nom_pdb/common/

parser.rs

// Copyright (c) 2020 Tianyi Shi
//
// This software is released under the MIT License.
// https://opensource.org/licenses/MIT

use crate::types::*;
use atoi::atoi;
use chrono::{
    format::{strftime::StrftimeItems, Parsed},
    NaiveDate,
};
use nom::{
    bytes::complete::{is_not, tag, take, take_while},
    character::complete::{anychar, char, line_ending, multispace1, not_line_ending},
    combinator::{map, map_res, peek},
    IResult,
};

pub trait FieldParser {
    type Output;
    fn parse(inp: &[u8]) -> IResult<&[u8], Self::Output>;
    fn parse_into<'a, 'b>(inp: &'a [u8], dst: &'b mut Self::Output) -> &'a [u8] {
        let (i, data) = Self::parse(inp).expect("parse error");
        *dst = data;
        i
    }
    fn parse_into_vec<'a>(inp: &'a [u8], dst: &mut Vec<Self::Output>) -> &'a [u8] {
        let (i, data) = Self::parse(inp).expect("parse error");
        dst.push(data);
        i
    }
    fn parse_into_option<'a>(inp: &'a [u8], dst: &mut Option<Self::Output>) -> &'a [u8] {
        let (i, data) = Self::parse(inp).expect("parse error");
        *dst = Some(data);
        i
    }
}

pub trait FieldParserWithModifiedTable {
    type Output;
    fn parse<'a>(
        inp: &'a [u8],
        modified_aa: &ModifiedAminoAcidTable,
        modified_nuc: &ModifiedNucleotideTable,
    ) -> IResult<&'a [u8], Self::Output>;
    fn parse_into<'a, 'b>(
        inp: &'a [u8],
        dst: &'b mut Self::Output,
        modified_aa: &ModifiedAminoAcidTable,
        modified_nuc: &ModifiedNucleotideTable,
    ) -> &'a [u8] {
        let (i, data) = Self::parse(inp, modified_aa, modified_nuc).expect("parse error");
        *dst = data;
        i
    }
    fn parse_into_vec<'a>(
        inp: &'a [u8],
        dst: &mut Vec<Self::Output>,
        modified_aa: &ModifiedAminoAcidTable,
        modified_nuc: &ModifiedNucleotideTable,
    ) -> &'a [u8] {
        let (i, data) = Self::parse(inp, modified_aa, modified_nuc).expect("parse error");
        dst.push(data);
        i
    }
}

// fn ws<'a, F: 'a, O, E: ParseError<&'a [u8]>>(inner: F) -> impl Fn(&'a [u8]) -> IResult<&'a [u8], O, E>
// where
//     F: Fn(&'a [u8]) -> IResult<&'a [u8], O, E>,
// {
//     preceded(multispace0, &inner)(i)
// }

pub(crate) fn jump_newline(inp: &[u8]) -> IResult<&[u8], ()> {
    let (inp, _) = not_line_ending(inp)?;
    let (inp, _) = line_ending(inp)?;
    Ok((inp, ()))
}

fn char_is_space(c: u8) -> bool {
    c == b' '
}

pub(crate) fn parse_date(i: &[u8]) -> IResult<&[u8], NaiveDate> {
    let (i, day) = take(2usize)(i)?;
    let (i, _) = take(1usize)(i)?;
    let (i, month) = parse_month(i)?;
    let (i, _) = take(1usize)(i)?;
    let (i, year) = take(2usize)(i)?;
    let mut year = atoi::<i32>(year).unwrap();
    if year < 50i32 {
        year += 2000
    } else {
        year += 1900
    }
    Ok((
        i,
        NaiveDate::from_ymd(year, month, atoi::<u32>(day).unwrap()),
    ))
}

fn parse_month(i: &[u8]) -> IResult<&[u8], u32> {
    map_res(take(3usize), |s: &[u8]| -> Result<u32, ()> {
        let s = unsafe { std::str::from_utf8_unchecked(s) };
        let mut parsed = Parsed::new();
        chrono::format::parse(&mut parsed, s, StrftimeItems::new("%b"))
            .expect("Failed to parse month");
        Ok(parsed.month.unwrap())
    })(i)
}

pub(crate) fn parse_right<'a, T>(i: &'a [u8], length: usize) -> IResult<&'a [u8], T>
where
    T: std::str::FromStr,
{
    let (i, s) = take_while(char_is_space)(i)?;
    let l = s.len();
    if l >= length {
        panic!("Failed to parse int")
    }
    let (i, digit) = take(length - l)(i)?;
    let digit = unsafe { std::str::from_utf8_unchecked(digit) };
    match digit.parse() {
        Err(_) => Err(nom::Err::Error((i, nom::error::ErrorKind::Digit))),
        Ok(x) => Ok((i, x)),
    }
}

