JensKrumsieck/ChemSharp

using System.Text;

namespace ChemSharp.Molecules.Extensions;

public static class AtomUtil
{
    /// <summary>
    ///     Calculates MolecularWeight of given Atoms collection
    /// </summary>
    /// <param name="atoms"></param>
    /// <returns></returns>
    public static double MolecularWeight(this IEnumerable<Atom> atoms) => atoms.Sum(s => s.AtomicWeight);

    /// <summary>
    ///     Creates Sum Formula from given atoms collection
    /// </summary>
    /// <param name="atoms"></param>
    /// <returns></returns>
    public static string SumFormula(this IEnumerable<Atom> atoms)
    {
        var groups = atoms.GroupBy(s => s.Symbol).OrderBy(s => s.Key);
        var formula = new StringBuilder();
        foreach (var g in groups)
        {
            var count = g.Count();
            formula.Append(g.Key);
            if (count != 1) formula.Append(count);
        }

        return formula.ToString();
    }

    /// <summary>
    ///     Gets Saturation of Atom a in Context of Molecule mol
    /// </summary>
    /// <param name="mol"></param>
    /// <param name="a"></param>
    /// <returns></returns>
    public static int Saturation(this Molecule mol, Atom a) => Saturation(mol.Bonds, a);

    /// <summary>
    ///     Gets Saturation of Atom in Context of Bond List
    /// </summary>
    /// <param name="bonds"></param>
    /// <param name="a"></param>
    /// <returns></returns>
    public static int Saturation(this IEnumerable<Bond> bonds, Atom a)
    {
        var selectedBonds = bonds.Bonds(a);
        return selectedBonds.Sum(s => s.Order);
    }

    /// <summary>
    ///     Get all Bonds for Atom a in Molecule
    /// </summary>
    /// <param name="mol"></param>
    /// <param name="a"></param>
    /// <returns></returns>
    public static IEnumerable<Bond> Bonds(this Molecule mol, Atom a) => Bonds(mol.Bonds, a);

    /// <summary>
    ///     Get all Bonds containing specific atom
    /// </summary>
    /// <param name="bonds"></param>
    /// <param name="a"></param>
    /// <returns></returns>
    public static IEnumerable<Bond> Bonds(this IEnumerable<Bond> bonds, Atom a) =>
        bonds.Where(s => s.Atom1.Equals(a) || s.Atom2.Equals(a));

    /// <summary>
    ///     Returns Neighboring atoms in context of molecule
    /// </summary>
    /// <param name="a"></param>
    /// <param name="ctx"></param>
    /// <returns></returns>
    public static IEnumerable<Atom> Neighbors(Atom a, Molecule ctx) => Neighbors(a, ctx.Bonds);

    /// <summary>
    ///     Returns Neighboring atoms in context of bond list
    /// </summary>
    /// <param name="a"></param>
    /// <param name="bonds"></param>
    /// <returns></returns>
    public static IEnumerable<Atom> Neighbors(Atom a, IEnumerable<Bond> bonds) =>
        bonds.Where(s => s.Atoms.Contains(a)).Select(s => s.Atoms.First(b => !b.Equals(a)));

    public static Dictionary<Atom, List<Atom>> BuildNeighborCache(IEnumerable<Atom> atoms, IEnumerable<Bond> bonds) =>
        atoms.ToDictionary(a => a, a => Neighbors(a, bonds).ToList());

    /// <summary>
    ///     Finds pair of atoms to prevent double looping
    /// </summary>
    /// <returns></returns>
    public static (Atom? a1, Atom? a2) FindPairwise(this IList<Atom> atoms, string a1, string a2)
    {
        Atom? atom1 = null;
        Atom? atom2 = null;
        for (var i = 0; i < atoms.Count; i++)
        {
            if (atoms[i].Title == a1) atom1 = atoms[i];
            if (atoms[i].Title == a2) atom2 = atoms[i];
        }

        return (atom1, atom2);
    }
}