public virtual void TestGetConnectedRings_IRing()
{
IRingSet ringset = (IRingSet)NewChemObject();
IAtom ring1Atom1 = ringset.Builder.NewAtom("C"); // rather artificial molecule
IAtom ring1Atom2 = ringset.Builder.NewAtom("C");
IAtom sharedAtom1 = ringset.Builder.NewAtom("C");
IAtom sharedAtom2 = ringset.Builder.NewAtom("C");
IAtom ring2Atom1 = ringset.Builder.NewAtom("C");
IAtom ring2Atom2 = ringset.Builder.NewAtom("C");
IBond ring1Bond1 = ringset.Builder.NewBond(ring1Atom1, ring1Atom2);
IBond ring1Bond2 = ringset.Builder.NewBond(sharedAtom1, ring1Atom1);
IBond ring1Bond3 = ringset.Builder.NewBond(sharedAtom2, ring1Atom2);
IBond sharedBond = ringset.Builder.NewBond(sharedAtom1, sharedAtom2);
IBond ring2Bond1 = ringset.Builder.NewBond(ring2Atom1, ring2Atom2);
IBond ring2Bond2 = ringset.Builder.NewBond(sharedAtom1, ring2Atom1);
IBond ring2Bond3 = ringset.Builder.NewBond(sharedAtom2, ring2Atom2);
IRing ring1 = ringset.Builder.NewRing();
ring1.Atoms.Add(ring1Atom1);
ring1.Atoms.Add(ring1Atom2);
ring1.Atoms.Add(sharedAtom1);
ring1.Atoms.Add(sharedAtom2);
ring1.Bonds.Add(ring1Bond1);
ring1.Bonds.Add(ring1Bond2);
ring1.Bonds.Add(ring1Bond3);
ring1.Bonds.Add(sharedBond);
IRing ring2 = ringset.Builder.NewRing();
ring2.Atoms.Add(ring2Atom1);
ring2.Atoms.Add(ring2Atom2);
ring2.Atoms.Add(sharedAtom1);
ring2.Atoms.Add(sharedAtom2);
ring2.Bonds.Add(ring2Bond1);
ring2.Bonds.Add(ring2Bond2);
ring2.Bonds.Add(ring2Bond3);
ring2.Bonds.Add(sharedBond);
ringset.Add(ring1);
ringset.Add(ring2);
Assert.AreEqual(1, ringset.GetConnectedRings(ring2).Count());
Assert.AreEqual(1, ringset.GetConnectedRings(ring1).Count());
}
/// <summary>
/// Perform a walk in the given RingSet, starting at a given Ring and
/// recursively searching for other Rings connected to this ring. By doing
/// this it finds all rings in the RingSet connected to the start ring,
/// putting them in newRs, and removing them from rs.
/// </summary>
/// <param name="rs">The RingSet to be searched</param>
/// <param name="ring">The ring to start with</param>
/// <param name="newRs">The RingSet containing all Rings connected to ring</param>
/// <returns>newRs The RingSet containing all Rings connected to ring</returns>
private static IRingSet WalkRingSystem(IRingSet rs, IRing ring, IRingSet newRs)
{
IRing tempRing;
var tempRings = rs.GetConnectedRings(ring);
rs.Remove(ring);
foreach (var container in tempRings)
{
tempRing = (IRing)container;
if (!newRs.Contains(tempRing))
{
newRs.Add(tempRing);
newRs.Add(WalkRingSystem(rs, tempRing, newRs));
}
}
return(newRs);
}
/// <summary>
/// Layout all rings in the given RingSet that are connected to a given Ring
/// </summary>
/// <param name="rs">The RingSet to be searched for rings connected to Ring</param>
/// <param name="ring">The Ring for which all connected rings in RingSet are to be layed out.</param>
public void PlaceConnectedRings(IRingSet rs, IRing ring, int handleType, double bondLength)
{
var connectedRings = rs.GetConnectedRings(ring);
// Debug.WriteLine(rs.ReportRingList(Molecule));
foreach (var container in connectedRings)
