knuckles_parse/records/
seqadv.rs

1#[cfg(feature = "serde")]
2use serde::{Deserialize, Serialize};
3
4use super::dbref::DBType;
5
6#[cfg(feature = "python")]
7use knuckles_macro::pydefault;
8
9#[cfg(feature = "python")]
10use pyo3::prelude::*;
11
12#[derive(Debug, Clone)]
13#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
14#[cfg_attr(feature = "python", pyclass(get_all, set_all))]
15#[cfg_attr(feature = "python", pydefault)]
16pub struct SeqAdvRecord {
17    pub id_code: String,
18    pub res_name: String,
19    pub chain_id: char,
20    pub seq_num: i32,
21    pub i_code: Option<char>,
22    pub database: DBType,
23    pub db_accession: String,
24    pub db_res: Option<String>,
25    pub db_seq: Option<i32>,
26    pub conflict: String,
27}
28
29impl SeqAdvRecord {
30    pub fn new(line: &str) -> Self {
31        // let db_res = line[39..42].trim().parse::<i32>().ok();
32        let database = DBType::new(&line[24..28]);
33        SeqAdvRecord {
34            id_code: line[7..11].trim().to_string(),
35            res_name: line[12..15].trim().to_string(),
36            chain_id: line.chars().nth(16).unwrap(),
37            seq_num: line[18..22].trim().parse().unwrap(),
38            i_code: line[22..23].trim().parse().ok(),
39            database,
40            db_accession: line[29..38].trim().to_string(),
41            db_res: line
42                .get(39..42)
43                .map(|str| str.trim().to_string())
44                .filter(|item| !item.is_empty()),
45            db_seq: line[43..48].trim().parse().ok(),
46            conflict: line[49..].trim().to_string(),
47        }
48    }
49}
50
51impl From<&str> for SeqAdvRecord {
52    fn from(value: &str) -> Self {
53        SeqAdvRecord::new(value)
54    }
55}
56
57#[cfg(test)]
58mod tests {
59    use super::*;
60
61    #[test]
62    fn test_new_seqdv_record() {
63        let line = "SEQADV 3ABC MET A   -1  UNP  P10725              EXPRESSION TAG";
64        let record = SeqAdvRecord::new(line);
65        assert_eq!("3ABC", record.id_code);
66        assert_eq!("MET", record.res_name);
67        assert_eq!('A', record.chain_id);
68        assert_eq!(-1, record.seq_num);
69        assert_eq!(None, record.i_code);
70        assert_eq!(DBType::UNP, record.database);
71        assert_eq!("P10725", record.db_accession);
72        assert_eq!(None, record.db_res);
73        assert_eq!(None, record.db_seq);
74        assert_eq!("EXPRESSION TAG", record.conflict);
75
76        let line = "SEQADV 3ABC GLY A   50  UNP  P10725    VAL    50 ENGINEERED";
77        let record = SeqAdvRecord::new(line);
78        assert_eq!("3ABC", record.id_code);
79        assert_eq!("GLY", record.res_name);
80        assert_eq!('A', record.chain_id);
81        assert_eq!(50, record.seq_num);
82        assert_eq!(None, record.i_code);
83        assert_eq!(DBType::UNP, record.database);
84        assert_eq!("P10725", record.db_accession);
85        assert_eq!(Some("VAL".to_string()), record.db_res);
86        assert_eq!(Some(50), record.db_seq);
87        assert_eq!("ENGINEERED", record.conflict);
88
89        let line = "SEQADV 2OKW LEU A   64  NOR  NOR00669  PHE    14 SEE REMARK 999";
90        let record = SeqAdvRecord::new(line);
91        assert_eq!("2OKW", record.id_code);
92        assert_eq!("LEU", record.res_name);
93        assert_eq!('A', record.chain_id);
94        assert_eq!(64, record.seq_num);
95        assert_eq!(None, record.i_code);
96        assert_eq!(DBType::NORINE, record.database);
97        assert_eq!("NOR00669", record.db_accession);
98        assert_eq!(Some("PHE".to_string()), record.db_res);
99        assert_eq!(Some(14), record.db_seq);
100        assert_eq!("SEE REMARK 999", record.conflict);
101    }
102}
knuckles_parse/records/seqadv.rs

knuckles_parse/records/
seqadv.rs
