/// <summary>
/// Completes the layout of a partially laid out ring.
/// </summary>
/// <param name="rset">ring set</param>
/// <param name="ring">the ring to complete</param>
/// <param name="bondLength">the bond length</param>
internal bool CompletePartiallyPlacedRing(IRingSet rset, IRing ring, double bondLength)
{
if (ring.IsPlaced)
{
return(true);
}
IRing partiallyPlacedRing = Molecule.Builder.NewRing();
foreach (IAtom atom in ring.Atoms)
{
if (atom.Point2D != null)
{
atom.IsPlaced = true;
}
}
AtomPlacer.CopyPlaced(partiallyPlacedRing, ring);
if (partiallyPlacedRing.Atoms.Count > 1 &&
partiallyPlacedRing.Atoms.Count < ring.Atoms.Count)
{
PlaceConnectedRings(rset, partiallyPlacedRing, RingPlacer.Fused, bondLength);
PlaceConnectedRings(rset, partiallyPlacedRing, RingPlacer.Bridged, bondLength);
PlaceConnectedRings(rset, partiallyPlacedRing, RingPlacer.Spiro, bondLength);
ring.IsPlaced = true;
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Place ring with user provided angles.
/// </summary>
/// <param name="ring">the ring to place.</param>
/// <param name="ringCenter">center coordinates of the ring.</param>
/// <param name="bondLength">given bond length.</param>
/// <param name="startAngles">a map with start angles when drawing the ring.</param>
public virtual void PlaceRing(IRing ring, Vector2 ringCenter, double bondLength, IReadOnlyDictionary <int, double> startAngles)
{
var radius = GetNativeRingRadius(ring, bondLength);
var addAngle = 2 * Math.PI / ring.RingSize;
var startAtom = ring.Atoms[0];
Vector2 p = new Vector2((ringCenter.X + radius), ringCenter.Y);
startAtom.Point2D = p;
var startAngle = Math.PI * 0.5;
// Different ring sizes get different start angles to have visually
// correct placement
int ringSize = ring.RingSize;
startAngle = startAngles[ringSize];
var bonds = ring.GetConnectedBonds(startAtom);
// Store all atoms to draw in consecutive order relative to the chosen bond.
var atomsToDraw = new List <IAtom>();
IAtom currentAtom = startAtom;
IBond currentBond = (IBond)bonds.First();
for (int i = 0; i < ring.Bonds.Count; i++)
{
currentBond = ring.GetNextBond(currentBond, currentAtom);
currentAtom = currentBond.GetOther(currentAtom);
atomsToDraw.Add(currentAtom);
}
AtomPlacer.PopulatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}
public void TriangleTest()
{
List <IAtom> atoms = new List <IAtom>
{
new Atom("C"),
new Atom("C"),
new Atom("C")
};
AtomPlacer placer = new AtomPlacer();
AtomPlacer.PopulatePolygonCorners(atoms, Vector2.Zero, 0, 10, 10);
foreach (var atom in atoms)
{
Assert.IsNotNull(atom.Point2D);
}
}
public void EmptyAtomsListTest()
{
List <IAtom> atoms = new List <IAtom>();
// switch on debugging, to see if NPE is thrown
AtomPlacer placer = new AtomPlacer();
bool npeThrown = false;
try
{
AtomPlacer.PopulatePolygonCorners(atoms, Vector2.Zero, 0, 10, 10);
}
catch (NullReferenceException)
{
npeThrown = true;
}
Assert.IsFalse(npeThrown, "Null pointer for emp.Y atoms list");
}
/// <summary>
/// Positions the aliphatic substituents of a ring system
/// </summary>
/// <param name="rs">The RingSystem for which the substituents are to be laid out</param>
/// <returns>A list of atoms that where laid out</returns>
public IAtomContainer PlaceRingSubstituents(IRingSet rs, double bondLength)
{
Debug.WriteLine("RingPlacer.PlaceRingSubstituents() start");
IRing ring = null;
IAtom atom = null;
IAtomContainer unplacedPartners = rs.Builder.NewAtomContainer();
IAtomContainer sharedAtoms = rs.Builder.NewAtomContainer();