{
IRing connectedRing = (IRing)container;
if (!connectedRing.IsPlaced)
{
// Debug.WriteLine(ring.ToString(Molecule));
// Debug.WriteLine(connectedRing.ToString(Molecule));
IAtomContainer sharedAtoms = AtomContainerManipulator.GetIntersection(ring, connectedRing);
int numSharedAtoms = sharedAtoms.Atoms.Count;
Debug.WriteLine("placeConnectedRings-> connectedRing: " + (ring.ToString()));
if ((numSharedAtoms == 2 && handleType == Fused) ||
(numSharedAtoms == 1 && handleType == Spiro) ||
(numSharedAtoms > 2 && handleType == Bridged))
{
Vector2 sharedAtomsCenter = GeometryUtil.Get2DCenter(sharedAtoms);
Vector2 oldRingCenter = GeometryUtil.Get2DCenter(ring);
Vector2 tempVector = sharedAtomsCenter;
Vector2 newRingCenterVector = tempVector;
newRingCenterVector -= oldRingCenter;
// zero (or v. small ring center)
if (Math.Abs(newRingCenterVector.X) < 0.001 && Math.Abs(newRingCenterVector.Y) < 0.001)
{
// first see if we can use terminal bonds
IAtomContainer terminalOnly = Molecule.Builder.NewAtomContainer();
foreach (IAtom atom in ring.Atoms)
{
if (ring.GetConnectedBonds(atom).Count() == 1)
{
terminalOnly.Atoms.Add(atom);
}
}
if (terminalOnly.Atoms.Count == 2)
{
newRingCenterVector = GeometryUtil.Get2DCenter(terminalOnly);
newRingCenterVector = oldRingCenter;
connectedRing.SetProperty(RingPlacer.SnapHint, true);
}
else
{
// project coordinates on 12 axis (30 degree snaps) and choose one with most spread
Vector2 vec = new Vector2(0, 1);
double bestLen = -double.MaxValue;
for (int i = 0; i < 12; i++)
{
Vector2 orth = new Vector2(-vec.Y, vec.X);
orth = Vector2.Normalize(orth);
double min = double.MaxValue, max = -double.MaxValue;
foreach (IAtom atom in sharedAtoms.Atoms)
{
// s: scalar projection
double s = Vector2.Dot(orth, atom.Point2D.Value);
if (s < min)
{
min = s;
}
if (s > max)
{
max = s;
}
}
double len = max - min;
if (len > bestLen)
{
bestLen = len;
newRingCenterVector = vec;
}
Rotate(vec, RAD_30);
}
}
}
Vector2 oldRingCenterVector = newRingCenterVector;
Debug.WriteLine($"placeConnectedRing -> tempVector: {tempVector}, tempVector.Length: {tempVector.Length()}");
Debug.WriteLine($"placeConnectedRing -> bondCenter: {sharedAtomsCenter}");
Debug.WriteLine($"placeConnectedRing -> oldRingCenterVector.Length: {oldRingCenterVector.Length()}");
Debug.WriteLine($"placeConnectedRing -> newRingCenterVector.Length: {newRingCenterVector.Length()}");
Vector2 tempPoint = sharedAtomsCenter;
tempPoint += newRingCenterVector;
PlaceRing(connectedRing, sharedAtoms, sharedAtomsCenter, newRingCenterVector, bondLength);
connectedRing.IsPlaced = true;
PlaceConnectedRings(rs, connectedRing, handleType, bondLength);
}
}
}
}
public virtual void TestGetConnectedRingsBug1772613()
{
// Build a bridged and fused norbomane like ring system
// C1CCC2C(C1)C4CC2C3CCCCC34
IRingSet ringSet = (IRingSet)NewChemObject();
IRing leftCyclohexane = ringSet.Builder.NewRing(6, "C");
IRing rightCyclopentane = ringSet.Builder.NewRing(5, "C");
IRing leftCyclopentane = ringSet.Builder.NewRing();
