/// <summary> /// Generate the intermediate <see cref="AtomSymbol"/> instances. /// </summary> /// <param name="container">structure representation</param> /// <param name="symbolRemap">use alternate symbols (used for Sgroup shortcuts)</param> /// <param name="visibility">defines whether an atom symbol is displayed</param> /// <param name="parameters">render model parameters</param> /// <returns>generated atom symbols (can contain <see langword="null"/>)</returns> private AtomSymbol[] GenerateAtomSymbols(IAtomContainer container, Dictionary <IAtom, string> symbolRemap, SymbolVisibility visibility, RendererModel parameters, ElementGroup annotations, Color foreground, double stroke, StandardDonutGenerator donutGen) { var scale = parameters.GetScale(); var annDist = parameters.GetAnnotationDistance() * (parameters.GetBondLength() / scale); var annScale = (1 / scale) * parameters.GetAnnotationFontScale(); var annColor = parameters.GetAnnotationColor(); var halfStroke = stroke / 2; var symbols = new AtomSymbol[container.Atoms.Count]; var builder = container.Builder; // check if we should annotate attachment point numbers (maxAttach>1) // and queue them all up for processing var attachPoints = new List <IPseudoAtom>(); int maxAttach = 0; for (int i = 0; i < container.Atoms.Count; i++) { var atom = container.Atoms[i]; if (IsHiddenFully(atom)) { continue; } if (atom is IPseudoAtom) { var attachNum = ((IPseudoAtom)atom).AttachPointNum; if (attachNum > 0) { attachPoints.Add((IPseudoAtom)atom); } if (attachNum > maxAttach) { maxAttach = attachNum; } } var remapped = symbolRemap.ContainsKey(atom); var bonds = container.GetConnectedBonds(atom); var neighbors = container.GetConnectedAtoms(atom); var visNeighbors = new List <IAtom>(); // if a symbol is remapped we only want to consider // visible neighbors in the alignment calculation, otherwise // we include all neighbors foreach (var neighbor in neighbors) { if (!remapped || !IsHidden(neighbor)) { visNeighbors.Add(neighbor); } } var auxVectors = new List <Vector2>(1); // only generate if the symbol is visible if (visibility.Visible(atom, bonds, parameters) || remapped) { var hPosition = HydrogenPositionTools.Position(atom, visNeighbors); if (atom.ImplicitHydrogenCount != null && atom.ImplicitHydrogenCount > 0) { auxVectors.Add(hPosition.Vector()); } if (remapped) { symbols[i] = atomGenerator.GenerateAbbreviatedSymbol(symbolRemap[atom], hPosition); } else if (donutGen.IsChargeDelocalised(atom)) { var charge = atom.FormalCharge; atom.FormalCharge = 0; // can't think of a better way to handle this without API // change to symbol visibility if (atom.AtomicNumber != 6) { symbols[i] = atomGenerator.GenerateSymbol(container, atom, hPosition, parameters); } atom.FormalCharge = charge; } else { symbols[i] = atomGenerator.GenerateSymbol(container, atom, hPosition, parameters); } if (symbols[i] != null) { // defines how the element is aligned on the atom point, when // aligned to the left, the first character 'e.g. Cl' is used. if (visNeighbors.Count < 4) { if (hPosition == HydrogenPosition.Left) { symbols[i] = symbols[i].AlignTo(AtomSymbol.SymbolAlignment.Right); } else { symbols[i] = symbols[i].AlignTo(AtomSymbol.SymbolAlignment.Left); } } var p = atom.Point2D; if (p == null) { throw new ArgumentException("Atom did not have 2D coordinates"); } symbols[i] = symbols[i].Resize(1 / scale, 1 / -scale).Center(p.Value.X, p.Value.Y); } } var label = GetAnnotationLabel(atom); if (label != null) { // to ensure consistent draw distance we need to adjust the annotation distance // depending on whether we are drawing next to an atom symbol or not. double strokeAdjust = symbols[i] != null ? -halfStroke : 0; var vector = NewAtomAnnotationVector(atom, bonds, auxVectors); var annOutline = GenerateAnnotation(atom.Point2D.Value, label, vector, annDist + strokeAdjust, annScale, font, emSize, symbols[i]); // the AtomSymbol may migrate during bond generation and therefore the annotation // needs to be tied to the symbol. If no symbol is available the annotation is // fixed and we can add it to the annotation ElementGroup right away. if (symbols[i] != null) { symbols[i] = symbols[i].AddAnnotation(annOutline); } else { annotations.Add(GeneralPath.ShapeOf(annOutline.GetOutline(), annColor)); } } } // label attachment points if (maxAttach > 1) { var attachNumOutlines = new List <TextOutline>(); double maxRadius = 0; foreach (IPseudoAtom atom in attachPoints) { int attachNum = atom.AttachPointNum; // to ensure consistent draw distance we need to adjust the annotation distance // depending on whether we are drawing next to an atom symbol or not. var strokeAdjust = -halfStroke; var vector = NewAttachPointAnnotationVector( atom, container.GetConnectedBonds(atom), new List <Vector2>()); var