// * MULTILINE PARSERS ---------------------------------------------------------

pub(crate) fn parse_multiline_list(inp: &[u8]) -> IResult<&[u8], Vec<String>> {
    // ! need improvement
    let (mut inp, _) = take(4usize)(inp)?; // 7 - 10
    let mut v: Vec<String> = Vec::new();
    loop {
        let (i, item) = take_while(|c| c != b',' && c != b'\n' && c != b'\r')(inp)?;
        let item = unsafe { std::str::from_utf8_unchecked(item) };
        v.push(item.trim().to_owned());
        let (i, comma_or_newline) = anychar(i)?; // consume \r or \n if newline
        if comma_or_newline == ',' {
            let (i, char_after_comma) = peek(anychar)(i)?;
            if char_after_comma == ' ' {
                let (i, second_char_after_comma) = peek(anychar)(anychar(i)?.0)?;
                if !second_char_after_comma.is_alphanumeric() {
                    // newline
                    inp = multispace1(i)?.0;
                    inp = take(10usize)(inp)?.0; // 1 - 10
                } else {
                    inp = i;
                }
            } else {
                inp = i;
            }
        } else {
            // end
            inp = take_while(|x| x == b'\n')(i)?.0;
            return Ok((inp, v));
        }
    }
}

pub(crate) fn parse_multiline_string<'a>(
    inp: &'a [u8],
    record_identifier: &[u8],
) -> IResult<&'a [u8], String> {
    // ! need improvement
    let (mut inp, _) = take(4usize)(inp)?; // 7 - 10
    let mut s = String::new();
    loop {
        let (i, item) = not_line_ending(inp)?;
        let item = std::str::from_utf8(item).unwrap();
        s.push_str(item.trim_end());
        let (i, _) = line_ending(i)?;
        if peek(take(6usize))(i)?.1 != record_identifier {
            return Ok((i, s));
        }
        let (i, _) = take(10usize)(i)?;
        inp = i;
    }
}

pub(crate) fn parse_multiline<'a, T, F>(
    inp: &'a [u8],
    record_identifier: &[u8],
    continuation: bool,
    parse_oneline: F,
) -> IResult<&'a [u8], Vec<T>>
where
    F: Fn(&'a [u8]) -> IResult<&'a [u8], T>,
{
    // ! need improvement
    let offset = if continuation { 10usize } else { 6usize };
    let (mut inp, _) = take(4usize)(inp)?; // 7 - 10
    let mut res = Vec::<T>::new();
    loop {
        let (i, item) = parse_oneline(inp)?;
        res.push(item);
        if peek(take(6usize))(i)?.1 != record_identifier {
            return Ok((i, res));
        }
        let (i, _) = take(offset)(i)?;
        inp = i;
    }
}

use std::collections::HashMap;

pub(crate) fn parse_residue<'a, 'b>(
    inp: &'a [u8],
    modified_aa: &'b ModifiedAminoAcidTable,
    modified_nuc: &'b ModifiedNucleotideTable,
) -> IResult<&'a [u8], Residue> {
    let (inp, residue) = take(3usize)(inp)?;
    let residue_s = unsafe { std::str::from_utf8_unchecked(residue).to_owned() };
    let residue = if let Some(res) = StandardAminoAcid::try_parse_fw3(&residue) {
        Residue::AminoAcid(AminoAcid::Standard(res))
    } else if let Some(_res) = modified_aa.get(&residue_s) {
        Residue::AminoAcid(AminoAcid::Modified(residue_s))
    } else if let Some(res) = StandardNucleotide::try_parse_fw3(&residue) {
        Residue::Nucleotide(Nucleotide::Standard(res))
    } else if let Some(_res) = modified_nuc.get(&residue_s) {
        Residue::Nucleotide(Nucleotide::Modified(residue_s))
    } else {
        match residue {
            b"HOH" => Residue::Water,
            b"UNX" => Residue::UnknownAtomOrIon,
            b"UNL" => Residue::UnknownLigand,
            _ => Residue::Other(residue_s),
        }
    };
    Ok((inp, residue))
}