IAtomContainer primaryAtoms = rs.Builder.NewAtomContainer();
IAtomContainer treatedAtoms = rs.Builder.NewAtomContainer();
for (int j = 0; j < rs.Count; j++)
{
ring = (IRing)rs[j]; // Get the j-th Ring in RingSet rs
for (int k = 0; k < ring.Atoms.Count; k++)
{
unplacedPartners.RemoveAllElements();
sharedAtoms.RemoveAllElements();
primaryAtoms.RemoveAllElements();
atom = ring.Atoms[k];
var rings = rs.GetRings(atom);
var centerOfRingGravity = GeometryUtil.Get2DCenter(rings);
AtomPlacer.PartitionPartners(atom, unplacedPartners, sharedAtoms);
AtomPlacer.MarkNotPlaced(unplacedPartners);
try
{
for (int f = 0; f < unplacedPartners.Atoms.Count; f++)
{
Debug.WriteLine("placeRingSubstituents->unplacedPartners: "
+ (Molecule.Atoms.IndexOf(unplacedPartners.Atoms[f]) + 1));
}
}
catch (Exception)
{
}
treatedAtoms.Add(unplacedPartners);
if (unplacedPartners.Atoms.Count > 0)
{
AtomPlacer.DistributePartners(atom, sharedAtoms, centerOfRingGravity, unplacedPartners, bondLength);
}
}
}
Debug.WriteLine("RingPlacer.PlaceRingSubstituents() end");
return(treatedAtoms);
}
public void Cumulated_x3()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 3));
m.Atoms.Add(Atom("C", 1));
m.Atoms.Add(Atom("C", 0));
m.Atoms.Add(Atom("C", 0));
m.Atoms.Add(Atom("C", 1));
m.Atoms.Add(Atom("C", 3));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Double);
m.AddBond(m.Atoms[2], m.Atoms[3], BondOrder.Double);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Double);
m.AddBond(m.Atoms[4], m.Atoms[5], BondOrder.Single);
m.Atoms[0].Point2D = Vector2.Zero;
m.Atoms[0].IsPlaced = true;
AtomPlacer atomPlacer = new AtomPlacer {
Molecule = m
};
var v = new Vector2(0, 1.5);
atomPlacer.PlaceLinearChain(m, ref v, 1.5);
Vector2 p1 = m.Atoms[1].Point2D.Value;
Vector2 p2 = m.Atoms[2].Point2D.Value;
Vector2 p3 = m.Atoms[3].Point2D.Value;
Vector2 p4 = m.Atoms[4].Point2D.Value;
Vector2 p2p1 = new Vector2(p1.X - p2.X, p1.Y - p2.Y);
Vector2 p2p3 = new Vector2(p3.X - p2.X, p3.Y - p2.Y);
Vector2 p3p2 = new Vector2(p2.X - p3.X, p2.Y - p3.Y);
Vector2 p3p4 = new Vector2(p4.X - p3.X, p4.Y - p3.Y);
p2p1 = Vector2.Normalize(p2p1);
p2p3 = Vector2.Normalize(p2p3);
p3p2 = Vector2.Normalize(p3p2);
p3p4 = Vector2.Normalize(p3p4);
//Assert.AreEqual(Math.PI, Math.Acos(p2p1.X * p2p3.X + p2p1.Y * p2p3.Y), 0.05);
//Assert.AreEqual(Math.PI, Math.Acos(p3p2.X * p3p4.X + p3p2.Y * p3p4.Y), 0.05);
Assert.AreEqual(-1, p2p1.X * p2p3.X + p2p1.Y * p2p3.Y, 0.001);
Assert.AreEqual(-1, p3p2.X * p3p4.X + p3p2.Y * p3p4.Y, 0.001);
}
public void Cumulated_x2()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 3));
m.Atoms.Add(Atom("C", 1));
m.Atoms.Add(Atom("C", 0));
m.Atoms.Add(Atom("C", 1));
m.Atoms.Add(Atom("C", 3));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Double);
m.AddBond(m.Atoms[2], m.Atoms[3], BondOrder.Double);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Single);
m.Atoms[0].Point2D = Vector2.Zero;
m.Atoms[0].IsPlaced = true;
AtomPlacer atomPlacer = new AtomPlacer {
Molecule = m
};
var v = new Vector2(0, 1.5);
atomPlacer.PlaceLinearChain(m, ref v, 1.5);
Vector2 p1 = m.Atoms[1].Point2D.Value;
Vector2 p2 = m.Atoms[2].Point2D.Value;
Vector2 p3 = m.Atoms[3].Point2D.Value;
Vector2 p2p1 = new Vector2(p1.X - p2.X, p1.Y - p2.Y);
Vector2 p2p3 = new Vector2(p3.X - p2.X, p3.Y - p2.Y);
p2p1 = Vector2.Normalize(p2p1);
p2p3 = Vector2.Normalize(p2p3);
double round = (float)(p2p1.X * p2p3.X + p2p1.Y * p2p3.Y); // rounding the value to avoid over 1 value.
