/// <summary>
/// Returns a BondDescriptor object describing the visual layout of the visual
/// </summary>
/// <param name="parent"></param>
/// <param name="startAtomVisual"></param>
/// <param name="endAtomVisual"></param>
/// <param name="modelXamlBondLength"></param>
/// <param name="ignoreCentroid"></param>
/// <returns></returns>
public static BondLayout GetBondDescriptor(Bond parent, AtomVisual startAtomVisual, AtomVisual endAtomVisual, double modelXamlBondLength, bool ignoreCentroid = false)
{
//check to see if it's a wedge or a hatch yet
var startAtomPosition = parent.StartAtom.Position;
var endAtomPosition = parent.EndAtom.Position;
Point?centroid = null;
Point?secondaryCentroid = null;
if (!ignoreCentroid)
{
if (parent.IsCyclic())
{
centroid = parent.PrimaryRing?.Centroid;
secondaryCentroid = parent.SubsidiaryRing?.Centroid;
}
else
{
centroid = parent.Centroid;
secondaryCentroid = null;
}
}
//do the straightforward cases first -discriminate by stereo
var parentStereo = parent.Stereo;
var parentOrderValue = parent.OrderValue;
var parentPlacement = parent.Placement;
return(GetBondDescriptor(startAtomVisual, endAtomVisual, modelXamlBondLength, parentStereo, startAtomPosition, endAtomPosition, parentOrderValue, parentPlacement, centroid, secondaryCentroid));
}
/// <summary>
/// Adjusts the StartPoint of a bond to avoid the atom visual
/// </summary>
/// <param name="startPoint">Moveable start point</param>
/// <param name="endPoint">Fixed end point</param>
/// <param name="av">AtomVisual to avoid</param>
public static void AdjustTerminus(ref Point startPoint, Point endPoint, AtomVisual av)
{
if (av != null && av.AtomSymbol != "")
{
if (startPoint != endPoint)
{
var displacement = endPoint - startPoint;
var intersection = av.GetIntersection(startPoint, endPoint);
if (intersection != null)
{
displacement.Normalize();
displacement = displacement * AtomVisual.Standoff;
var tempPoint = new Point(intersection.Value.X, intersection.Value.Y) + displacement;
startPoint = new Point(tempPoint.X, tempPoint.Y);
}
}
}
}
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>
/// Renders a bond to the display
/// </summary>
public override void Render()
{
//set up the shared variables first
Point startPoint = ParentBond.StartAtom.Position;
Point endPoint = ParentBond.EndAtom.Position;
double bondLength = ParentBond.Model.XamlBondLength;
bool firstVisualExists = ChemicalVisuals.ContainsKey(ParentBond.StartAtom);
bool secondVisualExists = ChemicalVisuals.ContainsKey(ParentBond.EndAtom);
//bale out in case we have a null start or end or zero length bond
if (startPoint != endPoint && firstVisualExists && secondVisualExists)
{
//now get the geometry of start and end atoms
AtomVisual startVisual = (AtomVisual)ChemicalVisuals[ParentBond.StartAtom];
AtomVisual 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;
}
}
//local function
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, 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);
}
}