static Vector2 NewAttachPointAnnotationVector(IAtom atom, IEnumerable <IBond> bonds, List <Vector2> auxVectors)
{
if (!bonds.Any())
{
return(new Vector2(0, -1));
}
else if (bonds.Count() > 1)
{
return(NewAtomAnnotationVector(atom, bonds, auxVectors));
}
// only one bond (as expected)
var bondVector = VecmathUtil.NewUnitVector(atom, bonds.First());
var perpVector = VecmathUtil.NewPerpendicularVector(bondVector);
// want the annotation below
if (perpVector.Y > 0)
{
perpVector = -perpVector;
}
var vector = new Vector2((bondVector.X + perpVector.X) / 2,
(bondVector.Y + perpVector.Y) / 2);
vector = Vector2.Normalize(vector);
return(vector);
}
public void TestNewUnitVector()
{
Vector2 unit = VecmathUtil.NewUnitVector(new Vector2(4, 2), new Vector2(6, 7));
Assert.AreEqual(0.371, unit.X, 0.01);
Assert.AreEqual(0.928, unit.Y, 0.01);
Assert.AreEqual(1, unit.Length(), 0.01);
}
public void TestNewUnitVectorFromBond()
{
var mock_a1 = new Mock <IAtom>(); var a1 = mock_a1.Object;
var mock_a2 = new Mock <IAtom>(); var a2 = mock_a2.Object;
mock_a1.Setup(n => n.Point2D).Returns(new Vector2(0, 1));
mock_a2.Setup(n => n.Point2D).Returns(new Vector2(1, 0));
var mock_bond = new Mock <IBond>(); var bond = mock_bond.Object;
mock_bond.Setup(n => n.GetOther(a1)).Returns(a2);
mock_bond.Setup(n => n.GetOther(a2)).Returns(a1);
Vector2 unit = VecmathUtil.NewUnitVector(a1, bond);
Assert.AreEqual(0.707, unit.X, 0.01);
Assert.AreEqual(-0.707, unit.Y, 0.01);
Assert.AreEqual(1, unit.Length(), 0.01);
}
private IRenderingElement GenerateSgroupBrackets(Sgroup sgroup,
IList <SgroupBracket> brackets,
IReadOnlyDictionary <IAtom, AtomSymbol> symbols,
string subscriptSuffix,
string superscriptSuffix)
{
// brackets are square by default (style:0)
var style = (int?)sgroup.GetValue(SgroupKey.CtabBracketStyle);
bool round = style != null && style == 1;
var result = new ElementGroup();
var atoms = sgroup.Atoms;
var crossingBonds = sgroup.Bonds;
// easy to depict in correct orientation, we just
// point each bracket at the atom of a crossing
// bond that is 'in' the group - this scales
// to more than two brackets
// first we need to pair the brackets with the bonds
var pairs = crossingBonds.Count == brackets.Count ? BracketBondPairs(brackets, crossingBonds) : Dictionaries.Empty <SgroupBracket, IBond>();
// override bracket layout around single atoms to bring them in closer
if (atoms.Count == 1)
{
var atom = atoms.First();
// e.g. 2 HCL, 8 H2O etc.
