JensKrumsieck/ChemSharp

using ChemSharp.Extensions;
using ChemSharp.Memory;

namespace ChemSharp.Molecules.Formats;

public partial class PDBFormat : FileFormat, IAtomFileFormat
{
    private const string Atom = "ATOM";
    private const string HetAtom = "HETATM";
    private PDBFormat(string path) : base(path) { }

    public List<Atom> Atoms { get; } = new();

    public Atom ParseAtom(ReadOnlySpan<char> line)
    {
        /*
         * http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
        COLUMNS        DATA  TYPE    FIELD        DEFINITION
        -------------------------------------------------------------------------------------
         1 -  6        Record name   "ATOM  "
         7 - 11        Integer       serial       Atom  serial number.
        13 - 16        Atom          name         Atom name.
        17             Character     altLoc       Alternate location indicator.
        18 - 20        Residue name  resName      Residue name.
        22             Character     chainID      Chain identifier.
        23 - 26        Integer       resSeq       Residue sequence number.
        27             AChar         iCode        Code for insertion of residues.
        31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
        39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
        47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
        55 - 60        Real(6.2)     occupancy    Occupancy.
        61 - 66        Real(6.2)     tempFactor   Temperature  factor.
        77 - 78        LString(2)    element      Element symbol, right-justified.
        79 - 80        LString(2)    charge       Charge  on the atom.
     */
        var title = line[12..16].Trim();
        var x = line[30..38].Trim();
        var y = line[38..46].Trim();
        var z = line[46..54].Trim();
        var symbol = line[76..78].Trim();
        var resName = line[17..20].Trim();
        var resId = line[22..26].Trim().ToInt();
        var chainIdRaw = line[21..22].Trim();
        var c = chainIdRaw.Length > 0 ? chainIdRaw[0] : default;
        return new Atom(symbol.ToString().UcFirst(), x.ToSingle(), y.ToSingle(), z.ToSingle())
        {
            Title = title.ToString(), Residue = resName.ToString(), ResidueId = resId, ChainId = c
        };
    }

    protected override void ParseLine(ReadOnlySpan<char> line)
    {
        line = line.Trim();
        if (line.StartsWith(Atom.AsSpan()) || line.StartsWith(HetAtom.AsSpan()))
            Atoms.Add(ParseAtom(line));
    }
}