23",1),
211            ("CA","N",1), ("H","N",1), ("H2","N",1), ("HXT","OXT",1)
212        ]);
213        m
214    })
215}
216
217static AMINO_ACIDS: OnceLock<HashSet<&'static str>> = OnceLock::new();
218static CARBOHYDRATES: OnceLock<HashSet<&'static str>> = OnceLock::new();
219static NUCLEOTIDES: OnceLock<HashSet<&'static str>> = OnceLock::new();
220
221fn get_amino_acids() -> &'static HashSet<&'static str> {
222    AMINO_ACIDS.get_or_init(|| include_str!("ccddata/amino_acids.txt").lines().collect())
223}
224
225fn get_carbohydrates() -> &'static HashSet<&'static str> {
226    CARBOHYDRATES.get_or_init(|| include_str!("ccddata/carbohydrates.txt").lines().collect())
227}
228
229fn get_nucleotides() -> &'static HashSet<&'static str> {
230    NUCLEOTIDES.get_or_init(|| include_str!("ccddata/nucleotides.txt").lines().collect())
231}
232
233pub(crate) fn is_amino_acid(symbol: &str) -> bool {
234    get_amino_acids().contains(symbol)
235}
236
237pub(crate) fn is_carbohydrate(symbol: &str) -> bool {
238    get_carbohydrates().contains(symbol)
239}
240
241pub(crate) fn is_nucleotide(symbol: &str) -> bool {
242    get_nucleotides().contains(symbol)
243}
244
245#[cfg(test)]
246mod tests {
247    use super::*;
248
249    #[test]
250    fn test_residue_checking() {
251        assert!(is_amino_acid("ALA"));
252        assert!(is_amino_acid("ARG"));
253        assert!(!is_amino_acid("ZZZ"));
254
255        assert!(is_carbohydrate("045"));
256        assert!(is_carbohydrate("05L"));
257        assert!(!is_carbohydrate("ZZZ"));
258
259        assert!(is_nucleotide("02I"));
260        assert!(is_nucleotide("05A"));
261        assert!(!is_nucleotide("ZZZ"));
262    }
263}
ferritin_core/info/constants.rs

ferritin_core/info/
constants.rs