double theta = Math.Acos(round);
Assert.AreEqual(Math.PI, theta, 0.05);
}
/// <summary>
/// Generated coordinates for a given ring, which is fused to another ring.
/// The rings share exactly one bond.
/// </summary>
/// <param name="ring">The ring to be placed</param>
/// <param name="sharedAtoms">The atoms of this ring, also members of another ring, which are already placed</param>
/// <param name="ringCenterVector">A vector pointing the the center of the new ring</param>
/// <param name="bondLength">The standard bondlength</param>
public virtual void PlaceFusedRing(IRing ring,
IAtomContainer sharedAtoms,
Vector2 ringCenterVector,
double bondLength)
{
Debug.WriteLine("RingPlacer.PlaceFusedRing() start");
IAtom beg = sharedAtoms.Atoms[0];
IAtom end = sharedAtoms.Atoms[1];
Vector2 pBeg = beg.Point2D.Value;
Vector2 pEnd = end.Point2D.Value;
// fuse the ring perpendicular to the bond, ring center is not
// sub-optimal if non-regular/convex polygon (e.g. macro cycle)
ringCenterVector = GetPerpendicular(pBeg, pEnd, ringCenterVector);
double radius = GetNativeRingRadius(ring, bondLength);
double newRingPerpendicular = Math.Sqrt(Math.Pow(radius, 2) - Math.Pow(bondLength / 2, 2));
ringCenterVector = Vector2.Normalize(ringCenterVector);
Debug.WriteLine($"placeFusedRing->: ringCenterVector.Length {ringCenterVector.Length()}");
ringCenterVector *= newRingPerpendicular;
Vector2 ringCenter = GetMidPoint(pBeg, pEnd);
ringCenter += ringCenterVector;
Vector2 originRingCenterVector = ringCenter;
pBeg -= originRingCenterVector;
pEnd -= originRingCenterVector;
double occupiedAngle = Angle(pBeg, pEnd);
double remainingAngle = (2 * Math.PI) - occupiedAngle;
double addAngle = remainingAngle / (ring.RingSize - 1);
Debug.WriteLine("placeFusedRing->occupiedAngle: " + Vectors.RadianToDegree(occupiedAngle));
Debug.WriteLine("placeFusedRing->remainingAngle: " + Vectors.RadianToDegree(remainingAngle));
Debug.WriteLine("placeFusedRing->addAngle: " + Vectors.RadianToDegree(addAngle));
IAtom startAtom;
double centerX = ringCenter.X;
double centerY = ringCenter.Y;
double xDiff = beg.Point2D.Value.X - end.Point2D.Value.X;
double yDiff = beg.Point2D.Value.Y - end.Point2D.Value.Y;
double startAngle;;
int direction = 1;
// if bond is vertical
if (xDiff == 0)
{
Debug.WriteLine("placeFusedRing->Bond is vertical");
//starts with the lower Atom
if (beg.Point2D.Value.Y > end.Point2D.Value.Y)
{
startAtom = beg;
}
else
{
startAtom = end;
}
//changes the drawing direction
if (centerX < beg.Point2D.Value.X)
{
direction = 1;
}
else
{
direction = -1;
}
}
// if bond is not vertical
else
{
//starts with the left Atom
if (beg.Point2D.Value.X > end.Point2D.Value.X)
{
startAtom = beg;
}
else
{
startAtom = end;
}
//changes the drawing direction
if (centerY - beg.Point2D.Value.Y > (centerX - beg.Point2D.Value.X) * yDiff / xDiff)
{
direction = 1;
}
else
{
direction = -1;
}
}
startAngle = GeometryUtil.GetAngle(startAtom.Point2D.Value.X - ringCenter.X, startAtom.Point2D.Value.Y - ringCenter.Y);
IAtom currentAtom = startAtom;
// determine first bond in Ring
// int k = 0;
// for (k = 0; k < ring.GetElectronContainerCount(); k++) {
// if (ring.GetElectronContainer(k) is IBond) break;
// }
IBond currentBond = sharedAtoms.Bonds[0];
var atomsToDraw = new List <IAtom>();
for (int i = 0; i < ring.Bonds.Count - 2; i++)
{
currentBond = ring.GetNextBond(currentBond, currentAtom);
currentAtom = currentBond.GetOther(currentAtom);
atomsToDraw.Add(currentAtom);
}
addAngle = addAngle * direction;
#if DEBUG
Debug.WriteLine("placeFusedRing->startAngle: " + Vectors.RadianToDegree(startAngle));
Debug.WriteLine("placeFusedRing->addAngle: " + Vectors.RadianToDegree(addAngle));
Debug.WriteLine("placeFusedRing->startAtom is: " + (Molecule.Atoms.IndexOf(startAtom) + 1));
Debug.WriteLine("AtomsToDraw: " + AtomPlacer.ListNumbers(Molecule, atomsToDraw));
#endif
AtomPlacer.PopulatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}
/// <summary>
/// Generated coordinates for a given ring, which is connected to a spiro ring.