if (IsUnsignedInt(subscriptSuffix) &&
!crossingBonds.Any() &&
symbols.ContainsKey(atom))
{
var prefix = new TextOutline('·' + subscriptSuffix, font, emSize).Resize(1 / scale, 1 / -scale);
var prefixBounds = prefix.LogicalBounds;
var symbol = symbols[atom];
var bounds = symbol.GetConvexHull().Outline.Bounds;
// make slightly large
bounds = new Rect(bounds.Bottom - 2 * stroke,
bounds.Left - 2 * stroke,
bounds.Width + 4 * stroke,
bounds.Height + 4 * stroke);
prefix = prefix.Translate(bounds.Bottom - prefixBounds.Top,
symbol.GetAlignmentCenter().Y - prefixBounds.CenterY());
result.Add(GeneralPath.ShapeOf(prefix.GetOutline(), foreground));
}
// e.g. CC(O)nCC
else if (crossingBonds.Count > 0)
{
var scriptscale = labelScale;
var leftBracket = new TextOutline("(", font, emSize).Resize(1 / scale, 1 / -scale);
var rightBracket = new TextOutline(")", font, emSize).Resize(1 / scale, 1 / -scale);
var leftCenter = leftBracket.GetCenter();
var rightCenter = rightBracket.GetCenter();
if (symbols.ContainsKey(atom))
{
var symbol = symbols[atom];
var bounds = symbol.GetConvexHull().Outline.Bounds;
// make slightly large
bounds = new Rect(bounds.Left - 2 * stroke,
bounds.Top - 2 * stroke,
bounds.Width + 4 * stroke,
bounds.Height + 4 * stroke);
leftBracket = leftBracket.Translate(bounds.Left - 0.1 - leftCenter.X,
symbol.GetAlignmentCenter().Y - leftCenter.Y);
rightBracket = rightBracket.Translate(bounds.Right + 0.1 - rightCenter.X,
symbol.GetAlignmentCenter().Y - rightCenter.Y);
}
else
{
var p = atoms.First().Point2D.Value;
leftBracket = leftBracket.Translate(p.X - 0.2 - leftCenter.X, p.Y - leftCenter.Y);
rightBracket = rightBracket.Translate(p.X + 0.2 - rightCenter.X, p.Y - rightCenter.Y);
}
result.Add(GeneralPath.ShapeOf(leftBracket.GetOutline(), foreground));
result.Add(GeneralPath.ShapeOf(rightBracket.GetOutline(), foreground));
var rightBracketBounds = rightBracket.GetBounds();
// subscript/superscript suffix annotation
if (subscriptSuffix != null && subscriptSuffix.Any())
{
TextOutline subscriptOutline = LeftAlign(MakeText(subscriptSuffix.ToLowerInvariant(),
new Vector2(rightBracketBounds.Right,
rightBracketBounds.Top - 0.1),
new Vector2(-0.5 * rightBracketBounds.Width, 0),
scriptscale));
result.Add(GeneralPath.ShapeOf(subscriptOutline.GetOutline(), foreground));
}
if (superscriptSuffix != null && superscriptSuffix.Any())
{
var superscriptOutline = LeftAlign(MakeText(superscriptSuffix.ToLowerInvariant(),
new Vector2(rightBracketBounds.Right,
rightBracketBounds.Bottom + 0.1),
new Vector2(-rightBracketBounds.Width, 0),
scriptscale));
result.Add(GeneralPath.ShapeOf(superscriptOutline.GetOutline(), foreground));
}
}
}
else if (pairs.Any())
{
SgroupBracket suffixBracket = null;
Vector2? suffixBracketPerp = null;
foreach (var e in pairs)
{
var bracket = e.Key;
var bond = e.Value;
var inGroupAtom = atoms.Contains(bond.Begin) ? bond.Begin : bond.End;
var p1 = bracket.FirstPoint;
var p2 = bracket.SecondPoint;
var perp = VecmathUtil.NewPerpendicularVector(VecmathUtil.NewUnitVector(p1, p2));
// point the vector at the atom group
var midpoint = VecmathUtil.Midpoint(p1, p2);
if (Vector2.Dot(perp, VecmathUtil.NewUnitVector(midpoint, inGroupAtom.Point2D.Value)) < 0)
{
perp = Vector2.Negate(perp);
}
perp *= bracketDepth;
if (round)
{
result.Add(CreateRoundBracket(p1, p2, perp, midpoint));
}
else
{
result.Add(CreateSquareBracket(p1, p2, perp));
}
if (suffixBracket == null)
{
suffixBracket = bracket;
suffixBracketPerp = perp;
}
else
{
// is this bracket better as a suffix?
