/// <summary>
/// draws the two parallel lines of a double bond
/// These bonds can either straddle the atom-atom line or fall to one or other side of it
/// </summary>
/// <param name="descriptor">DoubleBondDescriptor which is populated</param>
/// <param name="standardBondLength">Standard bond length as defined by the model</param>
/// <param name="standoff"></param>
/// <returns></returns>
public static void GetDoubleBondGeometry(DoubleBondLayout descriptor, double standardBondLength, double standoff)
{
//get the standard points for a double bond
GetDoubleBondPoints(descriptor, standardBondLength);
//adjust the line ends
if (descriptor.StartAtomHull != null)
{
AdjustTerminus(ref descriptor.Start, descriptor.End, descriptor.StartAtomHull, standoff);
AdjustTerminus(ref descriptor.SecondaryStart, descriptor.SecondaryEnd, descriptor.StartAtomHull, standoff);
}
if (descriptor.EndAtomHull != null)
{
AdjustTerminus(ref descriptor.End, descriptor.Start, descriptor.EndAtomHull, standoff);
AdjustTerminus(ref descriptor.SecondaryEnd, descriptor.SecondaryStart, descriptor.EndAtomHull, standoff);
}
//and draw it
var sg = new StreamGeometry();
using (var sgc = sg.Open())
{
sgc.BeginFigure(descriptor.Start, false, false);
sgc.LineTo(descriptor.End, true, false);
sgc.BeginFigure(descriptor.SecondaryStart, false, false);
sgc.LineTo(descriptor.SecondaryEnd, true, false);
sgc.Close();
}
sg.Freeze();
descriptor.DefiningGeometry = sg;
}
/// <summary>
/// Defines a double bond
/// </summary>
/// <param name="descriptor">DoubleBondDescriptor which is populated</param>
/// <param name="standardBondLength">Standard bond length as defined by the model</param>
/// <returns></returns>
public static void GetDoubleBondPoints(DoubleBondLayout descriptor, double standardBondLength)
{
Point?point3a;
Point?point4a;
//use a struct here to return the values
GetDefaultDoubleBondPoints(descriptor, standardBondLength);
if (descriptor.PrimaryCentroid != null)
//now, if there is a centroid defined, the bond is part of a ring
{
Point?workingCentroid = null;
//work out whether the bond is place inside or outside the ring
var bondvector = descriptor.PrincipleVector;
var centreVector = descriptor.PrimaryCentroid - descriptor.Start;
var computedPlacement = (BondDirection)Math.Sign(Vector.CrossProduct(centreVector.Value, bondvector));
if (descriptor.Placement != BondDirection.None)
{
if (computedPlacement == descriptor.Placement) //then we have nothing to worry about
{
workingCentroid = descriptor.PrimaryCentroid;
}
else //we need to adjust the points according to the other centroid
{
workingCentroid = descriptor.SecondaryCentroid;
}
}
if (workingCentroid != null)
{
//shorten the secondto fit neatly within the ring
point3a = BasicGeometry.LineSegmentsIntersect(descriptor.Start, workingCentroid.Value,
descriptor.SecondaryStart,
descriptor.SecondaryEnd);
point4a = BasicGeometry.LineSegmentsIntersect(descriptor.End, workingCentroid.Value,
descriptor.SecondaryStart,
descriptor.SecondaryEnd);
var tempPoint3 = point3a ?? descriptor.SecondaryStart;
var tempPoint4 = descriptor.SecondaryEnd = point4a ?? descriptor.SecondaryEnd;
descriptor.SecondaryStart = tempPoint3;
descriptor.SecondaryEnd = tempPoint4;
}
//get the boundary for hit testing purposes
descriptor.Boundary.Clear();
descriptor.Boundary.AddRange(new[]
{
descriptor.Start, descriptor.End, descriptor.SecondaryEnd,
descriptor.SecondaryStart
});
}
}
/// <summary>
/// Gets an unadjusted set of points for a double bond