outline = GenerateAnnotation(atom.Point2D.Value, attachNum.ToString(), vector, 1.75 * annDist + strokeAdjust, annScale, new Typeface(font.FontFamily, font.Style, WPF.FontWeights.Bold, font.Stretch), emSize, null); attachNumOutlines.Add(outline); var w = outline.GetBounds().Width; var h = outline.GetBounds().Height; var r = Math.Sqrt(w * w + h * h) / 2; if (r > maxRadius) { maxRadius = r; } } foreach (var outline in attachNumOutlines) { var group = new ElementGroup(); var radius = 2 * stroke + maxRadius; var shape = new EllipseGeometry(outline.GetCenter(), radius, radius); var area1 = Geometry.Combine(shape, outline.GetOutline(), GeometryCombineMode.Exclude, Transform.Identity); group.Add(GeneralPath.ShapeOf(area1, foreground)); annotations.Add(group); } } return(symbols); }
/// <inheritdoc/> public IRenderingElement Generate(IAtomContainer container, RendererModel parameters) { if (container.Atoms.Count == 0) { return(new ElementGroup()); } var symbolRemap = new Dictionary <IAtom, string>(); StandardSgroupGenerator.PrepareDisplayShortcuts(container, symbolRemap); var scale = parameters.GetScale(); var visibility = parameters.GetVisibility(); var coloring = parameters.GetAtomColorer(); var annotationColor = parameters.GetAnnotationColor(); var foreground = coloring.GetAtomColor(container.Builder.NewAtom("C")); // the stroke width is based on the font. a better method is needed to get // the exact font stroke but for now we use the width of the pipe character. var fontStroke = new TextOutline("|", font, emSize).Resize(1 / scale, 1 / scale).GetBounds().Width; var stroke = parameters.GetStrokeRatio() * fontStroke; var annotations = new ElementGroup(); var donutGenerator = new StandardDonutGenerator(container, font, emSize, parameters, stroke); var donuts = donutGenerator.Generate(); var symbols = GenerateAtomSymbols(container, symbolRemap, visibility, parameters, annotations, foreground, stroke, donutGenerator); var bondElements = StandardBondGenerator.GenerateBonds(container, symbols, parameters, stroke, font, emSize, annotations, donutGenerator); var style = parameters.GetHighlighting(); var glowWidth = parameters.GetOuterGlowWidth(); var backLayer = new ElementGroup(); var middleLayer = new ElementGroup(); var frontLayer = new ElementGroup(); // bond elements can simply be added to the element group for (int i = 0; i < container.Bonds.Count; i++) { var bond = container.Bonds[i]; if (IsHidden(bond)) { continue; } var highlight = GetHighlightColor(bond, parameters); if (highlight != null && style == HighlightStyle.OuterGlow) { backLayer.Add(MarkedElement.Markup(OuterGlow(bondElements[i], highlight.Value, glowWidth, stroke), "outerglow")); } if (highlight != null && style == HighlightStyle.Colored) { frontLayer.Add(MarkedElement.MarkupBond(Recolor(bondElements[i], highlight.Value), bond)); } else { middleLayer.Add(MarkedElement.MarkupBond(bondElements[i], bond)); } } // bonds for delocalised aromatic frontLayer.Add(donuts); // convert the atom symbols to IRenderingElements for (int i = 0; i < container.Atoms.Count; i++) { var atom = container.Atoms[i]; if (IsHidden(atom)) { continue; } var highlight = GetHighlightColor(atom, parameters); var color = GetColorOfAtom(symbolRemap, coloring, foreground, style, atom, highlight); if (symbols[i] == null) { // we add a 'ball' around atoms with no symbols (e.g. carbons) if (highlight != null && style == HighlightStyle.OuterGlow) { backLayer.Add(MarkedElement.Markup(new OvalElement(ToPoint(atom.Point2D.Value), 1.75 * glowWidth * stroke, true, highlight.Value), "outerglow")); } continue; } var symbolElements = new ElementGroup(); foreach (var shape in symbols[i].GetOutlines()) { GeneralPath path = GeneralPath.ShapeOf(shape, color); symbolElements.Add(path); } // add the annotations of the symbol to the annotations ElementGroup foreach (var shape in symbols[i].GetAnnotationOutlines()) { annotations.Add(MarkedElement.Markup(GeneralPath.ShapeOf(shape, annotationColor), "annotation")); } if (highlight != null && style == HighlightStyle.OuterGlow) { backLayer.Add(MarkedElement.Markup(OuterGlow(symbolElements, highlight.Value, glowWidth, stroke), "outerglow")); } if (highlight != null && style == HighlightStyle.Colored) { frontLayer.Add(MarkedElement.MarkupAtom(symbolElements, atom)); } else { middleLayer.Add(MarkedElement.MarkupAtom(symbolElements, atom)); } } // Add the Sgroups display elements to the front layer var sgroups = StandardSgroupGenerator.Generate(parameters, stroke, font, emSize, foreground, atomGenerator, symbols, container); frontLayer.Add(sgroups); // Annotations are added to the front layer. frontLayer.Add(annotations); var group = new ElementGroup { backLayer, middleLayer, frontLayer }; return(MarkedElement.MarkupMol(group, container)); }