private bool TrimLine(BondLine leftOrRight, BondLine line, bool isInRing)
{
bool dummy;
bool intersect;
Point intersection;
// Make a longer version of the line
Point startLonger = new Point(leftOrRight.Start.X, leftOrRight.Start.Y);
Point endLonger = new Point(leftOrRight.End.X, leftOrRight.End.Y);
CoordinateTool.AdjustLineAboutMidpoint(ref startLonger, ref endLonger, _medianBondLength / 5);
// See if they intersect at one end
CoordinateTool.FindIntersection(startLonger, endLonger, line.Start, line.End,
out dummy, out intersect, out intersection);
// If they intersect update the main line
if (intersect)
{
double l1 = CoordinateTool.DistanceBetween(intersection, leftOrRight.Start);
double l2 = CoordinateTool.DistanceBetween(intersection, leftOrRight.End);
if (l1 > l2)
{
leftOrRight.End = new Point(intersection.X, intersection.Y);
}
else
{
leftOrRight.Start = new Point(intersection.X, intersection.Y);
}
if (!isInRing)
{
l1 = CoordinateTool.DistanceBetween(intersection, line.Start);
l2 = CoordinateTool.DistanceBetween(intersection, line.End);
if (l1 > l2)
{
line.End = new Point(intersection.X, intersection.Y);
}
else
{
line.Start = new Point(intersection.X, intersection.Y);
}
}
}
return(intersect);
}
/// <summary>
/// Creates the lines for a bond
/// </summary>
/// <param name="bond"></param>
public void CreateLines(Bond bond)
{
IEnumerable <Ring> rings = bond.Rings;
int ringCount = 0;
foreach (Ring r in rings)
{
ringCount++;
}
Point bondStart = bond.StartAtom.Position;
Point bondEnd = bond.EndAtom.Position;
#region Create Bond Line objects
switch (bond.Order)
{
case Globals.OrderZero:
case "unknown":
m_BondLines.Add(new BondLine(BondLineStyle.Dotted, bond));
break;
case Globals.OrderPartial01:
m_BondLines.Add(new BondLine(BondLineStyle.Dashed, bond));
break;
case "1":
case Globals.OrderSingle:
switch (bond.Stereo)
{
case Globals.BondStereo.None:
m_BondLines.Add(new BondLine(BondLineStyle.Solid, bond));
break;
case Globals.BondStereo.Hatch:
m_BondLines.Add(new BondLine(BondLineStyle.Hatch, bond));
break;
case Globals.BondStereo.Wedge:
m_BondLines.Add(new BondLine(BondLineStyle.Wedge, bond));
break;
case Globals.BondStereo.Indeterminate:
m_BondLines.Add(new BondLine(BondLineStyle.Wavy, bond));
break;
default:
m_BondLines.Add(new BondLine(BondLineStyle.Solid, bond));
break;
}
break;
case Globals.OrderPartial12:
case Globals.OrderAromatic:
BondLine onePointFive;
BondLine onePointFiveDotted;
Point onePointFiveStart;
Point onePointFiveEnd;
switch (bond.Placement)
{
case Globals.BondDirection.Clockwise:
onePointFive = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(onePointFive);
onePointFiveDotted = onePointFive.GetParallel(BondOffset());
onePointFiveStart = new Point(onePointFiveDotted.Start.X, onePointFiveDotted.Start.Y);
onePointFiveEnd = new Point(onePointFiveDotted.End.X, onePointFiveDotted.End.Y);
CoordinateTool.AdjustLineAboutMidpoint(ref onePointFiveStart, ref onePointFiveEnd, -(BondOffset() / 1.75));
onePointFiveDotted = new BondLine(BondLineStyle.Dotted, onePointFiveStart, onePointFiveEnd, bond);
m_BondLines.Add(onePointFiveDotted);
break;
case Globals.BondDirection.Anticlockwise:
onePointFive = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(onePointFive);
onePointFiveDotted = onePointFive.GetParallel(-BondOffset());
onePointFiveStart = new Point(onePointFiveDotted.Start.X, onePointFiveDotted.Start.Y);
onePointFiveEnd = new Point(onePointFiveDotted.End.X, onePointFiveDotted.End.Y);
CoordinateTool.AdjustLineAboutMidpoint(ref onePointFiveStart, ref onePointFiveEnd, -(BondOffset() / 1.75));
onePointFiveDotted = new BondLine(BondLineStyle.Dotted, onePointFiveStart, onePointFiveEnd, bond);
m_BondLines.Add(onePointFiveDotted);