/// </summary>
/// <param name="descriptor">DoubleBondDescriptor which is populated</param>
/// <param name="standardBondLength">Standard bond length as defined by the model</param>
private static void GetDefaultDoubleBondPoints(DoubleBondLayout descriptor, double standardBondLength)
{
var v = descriptor.PrincipleVector;
var normal = v.Perpendicular();
normal.Normalize();
var distance = standardBondLength * BondOffsetPercentage;
//first, calculate the default bond points as if there were no rings involved
var tempStart = descriptor.Start;
//offset according to placement
switch (descriptor.Placement)
{
case BondDirection.None:
descriptor.Start = tempStart + normal * distance;
descriptor.End = descriptor.Start + v;
descriptor.SecondaryStart = tempStart - normal * distance;
descriptor.SecondaryEnd = descriptor.SecondaryStart + v;
break;
case BondDirection.Clockwise:
{
descriptor.SecondaryStart = tempStart - normal * 2 * distance;
descriptor.SecondaryEnd = descriptor.SecondaryStart + v;
break;
}
case BondDirection.Anticlockwise:
descriptor.SecondaryStart = tempStart + normal * 2 * distance;
descriptor.SecondaryEnd = descriptor.SecondaryStart + v;
break;
default:
descriptor.Start = tempStart + normal * distance;
descriptor.End = descriptor.Start + v;
descriptor.SecondaryStart = tempStart - normal * distance;
descriptor.SecondaryEnd = descriptor.SecondaryStart + v;
break;
}
}
/// <summary>
/// Draws the crossed double bond to indicate indeterminate geometry
/// </summary>
/// <param name="descriptor">BondLayout to hadle the physical bond shape</param>
/// <param name="standardBondLength">Model's standard bond length</param>
/// <param name="standoff">Boundary width between atom label and bond terminus</param>
public static void GetCrossedDoubleGeometry(DoubleBondLayout descriptor, double standardBondLength, double standoff)
{
var v = descriptor.PrincipleVector;
var normal = v.Perpendicular();
normal.Normalize();
Point point1, point2, point3, point4;
var distance = standardBondLength * Globals.BondOffsetPercentage;
point1 = descriptor.Start + normal * distance;
point2 = point1 + v;
point3 = descriptor.Start - normal * distance;
point4 = point3 + v;
if (descriptor.StartAtomHull != null)
{
AdjustTerminus(ref point1, point2, descriptor.StartAtomHull, standoff);
AdjustTerminus(ref point3, point4, descriptor.StartAtomHull, standoff);
}
if (descriptor.StartAtomHull != null)
{
AdjustTerminus(ref point2, point1, descriptor.StartAtomHull, standoff);
AdjustTerminus(ref point4, point3, descriptor.StartAtomHull, standoff);
}
var sg = new StreamGeometry();
using (var sgc = sg.Open())
{
sgc.BeginFigure(point1, false, false);
sgc.LineTo(point4, true, false);
sgc.BeginFigure(point2, false, false);
sgc.LineTo(point3, true, false);
sgc.Close();
}
sg.Freeze();
descriptor.DefiningGeometry = sg;
descriptor.Boundary.Clear();
descriptor.Boundary.AddRange(new[] { point1, point2, point4, point3 });
}
/// <summary>
/// Renders a bond to the display
/// </summary>
public override void Render()
{
//set up the shared variables first
Point startPoint, endPoint;
startPoint = ParentBond.StartAtom.Position;
endPoint = ParentBond.EndAtom.Position;
var bondLength = ParentBond.Model.XamlBondLength;
var cv1 = ChemicalVisuals.ContainsKey(ParentBond.StartAtom);
var cv2 = ChemicalVisuals.ContainsKey(ParentBond.EndAtom);
//bale out in case we have a null start or end
if (!cv1 || !cv2)
{
// Abort if either ChemicalVisual is missing !
