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);
}
}