break;
case Globals.BondDirection.None:
onePointFive = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(onePointFive.GetParallel(-(BondOffset() / 2)));
onePointFiveDotted = onePointFive.GetParallel(BondOffset() / 2);
onePointFiveDotted.SetLineStyle(BondLineStyle.Dotted);
m_BondLines.Add(onePointFiveDotted);
break;
}
break;
case "2":
case Globals.OrderDouble:
if (bond.Stereo == Globals.BondStereo.Indeterminate) //crossing bonds
{
// Crossed lines
BondLine d = new BondLine(BondLineStyle.Solid, bondStart, bondEnd, bond);
BondLine d1 = d.GetParallel(-(BondOffset() / 2));
BondLine d2 = d.GetParallel(BondOffset() / 2);
m_BondLines.Add(new BondLine(BondLineStyle.Solid, new Point(d1.Start.X, d1.Start.Y), new Point(d2.End.X, d2.End.Y), bond));
m_BondLines.Add(new BondLine(BondLineStyle.Solid, new Point(d2.Start.X, d2.Start.Y), new Point(d1.End.X, d1.End.Y), bond));
}
else
{
bool shifted = false;
if (ringCount == 0)
{
if (bond.StartAtom.Element as Element == Globals.PeriodicTable.C && bond.EndAtom.Element as Element == Globals.PeriodicTable.C)
{
shifted = false;
}
else
{
shifted = true;
}
}
if (bond.StartAtom.Degree == 1 | bond.EndAtom.Degree == 1)
{
shifted = true;
}
if (shifted)
{
BondLine d = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(d.GetParallel(-(BondOffset() / 2)));
m_BondLines.Add(d.GetParallel(BondOffset() / 2));
}
else
{
Point outIntersectP1;
Point outIntersectP2;
bool linesIntersect;
bool segmentsIntersect;
Point centre;
switch (bond.Placement)
{
case Globals.BondDirection.Anticlockwise:
BondLine da = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(da);
BondLine bla = da.GetParallel(-BondOffset());
Point startPointa = bla.Start;
Point endPointa = bla.End;
if (bond.PrimaryRing != null)
{
centre = bond.PrimaryRing.Centroid.Value;
// Diagnostics
//m_BondLines.Add(new BondLine(bondStart, centre, BondLineStyle.Dotted, null));
//m_BondLines.Add(new BondLine(bondEnd, centre, BondLineStyle.Dotted, null));
CoordinateTool.FindIntersection(startPointa, endPointa, bondStart, centre,
out linesIntersect, out segmentsIntersect, out outIntersectP1);
CoordinateTool.FindIntersection(startPointa, endPointa, bondEnd, centre,
out linesIntersect, out segmentsIntersect, out outIntersectP2);
m_BondLines.Add(new BondLine(BondLineStyle.Solid, outIntersectP1, outIntersectP2, bond));
}
else
{
CoordinateTool.AdjustLineAboutMidpoint(ref startPointa, ref endPointa, -(BondOffset() / 1.75));
m_BondLines.Add(new BondLine(BondLineStyle.Solid, startPointa, endPointa, bond));
}
break;
case Globals.BondDirection.Clockwise:
BondLine dc = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(dc);
BondLine blc = dc.GetParallel(BondOffset());
Point startPointc = blc.Start;
Point endPointc = blc.End;
if (bond.PrimaryRing != null)
{
centre = bond.PrimaryRing.Centroid.Value;
// Diagnostics
//m_BondLines.Add(new BondLine(bondStart, centre, BondLineStyle.Dotted, null));
//m_BondLines.Add(new BondLine(bondEnd, centre, BondLineStyle.Dotted, null));
CoordinateTool.FindIntersection(startPointc, endPointc, bondStart, centre,
out linesIntersect, out segmentsIntersect, out outIntersectP1);
CoordinateTool.FindIntersection(startPointc, endPointc, bondEnd, centre,
out linesIntersect, out segmentsIntersect, out outIntersectP2);
m_BondLines.Add(new BondLine(BondLineStyle.Solid, outIntersectP1, outIntersectP2, bond));
}
else
{
CoordinateTool.AdjustLineAboutMidpoint(ref startPointc, ref endPointc, -(BondOffset() / 1.75));
m_BondLines.Add(new BondLine(BondLineStyle.Solid, startPointc, endPointc, bond));
}
break;
default:
switch (bond.Stereo)
{
case Globals.BondStereo.Cis:
BondLine dcc = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(dcc);
