public static void GetSingleBondGeometry(BondLayout descriptor, double standoff)
{
var start = descriptor.Start;
var end = descriptor.End;
var sg = new StreamGeometry();
if (descriptor.StartAtomHull != null)
{
AdjustTerminus(ref start, end, descriptor.StartAtomHull, standoff);
}
if (descriptor.EndAtomHull != null)
{
AdjustTerminus(ref end, start, descriptor.EndAtomHull, standoff);
}
using (var sgc = sg.Open())
{
sgc.BeginFigure(start, false, false);
sgc.LineTo(end, true, false);
sgc.Close();
}
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)
{
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>
/// Quite ghastly routine to draw a wiggly bond
/// </summary>
/// <param name="descriptor">BondDescriptor which is populated</param>
/// <param name="standardBondLength">Standard bond length as defined by the model</param>
/// <param name="standoff"></param>
public static void GetWavyBondGeometry(BondLayout descriptor, double standardBondLength, double standoff)
{
var sg = new StreamGeometry();
//first do the adjustment for any atom visuals
if (descriptor.StartAtomHull != null)
{
AdjustTerminus(ref descriptor.Start, descriptor.End, descriptor.StartAtomHull, standoff);
}
if (descriptor.EndAtomHull != null)
{
AdjustTerminus(ref descriptor.End, descriptor.Start, descriptor.EndAtomHull, standoff);
}
//Work out the control points for a quadratic Bezier by sprouting alternately along the bond line
Vector halfAWiggle;
using (var sgc = sg.Open())
{
var bondVector = descriptor.PrincipleVector;
//come up with a number of wiggles that looks aesthetically sensible
var noOfWiggles = (int)Math.Ceiling(bondVector.Length / (standardBondLength * Globals.BondOffsetPercentage * 2));
if (noOfWiggles < 3)
{
noOfWiggles = 3;
}
//now calculate a wiggle vector that is 60 degrees from the bond angle
var wiggleLength = bondVector.Length / noOfWiggles;
halfAWiggle = bondVector;
halfAWiggle.Normalize();
halfAWiggle *= wiggleLength / 2;
//work out left and right sprouting vectors
var toLeft = new Matrix();
toLeft.Rotate(-60);
var toRight = new Matrix();
toRight.Rotate(60);
var leftVector = halfAWiggle * toLeft;
var rightVector = halfAWiggle * toRight;
var allpoints = new List <Point>();
//allpoints holds the control points for the bezier
allpoints.Add(descriptor.Start);
var lastPoint = descriptor.Start;
//move along the bond vector, sprouting control points alternately
for (var i = 0; i < noOfWiggles; i++)
{
var leftPoint = lastPoint + leftVector;
allpoints.Add(leftPoint);
allpoints.Add(lastPoint + halfAWiggle);
var rightPoint = lastPoint + halfAWiggle + rightVector;
allpoints.Add(rightPoint);
lastPoint += halfAWiggle * 2;
allpoints.Add(lastPoint);
}
allpoints.Add(descriptor.End);
BezierFromPoints(sgc, allpoints);
sgc.Close();
}
//define the boundary
descriptor.Boundary.Clear();
descriptor.Boundary.AddRange(new[]
{
descriptor.Start - halfAWiggle.Perpendicular(),
descriptor.End - halfAWiggle.Perpendicular(),
descriptor.End + halfAWiggle.Perpendicular(),
descriptor.Start + halfAWiggle.Perpendicular()
});
sg.Freeze();
descriptor.DefiningGeometry = sg;
//local function
void BezierFromPoints(StreamGeometryContext sgc, List <Point> allpoints)
{
sgc.BeginFigure(allpoints[0], false, false);
sgc.PolyQuadraticBezierTo(allpoints.Skip(1).ToArray(), true, true);
}
}
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);
}
}
