/// <summary>
/// Hide the repeated atoms and bonds of a multiple group. We hide al atoms that
/// belong to the group unless they are defined in the parent atom list. Any
/// bond to those atoms that is not a crossing bond or one connecting atoms in
/// the parent list is hidden.
/// </summary>
/// <param name="container">molecule</param>
/// <param name="sgroup">multiple group display shortcut</param>
private static void HideMultipleParts(IAtomContainer container, Sgroup sgroup)
{
var crossing = sgroup.Bonds;
var atoms = sgroup.Atoms;
var parentAtoms = (ICollection <IAtom>)sgroup.GetValue(SgroupKey.CtabParentAtomList);
foreach (var bond in container.Bonds)
{
if (parentAtoms.Contains(bond.Begin) && parentAtoms.Contains(bond.End))
{
continue;
}
if (atoms.Contains(bond.Begin) || atoms.Contains(bond.End))
{
StandardGenerator.Hide(bond);
}
}
foreach (var atom in atoms)
{
if (!parentAtoms.Contains(atom))
{
StandardGenerator.Hide(atom);
}
}
foreach (var bond in crossing)
{
StandardGenerator.Unhide(bond);
}
}
private static string GetSgroupPolymerKey(Sgroup sgroup)
{
switch (sgroup.Type)
{
case SgroupType.CtabStructureRepeatUnit:
return("n");
case SgroupType.CtabMonomer:
return("mon");
case SgroupType.CtabMer:
return("mer");
case SgroupType.CtabCopolymer:
string subtype = (string)sgroup.GetValue(SgroupKey.CtabSubType);
if (subtype == null)
{
return("co");
}
switch (subtype)
{
case "RAN":
return("ran");
case "ALT":
return("alt");
case "BLO":
return("blk");
}
goto case SgroupType.CtabCrossLink;
case SgroupType.CtabCrossLink:
return("xl");
case SgroupType.CtabModified:
return("mod");
case SgroupType.CtabMixture:
return("mix");
case SgroupType.CtabFormulation:
return("f");
case SgroupType.CtabAnyPolymer:
return("any");
case SgroupType.CtabGeneric:
return("gen");
case SgroupType.CtabComponent:
return("c");
case SgroupType.CtabGraft:
return("grf");
default:
throw new ArgumentException($"{sgroup.Type} is not proper.");
}
}
private IRenderingElement GenerateMixtureSgroup(Sgroup sgroup)
{
// draw the brackets
// TODO - mixtures normally have attached Sgroup data
// TODO - e.g. COMPONENT_FRACTION, ACTIVITY_TYPE, WEIGHT_PERCENT
var brackets = (IList <SgroupBracket>)sgroup.GetValue(SgroupKey.CtabBracket);
if (brackets != null)
{
var type = sgroup.Type;
string subscript = "?";
switch (type)
{
case SgroupType.CtabComponent:
var compNum = (int?)sgroup.GetValue(SgroupKey.CtabComponentNumber);
if (compNum != null)
{
subscript = "c" + compNum.ToString();
}
else
{
subscript = "c";
}
break;
case SgroupType.CtabMixture:
subscript = "mix";
break;
case SgroupType.CtabFormulation:
subscript = "f";
break;
}
return(GenerateSgroupBrackets(sgroup,
brackets,
null,
subscript,
null));
}
else
{
return(new ElementGroup());
}
}
private IRenderingElement GenerateMultipleSgroup(Sgroup sgroup)
{
// just draw the brackets - multiplied group parts have already been hidden in prep phase
var brackets = (IList <SgroupBracket>)sgroup.GetValue(SgroupKey.CtabBracket);
if (brackets != null)
{
return(GenerateSgroupBrackets(sgroup,
brackets,
Dictionaries.Empty <IAtom, AtomSymbol>(),
(string)sgroup.GetValue(SgroupKey.CtabSubScript),
null));
}
else
{
return(new ElementGroup());
}
}
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>
/// Generates polymer Sgroup elements.
/// </summary>
/// <param name="sgroup">the Sgroup</param>
/// <returns>the rendered elements (empty if no brackets defined)</returns>
private IRenderingElement GeneratePolymerSgroup(Sgroup sgroup, IReadOnlyDictionary <IAtom, AtomSymbol> symbolMap)
{
// draw the brackets
var brackets = (IList <SgroupBracket>)sgroup.GetValue(SgroupKey.CtabBracket);
if (brackets != null)
{
var type = sgroup.Type;
var subscript = (string)sgroup.GetValue(SgroupKey.CtabSubScript);
var connectivity = (string)sgroup.GetValue(SgroupKey.CtabConnectivity);
switch (type)
{
case SgroupType.CtabCopolymer:
subscript = "co";
string subtype = (string)sgroup.GetValue(SgroupKey.CtabSubType);
if (string.Equals("RAN", subtype, StringComparison.Ordinal))
{
subscript = "ran";
}
else if (string.Equals("BLK", subtype, StringComparison.Ordinal))
{
subscript = "blk";
}
else if (string.Equals("ALT", subtype, StringComparison.Ordinal))
{
subscript = "alt";
}
break;
case SgroupType.CtabCrossLink:
subscript = "xl";
break;
case SgroupType.CtabAnyPolymer:
subscript = "any";
break;
case SgroupType.CtabGraft:
subscript = "grf";
break;
case SgroupType.CtabMer:
subscript = "mer";
break;
case SgroupType.CtabMonomer:
subscript = "mon";
break;
case SgroupType.CtabModified:
subscript = "mod";
break;
case SgroupType.CtabStructureRepeatUnit:
if (subscript == null)
{
subscript = "n";
}
if (connectivity == null)
{
connectivity = "eu";
}
break;
}
// connectivity doesn't matter if symmetric... which is hard to test
// here but we can certainly ignore it for single atoms (e.g. methylene)
// also when we see brackets we presume head-to-tail repeating
if ("ht".Equals(connectivity) || sgroup.Atoms.Count == 1)
{
connectivity = null;
}
return(GenerateSgroupBrackets(sgroup,
brackets,
symbolMap,
subscript,
connectivity));
}
else
{
return(new ElementGroup());
}
}