BondLine blnewc = dcc.GetParallel(BondOffset());
Point startPointn = blnewc.Start;
Point endPointn = blnewc.End;
CoordinateTool.AdjustLineAboutMidpoint(ref startPointn, ref endPointn, -(BondOffset() / 1.75));
m_BondLines.Add(new BondLine(BondLineStyle.Solid, startPointn, endPointn, bond));
break;
case Globals.BondStereo.Trans:
BondLine dtt = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(dtt);
BondLine blnewt = dtt.GetParallel(BondOffset());
Point startPointt = blnewt.Start;
Point endPointt = blnewt.End;
CoordinateTool.AdjustLineAboutMidpoint(ref startPointt, ref endPointt, -(BondOffset() / 1.75));
m_BondLines.Add(new BondLine(BondLineStyle.Solid, startPointt, endPointt, bond));
break;
default:
BondLine dp = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(dp.GetParallel(-(BondOffset() / 2)));
m_BondLines.Add(dp.GetParallel(BondOffset() / 2));
break;
}
break;
}
}
}
break;
case Globals.OrderPartial23:
BondLine twoPointFive;
BondLine twoPointFiveDotted;
BondLine twoPointFiveParallel;
Point twoPointFiveStart;
Point twoPointFiveEnd;
switch (bond.Placement)
{
case Globals.BondDirection.Clockwise:
// Central bond line
twoPointFive = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(twoPointFive);
// Solid bond line
twoPointFiveParallel = twoPointFive.GetParallel(-BondOffset());
twoPointFiveStart = new Point(twoPointFiveParallel.Start.X, twoPointFiveParallel.Start.Y);
twoPointFiveEnd = new Point(twoPointFiveParallel.End.X, twoPointFiveParallel.End.Y);
CoordinateTool.AdjustLineAboutMidpoint(ref twoPointFiveStart, ref twoPointFiveEnd, -(BondOffset() / 1.75));
twoPointFiveParallel = new BondLine(BondLineStyle.Solid, twoPointFiveStart, twoPointFiveEnd, bond);
m_BondLines.Add(twoPointFiveParallel);
// Dotted bond line
twoPointFiveDotted = twoPointFive.GetParallel(BondOffset());
twoPointFiveStart = new Point(twoPointFiveDotted.Start.X, twoPointFiveDotted.Start.Y);
twoPointFiveEnd = new Point(twoPointFiveDotted.End.X, twoPointFiveDotted.End.Y);
CoordinateTool.AdjustLineAboutMidpoint(ref twoPointFiveStart, ref twoPointFiveEnd, -(BondOffset() / 1.75));
twoPointFiveDotted = new BondLine(BondLineStyle.Dotted, twoPointFiveStart, twoPointFiveEnd, bond);
m_BondLines.Add(twoPointFiveDotted);
break;
case Globals.BondDirection.Anticlockwise:
// Central bond line
twoPointFive = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(twoPointFive);
// Dotted bond line
twoPointFiveDotted = twoPointFive.GetParallel(-BondOffset());
twoPointFiveStart = new Point(twoPointFiveDotted.Start.X, twoPointFiveDotted.Start.Y);
twoPointFiveEnd = new Point(twoPointFiveDotted.End.X, twoPointFiveDotted.End.Y);
CoordinateTool.AdjustLineAboutMidpoint(ref twoPointFiveStart, ref twoPointFiveEnd, -(BondOffset() / 1.75));
twoPointFiveDotted = new BondLine(BondLineStyle.Dotted, twoPointFiveStart, twoPointFiveEnd, bond);
m_BondLines.Add(twoPointFiveDotted);
// Solid bond line
twoPointFiveParallel = twoPointFive.GetParallel(BondOffset());
twoPointFiveStart = new Point(twoPointFiveParallel.Start.X, twoPointFiveParallel.Start.Y);
twoPointFiveEnd = new Point(twoPointFiveParallel.End.X, twoPointFiveParallel.End.Y);
CoordinateTool.AdjustLineAboutMidpoint(ref twoPointFiveStart, ref twoPointFiveEnd, -(BondOffset() / 1.75));
twoPointFiveParallel = new BondLine(BondLineStyle.Solid, twoPointFiveStart, twoPointFiveEnd, bond);
m_BondLines.Add(twoPointFiveParallel);
break;
case Globals.BondDirection.None:
twoPointFive = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(twoPointFive);
m_BondLines.Add(twoPointFive.GetParallel(-BondOffset()));
twoPointFiveDotted = twoPointFive.GetParallel(BondOffset());
twoPointFiveDotted.SetLineStyle(BondLineStyle.Dotted);
m_BondLines.Add(twoPointFiveDotted);