/// The rings share exactly one atom.
/// </summary>
/// <param name="ring">The ring to be placed</param>
/// <param name="sharedAtoms">The atoms of this ring, also members of another ring, which are already placed</param>
/// <param name="sharedAtomsCenter">The geometric center of these atoms</param>
/// <param name="ringCenterVector">A vector pointing the center of the new ring</param>
/// <param name="bondLength">The standard bond length</param>
public virtual void PlaceSpiroRing(IRing ring, IAtomContainer sharedAtoms, Vector2 sharedAtomsCenter, Vector2 ringCenterVector, double bondLength)
{
var startAtom = sharedAtoms.Atoms[0];
var mBonds = Molecule.GetConnectedBonds(sharedAtoms.Atoms[0]).ToReadOnlyList();
var degree = mBonds.Count;
Debug.WriteLine($"placeSpiroRing: D={degree}");
// recalculate the ringCentreVector
if (degree != 4)
{
int numPlaced = 0;
foreach (var bond in mBonds)
{
var nbr = bond.GetOther(sharedAtoms.Atoms[0]);
if (!nbr.IsPlaced)
{
continue;
}
numPlaced++;
}
if (numPlaced == 2)
{
// nudge the shared atom such that bond lengths will be
// equal
startAtom.Point2D += ringCenterVector;
sharedAtomsCenter += ringCenterVector;
}
var theta = Math.PI - (2 * Math.PI / (degree / 2));
Rotate(ringCenterVector, theta);
}
var radius = GetNativeRingRadius(ring, bondLength);
var ringCenter = sharedAtomsCenter;
if (degree == 4)
{
ringCenterVector = Vector2.Normalize(ringCenterVector);
ringCenterVector *= radius;
}
else
{
// spread things out a little for multiple spiro centres
ringCenterVector = Vector2.Normalize(ringCenterVector);
ringCenterVector *= (2 * radius);
}
ringCenter += ringCenterVector;
var addAngle = 2 * Math.PI / ring.RingSize;
var currentAtom = startAtom;
var startAngle = GeometryUtil.GetAngle(
startAtom.Point2D.Value.X - ringCenter.X,
startAtom.Point2D.Value.Y - ringCenter.Y);
// Get one bond connected to the spiro bridge atom. It doesn't matter in which direction we draw.
var rBonds = ring.GetConnectedBonds(startAtom);
var currentBond = rBonds.First();
var atomsToDraw = new List <IAtom>();
// Store all atoms to draw in consequtive order relative to the chosen bond.