return;
}
//now get the geometry of start and end atoms
var startVisual = (AtomVisual)ChemicalVisuals[ParentBond.StartAtom];
var endVisual = (AtomVisual)ChemicalVisuals[ParentBond.EndAtom];
//first grab the main descriptor
BondDescriptor = GetBondDescriptor(ParentBond, startVisual, endVisual, bondLength);
_enclosingPoly = BondDescriptor.Boundary;
//set up the default pens for rendering
_mainBondPen = new Pen(Brushes.Black, BondThickness)
{
StartLineCap = PenLineCap.Round,
EndLineCap = PenLineCap.Round,
LineJoin = PenLineJoin.Miter
};
_subsidiaryBondPen = _mainBondPen.Clone();
switch (ParentBond.Order)
{
case Globals.OrderZero:
case Globals.OrderOther:
case "unknown":
// Handle Zero Bond
_mainBondPen.DashStyle = DashStyles.Dot;
using (DrawingContext dc = RenderOpen())
{
dc.DrawGeometry(Brushes.Black, _mainBondPen, BondDescriptor.DefiningGeometry);
//we need to draw another transparent rectangle to expand the bounding box
DrawHitTestOverlay(dc);
dc.Close();
}
DoubleBondLayout dbd = new DoubleBondLayout
{
Start = startPoint,
End = endPoint,
Placement = ParentBond.Placement
};
BondGeometry.GetDoubleBondPoints(dbd, bondLength);
_enclosingPoly = dbd.Boundary;
break;
case Globals.OrderPartial01:
_mainBondPen.DashStyle = DashStyles.Dash;
using (DrawingContext dc = RenderOpen())
{
dc.DrawGeometry(Brushes.Black, _mainBondPen, BondDescriptor.DefiningGeometry);
//we need to draw another transparent thicker line on top of the existing one
DrawHitTestOverlay(dc);
dc.Close();
}
//grab the enclosing polygon as for a double ParentBond - this overcomes a hit testing bug
DoubleBondLayout dbd2 = new DoubleBondLayout
{
Start = startPoint,
End = endPoint,
Placement = ParentBond.Placement
};
BondGeometry.GetDoubleBondPoints(dbd2, bondLength);
_enclosingPoly = dbd2.Boundary;
break;
case "1":
case Globals.OrderSingle:
// Handle Single bond
switch (ParentBond.Stereo)
{
case Globals.BondStereo.Indeterminate:
case Globals.BondStereo.None:
case Globals.BondStereo.Wedge:
using (DrawingContext dc = RenderOpen())
{
dc.DrawGeometry(Brushes.Black, _mainBondPen, BondDescriptor.DefiningGeometry);
//we need to draw another transparent rectangle to expand the bounding box
DrawHitTestOverlay(dc);
dc.Close();
}
break;
case Globals.BondStereo.Hatch:
using (DrawingContext dc = RenderOpen())
{
dc.DrawGeometry(GetHatchBrush(ParentBond.Angle), _mainBondPen, BondDescriptor.DefiningGeometry);
//we need to draw another transparent rectangle to expand the bounding box
DrawHitTestOverlay(dc);
dc.Close();
}
break;
}
break;
case Globals.OrderPartial12:
case Globals.OrderAromatic:
case "2":
case Globals.OrderDouble:
DoubleBondLayout dbd3 = (DoubleBondLayout)BondDescriptor;
Point? centroid = ParentBond.Centroid;
dbd3.PrimaryCentroid = centroid;
if (ParentBond.Order == Globals.OrderPartial12 || ParentBond.Order == Globals.OrderAromatic) // Handle 1.5 bond
{
_subsidiaryBondPen.DashStyle = DashStyles.Dash;
}
_enclosingPoly = dbd3.Boundary;
if (ParentBond.Stereo != Globals.BondStereo.Indeterminate)
{
using (DrawingContext dc = RenderOpen())
{
dc.DrawLine(_mainBondPen, BondDescriptor.Start, BondDescriptor.End);
dc.DrawLine(_subsidiaryBondPen,
dbd3.SecondaryStart,
dbd3.SecondaryEnd);
dc.Close();
}
}
else
{
using (DrawingContext dc = RenderOpen())
{
dc.DrawGeometry(_mainBondPen.Brush, _mainBondPen, BondDescriptor.DefiningGeometry);
dc.Close();
}
}
break;
case Globals.OrderPartial23:
case "3":
case Globals.OrderTriple:
if (ParentBond.Order == Globals.OrderPartial23) // Handle 2.5 bond
{
_subsidiaryBondPen.DashStyle = DashStyles.Dash;
}
var tbd = (BondDescriptor as TripleBondLayout);
using (DrawingContext dc = RenderOpen())
{
if (ParentBond.Placement == Globals.BondDirection.Clockwise)
{
dc.DrawLine(_mainBondPen, tbd.SecondaryStart, tbd.SecondaryEnd);
dc.DrawLine(_mainBondPen, tbd.Start, tbd.End);
