/// <summary> /// Select the best coordinates /// </summary> /// <param name="ps">template points</param> /// <param name="coords">best coordinates (updated by this method)</param> /// <param name="macrocycle">the macrocycle</param> /// <param name="ringset">rest of the ring system</param> /// <returns>offset into the coordinates</returns> private static int SelectCoords(IEnumerable <Vector2[]> ps, Vector2[] coords, IRing macrocycle, IRingSet ringset) { Debug.Assert(ps.Any()); var winding = new int[coords.Length]; MacroScore best = null; foreach (var p in ps) { var wind = Winding(p, winding); var score = BestScore(macrocycle, ringset, wind, winding); if (score.CompareTo(best) < 0) { best = score; Array.Copy(p, 0, coords, 0, p.Length); } } // never null return(best != null ? best.offset : 0); }
/// <summary> /// Select the best scoring template + offset for the given macrocycle. /// </summary> /// <param name="macrocycle">macrocycle</param> /// <param name="ringset">entire ring system</param> /// <param name="wind">winding of ring CW/CCW</param> /// <param name="winding">winding of each turn in the ring</param> /// <returns>the best scoring configuration</returns> private static MacroScore BestScore(IRing macrocycle, IRingSet ringset, int wind, int[] winding) { var numAtoms = macrocycle.Atoms.Count; var heteroIdxs = new List <int>(); var ringAttachs = new List <IList <int> >(); // hetero atoms for (int i = 0; i < numAtoms; i++) { if (macrocycle.Atoms[i].AtomicNumber != 6) { heteroIdxs.Add(i); } } foreach (var other in ringset) { if (other == macrocycle) { continue; } var shared = AtomContainerManipulator.GetIntersection(macrocycle, other); if (shared.Atoms.Count >= 2 && shared.Atoms.Count <= 4) { ringAttachs.Add(GetAttachedInOrder(macrocycle, shared)); } } // convex and concave are relative var convex = wind; var concave = -wind; MacroScore best = null; for (int i = 0; i < winding.Length; i++) { // score ring attachs int nRingClick = 0; foreach (var ringAttach in ringAttachs) { int r1, r2, r3, r4; switch (ringAttach.Count) { case 2: r1 = (ringAttach[0] + i) % numAtoms; r2 = (ringAttach[1] + i) % numAtoms; if (winding[r1] == winding[r2]) { if (winding[r1] == convex) { nRingClick += 5; } else { nRingClick++; } } break; case 3: r1 = (ringAttach[0] + i) % numAtoms; r2 = (ringAttach[1] + i) % numAtoms; r3 = (ringAttach[2] + i) % numAtoms; if (winding[r1] == convex && winding[r2] == concave && winding[r3] == convex) { nRingClick += 5; } else if (winding[r1] == concave && winding[r2] == convex && winding[r3] == concave) { nRingClick++; } break; case 4: r1 = (ringAttach[0] + i) % numAtoms; r2 = (ringAttach[1] + i) % numAtoms; r3 = (ringAttach[2] + i) % numAtoms; r4 = (ringAttach[3] + i) % numAtoms; if (winding[r1] == convex && winding[r2] == concave && winding[r3] == concave && winding[r4] == convex) { nRingClick++; } else if (winding[r1] == concave && winding[r2] == convex && winding[r3] == convex && winding[r4] == concave) { nRingClick++; } break; } } // score hetero atoms in concave positions int nConcaveHetero = 0; foreach (var heteroIdx in heteroIdxs) { var k = (heteroIdx + i) % numAtoms; if (winding[k] == concave) { nConcaveHetero++; } } int nCorrectStereo = 0; int nIncorrectStereo = 0; foreach (var se in macrocycle.StereoElements) { if (se.Class == StereoClass.CisTrans) { var bond = (IBond)se.Focus; var beg = bond.Begin; var end = bond.End; StereoConfigurations cfg; if (winding[(macrocycle.Atoms.IndexOf(beg) + i) % numAtoms] == winding[(macrocycle.Atoms.IndexOf(end) + i) % numAtoms]) { cfg = StereoConfigurations.Together; } else { cfg = StereoConfigurations.Opposite; } if (cfg == se.Configure) { nCorrectStereo++; } else { nIncorrectStereo++; } } } var score = new MacroScore(i, nConcaveHetero, nCorrectStereo, nRingClick); if (score.CompareTo(best) < 0) { best = score; } } return(best); }