JensKrumsieck/ChemSharp

using System.Numerics;
using ChemSharp.Mathematics;
using ChemSharp.Memory;

// ReSharper disable InconsistentNaming

namespace ChemSharp.Molecules.Formats;

public partial class CifFormat
{
    private const string AtomsLoopCCDC = "_atom_site_label";
    private const string BondsLoopCCDC = "_geom_bond";

    private const string HeaderLabelCCDC = "_atom_site_label";
    private const string HeaderSymbolCCDC = "_atom_site_type_symbol";
    private const string HeaderDisorderCCDC = "_atom_site_disorder_group";
    private const string HeaderFractX = "_atom_site_fract_x";
    private const string HeaderFractY = "_atom_site_fract_y";
    private const string HeaderFractZ = "_atom_site_fract_z";

    private const string LenghtLines = "_cell_length_";
    private const string AngleLines = "_cell_angle_";
    private readonly float[] _cellParams = new float[6];

    private Matrix4x4? _conversionMatrix;

    private Atom? ParseAtomCCDC(ReadOnlySpan<char> line)
    {
        var cols = line.WhiteSpaceSplit();
        //filter disorder
        var disorder = 0;
        if (_colDisorder != 0 && _colDisorder < cols.Length)
#if NETSTANDARD2_0
            int.TryParse(line.Slice(cols[_colDisorder].start, cols[_colDisorder].length).ToString(), out disorder);
#else
            int.TryParse(line.Slice(cols[_colDisorder].start, cols[_colDisorder].length).ToString(), out disorder);
#endif
        if (disorder == 2) return null;
        //parse atom
        var label = line.Slice(cols[_colLabel].start, cols[_colLabel].length);
        var symbol = line.Slice(cols[_colSymbol].start, cols[_colSymbol].length);
        var fractX = line.Slice(cols[_colX].start, cols[_colX].length).RemoveUncertainty().ToSingle();
        var fractY = line.Slice(cols[_colY].start, cols[_colY].length).RemoveUncertainty().ToSingle();
        var fractZ = line.Slice(cols[_colZ].start, cols[_colZ].length).RemoveUncertainty().ToSingle();

        var coords =
            FractionalCoordinates.FractionalToCartesian(new Vector3(fractX, fractY, fractZ), _conversionMatrix!.Value);
        return new Atom(symbol.ToString()) {Location = coords, Title = label.ToString()};
    }

    private void ExtractHeaderCCDC(ReadOnlySpan<char> line)
    {
        if (line.StartsWith(HeaderLabelCCDC.AsSpan())) _colLabel = _idh;
        if (line.StartsWith(HeaderSymbolCCDC.AsSpan())) _colSymbol = _idh;
        if (line.StartsWith(HeaderFractX.AsSpan())) _colX = _idh;
        if (line.StartsWith(HeaderFractY.AsSpan())) _colY = _idh;
        if (line.StartsWith(HeaderFractZ.AsSpan())) _colZ = _idh;
        if (line.StartsWith(HeaderDisorderCCDC.AsSpan())) _colDisorder = _idh;
        _idh++;
    }

    private void ParseCellParams(ReadOnlySpan<char> line)
    {
        var cols = line.WhiteSpaceSplit();
        _cellParams[_idx] = line[cols[1].start..].RemoveUncertainty().ToSingle();
        _idx++;

        if (_idx == 6)
            _conversionMatrix = FractionalCoordinates.ConversionMatrix(
                                                                       _cellParams[0],
                                                                       _cellParams[1],
                                                                       _cellParams[2],
                                                                       _cellParams[3],
                                                                       _cellParams[4],
                                                                       _cellParams[5]);
    }

    private void SetPickingIndicatorCCDC(ReadOnlySpan<char> line)
    {
        //determine whether to check for atoms or bonds
        if (line.StartsWith(AtomsLoopCCDC.AsSpan()))
        {
            _pickingAtoms = true;
            _pickingBonds = false;
        }
        else if (line.StartsWith(BondsLoopCCDC.AsSpan()))
        {
            _pickingBonds = true;
            _pickingAtoms = false;
        }
    }
}