dc.DrawLine(_subsidiaryBondPen, tbd.TertiaryStart, tbd.TertiaryEnd);
}
else
{
dc.DrawLine(_subsidiaryBondPen, tbd.SecondaryStart, tbd.SecondaryEnd);
dc.DrawLine(_mainBondPen, tbd.Start, tbd.End);
dc.DrawLine(_mainBondPen, tbd.TertiaryStart, tbd.TertiaryEnd);
}
dc.Close();
}
break;
}
void DrawHitTestOverlay(DrawingContext dc)
{
SolidColorBrush outliner = new SolidColorBrush(Colors.Salmon);
#if SHOWBOUNDS
outliner.Opacity = 0.2d;
#else
outliner.Opacity = 0d;
#endif
Pen outlinePen = new Pen(outliner, BondThickness * 5);
dc.DrawGeometry(outliner, outlinePen, BondDescriptor.DefiningGeometry);
}
}
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>
/// Defines a double bond
/// </summary>
/// <param name="descriptor">DoubleBondDescriptor which is populated</param>
/// <param name="standardBondLength">Standard bond length as defined by the model</param>
/// <returns></returns>
public static void GetDoubleBondPoints(DoubleBondLayout descriptor, double standardBondLength)
{
Point?descriptorSecondaryStart;
Point?descriptorSecondaryEnd;
//use a struct here to return the values
GetDefaultDoubleBondPoints(descriptor, standardBondLength);
if (descriptor.PrimaryCentroid != null)
{
//now, if there is a centroid defined, the bond is part of a ring
Point?workingCentroid = null;
//work out whether the bond is place inside or outside the ring
var bondvector = descriptor.PrincipleVector;
var centreVector = descriptor.PrimaryCentroid - descriptor.Start;
var computedPlacement = (Globals.BondDirection)Math.Sign(Vector.CrossProduct(centreVector.Value, bondvector));
if (descriptor.Placement != Globals.BondDirection.None)
{
if (computedPlacement == descriptor.Placement) //then we have nothing to worry about
{
workingCentroid = descriptor.PrimaryCentroid;
}
else //we need to adjust the points according to the other centroid
{
workingCentroid = descriptor.SecondaryCentroid;
}
}
if (workingCentroid != null)
{
var bondVector = (descriptor.End - descriptor.Start);
var midPoint = bondVector / 2 + descriptor.Start;
var perpAngle = Math.Abs(Vector.AngleBetween(workingCentroid.Value - midPoint, bondVector));
if (perpAngle >= 80 && perpAngle <= 100) //probably convex ring
{
//shorten the second bond to fit neatly within the ring
descriptorSecondaryStart = BasicGeometry.LineSegmentsIntersect(descriptor.Start, workingCentroid.Value,
descriptor.SecondaryStart,
descriptor.SecondaryEnd);
descriptorSecondaryEnd = BasicGeometry.LineSegmentsIntersect(descriptor.End, workingCentroid.Value,
descriptor.SecondaryStart,
descriptor.SecondaryEnd);
var tempPoint3 = descriptorSecondaryStart ?? descriptor.SecondaryStart;
var tempPoint4 = descriptorSecondaryEnd ?? descriptor.SecondaryEnd;
descriptor.SecondaryStart = tempPoint3;
descriptor.SecondaryEnd = tempPoint4;
}
else //probably concave ring, so shorten by half the bond offset value
{
if (descriptor.StartNeigbourPositions != null && descriptor.EndNeighbourPositions != null)
{
SplitBondAngles(ref descriptor.SecondaryStart, descriptor.SecondaryEnd,
descriptor.StartNeigbourPositions, descriptor.Start);
SplitBondAngles(ref descriptor.SecondaryEnd, descriptor.SecondaryStart,
descriptor.EndNeighbourPositions, descriptor.End);
}
}
}
else //no centroid so split the angles anyway
{
if (descriptor.StartNeigbourPositions != null && descriptor.EndNeighbourPositions != null)
{
SplitBondAngles(ref descriptor.SecondaryStart, descriptor.SecondaryEnd,
descriptor.StartNeigbourPositions, descriptor.Start);
SplitBondAngles(ref descriptor.SecondaryEnd, descriptor.SecondaryStart,
descriptor.EndNeighbourPositions, descriptor.End);
}
}
//get the boundary for hit testing purposes
descriptor.Boundary.Clear();
descriptor.Boundary.AddRange(new[]
{
descriptor.Start, descriptor.End, descriptor.SecondaryEnd,
descriptor.SecondaryStart
});
}
}
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);
}
}
