JensKrumsieck/ChemSharp

using ChemSharp.Memory;

namespace ChemSharp.Molecules.Formats;

public partial class MolFormat : FileFormat, IAtomFileFormat, IBondFileFormat
{
    private const string Version = "V2000";
    private int _idx;
    private int _noAtoms;
    private int _noBonds;

    private bool _pickingAtoms;
    private bool _pickingBonds;

    public MolFormat(string path) : base(path) { }

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

    public Atom ParseAtom(ReadOnlySpan<char> line)
    {
        var cols = line.WhiteSpaceSplit();
        var x = line.Slice(cols[0].start, cols[0].length).ToSingle();
        var y = line.Slice(cols[1].start, cols[1].length).ToSingle();
        var z = line.Slice(cols[2].start, cols[2].length).ToSingle();
        var symbol = line.Slice(cols[3].start, cols[3].length).ToString();
        return new Atom(symbol, x, y, z);
    }

    public List<Bond> Bonds { get; } = new();

    public Bond ParseBond(ReadOnlySpan<char> line)
    {
        var cols = line.WhiteSpaceSplit();
        var iA1 = line.Slice(cols[0].start, cols[0].length).ToInt();
        var iA2 = line.Slice(cols[1].start, cols[1].length).ToInt();
        var order = line.Slice(cols[2].start, cols[2].length).ToInt();
        var bond = new Bond(Atoms[iA1 - 1], Atoms[iA2 - 1]);
        if (order == 4)
        {
            bond.IsAromatic = true;
            order = 1;
        }

        bond.Order = order;
        return bond;
    }

    protected override void ParseLine(ReadOnlySpan<char> line)
    {
        line = line.Trim();
        if (_pickingAtoms && _idx < _noAtoms)
        {
            Atoms.Add(ParseAtom(line));
            _idx++;
            if (_idx == _noAtoms)
            {
                _pickingAtoms = false;
                _pickingBonds = true;
                _idx = 0;
            }
        }
        else if (_pickingBonds && _idx < _noBonds)
        {
            Bonds.Add(ParseBond(line));
            _idx++;
        }

        //get counts from information line
        if (line.EndsWith(Version.AsSpan()))
            GetFileInfo(line);
    }

    private void GetFileInfo(ReadOnlySpan<char> line)
    {
        var cols = line.WhiteSpaceSplit();
        _noAtoms = line.Slice(cols[0].start, cols[0].length).ToInt();
        _noBonds = line.Slice(cols[1].start, cols[1].length).ToInt();
        _pickingAtoms = true;
    }
}