private Globals.BondDirection?GetPlacement() { Globals.BondDirection dir = Globals.BondDirection.None; var vec = GetPrettyDoubleBondVector(); if (vec == null) { dir = Globals.BondDirection.None; } else { // Azure DevOps #713 if (double.IsNaN(vec.Value.X) || double.IsNaN(vec.Value.Y)) { dir = Globals.BondDirection.None; } else { dir = (Globals.BondDirection)Math.Sign(Vector.CrossProduct(vec.Value, BondVector)); } } return(dir); }
private Globals.BondDirection?GetPlacement() { Globals.BondDirection dir = Globals.BondDirection.None; var vec = GetPrettyDoubleBondVector(); if (vec == null) { dir = Globals.BondDirection.None; } else { dir = (Globals.BondDirection)Math.Sign(Vector.CrossProduct(vec.Value, BondVector)); } return(dir); }
/// <summary> /// Circles a ring /// </summary> /// <param name="start">Atom to start at</param> /// <param name="direction">Which direction to go in</param> /// <returns>IEnumerable<Atom> that iterates through the ring</returns> public IEnumerable <Atom> Traverse(Atom start = null, Globals.BondDirection direction = Globals.BondDirection.Anticlockwise) { HashSet <Atom> res = new HashSet <Atom>(); res.Add(start); Atom next; if (start == null) { start = Atoms.First(); } //start with the start atom, and find the other two adjacent atoms that are part of the ring var adj = from n in start.Neighbours where Atoms.Contains(n) select n; var nextatoms = adj.ToArray(); if (nextatoms.Length >= 2) { Vector v1 = nextatoms[0].Position - start.Position; Vector v2 = nextatoms[1].Position - start.Position; //make sure a positive angle is the direction in which we want to travel //multiply the angle by the direction to choose the correct atom double angle = (int)direction * Vector.AngleBetween(v1, v2); next = angle > 0 ? nextatoms[0] : nextatoms[1]; //circle the ring, making sure we ignore atoms we've visited already while (next != null) { yield return(next); res.Add(next); var candidates = next.NeighbourSet; //get the set of atoms around the next atom //get rid of all the atoms NOT in the ring or already in the set candidates.RemoveWhere(a => res.Contains(a) || !Atoms.Contains(a)); next = candidates.FirstOrDefault(); } } }
public static BondLayout GetBondDescriptor(AtomVisual startAtomVisual, AtomVisual endAtomVisual, double modelXamlBondLength, Globals.BondStereo parentStereo, Point startAtomPosition, Point endAtomPosition, double?parentOrderValue, Globals.BondDirection parentPlacement, Point?centroid, Point?secondaryCentroid) { if (parentStereo == Globals.BondStereo.Wedge || parentStereo == Globals.BondStereo.Hatch) { WedgeBondLayout wbd = new WedgeBondLayout() { Start = startAtomPosition, End = endAtomPosition, StartAtomVisual = startAtomVisual, EndAtomVisual = endAtomVisual }; var endAtom = endAtomVisual.ParentAtom; var otherBonds = endAtom.Bonds.Except(new[] { startAtomVisual.ParentAtom.BondBetween(endAtom) }).ToList(); Bond bond = null; if (otherBonds.Any()) { bond = otherBonds.ToArray()[0]; } bool chamferBond = (otherBonds.Any() && (endAtom.Element as Element) == Globals.PeriodicTable.C && endAtom.SymbolText == "" && bond.Order == Globals.OrderSingle); if (!chamferBond) { wbd.CappedOff = false; BondGeometry.GetWedgeBondGeometry(wbd, modelXamlBondLength); } else { var nonHPs = (from b in otherBonds select b.OtherAtom(endAtom).Position).ToList(); if (nonHPs.Any()) { wbd.CappedOff = true; BondGeometry.GetChamferedWedgeGeometry(wbd, modelXamlBondLength, nonHPs); } else { wbd.CappedOff = false; BondGeometry.GetWedgeBondGeometry(wbd, modelXamlBondLength); } } return(wbd); } //wavy bond if (parentStereo == Globals.BondStereo.Indeterminate && parentOrderValue == 1.0) { BondLayout sbd = new BondLayout { Start = startAtomPosition, End = endAtomPosition, StartAtomVisual = startAtomVisual, EndAtomVisual = endAtomVisual }; BondGeometry.GetWavyBondGeometry(sbd, modelXamlBondLength); return(sbd); } switch (parentOrderValue) { //indeterminate double case 2 when parentStereo == Globals.BondStereo.Indeterminate: DoubleBondLayout dbd = new DoubleBondLayout() { StartAtomVisual = startAtomVisual, EndAtomVisual = endAtomVisual, Start = startAtomPosition, End = endAtomPosition }; BondGeometry.GetCrossedDoubleGeometry(dbd, modelXamlBondLength); return(dbd); //partial or undefined bonds case 0: case 0.5: case 1.0: BondLayout sbd = new BondLayout { Start = startAtomPosition, End = endAtomPosition, StartAtomVisual = startAtomVisual, EndAtomVisual = endAtomVisual }; BondGeometry.GetSingleBondGeometry(sbd); return(sbd); //double bond & 1.5 bond case 1.5: case 2: DoubleBondLayout dbd2 = new DoubleBondLayout() { StartAtomVisual = startAtomVisual, EndAtomVisual = endAtomVisual, Start = startAtomPosition, End = endAtomPosition, Placement = parentPlacement, PrimaryCentroid = centroid, SecondaryCentroid = secondaryCentroid }; BondGeometry.GetDoubleBondGeometry(dbd2, modelXamlBondLength); return(dbd2); //triple and 2.5 bond case 2.5: case 3: TripleBondLayout tbd = new TripleBondLayout() { StartAtomVisual = startAtomVisual, EndAtomVisual = endAtomVisual, Start = startAtomPosition, End = endAtomPosition, Placement = parentPlacement, PrimaryCentroid = centroid, SecondaryCentroid = secondaryCentroid }; BondGeometry.GetTripleBondGeometry(tbd, modelXamlBondLength); return(tbd); default: return(null); } }
