1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100

use super::Element;
use serde::Serialize;
use strum::EnumString;

#[derive(Debug, Clone, Serialize)]
pub enum Residue {
    AminoAcid(AminoAcid),
    Nucleotide(Nucleotide),
    Water,
    Metal(Element),
    Molecule(Molecule),
    Other(String),
    UnknownAtomOrIon,
    UnknownLigand,
}

pub enum StandardResidue {
    AminoAcid(StandardAminoAcid),
    Nucleotide(StandardNucleotide),
    Unknown,
}

#[derive(Debug, Clone, Serialize)]
pub struct Molecule {
    code: String,
    description: String,
}

#[derive(Debug, Clone, Eq, PartialEq, Serialize)]
pub enum Nucleotide {
    Standard(StandardNucleotide),
    Modified(String),
    Unknown, // represented as "N" in PDB files
}

#[derive(Debug, Clone, Eq, PartialEq, Serialize, EnumString)]
pub enum StandardNucleotide {
    A,
    C,
    G,
    U,
    DA,
    DC,
    DG,
    DT,
}

#[derive(Debug, Clone, Eq, PartialEq, Serialize)]
pub enum AminoAcid {
    Standard(StandardAminoAcid),
    Modified(String),
    Unknown, // represented as "UNK" in PDB files
}

#[derive(Debug, Clone, Eq, PartialEq, Serialize)]
pub enum StandardAminoAcid {
    Ala,
    Arg,
    Asn,
    Asp,
    Cys,
    Gln,
    Glu,
    Gly,
    His,
    Ile,
    Leu,
    Lys,
    Met,
    Phe,
    Pro,
    Ser,
    Thr,
    Trp,
    Tyr,
    Val,
    Mse,
    Pyl, // https://www.wwpdb.org/news/news?year=2014#5764490799cccf749a90cddf
    Sec, // https://www.wwpdb.org/news/news?year=2014#5764490799cccf749a90cddf
}

#[derive(Debug, Clone, Eq, PartialEq, Serialize)]
pub struct ModifiedAminoAcid {
    pub standard: StandardAminoAcid,
    pub description: String,
}

pub trait Monomer {}

impl Monomer for AminoAcid {}

impl Monomer for Nucleotide {}

#[derive(Debug, Clone, Eq, PartialEq, Serialize)]
pub struct ModifiedNucleotide {
    pub standard: StandardNucleotide,
    pub description: String,
}

pub type ModifiedNucleotideList = Vec<ModifiedNucleotide>;