nom_pdb/title_section/
header.rs

1// Copyright (c) 2020 Tianyi Shi
2//
3// This software is released under the MIT License.
4// https://opensource.org/licenses/MIT
5
6//! Parsing the [Header](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#HEADER).
7//! The HEADER record uniquely identifies a PDB entry through the idCode field.
8//! This record also provides a classification for the entry. Finally, it contains
9//! the date when the coordinates were deposited to the PDB archive.
10//!
11//! # Record Format
12//!
13//! | COLUMNS | DATA  TYPE   | FIELD          | DEFINITION                                |
14//! |---------|--------------|----------------|-------------------------------------------|
15//! | 1 -  6  | Record name  | HEADER         |                                           |
16//! | 11 - 50 | String(40)/`String`   | `classification` | Classifies the molecule(s).               |
17//! | 51 - 59 | Date/`chrono::NaiveDate`         | `deposition_date`        | Deposition date. This is the date the coordinates  were received at the PDB.   |
18//! | 63 - 66 | IDcode/`String`      | `id_code`         | This identifier is unique within the PDB. |
19use crate::common::parser::{parse_date, take_trim_own, FieldParser};
20use crate::types::*;
21use nom::{bytes::complete::take, character::complete::multispace1, IResult};
22
23pub struct HeaderParser;
24
25impl FieldParser for HeaderParser {
26    type Output = Header;
27    fn parse(inp: &[u8]) -> IResult<&[u8], Self::Output> {
28        let inp = &inp[4..];
29        let (inp, classification) = unsafe { take_trim_own(inp, 40usize)? };
30        let (inp, deposition_date) = parse_date(inp)?;
31        let inp = &inp[3..];
32        let (inp, id_code) = take(4usize)(inp)?;
33        let (inp, _) = multispace1(inp)?;
34        Ok((
35            inp,
36            Header {
37                classification,
38                deposition_date,
39                id_code: unsafe { std::str::from_utf8_unchecked(id_code).to_owned() },
40            },
41        ))
42    }
43}
44
45pub struct HeaderParserStreaming;
46pub struct HeaderParserParallel;
47
48// #[cfg(test)]
49// mod tests {
50//     use super::*;
51//     use chrono::NaiveDate;
52//     #[test]
53//     fn test_parse_header() {
54//         let i = "    VIRAL PROTEIN                           27-MAR-98   1A8O              \nTITLE     HIV CAPSID C-TERMINAL DOMAIN                                          ";
55//         let (i, r) = HeaderParser::parse(i).unwrap();
56//         assert_eq!(
57//             i.to_owned(),
58//             "TITLE     HIV CAPSID C-TERMINAL DOMAIN                                          "
59//                 .to_owned()
60//         );
61//         assert_eq!(
62//             r,
63//             Header {
64//                 classification: "VIRAL PROTEIN".to_owned(),
65//                 deposition_date: NaiveDate::from_ymd(1998i32, 3u32, 27u32),
66//                 id_code: "1A8O".to_owned()
67//             }
68//         )
69//     }
70// }
nom_pdb/title_section/header.rs

nom_pdb/title_section/
header.rs