public static BondLayout GetBondDescriptor(AtomVisual startAtomVisual, AtomVisual endAtomVisual, double modelXamlBondLength, Globals.BondStereo parentStereo, Point startAtomPosition, Point endAtomPosition, double?parentOrderValue, Globals.BondDirection parentPlacement, Point?centroid, Point?secondaryCentroid, double standoff) { List <Point> startAtomHull = new List <Point>(); List <Point> endAtomHull = new List <Point>(); if (startAtomVisual.ParentAtom.SymbolText != "" || startAtomVisual.ShowAllCarbons) { startAtomHull = startAtomVisual.Hull; } if (endAtomVisual.ParentAtom.SymbolText != "" || endAtomVisual.ShowAllCarbons) { endAtomHull = endAtomVisual.Hull; } if ((parentStereo == Globals.BondStereo.Wedge || parentStereo == Globals.BondStereo.Hatch) && parentOrderValue == 1) { WedgeBondLayout wbd = new WedgeBondLayout { Start = startAtomPosition, End = endAtomPosition, StartAtomHull = startAtomHull, EndAtomHull = endAtomHull }; var endAtom = endAtomVisual.ParentAtom; var otherBonds = endAtom.Bonds.Except(new[] { startAtomVisual.ParentAtom.BondBetween(endAtom) }).ToList(); Bond bond = null; bool oblique = true; if (otherBonds.Any()) { bond = otherBonds.ToArray()[0]; Vector wedgevector = wbd.End - wbd.Start; foreach (Bond b in otherBonds) { Atom otherAtom = b.OtherAtom(endAtom); Vector v = wbd.End - otherAtom.Position; double angle = System.Math.Abs(Vector.AngleBetween(wedgevector, v)); if (angle < 109.5 || angle > 130.5) { oblique = false; break; } } } bool chamferBond = otherBonds.Any() && oblique && (endAtom.Element as Element) == Globals.PeriodicTable.C && endAtom.SymbolText == "" && bond.Order == Globals.OrderSingle; if (!chamferBond) { wbd.CappedOff = false; BondGeometry.GetWedgeBondGeometry(wbd, modelXamlBondLength, standoff); } else { var nonHPs = (from b in otherBonds select b.OtherAtom(endAtom).Position).ToList(); if (nonHPs.Any()) { wbd.CappedOff = true; BondGeometry.GetChamferedWedgeGeometry(wbd, modelXamlBondLength, nonHPs, standoff); } else { wbd.CappedOff = false; BondGeometry.GetWedgeBondGeometry(wbd, modelXamlBondLength, standoff); } } return(wbd); } //wavy bond if (parentStereo == Globals.BondStereo.Indeterminate && parentOrderValue == 1.0) { BondLayout sbd = new BondLayout { Start = startAtomPosition, End = endAtomPosition, StartAtomHull = startAtomHull, EndAtomHull = endAtomHull }; BondGeometry.GetWavyBondGeometry(sbd, modelXamlBondLength, standoff); return(sbd); } switch (parentOrderValue) { //indeterminate double case 2 when parentStereo == Globals.BondStereo.Indeterminate: DoubleBondLayout dbd = new DoubleBondLayout() { StartAtomHull = startAtomHull, EndAtomHull = endAtomHull, Start = startAtomPosition, End = endAtomPosition, StartNeigbourPositions = (from Atom a in startAtomVisual.ParentAtom.NeighboursExcept(endAtomVisual.ParentAtom) select a.Position).ToList(), EndNeighbourPositions = (from Atom a in endAtomVisual.ParentAtom.NeighboursExcept(startAtomVisual.ParentAtom) select a.Position).ToList() }; BondGeometry.GetCrossedDoubleGeometry(dbd, modelXamlBondLength, standoff); return(dbd); //partial or undefined bonds case 0: case 0.5: case 1.0: BondLayout sbd = new BondLayout { Start = startAtomPosition, End = endAtomPosition, StartAtomHull = startAtomHull, EndAtomHull = endAtomHull }; BondGeometry.GetSingleBondGeometry(sbd, standoff); return(sbd); //double bond & 1.5 bond case 1.5: case 2: DoubleBondLayout dbd2 = new DoubleBondLayout() { StartAtomHull = startAtomHull, EndAtomHull = endAtomHull, Start = startAtomPosition, End = endAtomPosition, Placement = parentPlacement, PrimaryCentroid = centroid, SecondaryCentroid = secondaryCentroid, StartNeigbourPositions = (from Atom a in startAtomVisual.ParentAtom.NeighboursExcept(endAtomVisual.ParentAtom) select a.Position).ToList(), EndNeighbourPositions = (from Atom a in endAtomVisual.ParentAtom.NeighboursExcept(startAtomVisual.ParentAtom) select a.Position).ToList() }; BondGeometry.GetDoubleBondGeometry(dbd2, modelXamlBondLength, standoff); return(dbd2); //triple and 2.5 bond case 2.5: case 3: TripleBondLayout tbd = new TripleBondLayout() { StartAtomHull = startAtomHull, EndAtomHull = endAtomHull, Start = startAtomPosition, End = endAtomPosition, Placement = parentPlacement, PrimaryCentroid = centroid, SecondaryCentroid = secondaryCentroid }; BondGeometry.GetTripleBondGeometry(tbd, modelXamlBondLength, standoff); return(tbd); default: return(null); } }