for (int i = 0; i < ring.Bonds.Count; i++)
{
currentBond = ring.GetNextBond(currentBond, currentAtom);
currentAtom = currentBond.GetOther(currentAtom);
if (!currentAtom.Equals(startAtom))
{
atomsToDraw.Add(currentAtom);
}
}
Debug.WriteLine($"currentAtom {currentAtom}");
Debug.WriteLine($"startAtom {startAtom}");
AtomPlacer.PopulatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}
private void PlaceBridgedRing(IRing ring, IAtomContainer sharedAtoms, Vector2 sharedAtomsCenter, Vector2 ringCenterVector, double bondLength)
{
IAtom[] bridgeAtoms = GetBridgeAtoms(sharedAtoms);
IAtom bondAtom1 = bridgeAtoms[0];
IAtom bondAtom2 = bridgeAtoms[1];
List <IAtom> otherAtoms = new List <IAtom>();
foreach (IAtom atom in sharedAtoms.Atoms)
{
if (atom != bondAtom1 && atom != bondAtom2)
{
otherAtoms.Add(atom);
}
}
bool snap = ring.GetProperty <bool>(SnapHint, false);
bool swap = snap ? Det(bondAtom1.Point2D.Value, GeometryUtil.Get2DCenter(otherAtoms), bondAtom2.Point2D.Value) < 0
: Det(bondAtom1.Point2D.Value, GeometryUtil.Get2DCenter(otherAtoms), bondAtom2.Point2D.Value) > 0;
if (swap)
{
IAtom tmp = bondAtom1;
bondAtom1 = bondAtom2;
bondAtom2 = tmp;
}
Vector2 bondAtom1Vector = bondAtom1.Point2D.Value;
Vector2 bondAtom2Vector = bondAtom2.Point2D.Value;
Vector2 midPoint = GetMidPoint(bondAtom1Vector, bondAtom2Vector);
Vector2 ringCenter;
double radius = GetNativeRingRadius(ring, bondLength);
double offset = 0;
if (snap)
{
ringCenter = midPoint;
ringCenterVector = GetPerpendicular(bondAtom1Vector, bondAtom2Vector,
new Vector2(midPoint.X - sharedAtomsCenter.X, midPoint.Y - sharedAtomsCenter.Y));
offset = 0;
foreach (IAtom atom in otherAtoms)
{
double dist = Vector2.Distance(atom.Point2D.Value, midPoint);
if (dist > offset)
{
offset = dist;
}
}
}
else
{
ringCenter = sharedAtomsCenter;
}
Vector2.Normalize(ringCenterVector);
ringCenterVector = ringCenterVector * (radius - offset);
ringCenter += ringCenterVector;
bondAtom1Vector -= ringCenter;
bondAtom2Vector -= ringCenter;
int numUnplaced = ring.RingSize - sharedAtoms.Atoms.Count;
double dot = bondAtom2Vector.X * bondAtom1Vector.X + bondAtom2Vector.Y * bondAtom1Vector.Y;
double det = bondAtom2Vector.X * bondAtom1Vector.Y - bondAtom2Vector.Y * bondAtom1Vector.X;
// theta remain/step
double tRemain = Math.Atan2(det, dot);
if (tRemain < 0)
{
tRemain = Math.PI + (Math.PI + tRemain);
}
double tStep = tRemain / (numUnplaced + 1);
Debug.WriteLine($"placeBridgedRing->tRemain: {Vectors.RadianToDegree(tRemain)}");
Debug.WriteLine($"placeBridgedRing->tStep: {Vectors.RadianToDegree(tStep)}");
double startAngle;
startAngle = GeometryUtil.GetAngle(bondAtom1.Point2D.Value.X - ringCenter.X, bondAtom1.Point2D.Value.Y - ringCenter.Y);
IAtom currentAtom = bondAtom1;
IBond currentBond = sharedAtoms.GetConnectedBonds(currentAtom).First();
List <IAtom> atoms = new List <IAtom>();
for (int i = 0; i < ring.Bonds.Count; i++)
{
currentBond = ring.GetNextBond(currentBond, currentAtom);
currentAtom = currentBond.GetOther(currentAtom);
if (!sharedAtoms.Contains(currentAtom))
{
atoms.Add(currentAtom);
}
}
#if DEBUG
Debug.WriteLine($"{nameof(PlaceBridgedRing)}->atomsToPlace: {AtomPlacer.ListNumbers(Molecule, atoms)}");
Debug.WriteLine($"{nameof(PlaceBridgedRing)}->startAngle: {Vectors.RadianToDegree(startAngle)}");
Debug.WriteLine($"{nameof(PlaceBridgedRing)}->tStep: {Vectors.RadianToDegree(tStep)}");
#endif
AtomPlacer.PopulatePolygonCorners(atoms, ringCenter, startAngle, -tStep, radius);
}
