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(C) 2022 Cadence Design Systems, Inc. (Cadence) 
All rights reserved.
TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
provided to current licensees or subscribers of Cadence products or
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Customer is hereby permitted to use, copy, and modify the Sample Code,
subject to these terms. Cadence claims no rights to Customer's
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THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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liable for any damages or liability in connection with the Sample Code
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*/

// This example reads in a reference molecule and a few fit
// molecules, performs overlay optimization, and uses 2 iterators to
// show all the results.
// With the default options, OEOverlay optimizes both shape and color.

using System;
using OpenEye.OEChem;
using OpenEye.OEGrid;
using OpenEye.OEShape;

public class OverlayAllRes
{
    public static void Main(string [] args)
    {
        if (args.Length != 2)
            OEChem.OEThrow.Usage("OverlayAllRes <reffile> <fitfile>");

        oemolistream reffs = new oemolistream(args[0]);
        oemolistream fitfs = new oemolistream(args[1]);

        OEMol refmol = new OEMol();
        OEChem.OEReadMolecule(reffs, refmol);
        Console.WriteLine("Ref. title: {0} Num Confs: {0}\n",
                          refmol.GetTitle(), refmol.NumConfs());

        // Prepare reference molecule for calculation
        // With default options this will remove any explicit
        // hydrogens present and add color atoms
        OEOverlapPrep prep = new OEOverlapPrep();
        prep.Prep(refmol);

        OEMultiRefOverlay overlay = new OEMultiRefOverlay();
        overlay.SetupRef(refmol);

        foreach (OEMol fitmol in fitfs.GetOEMols())
        {
            Console.WriteLine("Fit. title: {0}  Num Confs: {1}",
                         fitmol.GetTitle(), fitmol.NumConfs());

            int resCount = 0;

            // double loop over results and scores to obtain all scores
            foreach (OEBestOverlayResults res in overlay.Overlay(fitmol))
            {
                foreach (OEBestOverlayScore score in res.GetScores())
                {
                    Console.WriteLine("FitConfIdx: {0}  RefConfIdx: {1}  Tanimoto Combo: {2}",
                                        score.GetFitConfIdx(), score.GetRefConfIdx(), score.GetTanimotoCombo());
                    ++resCount;
                }
            }
            Console.WriteLine(resCount+" results returned.");
        }
    }
}