pub(crate) unsafe fn take_trim_own(inp: &[u8], n: usize) -> IResult<&[u8], String> {
    let (inp, x) = take(n)(inp)?;
    Ok((inp, std::str::from_utf8_unchecked(x).trim().to_owned()))
}

pub(crate) unsafe fn take_trim_start_own(inp: &[u8], n: usize) -> IResult<&[u8], String> {
    let (inp, x) = take(n)(inp)?;
    Ok((
        inp,
        std::str::from_utf8_unchecked(x).trim_start().to_owned(),
    ))
}

// pub(crate) unsafe fn take_trim_end_own(inp: &[u8], n: usize) -> IResult<&[u8], String> {
//     let (inp, x) = take(n)(inp)?;
//     Ok((inp, std::str::from_utf8_unchecked(x).trim_end().to_owned()))
// }

// pub(crate) fn parse_specification(inp: &[u8]) -> IResult<&[u8], Token> {
//     let (mut inp, _) = take(4usize)(inp)?;
//     let (inp, token) = is_not(":")(inp)?;
// }

// Represents keys of CMPND and SOURCE records
// #[derive(Debug, PartialEq, Clone)]
// pub enum Token {
//     MoleculeId(u32),
//     Molecule(String),
//     Chain { identifiers: Vec<String> },
//     Fragment(String),
//     Synonym { synonyms: Vec<String> },
//     Ec { commission_numbers: Vec<String> },
//     Engineered(bool),
//     Mutation(bool),
//     OtherDetails(String),
//     Synthetic(String),
//     OrganismScientific(String),
//     OrganismCommon { organisms: Vec<String> },
//     OrganismTaxId { id: Vec<u32> },
//     Strain(String),
//     Variant(String),
//     CellLine(String),
//     Atcc(u32),
//     Organ(String),
//     Tissue(String),
//     Cell(String),
//     Organelle(String),
//     Secretion(String),
//     CellularLocation(String),
//     Plasmid(String),
//     Gene { gene: Vec<String> },
//     ExpressionSystem(String),
//     ExpressionSystemCommon { systems: Vec<String> },
//     ExpressionSystemTaxId { id: Vec<u32> },
//     ExpressionSystemStrain(String),
//     ExpressionSystemVariant(String),
//     ExpressionSystemCellLine(String),
//     ExpressionSystemAtcc(u32),
//     ExpressionSystemOrgan(String),
//     ExpressionSystemTissue(String),
//     ExpressionSystemCell(String),
//     ExpressionSystemOrganelle(String),
//     ExpressionSystemCellularLocation(String),
//     ExpressionSystemVectorType(String),
//     ExpressionSystemVector(String),
//     ExpressionSystemPlasmid(String),
//     ExpressionSystemGene(String),
// }

// /// Represents a modification made to this pdb entry.
// #[derive(Debug, Clone)]
// pub struct Revdat {
//     pub modification_number: u32,
//     pub modification_date: NaiveDate,
//     pub idcode: String,
//     pub modification_type: ModificationType,
//     pub modification_detail: Vec<String>,
// }

// /// modification type of REVDAT record
// #[derive(Debug, Clone)]
// pub enum ModificationType {
//     /// initial release of the entry. Indicated as 0
//     /// in a REVDAT record
//     InitialRelease,
//     /// modifications other than initial release
//     /// Indicated with 1 in a REVDAT record.
//     OtherModification,
//     /// modification type other than 0 or 1
//     UnknownModification,
// }

// /// Serial Number Type of a JRNL REFN record
// #[derive(Debug, Clone, PartialEq)]
// pub enum SerialNumber {
//     Issn,
//     Essn,
// }

// /// contains HEADER recor information
// #[derive(Debug, Clone)]
// pub struct Header {
//     pub classification: String,
//     pub deposition_date: NaiveDate,
//     pub id_code: String,
// }

// impl std::default::Default for Header {
//     fn default() -> Self {
//         Header {
//             classification: String::default(),
//             deposition_date: NaiveDate::from_ymd(1900, 1, 1),
//             id_code: String::default(),
//         }
//     }
// }

// /// result of a TITLE record
// #[derive(Debug, Clone, Default)]
// pub struct Title {
//     pub title: String,
// }

