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);
}
}