break;
}
break;
case "3":
case Globals.OrderTriple:
BondLine tripple = new BondLine(BondLineStyle.Solid, bond);
m_BondLines.Add(tripple);
m_BondLines.Add(tripple.GetParallel(BondOffset()));
m_BondLines.Add(tripple.GetParallel(-BondOffset()));
break;
default:
// Draw a single line, so that there is something to see
m_BondLines.Add(new BondLine(BondLineStyle.Solid, bond));
break;
}
#endregion Create Bond Line objects
}
/// <summary>
/// Creates the lines for a bond
/// </summary>
/// <param name="wordprocessingGroup1">Where to add the bond lines</param>
/// <param name="bond"></param>
public void CreateLines(Bond bond)
{
//Debug.WriteLine("Bond: " + bond.Id);
//IEnumerable<Atom> bondatoms = bond.GetAtoms();
IEnumerable <Ring> rings = bond.Rings;
int ringCount = 0;
foreach (Ring r in rings)
{
ringCount++;
}
//Debug.WriteLine(" Ring Count: " + ringCount);
Point bondStart = bond.StartAtom.Position;
Point bondEnd = bond.EndAtom.Position;
//IEnumerable<CmlBond> toAtomBonds = toAtom.GetLigandBonds();
//int toAtomBondCount = toAtomBonds.ToArray<CmlBond>().Length;
//Debug.WriteLine(" From : " + fromAtom.ElementType + " [" + fromAtom.Id + "] at " + bondStart.X + ", " + bondStart.Y);
//Debug.WriteLine(" To : " + toAtom.ElementType + " [" + toAtom.Id + "] at " + bondEnd.X + ", " + bondEnd.Y);
#region Create Bond Line objects
switch (bond.Order)
{
case Bond.OrderZero:
case "unknown":
m_BondLines.Add(new BondLine(bondStart, bondEnd, BondLineStyle.Dotted, bond.Id));
break;
case Bond.OrderPartial01:
m_BondLines.Add(new BondLine(bondStart, bondEnd, BondLineStyle.Dashed, bond.Id));
break;
case "1":
case Bond.OrderSingle:
switch (bond.Stereo)
{
case BondStereo.None:
m_BondLines.Add(new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id));
break;
case BondStereo.Hatch:
m_BondLines.Add(new BondLine(bondStart, bondEnd, BondLineStyle.Hash, bond.Id));
break;
case BondStereo.Wedge:
m_BondLines.Add(new BondLine(bondStart, bondEnd, BondLineStyle.Wedge, bond.Id));
break;
case BondStereo.Indeterminate:
m_BondLines.Add(new BondLine(bondStart, bondEnd, BondLineStyle.Wavy, bond.Id));
break;
default:
m_BondLines.Add(new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id));
break;
}
break;
case Bond.OrderPartial12:
//case "A":
BondLine a = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
m_BondLines.Add(a);
BondLine a1 = a.GetParallel(-BondOffset());
Point newStarta = new Point(a1.Start.X, a1.Start.Y);
Point newEnda = new Point(a1.End.X, a1.End.Y);
CoordinateTool.AdjustLineAboutMidpoint(ref newStarta, ref newEnda, -(BondOffset() / 1.75));
a1 = new BondLine(newStarta, newEnda, BondLineStyle.Dotted, bond.Id);
m_BondLines.Add(a1);
break;
case Bond.OrderDouble:
if (bond.Stereo == BondStereo.Indeterminate) //crossing bonds
{
// Crossed lines
BondLine d = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
BondLine d1 = d.GetParallel(-(BondOffset() / 2));
BondLine d2 = d.GetParallel(BondOffset() / 2);
m_BondLines.Add(new BondLine(new Point(d1.Start.X, d1.Start.Y), new Point(d2.End.X, d2.End.Y), BondLineStyle.Solid, bond.Id));
m_BondLines.Add(new BondLine(new Point(d2.Start.X, d2.Start.Y), new Point(d1.End.X, d1.End.Y), BondLineStyle.Solid, bond.Id));
}
else
{
bool shifted = false;
if (ringCount == 0)
{
if (bond.StartAtom.Element as Element == Globals.PeriodicTable.C && bond.EndAtom.Element as Element == Globals.PeriodicTable.C)
{
shifted = false;
}
else
{
shifted = true;
}
}
if (bond.StartAtom.Degree == 1 | bond.EndAtom.Degree == 1)
{
shifted = true;
}
if (shifted)
{
BondLine d = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
m_BondLines.Add(d.GetParallel(-(BondOffset() / 2)));
m_BondLines.Add(d.GetParallel(BondOffset() / 2));
}
else
{