IBond leftCyclohexane0RightCyclopentane4 = ringSet.Builder.NewBond(leftCyclohexane.Atoms[0], rightCyclopentane.Atoms[4]);
IBond leftCyclohexane1RightCyclopentane2 = ringSet.Builder.NewBond(leftCyclohexane.Atoms[1], rightCyclopentane.Atoms[2]);
leftCyclopentane.Atoms.Add(leftCyclohexane.Atoms[0]);
leftCyclopentane.Atoms.Add(leftCyclohexane.Atoms[1]);
leftCyclopentane.Atoms.Add(rightCyclopentane.Atoms[2]);
leftCyclopentane.Atoms.Add(rightCyclopentane.Atoms[3]);
leftCyclopentane.Atoms.Add(rightCyclopentane.Atoms[4]);
leftCyclopentane.Bonds.Add(leftCyclohexane.GetBond(leftCyclohexane.Atoms[0], leftCyclohexane.Atoms[1]));
leftCyclopentane.Bonds.Add(leftCyclohexane1RightCyclopentane2);
leftCyclopentane.Bonds.Add(rightCyclopentane.GetBond(rightCyclopentane.Atoms[2], rightCyclopentane.Atoms[3]));
leftCyclopentane.Bonds.Add(rightCyclopentane.GetBond(rightCyclopentane.Atoms[3], rightCyclopentane.Atoms[4]));
leftCyclopentane.Bonds.Add(leftCyclohexane0RightCyclopentane4);
IRing rightCyclohexane = ringSet.Builder.NewRing();
IAtom rightCyclohexaneAtom0 = ringSet.Builder.NewAtom("C");
IAtom rightCyclohexaneAtom1 = ringSet.Builder.NewAtom("C");
IAtom rightCyclohexaneAtom2 = ringSet.Builder.NewAtom("C");
IAtom rightCyclohexaneAtom5 = ringSet.Builder.NewAtom("C");
IBond rightCyclohexaneAtom0Atom1 = ringSet.Builder.NewBond(rightCyclohexaneAtom0,
rightCyclohexaneAtom1);
IBond rightCyclohexaneAtom1Atom2 = ringSet.Builder.NewBond(rightCyclohexaneAtom1,
rightCyclohexaneAtom2);
IBond rightCyclohexane2rightCyclopentane1 = ringSet.Builder.NewBond(rightCyclohexaneAtom2, rightCyclopentane.Atoms[1]);
IBond rightCyclohexane5rightCyclopentane0 = ringSet.Builder.NewBond(rightCyclohexaneAtom5, rightCyclopentane.Atoms[0]);
IBond rightCyclohexaneAtom0Atom5 = ringSet.Builder.NewBond(rightCyclohexaneAtom0,
rightCyclohexaneAtom5);
rightCyclohexane.Atoms.Add(rightCyclohexaneAtom0);
rightCyclohexane.Atoms.Add(rightCyclohexaneAtom1);
rightCyclohexane.Atoms.Add(rightCyclohexaneAtom2);
rightCyclohexane.Atoms.Add(rightCyclopentane.Atoms[1]);
rightCyclohexane.Atoms.Add(rightCyclopentane.Atoms[0]);
rightCyclohexane.Atoms.Add(rightCyclohexaneAtom5);
rightCyclohexane.Bonds.Add(rightCyclohexaneAtom0Atom1);
rightCyclohexane.Bonds.Add(rightCyclohexaneAtom1Atom2);
rightCyclohexane.Bonds.Add(rightCyclohexane2rightCyclopentane1);
rightCyclohexane.Bonds.Add(rightCyclopentane.GetBond(rightCyclopentane.Atoms[0], rightCyclopentane.Atoms[1]));
rightCyclohexane.Bonds.Add(rightCyclohexane5rightCyclopentane0);
rightCyclohexane.Bonds.Add(rightCyclohexaneAtom0Atom5);
ringSet.Add(leftCyclohexane);
ringSet.Add(leftCyclopentane);
ringSet.Add(rightCyclopentane);
ringSet.Add(rightCyclohexane);
// Get connected rings
var connectedRings = ringSet.GetConnectedRings(leftCyclohexane);
// Iterate over the connectedRings and fail if any duplicate is found
IList <IRing> foundRings = new List <IRing>();
foreach (var container in connectedRings)
{
IRing connectedRing = (IRing)container;
if (foundRings.Contains(connectedRing))
{
Assert.Fail("The list of connected rings contains duplicates.");
}
foundRings.Add(connectedRing);
}
}