var sp1 = suffixBracket.FirstPoint;
var sp2 = suffixBracket.SecondPoint;
var bestMaxX = Math.Max(sp1.X, sp2.X);
var thisMaxX = Math.Max(p1.X, p2.X);
var bestMaxY = Math.Max(sp1.Y, sp2.Y);
var thisMaxY = Math.Max(p1.Y, p2.Y);
// choose the most eastern or.. the most southern
var xDiff = thisMaxX - bestMaxX;
var yDiff = thisMaxY - bestMaxY;
if (xDiff > EQUIV_THRESHOLD || (xDiff > -EQUIV_THRESHOLD && yDiff < -EQUIV_THRESHOLD))
{
suffixBracket = bracket;
suffixBracketPerp = perp;
}
}
}
// write the labels
if (suffixBracket != null)
{
var subSufPnt = suffixBracket.FirstPoint;
var supSufPnt = suffixBracket.SecondPoint;
// try to put the subscript on the bottom
var xDiff = subSufPnt.X - supSufPnt.X;
var yDiff = subSufPnt.Y - supSufPnt.Y;
if (yDiff > EQUIV_THRESHOLD || (yDiff > -EQUIV_THRESHOLD && xDiff > EQUIV_THRESHOLD))
{
var tmpP = subSufPnt;
subSufPnt = supSufPnt;
supSufPnt = tmpP;
}
// subscript/superscript suffix annotation
if (subscriptSuffix != null && subscriptSuffix.Any())
{
var subscriptOutline = LeftAlign(MakeText(subscriptSuffix.ToLowerInvariant(), subSufPnt, suffixBracketPerp.Value, labelScale));
result.Add(GeneralPath.ShapeOf(subscriptOutline.GetOutline(), foreground));
}
if (superscriptSuffix != null && superscriptSuffix.Any())
{
var superscriptOutline = LeftAlign(MakeText(superscriptSuffix.ToLowerInvariant(), supSufPnt, suffixBracketPerp.Value, labelScale));
result.Add(GeneralPath.ShapeOf(superscriptOutline.GetOutline(), foreground));
}
}
}
else if (brackets.Count == 2)
{
var b1p1 = brackets[0].FirstPoint;
var b1p2 = brackets[0].SecondPoint;
var b2p1 = brackets[1].FirstPoint;
var b2p2 = brackets[1].SecondPoint;
var b1vec = VecmathUtil.NewUnitVector(b1p1, b1p2);
var b2vec = VecmathUtil.NewUnitVector(b2p1, b2p2);
var b1pvec = VecmathUtil.NewPerpendicularVector(b1vec);
var b2pvec = VecmathUtil.NewPerpendicularVector(b2vec);
// Point the vectors at each other
if (Vector2.Dot(b1pvec, VecmathUtil.NewUnitVector(b1p1, b2p1)) < 0)
{
b1pvec = Vector2.Negate(b1pvec);
}
if (Vector2.Dot(b2pvec, VecmathUtil.NewUnitVector(b2p1, b1p1)) < 0)
{
b2pvec = Vector2.Negate(b2pvec);
}
// scale perpendicular vectors by how deep the brackets need to be
b1pvec *= bracketDepth;
b2pvec *= bracketDepth;
// bad brackets
if (double.IsNaN(b1pvec.X) || double.IsNaN(b1pvec.Y) ||
double.IsNaN(b2pvec.X) || double.IsNaN(b2pvec.Y))
{
return(result);
}
{
var path = new PathGeometry();
if (round)
{
{
// bracket 1 (cp: control point)
var pf = new PathFigure
{
StartPoint = new Point(b1p1.X + b1pvec.X, b1p1.Y + b1pvec.Y)
};
Vector2 cpb1 = VecmathUtil.Midpoint(b1p1, b1p2);
cpb1 += VecmathUtil.Negate(b1pvec);
var seg = new QuadraticBezierSegment
{
Point1 = new Point(cpb1.X, cpb1.Y),
Point2 = new Point(b1p2.X + b1pvec.X, b1p2.Y + b1pvec.Y)
};
pf.Segments.Add(seg);
path.Figures.Add(pf);
}
{
// bracket 2 (cp: control point)
var pf = new PathFigure
{
StartPoint = new Point(b2p1.X + b2pvec.X, b2p1.Y + b2pvec.Y)
};
