private static Globals.BondStereo BondStereoFromMolfile(int molfileBondStereo)
{
//Translates from a molfile convention bond stereochemistry number to the enumeration used in the model
//The opposite of BondStereoFromModel
Globals.BondStereo modelStereo = 0;
//MOLFILE: 0 is NOT stereo, 1 is UP, 6 is DOWN, 4 is EITHER
//MODEL : 0 is None, 1 is Wedge, 2 is Hatch, 3 is Indeterminate
switch (molfileBondStereo)
{
case 0:
modelStereo = Globals.BondStereo.None;
break;
case 1:
modelStereo = Globals.BondStereo.Wedge;
break;
case 4:
modelStereo = Globals.BondStereo.Indeterminate;
break;
case 6:
modelStereo = Globals.BondStereo.Hatch;
break;
default:
modelStereo = Globals.BondStereo.None;
break;
}
return(modelStereo);
}
private static int BondStereoFromModel(Globals.BondStereo modelBondStereo)
{
//Translates from the model enumerated bond stereochemistry to the molfile convention
//The opposite of BondStereoFromMolfile
int molfileStereo = 0;
//MODEL : 0 is None, 1 is Wedge, 2 is Hatch, 3 is Indeterminate
//MOLFILE: 0 is NOT stereo, 1 is UP, 6 is DOWN, 4 is EITHER
switch (modelBondStereo)
{
case Globals.BondStereo.None:
molfileStereo = 0;
break;
case Globals.BondStereo.Wedge:
molfileStereo = 1;
break;
case Globals.BondStereo.Hatch:
molfileStereo = 6;
break;
case Globals.BondStereo.Indeterminate:
molfileStereo = 4;
break;
default:
molfileStereo = 4;
break;
}
return(molfileStereo);
}
private static int MdlBondStereo(Globals.BondStereo code)
{
int stereo;
switch (code)
{
case Globals.BondStereo.None:
stereo = 0;
break;
case Globals.BondStereo.Wedge:
stereo = 1;
break;
case Globals.BondStereo.Hatch:
stereo = 6;
break;
case Globals.BondStereo.Indeterminate:
stereo = 4;
break;
default:
stereo = 0;
break;
}
return(stereo);
}
private static int MdlBondStereo(Globals.BondStereo code)
{
int stereo = 0;
if (code == Globals.BondStereo.None)
{
stereo = 0;
}
else if (code == Globals.BondStereo.Wedge)
{
stereo = 1;
}
else if (code == Globals.BondStereo.Hatch)
{
stereo = 6;
}
else
{
stereo = 0;
}
return(stereo);
}
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);
}
}
public BondLayout GetBondLayout(Point startPoint, Point endPoint, double bondLength,
Globals.BondStereo stereo, string order, Ring existingRing = null,
Ring subsidiaryRing = null)
{
BondLayout descriptor = null;
//check to see if it's a wedge or a hatch yet
if (stereo == Globals.BondStereo.Wedge || stereo == Globals.BondStereo.Hatch)
{
var wbd = new WedgeBondLayout {
Start = startPoint, End = endPoint
};
BondGeometry.GetWedgeBondGeometry(wbd, bondLength, CurrentEditor.ViewModel.Standoff);
return(wbd);
}
if (stereo == Globals.BondStereo.Indeterminate && (order == Globals.OrderSingle))
{
descriptor = new BondLayout {
Start = startPoint, End = endPoint
};
BondGeometry.GetWavyBondGeometry(descriptor, bondLength, CurrentEditor.ViewModel.Standoff);
return(descriptor);
}
var ordervalue = Bond.OrderToOrderValue(order);
//single or dotted bond
if (ordervalue <= 1)
{
descriptor = new BondLayout {
Start = startPoint, End = endPoint
};
BondGeometry.GetSingleBondGeometry(descriptor, CurrentEditor.ViewModel.Standoff);
}
//double bond
if (ordervalue == 2 || ordervalue == 1.5)
{
DoubleBondLayout dbd = new DoubleBondLayout {
Start = startPoint, End = endPoint
};
if (stereo == Globals.BondStereo.Indeterminate)
{
BondGeometry.GetCrossedDoubleGeometry(dbd, bondLength, CurrentEditor.ViewModel.Standoff);
}
else
{
dbd.PrimaryCentroid = existingRing?.Centroid;
dbd.SecondaryCentroid = subsidiaryRing?.Centroid;
BondGeometry.GetDoubleBondGeometry(dbd, bondLength, CurrentEditor.ViewModel.Standoff);
}
descriptor = dbd;
}
//tripe bond
if (ordervalue == 2.5 || ordervalue == 3)
{
var tbd = new TripleBondLayout {
Start = startPoint, End = endPoint
};
BondGeometry.GetTripleBondGeometry(tbd, bondLength, CurrentEditor.ViewModel.Standoff);
descriptor = tbd;
}
return(descriptor);
}