// /// contains pdb entry ids which removed
// /// this one from PDB
// #[derive(Debug, Clone)]
// pub struct Obslte {
//     pub replacement_date: NaiveDate,
//     pub replacement_ids: Vec<String>,
// }

// impl std::default::Default for Obslte {
//     fn default() -> Self {
//         Obslte {
//             replacement_date: NaiveDate::from_ymd(1900, 1, 1),
//             replacement_ids: Vec::new(),
//         }
//     }
// }

// /// if this entry is a part of bigger
// /// structure, this struct holds ids of other
// /// parts of the bigger structure
// #[derive(Debug, Clone, Default)]
// pub struct Split {
//     pub id_codes: Vec<String>,
// }

// /// fallacies of this entry
// #[derive(Debug, Clone, Default)]
// pub struct Caveat {
//     pub id_code: String,
//     pub comment: String,
// }

// /// pdb entry ids made obsolete by this entry
// #[derive(Debug, Clone)]
// pub struct Sprsde {
//     pub sprsde_date: NaiveDate,
//     pub id_code: String,
//     pub superseeded: Vec<String>,
// }

// impl std::default::Default for Sprsde {
//     fn default() -> Self {
//         Sprsde {
//             sprsde_date: NaiveDate::from_ymd(1900, 1, 1),
//             superseeded: Vec::new(),
//             id_code: String::default(),
//         }
//     }
// }

// #[derive(Debug, Clone, Default)]
// pub struct Seqres {
//     pub chain_id: Option<char>,
//     pub residues: Vec<String>,
// }

// /// model type of the entry
// #[derive(Debug, Clone, Default)]
// pub struct Mdltyp {
//     pub structural_annotation: Vec<String>,
// }

// /// collection of revisions
// #[derive(Debug, Clone, Default)]
// pub struct Revdats {
//     pub revdat: Vec<Revdat>,
// }

// /// collection of tokens in a CMPND record
// #[derive(Debug, Clone, Default)]
// pub struct Cmpnd {
//     pub tokens: Vec<Token>,
// }

// /// collection of tokens in a SOURCE record
// #[derive(Debug, Clone, Default)]
// pub struct Source {
//     pub tokens: Vec<Token>,
// }

// /// keywords related to the entry
// #[derive(Debug, Clone, Default)]
// pub struct Keywds {
//     pub keywords: Vec<String>,
// }

// /// journal author collection
// #[derive(Debug, Clone, Default)]
// pub struct JournalAuthors<'a> {
//     pub authors: Vec<&'a [u8]>,
// }

// /// journal title
// #[derive(Debug, Clone, Default)]
// pub struct JournalTitle {
//     pub title: String,
// }

// /// journal editor collection
// #[derive(Debug, Clone, Default)]
// pub struct JournalEditors<'a> {
//     pub name: Vec<&'a [u8]>,
// }

// /// journal reference
// #[derive(Debug, Clone, Default)]
// pub struct JournalReference {
//     pub publication_name: String,
//     pub volume: Option<u32>,
//     pub page: Option<u32>,
//     pub year: Option<u32>,
// }

// /// journal Citation fields
// #[derive(Debug, Clone, Default)]
// pub struct JournalCitation {
//     pub serial_type: Option<SerialNumber>,
//     pub serial: Option<String>,
// }

// /// journal publication fields
// #[derive(Debug, Clone, Default)]
// pub struct JournalPublication {
//     pub publication: String,
// }

// /// journal PubMed id
// #[derive(Debug, Clone, Default)]
// pub struct JournalPubMedId {
//     pub id: u32,
// }

// /// digital object identifier of related e-pub
// #[derive(Debug, Clone, Default)]
// pub struct JournalDoi {
//     pub id: String,
// }

// /// number of models in this file
// #[derive(Debug, Clone, Default)]
// pub struct Nummdl {
//     pub num: u32,
// }

// /// cross references to other sequence databases
// #[derive(Debug, Clone, Default)]
// pub struct Dbref {
//     pub idcode: String,
//     pub chain_id: char,
//     pub seq_begin: u32,
//     pub initial_sequence: Option<char>,
//     pub seq_end: u32,
//     pub ending_sequence: Option<char>,
//     pub database: String,
//     pub db_accession: String,
//     pub db_idcode: String,
//     pub db_seq_begin: u32,
//     pub idbns_begin: Option<char>,
//     pub db_seq_end: u32,
//     pub dbins_end: Option<char>,
// }