/// <summary>
/// Returns the geometry of a wedge bond. Hatch bonds use the same geometry
/// but a different brush.
/// </summary>
/// <param name="desc">Descriptor defining the bond shape</param>
/// <param name="perp">perpendicular vector to the bond</param>
public static void GetWedgePoints(WedgeBondLayout desc, Vector perp)
{
desc.FirstCorner = desc.End + perp;
desc.SecondCorner = desc.End - perp;
desc.Boundary.AddRange(new[] { desc.Start, desc.FirstCorner, desc.SecondCorner });
}
/// <summary>
/// Gets the geometry of a wedge bond.
/// </summary>
/// <param name="desc">WedgeBondDescriptor which is populated</param>
/// <param name="standardBondLength">Standard bond length as defined by the model</param>
/// <param name="standoff">Boundary width between atom label and bond terminus</param>
public static void GetWedgeBondGeometry(WedgeBondLayout desc, double standardBondLength, double standoff)
{
//get the width of the wedge bond's thick end
var bondVector = desc.PrincipleVector;
var perpVector = bondVector.Perpendicular();
perpVector.Normalize();
perpVector *= standardBondLength * Globals.BondOffsetPercentage;
// shrink the bond so it doesn't overlap any AtomVisuals
AdjustTerminus(ref desc.Start, desc.End, desc.StartAtomHull, standoff);
AdjustTerminus(ref desc.End, desc.Start, desc.EndAtomHull, standoff);
//then draw it
GetWedgePoints(desc, perpVector);
//and pass it back as a Geometry
StreamGeometry sg;
sg = desc.GetOutline();
sg.Freeze();
desc.DefiningGeometry = sg;
}
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);
}
}
/// <summary>
/// Chamfers or forks the end of a wedge bond under special circumstances
/// (one or more incoming single bonds)
/// </summary>
/// <param name="descriptor"> WedgeBondDescriptor to be populated</param>
/// <param name="standardBondLength">Standard bond length as defined by the model</param>
/// <param name="otherAtomPoints">List of positions of atoms splaying from the end atom</param>
/// <param name="standoff"></param>
public static void GetChamferedWedgeGeometry(WedgeBondLayout descriptor,
double standardBondLength,
List <Point> otherAtomPoints, double standoff)
{
var bondVector = descriptor.PrincipleVector;
//first get an unaltered bond
GetWedgeBondGeometry(descriptor, standardBondLength, standoff);
var firstEdgeVector = descriptor.FirstCorner - descriptor.Start;
var secondEdgeVector = descriptor.SecondCorner - descriptor.Start;
//get the two bonds with widest splay
var widestPoints = from Point p in otherAtomPoints
orderby Math.Abs(Vector.AngleBetween(bondVector, p - descriptor.End)) descending
select p;
//the scaling factors are what we multiply the bond edge vectors by
double firstScalingFactor = 0d;
double secondScalingFactor = 0d;
//work out the biggest scaling factor for either long edge
foreach (var point in widestPoints)
{
BasicGeometry.IntersectLines(descriptor.Start,
descriptor.FirstCorner,
descriptor.End,
point, out var firstEdgeCut, out var otherBond1Cut);
BasicGeometry.IntersectLines(descriptor.Start,
descriptor.SecondCorner,
descriptor.End,
point, out var secondEdgeCut, out var otherBond2Cut);
if (otherAtomPoints.Count == 1)
{
if (firstEdgeCut > firstScalingFactor)
{
firstScalingFactor = firstEdgeCut;
}
if (secondEdgeCut > secondScalingFactor)
{
secondScalingFactor = secondEdgeCut;
}
}
else
{
if (firstEdgeCut > firstScalingFactor && otherBond1Cut < 1d && otherBond1Cut > 0d)
{
firstScalingFactor = firstEdgeCut;
}
if (secondEdgeCut > secondScalingFactor && otherBond2Cut < 1d && otherBond2Cut > 0d)
{
secondScalingFactor = secondEdgeCut;
}
}
}
//and multiply the edges by the scaling factors
descriptor.FirstCorner = firstEdgeVector * firstScalingFactor + descriptor.Start;
descriptor.SecondCorner = secondEdgeVector * secondScalingFactor + descriptor.Start;
descriptor.CappedOff = true;
var sg = descriptor.GetOutline();
sg.Freeze();
descriptor.DefiningGeometry = sg;
}
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);
}
}