var cpb2 = VecmathUtil.Midpoint(b2p1, b2p2);
cpb2 += VecmathUtil.Negate(b2pvec);
var seg = new QuadraticBezierSegment
{
Point1 = new Point(cpb2.X, cpb2.Y),
Point2 = new Point(b2p2.X + b2pvec.X, b2p2.Y + b2pvec.Y)
};
pf.Segments.Add(seg);
path.Figures.Add(pf);
}
}
else
{
{
// bracket 1
var pf = new PathFigure
{
StartPoint = new Point(b1p1.X + b1pvec.X, b1p1.Y + b1pvec.Y)
};
var seg = new PolyLineSegment();
seg.Points.Add(new Point(b1p1.X, b1p1.Y));
seg.Points.Add(new Point(b1p2.X, b1p2.Y));
seg.Points.Add(new Point(b1p2.X + b1pvec.X, b1p2.Y + b1pvec.Y));
pf.Segments.Add(seg);
path.Figures.Add(pf);
}
{
// bracket 2
var pf = new PathFigure
{
StartPoint = new Point(b2p1.X + b2pvec.X, b2p1.Y + b2pvec.Y)
};
var seg = new PolyLineSegment();
seg.Points.Add(new Point(b2p1.X, b2p1.Y));
seg.Points.Add(new Point(b2p2.X, b2p2.Y));
seg.Points.Add(new Point(b2p2.X + b2pvec.X, b2p2.Y + b2pvec.Y));
pf.Segments.Add(seg);
path.Figures.Add(pf);
}
}
result.Add(GeneralPath.OutlineOf(path, stroke, foreground));
}
// work out where to put the suffix labels (e.g. ht/hh/eu) superscript
// and (e.g. n, xl, c, mix) subscript
// TODO: could be improved
var b1MaxX = Math.Max(b1p1.X, b1p2.X);
var b2MaxX = Math.Max(b2p1.X, b2p2.X);
var b1MaxY = Math.Max(b1p1.Y, b1p2.Y);
var b2MaxY = Math.Max(b2p1.Y, b2p2.Y);
var subSufPnt = b2p2;
var supSufPnt = b2p1;
var subpvec = b2pvec;
var bXDiff = b1MaxX - b2MaxX;
var bYDiff = b1MaxY - b2MaxY;
if (bXDiff > EQUIV_THRESHOLD || (bXDiff > -EQUIV_THRESHOLD && bYDiff < -EQUIV_THRESHOLD))
{
subSufPnt = b1p2;
supSufPnt = b1p1;
subpvec = b1pvec;
}
var xDiff = subSufPnt.X - supSufPnt.X;
var yDiff = subSufPnt.Y - supSufPnt.Y;
if (yDiff > EQUIV_THRESHOLD || (yDiff > -EQUIV_THRESHOLD && xDiff > EQUIV_THRESHOLD))
{
var tmpP = subSufPnt;
subSufPnt = supSufPnt;
supSufPnt = tmpP;
}
// subscript/superscript suffix annotation
if (subscriptSuffix != null && subscriptSuffix.Any())
{
var subscriptOutline = LeftAlign(MakeText(subscriptSuffix.ToLowerInvariant(), subSufPnt, subpvec, labelScale));
result.Add(GeneralPath.ShapeOf(subscriptOutline.GetOutline(), foreground));
}
if (superscriptSuffix != null && superscriptSuffix.Any())
{
var superscriptOutline = LeftAlign(MakeText(superscriptSuffix.ToLowerInvariant(), supSufPnt, subpvec, labelScale));
result.Add(GeneralPath.ShapeOf(superscriptOutline.GetOutline(), foreground));
}
}
return(result);
}
/// <summary>
/// Generate a new annotation vector for an atom using the connected bonds and any other occupied
/// space (auxiliary vectors). The fall back method is to use the largest available space but
/// some common cases are handled differently. For example, when the number of bonds is two
/// the annotation is placed in the acute angle of the bonds (providing there is space). This
/// improves labelling of atoms saturated rings. When there are three bonds and two are 'plain'
/// the label is again placed in the acute section of the plain bonds.