Debug.WriteLine($"bond.Placement {bond.Placement}");
Point outIntersectP1;
Point outIntersectP2;
bool linesIntersect;
bool segmentsIntersect;
Point centre;
switch (bond.Placement)
{
case BondDirection.Anticlockwise:
BondLine da = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
m_BondLines.Add(da);
BondLine bla = da.GetParallel(-BondOffset());
Point startPointa = bla.Start;
Point endPointa = bla.End;
if (bond.PrimaryRing != null)
{
centre = bond.PrimaryRing.Centroid.Value;
// Diagnostics
//m_BondLines.Add(new BondLine(bondStart, centre, BondLineStyle.Dotted, null));
//m_BondLines.Add(new BondLine(bondEnd, centre, BondLineStyle.Dotted, null));
CoordinateTool.FindIntersection(startPointa, endPointa, bondStart, centre,
out linesIntersect, out segmentsIntersect, out outIntersectP1);
CoordinateTool.FindIntersection(startPointa, endPointa, bondEnd, centre,
out linesIntersect, out segmentsIntersect, out outIntersectP2);
m_BondLines.Add(new BondLine(outIntersectP1, outIntersectP2, BondLineStyle.Solid, bond.Id));
}
else
{
CoordinateTool.AdjustLineAboutMidpoint(ref startPointa, ref endPointa, -(BondOffset() / 1.75));
m_BondLines.Add(new BondLine(startPointa, endPointa, BondLineStyle.Solid, bond.Id));
}
break;
case BondDirection.Clockwise:
BondLine dc = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
m_BondLines.Add(dc);
BondLine blc = dc.GetParallel(+BondOffset());
Point startPointc = blc.Start;
Point endPointc = blc.End;
if (bond.PrimaryRing != null)
{
centre = bond.PrimaryRing.Centroid.Value;
// Diagnostics
//m_BondLines.Add(new BondLine(bondStart, centre, BondLineStyle.Dotted, null));
//m_BondLines.Add(new BondLine(bondEnd, centre, BondLineStyle.Dotted, null));
CoordinateTool.FindIntersection(startPointc, endPointc, bondStart, centre,
out linesIntersect, out segmentsIntersect, out outIntersectP1);
CoordinateTool.FindIntersection(startPointc, endPointc, bondEnd, centre,
out linesIntersect, out segmentsIntersect, out outIntersectP2);
m_BondLines.Add(new BondLine(outIntersectP1, outIntersectP2, BondLineStyle.Solid, bond.Id));
}
else
{
CoordinateTool.AdjustLineAboutMidpoint(ref startPointc, ref endPointc, -(BondOffset() / 1.75));
m_BondLines.Add(new BondLine(startPointc, endPointc, BondLineStyle.Solid, bond.Id));
}
break;
default:
switch (bond.Stereo)
{
case BondStereo.Cis:
BondLine dcc = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
m_BondLines.Add(dcc);
BondLine blnewc = dcc.GetParallel(+BondOffset());
Point startPointn = blnewc.Start;
Point endPointn = blnewc.End;
CoordinateTool.AdjustLineAboutMidpoint(ref startPointn, ref endPointn, -(BondOffset() / 1.75));
m_BondLines.Add(new BondLine(startPointn, endPointn, BondLineStyle.Solid, bond.Id));
break;
case BondStereo.Trans:
BondLine dtt = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
m_BondLines.Add(dtt);
BondLine blnewt = dtt.GetParallel(+BondOffset());
Point startPointt = blnewt.Start;
Point endPointt = blnewt.End;
CoordinateTool.AdjustLineAboutMidpoint(ref startPointt, ref endPointt, -(BondOffset() / 1.75));
m_BondLines.Add(new BondLine(startPointt, endPointt, BondLineStyle.Solid, bond.Id));
break;
default:
BondLine dp = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
m_BondLines.Add(dp.GetParallel(-(BondOffset() / 2)));
m_BondLines.Add(dp.GetParallel(BondOffset() / 2));
break;
}
break;
}
}
}
break;
case "3":
case "T":
// Draw main bond line
BondLine t = new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id);
m_BondLines.Add(t);
m_BondLines.Add(t.GetParallel(BondOffset()));
m_BondLines.Add(t.GetParallel(-BondOffset()));
break;
default:
m_BondLines.Add(new BondLine(bondStart, bondEnd, BondLineStyle.Solid, bond.Id));
break;
}
#endregion Create Bond Line objects
}