/// </summary>
/// <param name="atom">the atom having an annotation</param>
/// <param name="bonds">the bonds connected to the atom</param>
/// <param name="auxVectors">additional vectors to avoid (filled spaced)</param>
/// <returns>unit vector along which the annotation should be placed.</returns>
/// <seealso cref="IsPlainBond(IBond)"/>
/// <seealso cref="VecmathUtil.NewVectorInLargestGap(IList{Vector2})"/>
internal static Vector2 NewAtomAnnotationVector(IAtom atom, IEnumerable <IBond> bonds, List <Vector2> auxVectors)
{
var vectors = new List <Vector2>();
foreach (var bond in bonds)
{
vectors.Add(VecmathUtil.NewUnitVector(atom, bond));
}
if (vectors.Count == 0)
{
// no bonds, place below
if (auxVectors.Count == 0)
{
return(new Vector2(0, -1));
}
if (auxVectors.Count == 1)
{
return(VecmathUtil.Negate(auxVectors[0]));
}
return(VecmathUtil.NewVectorInLargestGap(auxVectors));
}
else if (vectors.Count == 1)
{
// 1 bond connected
// H0, then label simply appears on the opposite side
if (auxVectors.Count == 0)
{
return(VecmathUtil.Negate(vectors[0]));
}
// !H0, then place it in the largest gap
vectors.AddRange(auxVectors);
return(VecmathUtil.NewVectorInLargestGap(vectors));
}
else if (vectors.Count == 2 && auxVectors.Count == 0)
{
// 2 bonds connected to an atom with no hydrogen labels
// sum the vectors such that the label appears in the acute/nook of the two bonds
var combined = VecmathUtil.Sum(vectors[0], vectors[1]);
// shallow angle (< 30 deg) means the label probably won't fit
if (Vectors.Angle(vectors[0], vectors[1]) < Vectors.DegreeToRadian(65))
{
combined = Vector2.Negate(combined);
}
else
{
// flip vector if either bond is a non-single bond or a wedge, this will
// place the label in the largest space.
// However - when both bonds are wedged (consider a bridging system) to
// keep the label in the nook of the wedges
var bonds_ = bonds.ToList();
if ((!IsPlainBond(bonds_[0]) || !IsPlainBond(bonds_[1])) &&
!(IsWedged(bonds_[0]) && IsWedged(bonds_[1])))
{
combined = Vector2.Negate(combined);
}
}
combined = Vector2.Normalize(combined);
// did we divide by 0? whoops - this happens when the bonds are collinear
if (double.IsNaN(combined.Length()))
{
return(VecmathUtil.NewVectorInLargestGap(vectors));
}
return(combined);
}
else
{
if (vectors.Count == 3 && auxVectors.Count == 0)
{
// 3 bonds connected to an atom with no hydrogen label
// the easy and common case is to check when two bonds are plain
// (i.e. non-stereo sigma bonds) and use those. This gives good
// placement for fused conjugated rings
var plainVectors = new List <Vector2>();
var wedgeVectors = new List <Vector2>();
foreach (var bond in bonds)
{
if (IsPlainBond(bond))
{
plainVectors.Add(VecmathUtil.NewUnitVector(atom, bond));
}
if (IsWedged(bond))
{
wedgeVectors.Add(VecmathUtil.NewUnitVector(atom, bond));
}
}
if (plainVectors.Count == 2)
{
return(VecmathUtil.Sum(plainVectors[0], plainVectors[1]));
}
else if (plainVectors.Count + wedgeVectors.Count == 2)
{
plainVectors.AddRange(wedgeVectors);
return(VecmathUtil.Sum(plainVectors[0], plainVectors[1]));
}
}
// the default option is to find the largest gap
if (auxVectors.Count > 0)
{
vectors.AddRange(auxVectors);
}
return(VecmathUtil.NewVectorInLargestGap(vectors));
}
}